Agenda 12/15/2009 Item #10F
Agenda Item No. 10F
December 15, 2009
Page 1 of 133
EXECUTIVE SUMMARY
Recommendation to approve actions required to complete the development of a
comprehensive management plan for the Clam Bay Estuary
OBJECTIVE: To obtain approval of activities that are required to complete the
development of a comprehensive, long term management plan for the Clam Bay estuary
including ratification of the Clam Bay Advisory Committee update report dated September
25,2009; extension of the term of the Clam Bay Advisory Committee to June 30, 2010;
approval of the proposed FY 2010 budget of $234,917; approval of the Clam Bay System
Data Collection and Analysis Report recommendations and approval of a peer review of
this report conducted by an independent expert jointly selected by Coastal Zone
Management and the Pelican Bay Services Division. .
CONSIDERATIONS: The Clam Bay Advisory Committee, (County Ordinance 2008-48),
is charged with developing a Masfer Plan for the health, management and long term
viability of the Clam Bay Esfuary. The Committee is scheduled fo sunset by December
31,2009 unless extended by the BCC.
The attached status report and budget funding request dated 9/25/2009 was sent to the
BCC as required to meet the October 20, 2009 deadline as outlined in County Ordinance
2008-48. This report highlights the Committee's major activity on its mission items and
. makes recommendations for BCC consideration.
In order to accomplish CBAC's mission as directed and approved by the BCC on 5/26/09,
water quality standards, monitoring programs, mixing, flushing, and circulation data, along
with natural resources characterizations, must still be performed. The CBAC is requesting
that this advisory committee be exfended until the Management Plan for Clam Pass/Clam
Bay has been developed, vetted within the community and approved by the BCC. This
will require a first extension of the CBAC by the BCC through June 30, 2010. This time
extension is due to delays experienced in forming the committee and effort consumed in
resolving the new 1 O-year permit and navigational markers.
Three members of the current nine-member Clam Bay Advisory Committee have
indicated their intent to resign as of December 2009. Replacement members as outlined
in County Ordinance 2008-48 will need to be solicited and appointed by the BCC.
On 6/23/09, the BCC authorized the expenditure of $120,000 to evaluate all existing data
and move forward with the data collection phase of the Water Quality Study. The City of
Naples provided $23,644 to perform the water quality program and together this funding
was sufficient to complete the data review and the data collection phase of this project.
These items were:
· Development of a Water quality program - $23,644: This included the review of all
the existing water quality data and all previous modeling studies along with
proposing water quality standards in Clam Bay in consultation with FDEP and
recommendations for a sampling program.
Agenda Item No. 10F
December 15, 2009
Page 2 of 133
· Sediment and Biological Characterization - $20,804: This included sediment
sampling along with identification and characterization of the sediment in Clam
Bay.
· Physical Data Collection - $95,994: This included subsurface topography along
with flow, tidal and current information at various locations within Clam Pass and
Bay.
Results of these activities are complete and detailed in the Clam Bay System Data
Collection and Analysis Report. The recommendations of this report have been approved
by the Clam Bay Advisory Committee as follows:
· Move forward with a water monitoring program as outlined in the report.
· Move forward with additional sediment toxicology and aging data collection and
analysis for Clam Bay.
. Conduct the water circulation/flushing modeling program.
Staff is asking that the BCC approve the recommendations as outlined above.
It is also recommend that independent peer review, of the Clam Bay Water
Circulation/Flushing Modeling Program and the Clam Bay System Data Collection
Analysis Report recently completed by PBS&J be performed by a recognized expert.
This expert, jointly selected by Pelican Bay Services Division and Coastal Zone
Management, will be from an academic/university background and not directly
involved with any consulting firm. The review of the Clam Bay Data Collection and
Analysis Report is proposed to be conducted early in the development of the
flushing/circulation model. It is also recommended that the cost of this effort and any
future phased peer review be split between the Pelican Bay Services Division and
Coastal Zone Management.
Funding required to complete the Master Plan for Clam Bay are:
Fund 111 . Unincorporated Collier County
Court Recording and Documentation Costs
Water Quality Monitoring in Clam Bay System
Chemicals and YSI probes
lab Fees (9 locations for 12 months)
Consulting and Analysis Support
Public Outreach and Communication
Peer Review
Sediment toxicology
Installation of Beach and Inlet Safety signs and Permitting
Permitting and Installation of Navigational Markers in Clam Bay
Estuary Wildlife and Habitat Preliminary Analysis
Fund 111 Subtotal
System ModelinQ (Fund 195. TOC)
Optimization of tidal flushing, water quality and mixing
$3,400
$1,000
$18,000
$4,000
$1,000
$5,000
$30,000
$5,000
$15,000
$20,000
$102,400
$86,017
Agenda Item NO.1 OF
December 15, 2009
Page 3 of 133
Optimize of pass/cross sections including sediment bypassing am
transport modeling $38,500
Existing model review and analysis $8,000
Fund 195 Subtotal $132,517
Total FY10 Funding Requirements $234,917
ADVISORY COMMITTEE RECOMMENDATIONS: The Clam Bay Advisory Committee
recommended (5-0) for approval and complete funding of this proposal at the October 8,
2009 meeting. The Coastal Advisory Committee recommended approval (8-0) of this
item at their October 8, 2009 meeting. The Clam Bay Advisory Committee also
recommended approval of the recommendations in the Clam Bay System Data and
Analysis Report conducted by PBS&J as outlined above.
FISCAL IMPACT: The total FY 2010 budget requirements for this program are estimated
at $234,917. A combination of project eligible Category "A" tourist tax dollars and
Unincorporated Area MSTD Fund (111) reserve dollars are proposed as the funding
source. A budget amendment in the amount of $102,400 will be necessary moving
budget from Fund (111) reserves to the Coastal Zone Management appropriation unit
within Fund (111). A draw of this amount will reduce Fund (111) confingency reserves to
$1,302,000.
GROWTH MANAGEMENT IMPACT: This item funds studies that will be used in the
development of a comprehensive master plan for the Clam Bay Estuary and ultimately be
approved by the Clam Bay Advisory Committee, the Coastal Advisory Committee and the
Board of County Commissioners. This master plan will conform to the Growth
Management Plan and the Land Development Codes and Ordinances of Collier County.
LEGAL CONSIDERATIONS: This item has been reviewed and approved by the County
Attorney's Office. This item is legally sufficient for Board action. - CMG
RECOMMENDATION: To approve the following actions required to complete the
development of a comprehensive, long term management plan for the Clam Bay estuary:
1. Ratify the previously provided Clam Bay Advisory Committee update report dated
September 25,2009.
2. Extend the term of the Clam Bay Advisory Committee to June 30, 2010.
3. Approve the proposed FY 2010 budget of $234,917 and all necessary budget
amendments.
4. Approve the Clam Bay System Data Collection and Analysis Report
recommendations and a peer review of this report conducted by an independent
expert jointly selected by Coastal Zone Management and the Pelican Bay Services
Division.
5. Approve of all necessary budget amendments.
PREPARED BY: J. Gary McAlpin, CZM Director
Agenda Item No. 10F
December 15, 2009
Page 4 of 133
COLLIER COUNTY
BOARD OF COUNTY COMMISSIONERS
Item Number:
Item Summary:
10F
Meeting Date:
This item to be heard at 2:30 p.m. Recommendation to approve actions required to complete
the development of a comprehensive management plan for the Clam Bay Estuary. (Gary
McAlpin, Coastal Zone Management Director)
12/15/20099:00:00 AM
Approved By
Colleen Greene
Assistant County Attorney
Date
County Attorney
County Attorney
10/12/20092:53 PM
Approved By
Marla Ramsey
Administrator - Public Services
Date
Public Services Division
Public Services Division
10/13/200912:03 PM
Approved By
Jeff Klatzkow
County Attorney
Date
10/16/20094:11 PM
Approved By
Kathy Carpenter
Executive Secretary
Date
Public Services
Public Services Admin.
10/20/20094:41 PM
Approved By
Gary McAlpin
Director - Coastal Management Programs
Date
Public Services Division
Coastal Zone Management
10/30/2009 10:06 AM
Approved By
OMS Coordinator
Date
County Manager's Office
Office of Management & Budget
12/2/2009 9:23 AM
Approved By
Mark Isackson
ManagemenUBudget Analyst, Senior
Date
Office of Management &
Budget
Office of Management & Budget
1214/20099:15 AM
Agenda Item NO.1 OF
December 15, 2009
Page 5 of 133
CLAM BAY ADVISORY COMMITTEE - STATUS REPORT
The Clam Bay Advisory Committee, as outlined in County Ordinance 2008-48, is charged with
developing a Master Plan for the health, management and long term viability of the Clam Bay
Estuary. The following is a summary of the Mission, Functions and Duties of this Advisory
Committee and the progress accomplished to date towards the development of a Management
Pian. This summary also addresses management plan completion dates, funding requirements
and recommendations on the long term management of this valuable County asset.
Mission: The Clam Bay Advisory Committee developed the following Mission Statement that
was approved by the Clam Bay Advisory Committee, the Coastal Advisory Committee and the
Board of County Commissioners. The approved mission is as follows:
1. The Committee's mission is to advise, assist and make joint recommendations to the Board
of County Commissioners ("BCC") and the Coastal Advisory Committee ("CAC") with all
major issues affecting the management, use. direction, health and long term viability of the
Clam Bay Estuary in accordance with the protection afforded Clam Pass and Clam Bay's
NRPA and conservation designations as delineated in the Future Land Use Element of the
Collier County Growth Plan and Coastal Zone Management Plan. In doing so, the Committee
will formulate recommendations for review and recommend possible funding sources that
may be required by such recommendations.
2. The Committee's powers and functions are as an advisory group with the responsibility of
making recommendations pertinent to the Estuary.
3. The Committee has defined its specific duties and scope of work relative to its defined
mission as the review and recommendations associated with, but not limited to, the major
issues listed below. The Committee plans on integrating their recommendations on these
specific issues into a comprehensive long term management plan as well as suggested
guidelines for the day-to-day operation of the Estuary.
. Permit issues, requirements and compliance
. Water quality and sampling programs
. Tidal flushing and mixing
. Mangrove maintenance
. Maintenance of hand dug channels
. Nutrient loadings and runoff control
. Maintenance of Clam Pass
. Sand bypassing at Clam Pass
. Navigational use and marking
. Estuarine wildlife and habitat optimization
Clam Bay Advisory Committee Update and Recommendations - 9/25/2009
Page 1
Agenda Item NO.1 OF
December 15, 2009
Page 6 of 133
· Public education and outreach
. Funding
4. The Committee is scheduled to sunset by December 31, 2009 unless extended by the BCe. The
Committee is to submit a compiete status report on their mission to the BCC by October 20, 2009
and make recommendations on its possible continuance. This report highlights the Committees
major actions on Its numerous mission items and makes the required recommendations for BCC
consideration.
Permits
Task: Review navigationai issues associated with Clam Pass for the specific purpose of
compliance with old permit conditions and the closing out of such permits. This
subcommittee will also complete the required application for a new dredging permit for
Clam Pass that enables minimal dredging for tidal flushing.
Status:
1. Regulatory Agencies in official correspondence has directed Collier County to come into
compliance with USACE permit conditions requiring Clam Pass/Bay to be marked for
navigation per USCG standards. A navigational marker plan has been prepared and
approved by the Clam Bay Advisory Committee, the Coastal Advisory Committee and
the Board of County Commissioners. . Florida Department of Environmental Protection
has approved our permit request by "Consent Rule" for the installation of these
navigational markers citing that since these markers are on sovereign submerged land,
any restrictive covenants between Collier County and the Pelican Bay Foundation do not
apply. The Peiican Bay Foundation and several individuals have challenged this ruling
and petitioned for a Formal Administrative Hearing. Additionally, staff has applied for
and received the USCG permit to install these markers. It is anticipated that resolution
of this item will not be resolved until the Administrative law Judge rules on this petition.
2. For tidal flushing maintenance dredging of Clam Pass. a new 10-year permit application
on exactly the same technical basis as the previously granted permit has been submitted
to FDEP and the USACE. Collier County is currently answering FDEP's Request for
Additional Information in an attempt to perfect the permit application. It is anticipated
that the permit process will take an additional 9-12 months. FDEP refused a second
one-year permit extension and no tidal flushing maintenance dredging or emergency
storm dredging work can occur without this permit in place. To date, no individual or
organization has filed a request for an Administrative Hearing on this permit application.
FDEP is strongly considering requiring Collier County to model the system to obtain the
exact cross section of the pass cut. If this is required, it could lengthen the permitting
Clam Bay Advisory Committee Update and Recommendations - 9/25/2009
Page 2
Agenda Item NO.1 OF
December 15, 2009
Page 7 of 133
time frame considerably due to, among other issues, the controversy associated with
the ebb shoal and the width of the cut at Clam Pass.
3. Safety signage in Clam Pass is a critical issue. Clam Pass is a County pass where
swimmer and boater directly interface. The County and The Pelican Bay Foundation
have agreed to work together to protect all the residents of Collier County by installing
two Informational safety markers/signs on the beach and two informational markers
within and outside the pass to warn boaters and swimmers of potential safety issues.
Proposed locations and size have been agreed upon and wording is being worked with
FWC in Tallahassee. FWC will be required to permit the signage. These signs should be
installed by 11/1/2009.
Future Action: All committee required action has been completed with the exception of
monitoring the progress to assure proper implementation.
Water Qualitv. MixinE! and Runoff/OrainaE!e
Task: In order to accomplish the mission of the Clam Bay Advisory Committee; water quality
standards, monitoring programs, mixing, flushing, tidal modeling and circulation data, along
with natural resources characterizations, must be performed as outlined below:
1. Water Quality and Sampling activities to include the review of prior water quality data,
technical reports, quality assurance and control procedures, laboratory certifications, state
reporting requirements and investigate water quality trends and impact on estuarine
wildlife and vegetation. Make recommendations on required water sampling and testing to
assure the long term viability of the Estuary. Make recommendations on the sampling
protocol to be consistent with other water quality programs.
2. Tidal Flushing and Mixing study to review all available technical data and make
recommendations on studies that could be undertaken to improve the overall health of the
Estuary by the identification and optimization of tidal flushing and mixing within the entire
estuary. Overall optimization of the entire system is required to enhance estuarine wildlife.
Habitat and restoration recommendations, if appropriate, are also to be considered.
3. Nutrient loading and Runoff/Drainage Control identification is the third major portion of
this analysis. This analysis will review previous reports on the sources and impact of run off
on the Estuary's water quality, mangroves and estuarine wildlife and habitat. This will
include a complete review of nutrient loadings, an identification of the major sources of
runoff/drainage and recommended actions to reduce runoff/drainage that may have a
negative impact on the Estuary.
Clam Bay Advisory Committee Update and Recommendations - 9/25/2009
Page 3
Agenda Item No. 10F
December 15, 2009
Page 8 of 133
Status: Staff and the CBAC began working with PBS&J over a nine months period to develop the
methodology and scope for water quality studies within Clam Bay. PBS&J was selected because
they were currently under contract with the County; they possessed extensive knowledge and
expert staff credentials working in similar estuaries in SW Florida. The Clam Bay Advisory
Committee felt that they were qualified to effectively collect and analyze the scientific data and
make recommendations based on the best science available.
In addition, a Best Value Offer was solicited from all firms under the Coastal Zone Management
Consulting Contract. PBS&J and Johnson Engineering responded to the solicitation and PBS&J
was selected by an independent selection committee utilizing standard criteria.
At the June 23, 2009 BCC meeting, the Board of County Commission authorized $120,000 to
evaluate all existing data and move forward with the data collection phase of the Water Quality
Study program that was recommended by the CBAC. In addition, the City of Naples authorized
$23,644 to the 'water quality program. With the City of Naples money and funds from the
Commission, enough funding was available to complete the data review and the data collection
phase of this project. This is the first three scope/work items of the PBS&J proposal and
includes:
1. Development of a Water quality program - $23,644: This includes a review of all the
existing water quality data and all previous modeling studies along with proposing water
quality standards in Clam Bay in consultation with FDEP and recommendations for a
sampling program.
2. Sediment and Biological Characterization - $20,804: This included sediment sampling
along with identification and characterization of the sediment in Clam Bay.
3. Physical Data Collection - $95,994: This includes subsurface topography along with flow,
tidal and current information at various locations within Clam pass and bay.
These work items should be completed and a draft report available by mid October 2009.
Future Action: The CBAC will review the final phase 1 report and submit appropriate
recommendations along with costs for the next phase to the CAC and the BCC in December,
2009. If the Committee finds that any of the existing data or models can be used more
extensively than previously thought, they will be incorporated into the next phase. The second
phase of this program, after BCC authorization to proceed, will be as follows:
. Development of a Circulation model (4a) - $86,017
. Sediment bypassing and Transport modeling (4B) - $38.550
. Peer Review - $5,000
The complete report along with recommendations from the water quality study should be
completed in 2010.
Clam Bay Advisory Committee Update and Recommendations - 9/25/2009
Page 4
Agenda Item NO.1 OF
December 15, 2009
Page 9 of 133
ManErove Maintenance and Estuarv Habitat
Task: Review and submit recommendations for ongoing mangrove maintenance and
maintenance of the hand dug channels.
Status: The Committee is working with the Pelican Bay Services Division to review their
successful mangrove maintenance program. To accomplish this, prior technical reports on the
condition ofthe mangroves, trend analysis and previously recommended actions will be were
reviewed to assure long term health of the mangrove community. The Committee has accepted
the past practices as a basis for future mangrove maintenance. However, specific firms
contracted for implementation may vary based on the cost effectiveness of proposals received
at the time of implementation. Review of the benthic community has already begun with the
sediment samples/analysis performed in the data collection phase of this project.
Future Action: Action required is as follows:
1. Review and approve the future mangrove maintenance plan.
2. Review historical, biological and ecological data; identify gaps in data sets; and make preliminary
recommendations based on these reviews to determine future direction in regard to improving
the health of the estuary.
3. Develop and recommend a budget to accomplish this activity.
These activities will be completed and integrated into the final management plan issued in
2010.
Maintenance DredEinE and Sand BvpassinE
Task: This activity will consist of reviewing previous reports on channel related issues and the
evaluation of various dredging cross sections to stabilize Clam Pass and determine the optimum
flushing levels of Clam Bay.
Status: This work was not planned to start until the 10 year permit was finalized and would be
the second portion of the modeling program. FDEP is leaning towards completion of the
modeling program as part of the lO-year permit. If this is the case, modeling of the system will
be a permit condition and will begin as soon as the data collection is completed.
Future Action: It is anticipated that this item will be included in the final management pian that
will be presented to the BCC in 2010.
Clam Bay Advisory Committee Update and Recommendations - 9/25/2009
Page 5
Agenda Item No. 10F
December 15, 2009
Page 10 of 133
Public Education and Outreach
~ This activity will prepare outlines of a proposed education plan for the public, local
residences and stakeholders of the Estuary waters. The plan will include suggested material
needs and methods for reaching all of the Estuary users. The focus of the public outreach
program will involve all stakeholders on the need for public involvement and action to help
assure the long-term viability of the Estuary.
Status: A special committee consisting of CBAC leadership with members of the public residing
in Sea Gate and Pelican Bay was formed to develop a public education and outreach program.
The highlights oftheir recommendations are as follows:
1. That an open letter be sent from CBAC's chairperson to the Pelican Bay, Sea gate, and
Naples Cay communities to update them on the status of Clam Bay and Clam Pass activities.
This direct mailing would assure maximum exposure to some 8,500 households on and
contiguous to Clam Bay. Mailed updates may follow as needed until the CBAC ceases to
exist and/or the projects are completed. Additionally, every effort should be made to place
similar information in all available traditional media and community outlets.
2. Likewise, that a direct, informational communication be placed on every available, relevant
web site, starting with Collier County's own, with postings updates to follow regularly as
projects are completed or as new developments occur.
3. That the educational component of Clam Bay and Clam Pass should be showcased to
enhance the public understanding of this valuable estuary system. To that end, a critical
review should be made of all informational and instructional signage on and around Clam
Bay with an eye toward adequacy, effectiveness, and modernization.
Future Action: The recommendations of the special committee will be finalized and included in
the final report to the BCC in 2010.
Budl1:et and Fundinl1: Sources
Task: This activity reviews all of the recommendations of the Clam Bay Advisory Committee
and formulates estimated funding requirements and sources offunds to enable
implementation ofthe recommended management plan. It identifies possible funding sources
such as the Tourist Development Council, local City governments and associations, national,
state and county governments and a review of availability of grants from all possible sources.
Clam Bay Advisory Committee Update and Recommendations - 9/25/2009
Page 6
Agenda Item NO.1 OF
December 15, 2009
Page 11 of 133
Status: A copy of the funding requirements through the development of a management plan is
attached.
Future Action: Receive approval from the BCC for this final long term budget and funding plan.
Committee Future
Task: Per Ordinance, the Clam Bay Advisory Committee is schedule to sunset on 12/31/2009
unless an extension of the sunsetting provision is requested of the BCC by the CBAC by
10/20/2009.
Status: As noted in this status report the CBAC requires time beyond 2009 to complete its
testing, its review of data, its completion of a long term management plan for the Estuary and
its recommendations on the management of such plan.
Future Action: The Clam Bay Advisory Committee is requesting that this advisory committee
not be sunsetted until the Management Plan for Clam Pass/Clam Bay has been developed,
vetted within the community and approved by the BCe. This will require a first extension of the
Committee by the BCC through June 30, 2010. Additional extensions or permanent status may
be considered by the Bee at that time.
Clam Bay Advisory Committee Update and Recommendations - 9/25/2009
Page 7
~
Clam Bay AdYisory Committee
Agenda Item No. 10F
December 15, 2009
Page 12 of 133
Operational Bud/!et and Capital Reauirements - Au/!ust 2009 throu/!h July 2010
Fundin/! Reauirements - Au/!ust 2009 throu/!h July 2010
ManR'fOVe Maintenance (Fund 320 M Pelican Bav Services Division)
The Board of County Commissioners and the Pelican Bay MSTBU has equally funded
Clam Bay mangrove maintenance for FY 09 and FYIO through the Pelican Bay
Services Division. $170,000 has been budgeted for mangrove maintenance for
FY2010. Funding and responsibility for future years is yet to be determined. No
funds are included in the budget of the Clam Bay Advisory Committee for this
activity.
,,--.
Fund 111 - UnincOfDorated Collier (ountv
Court Recording and Oocumentation Costs (12 months at $300/mo.)
Water Quality Monitoring in Clam Bay System
Chemicals and YSI probes
lab Fees (9 locations for 12 months)
Consulting and Analysis Support
Public Outreach and Communciations
Peer Review
Sediment toxicology
Installation of Beach and Inlet Safety signs and Permitting
Permitting and Installation of Navigational Markers in Clam Bay
Estuary Wildlife and Habitat Preliminary Analysis
Fund 111 Subtotal
Svstem Modelin. (Fund 19S - TOe)
Optimization of tidal flushing, water quality and mixing
Optimize of pass/cross sections including sediment bypassing and
transport modeling
Existing model review and analysis
19S Fund Subtotal
Total FY10 Funding Requirements
Previously Funded Activities
Mangrove Maintenance FY 2010 (Fund 320)
Water Quality and Model Data Review/Anaylsis - (Fund 1111
Water Quality and Model Data Review/Anaylsis - City of Naples
lO-year Permit Application (Fund 19S)
Total FYlO Funding Req and Previously Funded Activities
,-
$3,400
$1,000
$18,000
$4,000
$1,000
$S,OOO
$30,000
$s,OOO
$1S,000
$20,000
$86,017
$38,500
$8,000
$170,000
$120,000
$23,644
$115,700
$
$
$0
$102,400
$132,517
$234,917
$429,344
$664,261
c;f7fuT County
Agenda Item NO.1 OF
December 15, 2009
Page 14 of 133
Executive Summary
The project conducted by PBS&J included the following elements: an assessment of the status
and trends (if any) in water quality and the general biological features of Clam Bay and
Moorings Bay and recommendations on the design of future monitoring efforts, a review of
existing circnlation models for Clam Bay, and the collection and analysis of hydrodynamic data
from Clam Bay and MOOlings Bay. These elements are summarized below.
Review of the existing Water Quality Data within the Clam Bay System indicates:
1. While there are numerous water quality monitoring programs throughout the Clam and
Moorings Bays systems, the water quality data from efforts in Clam Bay is not being
placed into the State of Florida's Storage and Retrieval (STORET) database. This is
inconsistent with guidance given to 'local governments through Florida Administrative
Code (FAC 62-40.540(3)) and Florida Statutes (FS 373.026(2)). Data collected by the
City of Naples for Moorings Bay is being placed into STORET.
2. The lack of data placed in the STORET system could trigger FDEP to perform its own
data collection program similar to recent efforts in Rookery Bay and the Gordon River.
In both these instances, state-directed sampling and/or data interpretation resulted in
impaired water body classification, and a state mandated/directed remediation plan was
developed for the Gordon River.
3. Water quality data collected by the Conservancy of Southwest Florida does not meet the
requirements for parameter lists that are required by both the State of Florida's Impaired
Waters Rule (IWR) and Total Maximum Daily Loads (TMDL) program. The database
for water quality data collected by the Pelican Bay Services Division (Division) includes
obvious errors, although more recent data (as of 2005) appear to not have these same
problems. The collection sites visited by the Division are for permit-required monitoring
efforts and most locations are not suitable for baseline ambient water qnality monitoring
programs. Five of the sites visited by the Division were used here for further ambient
water quality analysis, despite limitations due to sample locations.
4. Data from these five locations, while not properly located for ambient monitoring
purposes, clearly indicate that Clam Bay would be classified as a "VeJified Impaired" for
water quality. Levels of dissolved oxygen (DO) are frequently below standards set in the
IWR (FAC 62-302.530). Additionally, the data indicates that portions of Clam Bay
exceed threshold values of chlorophyll-a established in the IWR (FAC 62-302.530). As
such, Clam Bay would be classified as "Verified Impaired" for both DO and nutrients.
However, both the DO and the ch10rophyll-a standards set by the State of Florida can be
inappropriate for Southwest Florida water bodies; Collier County should work with staff
from the Florida Department of Environmental Protection to develop site specific
alternative criteria for both these parameters. This would allow Collier County to respond
PBS.'
.,
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Executive Suil'lmat9f 133
to actual water quality problems, without diluting its efforts by pursumg "fixes" to
impairments that are naturally occurring.
5. Chlorophyll-a is an indicator of phytoplankton abnndance and is frequently characterized
as an indicator of how green the water appears. To control Chlorophyll-a in Clam Bay,
three critical parameters need to be addressed; Total Nitrogen, Total Phosphorus and
Retention Time.
6. A draft water quality monitoring program for Clam Bay is outlined within this report. It
is strongly recommended that such a program be implemented and information collected
be entered into STORET. Additional information on nitrogen and phosphorus (organic
or inorganic) and retention time is needed before any recommendations related to system-
wide restoration can be made.
One of the critical indicators of the biological health of the estuary is how deep oxygen can
penetrate into the sediments. Deeper penetration of oxygen into the sediment layer generally
indicates a system with a greater diversity of life (Flora and Fauna) to support a variety of marine
organisms.
A general biological survey of Clam Bay and Moorings Bay found that:
I. The Redox layer, an indicator of how deep into the sediments oxygen can penetrate, was
much deeper on average in Moorings Bay than in Clam Bay. Upper Clam Bay had the
shallowest Redox depths, followed by Outer Clam Bay and then Inner Clam Bay.
2. A fine-grained sediment layer was found in most locations of Outer Clam Bay. This
sediment depth was approximately 5 feet in the arca of the Seagate canals, was not
prevalent in Moorings Bay, and varied in depth in Outer, Inner and Uppcr Clam Bays.
3. It is not known at this time if the fine-grained sediment layer is naturally occun'ing, or
occuning as a result of man-made changes to the Clam Bay system. It is, however,
known that the sediment layer in the Seagate canals has accumulated since the canals
were dug in the 1950s.
4. Fine-grained sediments similar to the ones found throughout Clam Bay typically attract
contaminants. A 1997 study by Collier County confirmed elevated levels of various
contaminants in the sediments of Clam Bay, at levels expected to adversely impact the
health of benthic communities. It is strongly rccommended that more recent contaminant
levels and the age of the sediment layer be determined to indicate if contaminant levels
are increasing, and if the sediment layer is naturally occurring or a rcsu]t of reduced
circulation.
5. These same sediments appear to create conditions that limit the diffusion of dissolved
oxygen into the bottom.
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6, The shallow Redox layer depths in most of Clam Bay, in combination with the fine-
grained sediments found in most locations, suggest that benthic (i.e., "bottom-dwelling")
communities in Clam Bay wonld be expected to be less diverse than in Moorings Bay.
7. Clam Bay and Moorings Bay are functionally different systems, and it is neither possible
nor appropriate to expect these two systems to have similar ecological functions; an
appropriate question is not whether or not Clam Bay is different from Moorings Bay, but
whether the water quality and sediment composition of Clam Bay is a natural condition
or the result of changes in pollutant loads and/or circulation patterns,
8, It is highly recommended that Collier County pursue a sediment toxicology and sediment
aging study within the Clam Bay system.
In reviewing the previous circulation model for Clam Bay completed by Humiston & Moore as
well as the flow calculations by Tackney & Associates, the following key points are offered:
1. The previous circulation model was completed in 2003 by Hnmiston and Moore for Clam
Bay was sufficient and effective for its purpose at the time. Its purpose was to investigate
the freshwater and saltwater flows required to address mangrove die-off in the north of
the estuary. It was never designed as a comprehensive model to improve tidal flushing
for the health of the entire estuary.
2. A number of critical issues limit the Humiston & Moore model's ability to function as a
comprehensive model for the Clam Bay and Moorings Bay system. These limitations
include:
a. The model boundary ended at Seagate Drive, and did not include exchange
between Clam Bay and Moorings Bay,
b. The model domain does not include water movement into (and then out of) the
mangrove forest during normal tidal cycles and high water events.
c. Only one stormwater input is included in the model's water budget.
d. The model's offshore tidal boundary was limited in both amplitude and duration.
e. The model was calibrated for tidal range only, not flow velocities.
3. Modifying the Humiston and Moore's model to fnnction as a comprehensive model will
essentially require starting from scratch with the model development.
4. If staI1ing from scratch is required, then it is desirable to have the capability for varying
models (circulation, constituent transport, morphology, etc.) to be linked together on a
common platform.
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5. The 1996 report by Tackney & Associates includes basic theoretical calculations
regarding tidal attenuation and water level setup within the Clam Bay system, supported
by a field data collection effort. Also included is a discussion about inlet stability, and
while this discussion is theoretically sound, the rep0l1 provides limited to no calculations
or analysis to relate these conjectures specifically to Clam Pass. A preliminary model
was mentioned, but no report or model could be located.
6. The Tackney report measured currents at the Seagate Dr culverts, and used a basic
estimation of flow variation to conclude that flow is uniform in both directions, resulting
in little net exchange. The field work effort of August 2009 showed that this is not the
case; due to tidal elevation and phase differences between Clam Bay and Moorings Bay,
southerly flow dominates at Seagate Dr, and net water exchange is southerly from Clam
Bay into Moorings Bay.
With respect to water circulation and flushing in the system:
1. The Clam Bay system was impacted in the early 1950s by construction of two roads;
Vanderbilt Beach Road to the north, and Seagate Drive to the south. As it was originally
configured, Seagate Drive closed tidal connections to the south, and Clam Pass was left
as the only connection between Upper, Inner and Outer Clam Bays and the Gulf of
Mexico.
2. In response to water quality concerns, culverts were placed under Seagate Drive in 1976
to allow for tidal exchange between Clam and Moorings Bays. Originally, the culverts
were intended to allow flows only from Moorings Bay into Clam Bay, but their
construction was such that flows actually could occur in both directions. In the 1980s,
the tidal connection between Upper Clam Bay and Vanderbilt Lagoon was severed due to
development activities (Collier County, 1997).
3. Although Clam Bay's watershed had been developed rather extensively, the shoreline
features of Clam Bay have not been altered nearly as much as the shoreline features of
Moorings Bay, which had undergone significant modifications due to dredge and fill
activities as early as the 1970s.
4. In the late 1990s, as a result of observed mangrove die-offs, a permit was obtained to
conduct dredging activity within Clam Pass and Clam Bay. Three dredging events have
taken place over the past 10 years. The dredging activity focused on improving water
circulation and flushing, largely to Upper and Inner Clam Bays, by deepening the Pass
and interior channels within the estuary.
5. Hydrographic data (currents and water levels) was collected in the Clam Bay and
Moorings Bay systems over an eight day period in August 2009. In Clam Bay, tidal
ranges declined in amplitude and lagged in phase with increased distance from Clam
Pass, a result of channel meandering, constrictions, and friction losses in the system.
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Conversely, in Moorings Bay, there was little to no tidal amplitude attenuation and little
phase lag with respect to Doctor's Pass.
6. The tidal range in Moorings Bay was greater than the tidal range observed in Clam Bay,
indicating Moorings Bay experiences greater water circulation and flushing than Clam
Bay. In addition, Moorings Bay experiences less tidal lag then found in Clam Bay.
7. In the area of Seagate Drive, maximum current velocities were ten times greater in the
southerly direction than in the northerly direction, and water levels at low tide were up to
].5 ft higher on the north side (Clam Bay) versus the south side (Moorings Bay),
resulting in a net flow of water southward of 969,000 cubic feet per tidal cycle from
Clam Bay into Moorings Bay. Due to the net southerly exchange, it would appear that
water quality in Clam Bay is not strongly affected by Moorings Bay.
8. In order to analyze potential changes to the system to optimize circulation and dissolved
oxygen (DO) within Clam Bay, a hydrodynamic model will need to be developed to
understand the interactions between Clam Bay (Upper, Inner and Outer), Clam Pass,
Moorings Bay, and Doctor's Pass.
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Table of Contents
1 .0 Introduction........................................................................,............................................ ............,... 1
1.1 Clam Bay and Moorings Bay Issues ..................................,............................................... 1
1.2 Outline of Present Study............. ............. .......................................................................5
2.0 Methods................,..............................................................................................................,.......... 7
2.1 Task 1 - Development of a Water Quality Monitoring Program ........................................7
2.2 Task 2 - Status and Trends of Water Quality within Clam Bay and Moorings Bay........... 7
2.3 Task 3 - Sediment and Biological Health Characterization............................................... 7
2.4 Task 4 - Physical Data Collection .....................................................................................8
Hydrographic Survey.... ................... ............... ................ ...................................8
Currents/Water levels.. ................ ................... ................ ............... ..............................8
3.0 Water Quality Review and Analysis .............................................................................................. 10
3.1 Task 1 - Development of a Quality Monitoring Program .......... .............. .......................10
3.2 Task 2 - Status and Trends of Water Quality within Clam and Moorings Bays ..............13
Dissolved Oxygen......................................................................,.... .................................14
Chlorophyll a............ ............... ................ ......................................................................17
limiting Nutrient... ............. ..................... ................. .............. ................20
Total Nitrogen.. . ...................................... ................. ................. .............. ...............23
Total Phosphorus... ..... .................... . .........._.................................................. 25
3.3 Task 3 - Sediment and Biological Health Characterization.. .............. ..........28
General Biological Survey Results.. ............... .................... ............. ............. ...............28
4.0
Water Quality Discussion and Recommendations..
................,....32
5.0 Model Review.... ......................................... ....................................................... ......... 37
5.1 Review of RMA2 model of Clam Bay, Humiston & Moore (2003) ...................................37
Summary.........................................................................................................,................ 37
Model Report Overview...... .................... ................. ................................ ................ ...37
Model Restrictions and limitations ...... ................. ................. ............. ................... .....38
5.2 Review of Clam Bay hydrographic assessment report, Tackney & Associates
(1996) ...................... ............... ................. .........................................................40
Report Overview........ ..................... .................. ................................ ..............40
Report Review .................. ................. .............. ................. .........41
6.0
Hydrographic Data Collection
....................42
7.0 Hydrographic Data Analysis...........................................................,...................................... ........ 45
7.1 Introduction................ ................. ..................................,................,............ ................... 45
7.2 Water levels ............. .............. ...................... .............. .................... ...45
7.3 Current Velocities and Flow Rates..... ............... ................. ............... ................... .......62
7.4 Conclusions...................... ... ......... ................. ............................................................ 76
8.0
References................ .....
.......78
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October 2009
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List of Figures
Figure 1.1. Aerial Photo (circa 1940s) of Outer Clam Bay and immediate watershed ................2
Figure 1.2. Aerial Photo (1958) of northern Moorings Bay and Outer Clam Bay (photo from
Antonini et a!., 2003). ................ ................................................................................. 2
Figure 1.3. Aerial photograph (2006) of Clam Bay and immediate watershed ............................ 3
Figure 1.4. Aerial photograph (1970s) of Moorings Bay and immediate watershed (photo from
Antonini et a!., 2003). ........ -... ......................................................................................4
Figure 1.5. Project Area and Location Names for Clam and Moorings Bays. .............................6
Figure 3.1. Timeline of Various Water Quality Monitoring Efforts in Clam and Moorings Bays.
...........................................................................................................................10
Figure 3.2. Station Locations for Various Water Quality Monitoring Efforts in Clam Bay (left)
and Moorings Bay (right). Pelican Bay Services Division stations in blue, PBS&J (2008)
sites in red, Conservancy of Southwest Florida stations in white, and City of Naples
stations in yellow. ........................ ..........................................................................11
Figure 3.3. Sample Site Locations for Trend Analysis in Clam Bay.......................................... 14
Figure 3.4. Dissolved Oxygen over the period of record in Clam Bay. Erroneous Values are
Evident between August 2001 and August 2002............................................................. 15
Figure 3.5. Dissolved Oxygen in Clam Bay with the y-axis Truncated. The Black Line denotes
4.0 mgIL, the Threshold for Impairment from FDEP. ....................................................16
Figure 3.6. Average and Median Dissolved Oxygen Levels in Clam Bay over the Period of
Record (left axis). The Percent of DO Values Lower Than the IWR Threshold for
Marine Waters (4.0 mg/L; right axis). ............................................................................. 17
Figure 3.7. Chlorophyll a Concentration over the Period of Record in Clam Bay..................... 18
Figure 3.8. Chlorophyll a Concentration Over the Period of Record in Clam Bay With the y-axis
Truncated (the orange line denotes 361lg/L, the upper 90% value for Florida estuaries;
the red line indicates the median value for Florida estuaries; 9 mg/L)............................19
Figure 3.9. Annual Average Chlorophyll a Concentration for 2005, 2006, 2007 and 2008 (the
black line denotes 11 Ilg/L, the threshold for impainnent from FDEP's IWR; the red line
indicates the median value for Florida estuaries; 9 mg/L)............................................... 20
Figure 3.10. TN:TP Ratios for Clam Bay from January 2005 to May 2009 (the shaded area
indicates the range for a co-limited system). ................................................................... 21
Figure 3.11. Relationship Between Chlorophyll a and Total Nitrogen in Clam Bay (figure from
PBS&J [2008]). ................. ....................................................................................... 22
Figure 3.12. Relationship Between Chlorophyll a and Total Phosphorus in Clam Bay (figure
from PBS&J [2008]). ................... ............................................................................ 23
Figure 3.13. Total Nitrogen Levels in Clam Bay (the orange line denotes 1.6 mg/L, the upper
90% level for Florida estuaries; the red line indicates the median value for Florida
estuaries [0.8 mg/LJ). .................. ............................................................................. 24
Figure 3.14. Mean and Median TN concentrations (left axis). Percent of TN Values Greater
than the Median for Florida estuaries (0.8 mg/L; right axis). .......................................... 25
Figure 3.15. Total Phosphorus Levels in Clam Bay (the orange line denotes 0.2 mg/L, the upper
90% level for Florida estuaries; the red line indicates the median value for Florida
estuaries [0.07 mg/L]). .................... ......................................................................... 26
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Figure 3.16. Mean and Median TP concentrations (left axis). Percent of TN Values Greater than
the Median for Florida estuaries (0.07 mg/L; right axis)................................................. 27
Figure 3.17. Results of Redox Depth Survey in Clam Bay (left) and Moorings Bay (right). Red
symbols represent Redox layer at surface, Orange represent Redox layer < 20 em, Green
symbols represent Redox layer> 20 em. ......................................................................... 28
Figure 3.18. Results of Seagrass Survey in Clam Bay (left) and Moorings Bay (right). Green
symbols represent presence of seagrass, Red symbols represent absence of seagrass)... 29
Figure 3.19. Results of Macroalgae Survey in Clam Bay (left) and Moorings Bay (right). Green
symbols represent presence of seagrass, Red symbols represent absence of seagrass)... 31
Figure 4.1. Recommended Sampling Locations for Upper, Inner and Outer Clam Bay. ........... 35
Figure 6.]. Coastal Leasing MicroTide Gauge and concrete base. ............................................ 42
Figure 6.2. Elevating Tide Gauge with RTK GPS......................................................................43
Figure 6.3. SonTek ADCP on concrete base. .............................................................................44
Figure 7.1. Instrument deployment locations for Clam Bay data collection; August 15 to Angust
23,2009. ............................. .................................................................................. 47
Figure 7.2. Water surface elevations in Upper Clam Bay; August 15 to August 23, 2009. .......48
Figure 7.3. Water surface elevations in Inner Clam Bay; Augnst 15 to August 23, 2009. ........49
Figure 7.4. Water surface elevations at North Bridge; August 15 to August 23,2009.............. 50
Figure 7.5. Water surface elevations at Gulfside Clam Pass; August 15 to August 23, 2009....51
Figure 7.6. Water surface elevations in Clam Pass; August 15 to August 23, 2009.................. 52
Figure 7.7. Water surface elevations at South Bridge; August 15 to August 23, 2009. .............53
Figure 7.8. Water surface elevations in Outer Clam Bay; August 15 to August 23,2009. ........ 54
Figure 7.9. Water surface elevations at North Seagate Dr; August 15 to August 23, 2009. ...... 55
Figure 7.10. Water surface elevations at Seagate Dr; August 15 to August 23, 2009................56
Figure 7.11. Water surface elevations at South Seagat~ Dr; August 15 to August 23, 2009. .... 57
Figure 7.12. Water surface clevations at Park Shore Dr; August 15to August 23,2009. .........58
Figure 7.13. Water surface elevations at Harbour Dr; August 15 to August 23, 2009............... 59
Figure 7.14. Water surface elevations at Gulfside Doctor's Pass; August 15 to August 23,
2009....................................... ............................................................................. 60
Figure 7.15. Current velocity and water surface elevation at North Bridge; August 15 to August
23,2009. ............................. ................................................................................ 63
Figure 7.16. CUITent velocity at NOlth Bridge; August 15 to August 23,2009..........................64
Figure 7.17. Current velocity and water surface clevation at Clam Pass; August 15to August 23,
2009. ................................. ................................................................................... 65
Figure 7.18. Current velocity at Clam Pass; August 15 to August 23, 2009.............................. 66
Figure 7.] 9. Current velocity and water surface elevation at South Bridge; August 15 to August
23,2009. ................................. ............................................................................. 67
Figure 7.20. Current velocity at South Bridge; August 15 to August 23,2009..........................68
Figure 7.21. Current velocity components at South Seagate Dr; August 15 to August 23,2009.
..............................................................................................~
Figure 7.22. Current velocity magnitude at South Seagate Dr; August 15 to August 23, 2009. 70
Figure 7.23. Current velocity components at Park Shore Dr; August 15 to August 23,2009.... 71
Figure 7.24. Current velocity magnitude at Park Shore Dr; August 15 to August 23, 2009. ..... 72
Figure 7.25. Current velocity componcnts at Harbour Dr; August 15 to August 23, 2009. ....... 73
Figure 7.26. Current velocity magnitude at Harbour Dr; August 15 to August 23, 2009. .........74
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List of Tables
Table 3.1. Water Quality Parameter List for Various Monitoring Programs, Compared to Data
Requirements for the State of Florida's TMDL Prof,'fam. ...............................................12
Table 4.1. Recommended Parameter List for Ambient Waler Quality Monitoring Program for
Clam and Moorings Bays. .............. ........................................................................... 36
Table 7.1. Water level parameters in Clam Bay; August 15 to August 23, 2009.......................46
Table 7.2. Current velocity and flow rate parameters in Clam Bay; August 15 to August 23,
2009. ................................... ................................................................................ 75
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1.0 Introduction
1.1 Clam Bay and Moorings Bay Issues
Clam Bay and Moorings Bay are important natural features in Collier County. Associated with
the increased development of Collier County, there has been concern among the public that Clam
Bay and Moorings Bay have perhaps been adversely impacted by environmental pressures that
accompany development.
In its historical configuration, Clam Bay and Moorings Bay would have had fresh water
discharges mostly via small tidal creeks and groundwater inflow. Watershed development most
likely increased both the amount of freshwater discharged into these systems as well as the
amount of total suspended solids, nitrogen and phosphorus (PBS&J, 2008). Additionally, it was
likely that in their historical configurations, the inlets that connected Clam Bay and Moorings
Bay to the Gulf of Mexico likely migrated and closed periodically due to the influence of various
tropical storm events (Collier County, 1997). More recently, water quality changes that typically
accompany the closing of such inlets are viewed as unacceptable to the general public, and so
Clam Pass in particular has been the focns of much activity to keep it open since at least the
1970s (Collier County, 1997).
In the late 1990s, as a result of observed mangrove die-offs, a permit was obtained to conduct
dredging activity within Clam Pass and Clam Bay. Three dredging events have taken place over
the past 10 years (1999, 2002 & 2007). The dredging activity focused on improving water
circulation and flushing, largely to Upper and Inner Clam Bays, by deepening the Pass and
interior channels within the estuary.
The Clam Bay watershed, like much of Collier County, has experienced dramatic changes over
the past 60 years. In the 1940s, there was little evidence of human modifications to Clam Bay
and its immediate watershed (Figure I. I). In contrast, much of the shoreline of Moorings Bay
was significantly altered through dredge and fill activity, such that natural shoreline features in
the northern portions of Moorings Bay were mostly absent by the 1950s (Figures 1.2 and 1.3).
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Figure 1.1. Aerial Photo (circa 1940s) of Outer Clam Bay and immediate
watershed
Figure 1.2. Aerial Photo (1958) of northern Moorings Bay and Outer Clam Bay
(photo from Antonini et aI., 2003).
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In its pre-development condition, both Doctor's Pass and Clam Pass were small natnral tidal
inlets, and both were subject to migration and closure (Antonini et a!., 2003). The Clam Bay and
Moorings Bay systems were also connected to each other via narrow and winding tidal creeks in
the vicinity of today' s Seagate Drive.
The Clam Bay system was impacted in the early 1950s by construction of two roads; Vanderbilt
Beach Road to the north and Seagate Drive to the south. As it was originally configured, Seagate
Drive closed tidal connections to the south, and Clam Pass was left as the only connection of
Upper, Inner and Outer Clam Bays to the Gulf. In response to water quality concerns, culverts
were placed under Seagate Drive in 1976 to allow for tidal exchange between Clam and
Moorings Bays.
Originally, the culverts were intended to allow flows only from Moorings Bay into Clam Bay,
but their construction was such that flows actually could occnr in both directions (Collier
County, 1997). In the 1980s, the tidal connection between Upper Clam Bay arid Vanderbilt
Lagoon was severed due to development activities (Collier County, 1997).
Although Clam Bay's watershed had been developed rather extensively, the shoreline featnres of
Clam Bay (Figure 1.3) have not been altered nearly as much as the shoreline features of
Moorings Bay, which had undergone significant modifications due to dredge and fill activities as
early as the] 970s (Figure 1.4).
Figure 1.3. Aerial photograph (2006) of Clam Bay and immediate watershed
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Figure 1.4. Aerial photograph (1970s) of Moorings Bay and immediate watershed
(photo from Antonini et aI., 2003).
Prior studies in similar lagoonal systems in Southwest Florida suggest that increased
urbanization brings about increased freshwater inflows and substantial increases in nonpoint
sources of both nitrogen and phosphorus (i.e., Lemon Bay; Tomasko et aI., 2001).
In the early 1990s, an area of mangrove die-off of approximately seven acres was discovered in
Upper Clam Bay, north of Clam Pass. By the mid-I990s, the area of die-off (affecting mostly
black mangroves) had expanded to approximately 50 acres. In response to the die-off, Pelican
Bay residents acquired the services of a series of consultants to develop a plan of action to
remediate the mangrove loss. In the meantime, various intermediate measures were performed,
including the dredging of Clam Pass in April 1996 and the clearing of several channels by hand
evacuation in August and November 1996 (Conservancy of Southwest Florida, 1997).
Based on assessments of water quality data collected by Collier County Environmental Services
and the Pelican Bay Services District, there did not appear to be evidence that mangrove
mortality was caused by elevated levels of any toxic chemicals, nor did the data suggest changes
in nutrient concentrations would have been a likely factor in die-off. Instead, the conclusion was
reached that die-off was likely due to excessive freshwater input to the system from the adjacent
developed uplands and an inadequate dispersion of the increased freshwater input due to severely
constricted tidal channels in the mangrove forest. As a result, the mangrove forest became
inundated with water levels higher than the tops of the black mangrove pneumatophores. The
duration of increased water levels was sufficient to kill the trees by blocking oxygen exchange to
the below ground tissues. In 1998, the Collier County-Pelican Bay Services Division was issued
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a permit to restore and manage the Clam Bay Natural Resource Protection Area based on the
Clam Bay Restoration and Management Plan (Brown and Hillestad, 1998).
The management component of the Clam Bay Restoration and Management Plan consists of four
major activities:
1. Retrofitting of the culverts under Seagate Drive with flap gates, such that flow only goes
north.
2. Re-dredging of Clam Pass.
3. Excavation of tidal connections in interior portions of Upper Clam Bay.
4. Development of stormwater best management plans for on-site retention of water from
surrounding development.
1.2 Outline of Present Study
In response to concerns related to the issues of water quality and circulation in the Clam Bay and
Moorings Bay systems, Collier County requested PBS&J prepare a proposal to conduct a
circulation and water qnaJity study to determine the following:
. What is the extent and relative health of the natural resources in Clam Bay and Moorings
Bay?
. What do historical data suggest, in tenns of status and trends, about the health of Clam
Bay and Moorings Bay?
· How do circulation patterns and nutrient delivery interact to create spatial patterns of
water quality in Clam Bay and Moorings Bay, and how these patterns affect the estuarine
flora and fauna?
· How will changes in circulation within Clam Bay and between Clam Bay and Moorings
Bay affect the overall estuary (as defined in Figure 1.5)?
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Figure 1.5. Project Area and Location Names for Clam and Moorings Bays.
This report summarizes results obtained to-date on these questions.
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2.0 Methods
2.1 Task 1 - Development of a Water Quality Monitoring Program
The City of Naples currently conducts water quality monitoring at four stations in Moorings Bay,
immediately to the south of Clam Bay. In addition, water quality monitoring in Clam Bay has
been conducted by the Pelican Bay Services Division (PBSD) since 1991, and was conducted by
the Pelican Bay Improvement District prior to that date. This portion of the project was to
determine station locations, water quality parameters, and sampling frequencies that would allow
for the development of an integrated water quality monitoring program for both Clam Bay and
Moorings Bay.
2.2 Task 2 - Status and Trends of Water Quality within Clam Bay and Moorings
Bay
Based on a collaborative effort between major stakeholders and County staff, a list of contacts
that might possess appropriate water quality data sets was developed. Water quality data sets
were then asked for and received from the Pelican Bay Services Division, Collier County, the
City of Naples, and the Conservancy of Southwest Florida. Water quality stations were
identified as to their geographic location, and data were analyzed to determine the status and
trends (if any) in water quality over time.
2.3 Task 3 - Sediment and Biological Health Characterization
This characterization involved the investigation of Redox depths, seagrass coverage, and
macroalgal coverage throughout the Clam and Moorings Bays system. Field sampling occulTed
during a 2 day period in August 2009. Sample locations were randomly assigned using ArcGIS,
but were stratified such that different energy/circulation regimes throughout the project area
would be visited, i.e. dead-end channels, shallow vegetated areas, shoal locations, navigation
canals, tidal canals, etc. Samples were collected by inse11ing a clear PVC tube - sediment
sampler into the bottom sediments until penetration through any potential organic-rich layers.
Following recovery, the samples were measured for depth to any visible Redox layers (an
indicator of oxygen availability).
At each site, observations were made of the general biological community structure and health
(i.e., presence of bivalve siphons, seagrass and/or macroalgal abundance, etc.).
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2.4 Task 4 - Physical Data Collection
Hydrographic Survey
This task consisted of completing a bathymetric survey of a portion of the project area. The
bathymetric survey of the project area included Clam Pass (including the ebb shoal complex),
Upper, Inner, and Outer Clam Bay, and Moorings Bay. The purpose of the survey was to
delineate the existing bottom topography in order to create an np-to-date elevation data set.
Existing published benchmarks were utilized. The horizontal datum (coordinates) were
referenced to the North American Datum 1983 (NAD83) Florida State Plane Coordinate System.
The vertical datum (elevations) was referenced to the North American Vertical Datum of 1988
(NA VD88) and will be based on published horizontal and vertical control points. Drawings
. were prepared showing the bottom elevations and contours. Cross-sections were created
indicating measured water depths, tide information, and existing bottom grades.
Standard survey quality depth sounding equipment was used to record water depth data where
possible for the project area. Differential GPS and a high frequency single beam digital
fathometer linked to Hypack data collection software were utilized. Cross sections were taken at
a maximum 200 foot interval throughout the survey area.
Currents/Water levels
CmTent and water level measurements were taken within the project area over a period of 8 days
for use in a planning level circulation analysis. This data can also be used for the calibration of a
potential hydrodynamic numerical model. Cnrrents and water levels were measured at five and
seven locations within the project area, respectively. These measurements were obtained
through a field deployment using the following instruments:
· Coastal Leasing Microtide Gauges (7)
o Placed: (I) Upper Clam Bay, (2) Inner Clam Bay, (3) Outer Clam Bay, (4)
Gulfside Clam Pass, (5) Gulf side Doctor's Pass, (6) north of Seagate Drive in
Outer Clam Bay, (7) south of Seagate Drive in Moorings Bay.
· Workhorse Sentinel (3) and Sontek SW (3) current meters with water level
o Velocity and water level at five locations throughout domain: (I) Clam Pass
throat, (2) Clam Bay north pedestrian bridge, (3) Clam Bay south pedestrian
bridge, (4) South of Seagate Drive culvert, (5) Park Shore Drive bridge, and (6)
Harbour Drive bridge
Key issues to be addressed using the results include:
· Velocities and flow rates through Clam Pass
· Flow exchange volume and direction between Clam Bay and Venetian Bay through the
Seagate Driveculvel1
PHS1
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Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15. 2009
M~hti'dSf 133
· Water level differences and tidal phase lag between Clam Pass, Clam Bay, Venetian Bay,
Moorings Bay, and Doctor's Pass
Graphics were prepared showing the above parameters during the time of deployment. This
information may be used to gain a working understanding of the circulation patterns in the Clam
Bay and adjacent water bodies, as well as develop alternatives for enhancing restoration efforts
within Clam Bay through a comprehensive numerical modeling effort.
PBSl
9
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Page 32 of 133
3.0 Water Quality Review and Analysis
3.1 Task 1 - Development of a Quality Monitoring Program
Results from an analysis of water quality monitoring data sets are shown in Figure 3.1. The
water quality monitoring efforts of the City of Naples, in Moorings Bay, are the most recently-
initiated efforts. A short-term water quality data set from PBS&J, focused on Outer Clam Bay,
was conducted in 2007 only. In contrast, there are much longer timelines for water quality data
collection efforts by both the Conservancy of Southwest Florida (Conservancy) and the Pelican
Bay Services Division (Pelican Bay).
Figure 3.1. Timeline of Various Water Quality Monitoring Efforts in Clam
and Moorings Bays.
City of Naples . PBS] ~ PBSD .. Southwest Conservancy (Clam Bay) . Southwest Conservancy (Moorings Bay)
. I
1:1II11
.-
......
---..-------.----...............-............... .. .. .. .. .
~
Nov-8t May-87
Nov-92
May-98
Nov-03 Jun-09
In addition to information related to the duration of sampling efforts, station locations were also
plotted, as shown in Figure 3.2.
PBSI
10
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15. 2009
Water Quality Review and ARalrySlsf 133
Figure 3.2. Station Locations for Various Water Quality Monitoring Efforts
in Clam Bay (left) and Moorings Bay (right). Pelican Bay Services Division
stations in blue, PBS&J (2008) sites in red, Conservancy of Southwest
Florida stations in white, and City of Naples stations in yellow.
There is no single water quality monitoring program throughout thc cntire Clam and Moorings
Bays system. The Pelican Bay monitoring program, which was originally designed to answcr
specific permit-related water quality questions, includes stations that are appropriate for
permitting needs but would not be appropriate for an ambient monitoring program; a smaller
subset of stations (described below) were thc focus of trend analysis efforts. In contrast, stations
used by the Conservancy for its monitoring efforts tcnd to be located in more open-water
locations, and are, on the whole, appropriately sited for a monitoring eff0l1. Station locations
used by PBS&J (2008) were in adequate locations for Outer Clam Bay, and could be useful
locations for further sampling efforts. Sampling locations used by the City of Naples appear to
be in appropriate locations for an ambient monitoring program.
PHSI
11
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item No.1 OF
December 15, 2009
Water Quality Review and Afii!d,StSf 133
A further factor, needed for examining the appropriateness of existing water quality efforts, was
to examine the parameters examined; particularly in relation to data requirements associated with
State of Florida efforts to implement the Total Maximum Daily Loads (TMDL) program (Table
3.1).
Table 3.1. Water Quality Parameter List for Various Monitoring Programs,
Compared to Data Requirements for the State of Florida's TMDL Program.
[-~-~~-~---r--
Water Qualit Cit les PBSJ
Chtorophvll a
~_~eophYl~____
Nitrate
"--~----
Nitrite
~t;~te-Nitri~.---
---- ...._--_..,..,"~_.._-----
~TnlalKjeldahl Nilrogen
Total Nitroo-en
Orthol'hosphal~__
IotaJJ'hgsphorus __
i9i~~~~_~_~d o~~g~_,_""
'Fecal Coliform
Ammonia
IArsenic
..----.------.--.~---=_r--.---
I !Pelic3n Bay I
iSouthwest Services jRequired for
,Conservanc !Division 'TMDL
BOD
:C~i-~'iurn ------
-'--'-'-'-'--'-"---'-
'Chloride
Co]~~
i~g~
Enterococci
,-------~-
,Hardncss- Calculated
e;--"
:Mao-nesium
i,.-......./:;'.----...------
TOlal Organic Carbon
r..........--..--..... .-..'-.,-----..-
[1I:>tal Suspended Solids
Turbidity
i-----n- ,
~~_!~til~~~~ndc::~ So!~~
TOlal Dissolved Solids I
~1!I~;te ---=----=-===-"1--------._-
~S_~linity"---~-
IConductivit
~H
I
~,~.!!1pcratur~._
Secchi
I ----
,Photosynthetically Active
~adiation (PAR)
Depl~____.____" ___ ____.______
i --~._.--_J
,____.~L._~,_~,._~_~
PHSI
12
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Water Quality Review and AR~SiSlf 133
Of all the water quality monitoring programs, past and cunent, only the Pelican Bay, PBS&J and
City of Naples programs contain all (or nearly all) the water quality parameters needed for the
State of Florida's TMDL program. Of particular note, the nutrient data collected and reported by
the Conservancy only includes inorganic nutrients (both nitrogen and phosphorus). Inorganic
nutrient levels are not adequate for rep011ing on nutrient loading and/or nutrient enrichment, as
levels of inorganic nutrients can be low because of low input, or low due to rapid uptake,
concepts established by numerous prior researchers (e.g., Smith et al. 1981, Valiela et al. 1990,
Tomasko and Lapointe 199 I). For this reason and others, the data collected by the Conservancy
cannot be used for assessing the health of the Clam and Moorings Bays systems as related to
nutrient issues.
3.2 Task 2 - Status and Trends of Water Quality within Clam and Moorings
Bays
Pelican Bay has the most extensive dataset available for the Clam Bay system. The Pelican Bay
sampling effort began in November 198] with water samples continuing to be sampled monthly.
A large suite of water quality parameters are analyzed including: total Kjeldahl nitrogen (TKN),
nitrate (N03), nitrite (NOe), total phosphorus (TP), chlorophyll a (ChI a) and dissolved oxygen
(DO). Sampling sites were located in both the mangrove fringe as well as near the open water of
the bays. As the berm locations are insufficient for analysis for an ambient water quality
monitoring program (although they are useful for permit compliance issues) a subset of 5
sampling sites were identified for status and trend analysis (Figure 3.3). These stations are
labeled as UCBRK (in the northcrnmost portions of Upper Clam Bay, along the shoreline) W-7
(at the n011hern trolley bridge), W-6 (at the trolley bridge n011h of Clam Pass), W-1 (at the canoe
ramp at the park), and Seagate (at Seagate Drive).
PBSI
13
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Water Quality Review and AR~'Y~Sf 133
Figure 3.3. Sample Site Locations for Trend Analysis in Clam Bay.
Dissolved Oxygen
Dissolved Oxygen (DO) data are available from November 1981 to May 2009 at the W-l, W-6
and W-7 sites (Figure 3.4). Sampling for the UCBRK and Seagate sites began in October 1996.
Extremely elevated concentrations of DO were observed between August 2001 and August 2002;
these data must have been reported inaccurately, and cannot be representative of the ambient DO
readings at that time. To accommodate this data problem, Figure 3.5 was created, where the y_
axis was truncated at a more realistic maximum DO level of 10 mg/l.
PBSI
14
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Water Quality Review and AI9a1ySisf 133
Figure 3.4. Dissolved Oxygen over the period of record in Clam Bay. Erroneous
Values are Evident between August 2001 and August 2002.
100
-.-W6 ~W-7 -:::;- W-l --:-UCBRK ~Seagate
80
"'-
'" GO
E-
o
.
'"
>-
.
o
"
.
>-
'0
~ 40
is
20
. t.,.' ~............... 'II
6.~ -.'. '~;'<"Jliil;.,~fliltj,~i;, .GIi: rj1 "...'.. .'" .....~ i 'I'
o ~,.~p -.it~ i! 'lIr'i~r. "-, ~
Sep-81
Mar 1)5
Au!; 88
101 n~\2
JulljS
Dee 1,;18
Jun-02
Nov-OS
Apr-09
PBSI
15
Clam Say System Data Collection and Analysis
October 2009
Agenda Item No. 10F
December 15, 2009
Water Quality Review and AflalY!fisf 133
Figure 3.5. Dissolved Oxygen in Clam Bay with the y-axis Truncated. The Black
Line denotes 4.0 mg/L, the Threshold for Impairment from FDEP.
. ------'---_..__.._-_.._--------~
-+-W-6
___W.7
-z--W.l
-UC:8RK
~S('ag<lte
10
~
K 6
o
.
"
>
x
o
'C
.
>
~ 4
is
~
~
~
8
2 -.---.. -. ~
,
"'. ---.-...--..,;
.
L
.
I
"
....
.
o
Sep8l
Mar8S
Aug-88
Jan 92
Jul-95
Dec 98
Jun02
Nov-OS
Apr-09
PBSI
16
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15. 2009
Water Quality Review and Afi~Slsf 133
Figure 3.6. Average and Median Dissolved Oxygen Levels in Clam Bay over the
Period of Record (left axis). The Percent of DO Values Lower Than the IWR
Threshold for Marine Waters (4.0 mg/L; right axis).
10
. ^Vl'rilge
I: Median
GO
.i: % Values < 4.0 mgjt
I A
8 ,--.----.. - -- ------------- ----- -
!
"'-
" 6
..s
c
~
"
>-
x
o
'"
~
>
~ 4
o
2
o
UCBR.1<
1/\".7
SCC!f;<lte
W.(l
WI
DO values at all sites sampled in Clam Bay were consistently less than the required DO level of
4.0 mg/l in marine water bodies. DO concentrations were less than 4.0 mg/L sufficiently
frequently that based on FDEP's IWR, Clam Bay would be classified as "impaired" for DO
levels.
Chlorophyll a
Chlorophyll a data are available from January 1996 until May 2009 at the W-I, W-6 and W-7
sites (Figure 3.7). Sampling for the Seagate sites began in January 2001 and chlorophyll a data
only available at the UCBRK site from October 1996 until September 1997. Isolated elevated
concentrations of chlorophyll a have been observed at the W-6 and W-l sites, however, the
concentration observed on September 1996 at the W -6 site (299 llg/L) is unlikely in the marine
waters, and so the data are displayed (Figure 3.8) with a truncated y-axis.
PBSI
17
Clam Bay System Data Collection and Analysis
October 2009
so
40
~
v
C
.
'"
30 &:
v
x
~
#.
20
-10
Agenda Item NO.1 OF
December 15, 2009
Water Quality Review and AI9&l~Sf 133
Figure 3.7. Chlorophyll a Concentration over the Period of Record in Clam Bay.
350
-+-W-6 -fl-W~7 ~W-l ---UCBRK -"-Seagate
300
~-"----"--"""-------""'~"---" -.---.-----------,.-
250
"'-
~ 200
.
>C
~
"
o
15 150
:c
v
- -----..---.--..---... -------- ',' -------- ___n_m...._______n.u. ______ _ _______ _. ______ ..___,......._____. _____... ______n._.....__
100
- -- ------- ... -.----, - _______._n____ _____ _'...m____ __ _ __ _ _____...______._________.._______....___
50
,
,
o
Oct 95
Dee 99
Jail 04
Feb-08
Fignre 3.8 compares the Chl-a data to the median and 90% value for all Florida estuaries (FDEP
1996; 9 and 36 flg/L, respectively). Values were consistently greater than the median with
occasional spikes above the upper 90% value of 36 ugll. Upon displaying the data as annual
average values, the UCBRK site was excluded due to a lack of recent data (Figure 3.9).
PBSI
18
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item No.1 OF
December 15, 2009
Water Quality Review and AI1~isf 133
Figure 3.8. Chlorophyll a Concentration Over the Period of Record in Clam Bay
With the y-axis Truncated (the orange line denotes 36 I-lg/L, the upper 90% value
for Florida estuaries; the red line indicates the median value for Florida estuaries;
9 mg/L).
50
6 ....W-7 -r-W-l -UCBRK -t-Scagate
':0
J
.
~ 30
w
2-
.
>-
~
~
o
E
'6 20
10
o ,:.
Oct 95
D0(-99
I,m 04
Fob-OS
PES'
,
19
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Water Quality Review and ARl!l:J~Sf 133
Figure 3.9. Annual Average Chlorophyll a Concentration for 2005, 2006, 2007 and
2008 (the black line denotes 111JQ/L, the threshold for impairment from FDEP's
IWR; the red line indicates the median value for Florida estuaries; 9 mg/L).
I-
I 12
I
I
i
I
_2005
B
'"
~
-=-
.
>-
~
0-
e
0
:c
u
4
W7
_2006
... 2007
_ 2008
-Median -11 ug/l
^~-----l
I
I
_______'_. ._....___.__ .M______. _.__.....___..,_~..._...____ _...______...,~____..,.______
---,
SCClgatC'
Site W-7 exceeded an annual average Chl-a concentration of 11 Ilg/L during both 2005 and
2007. Based upon existing criteria from FDEP, Clam Bay would likely be declared verified
impaired due to elevated chlorophyll a concentrations.
Limiting Nutrient
W6
Station
WI
Multiple techniqnes are available to assist in the identification of the limiting nutrient responsible
for phytoplankton production. The ratio between TN and TP was calculated for each site from
January 1005 until May 2009 (Figure 3.10). A co-limited system generally has TN:TP values
between 10 and 30 (FDEP, 1996). A ratio greater than 30 indicates a phosphorus-limited system
whereas a ratio below 10 indicates a nitrogen-limited system. In Clam Bay, overall the TN:TP
ratio indicate a co-limited system with periods of both niLrogen and phosphorus limitation.
Additionally, the relationship between chlorophyll a and TN or TP was evaluated in PBS&J
(2008) to further evaluate the limited nutrient (Figure 3. 1 I and 3.12, respectively).
PHSl
20
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Water Quality Review and Afi~Sf 133
Figure 3.10. TN:TP Ratios for Clam Bay from January 2005 to May 2009 (the
shaded area indicates the range for a co-limited system).
80
-+-W-5 ___W7 -yt- W-l ~UCBRK -Seagate
70 -------- ~------------- - ------ -------------------- - ---------
GO
50
Q.
ii 40
~
T
I
,
\
-\
10
30 '-----
20
o
),11)-05
J,1n05
J<lnU7
]O)n08
Doc 08
PBSJ
21
Clam Bay System Data Collection and Analysis
October 2009
Agenda item No.1 OF
December 15, 2009
Water Quality Review and AfialySisf 133
Figure 3.11. Relationship Between Chlorophyll a and Total Nitrogen in Clam Bay
(figure from PBS&J [2008]).
16
Chl-a = 4.33 +S.03(TN); R' = 0.13; P = 0.045
14 .
.
.
~ 12
~ .
~ . .
~ 10
OJ .
~ .
1 8 .
>.
-c .
C. .
0 6 .
~
.Q .
-c .
l) 4
. . . . ..
2
0
0.0 0.2 0.4 0.6 0.8 1.0 1.2
TN (mg / liter)
PHS]
22
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Water Quality Review and Atl~~sf 133
Figure 3.12. Relationship Between Chlorophyll a and Total Phosphorus in Clam
Bay (figure from PBS&J [2008]).
16
Chl-a = -0.29 + 156.4(TP); R' = 0.42; p = 0.0001
14 .
.
~ 12
~
Q)
..", .
~ 10
OJ .
.E,
CIl .
-!.. 8 .
>-
L
Q.
0 6 .
~
0 .
L
0 4
.
2
0
0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09
TP (mg / liter)
While the TN:TP data suggest that Clam Bay is mostly a co-limited system, these ratios are only
an indicator of nutrient limitation, not proof itself. The cOITelation between TP and chlorophyll a
is stronger than that between TN and chlorophyll a, indicating that nitrogen is not as strong a
limiting factor to phytoplankton growth as phosphorus. While phosphorus may be the more
strongly limiting nutrient, it would be prudent to not focus nutrient management strategies on
phosphorus alone. When examining the status and trends in nitrogen and phosphorus, it would
be useful to consider that the abundance of both nutrients should be of concern.
Total Nitrogen
For each of the sites of interest, total nitrogen was calculated by the summation of TKN, N03
and N02 (Figure 3.13). Total nitrogen data are available for sites W-6, W-7 and W-I from
November 1981 to May 2009. Data for the UCBRK and Seagate sites began in October 1996.
The data were compared to the median and 90% value for all Florida estuaries (FDEP, 1996; 0.8
and 1.6 mgfL, respectively). The greatest TN concentration was found at the UCBRK site with
concentrations decreasing the further south in the watershed sampled (Figure 3.14).
PHSI
23
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item No.1 OF
December 15, 2009
Water Quality Review and ARa1~Sf 133
Figure 3.13. Total Nitrogen Levels in Clam Bay (the orange line denotes 1.6 mg/L,
the upper 90% level for Florida estuaries; the red line indicates the median value
for Florida estuaries [0.8 mg/L]).
110 -~--
i __W6
___W-7
"""*'" W-l -UCBRK -!-Seagate
8 .~ ---
""-- --....._--_._..._-_..._~.._--- - --.----........---..- - ------.-...,-.--,....-."-
<:. 6
"
E-
o
.
"
g
z
..
;2 4 ^-____.__._.___.__...,....__
2 L_~__ '-r J.;- ..-------- t
'T~~ . ~ --------~~
:
i ,I!.,
.
o
Sep81
Milr85
Aug 88
JOIn 92
Jul95
D(;'(98
Jun02
NovOS
Apr 09
PBSl
24
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item No. lOF
December 15, 2009
Water Quality Review and ARalcySlSf 133
Figure 3.14. Mean and Median TN concentrations (left axis). Percent of TN
Values Greater than the Median for Florida estuaries (0.8 mg/L; right axis).
,
~
.s.
c
.
g 0.8
Z
"
;2
1.6
1.2
0.4
Total Phosphorus
Total phosphorus data are available from November 1981 to May 2009 at the W- 1, W-6 and W-7
sites, although extremely elevated levels in the early to mid 1990s required the use of a truncated
y-axis to display the data (Figure 3.15). Sampling for the UCBRK and Seagate sites began in
October 1996. Elevated concentrations of total phosphorus were observed between July 1992
and January 1995. Figure 5 compares the TP data to the median and 90% value for all Florida
estuaries (FDEP, 1996; 0.07 and 0.2 mg/L, respectively). Values were consistently greater than
the median with occasional spikes above the 90%.
PBSl
25
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item No.1 OF
December 15, 2009
Water Quality Review and AR~Sf 133
Figure 3.15. Total Phosphorus Levels in Clam Bay (the orange line denotes 0.2
mg/L, the upper 90% level for Florida estuaries; the red line indicates the median
value for Florida estuaries [0.07 mg/L]).
-~'----'''--'---'-'-'-''''''-'-'-'--'-----'----'-- - ---..-...,..-------". -.----.........----.--.-..---.-..-."..-----.-..-.-.--.-'-'-""-"----'--.-.---
1 ,-----
"' ------- ...,..------.--, ----, .....-..-- --... -- -----,--------. -- - ------ '- ---~- ----- --_._---_....._---_._._.__._.~-
-t-W.6 -ll-W7 ~W-l ......,.....UCBRK .....;.r.....Seagate
0.8
~ 0.6
.s
.
,
:;
~
"
o
~
0-
] 0.4
,E
0.2
t
Sep81
Mar8S
Aug-88
Jan ~)2
lul95
Dcc~)8
Jun-02
Nov-OS
Apr-09
When mean and median values are calculated for each site, a similar pattern was found for TP as
in TN, with the highest TP concentrations at UCBRK, and concentrations mostly decreasing
further south (Figure 3.16).
PHSI
26
Clam Say System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Water Quality Review and Afi~Sf 133
Figure 3.16. Mean and Median TP concentrations (left axis). Percent of TN Values
Greater than the Median for Florida estuaries (0.07 mg/L; right axis).
0.08
"'-
~
E.
.
,
~
~
"
0
~
"-
m
~
0,04
012
W7
. Avera[3c
Wb
. Median
.i. % VJlues> 0.07 mli/I
W1
Se<1[;CltC'
90
80
70
60
.
50 ~
.
"
.
.
u
x
40 *
30
. 20
10
o
PBSI
o
UCBRK
27
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Water Quality Review and Afil!ll~Sf 133
3.3 Task 3 - Sediment and Biological Health Characterization
General Biological Survey Results
Figure 3.17 summarizes the results of the Redox depth survey undeJ1aken in Clam and Moorings
Bays.
Figure 3.17. Results of Redox Depth Survey in Clam Bay (left) and Moorings Bay
(right). Red symbols represent Redox layer at surface, Orange represent Redox
layer < 20 em, Green symbols represent Redox layer> 20 cm.
Redox layers were at or close to the surface (< 20 em) in both Upper and Outer Clam Bay. In
contrast, Redox layers were typically deeper than 20 em in Inner Clam Bay and Moorings Bay.
PHSI
28
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item No. 10F
December 15, 2009
Water Quality Review and ARMySisf 133
These data suggest that benthic communities would be expected to be of lower diversity (if not
abundance) in both Upper and Outer Clam Bays.
Figures 3.18 and 3.19 summarize the results of the seagrass and macroalgae surveys,
respectively, undertaken in Clam and Moorings Bays.
Figure 3.18. Results of Seagrass Survey in Clam Bay (left) and Moorings Bay
(right). Green symbols represent presence of seagrass, Red symbols represent
absence of seagrass).
Seagrass was only rarely encountered in the Clam and Moorings Bays system. In contrast to the
findings in the Clam Bay seagrass study conducted by PBS&J (2008) seagrass was not found in
most of the stations visited in Outer Clam Bay, perhaps due to the relatively ephemeral nature of
the species previously documented, Halophila decipiens. This species, as opposed to shoal grass
PBSJ
,
29
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Water Quality Review and AR~Sf 133
, (Halodule wrightii) or turtle grass (Thalassia testudinum) does not form persistent meadows, and
it typically propagates via sexual reproduction, which is relatively rare among most species of
seagrass in Florida (e.g., Dawes et al. 1989).
In contrast to seagrass, macroalgae were commonly encountered in all regions surveyed except
for Upper and Outer Clam Bays (Figure 3.] 9).
PBSI
30
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Water Quality Review and ARa1~gf 133
Figure 3.19. Results of Macroalgae Survey in Clam Bay (left) and Moorings Bay
(right). Green symbols represent presence of seagrass, Red symbols represent
absence of seagrass).
PBSI
31
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15. 2009
Page 54 of 133
4.0 Water Quality Discussion and
Recommendations
The biological conditions of the Clam Bay and Moorings Bay systems can be summarized as
follows:
Upper Clam Bay-
· Redox layer at or very close to the surface, indicating reduced DO levels in sediments
· Little to no macro algae or seagrass
· Benthic communities likely those expected for systems with reduced levels of DO, food
chain dependent on heterotrophs, not autotrophs
Middle Clam Bay
· Redox layer typically deeper than 20 em, indicating sufficient DO levels in sediments
· Macroalgae not uncommon, but little to no seagrass
· Benthic communities likely those expected for systems with adequate levels of DO in
sediments, food chain dependent upon both heterotrophs and autotrophs
Outer Clam Bay
· Redox layer typically at surface or shallow (< 20 em), indicating reduced DO levels in
sediments
· Limited and/or coverage by seagrasses, mostly Halophila decipiens with likely ephemeral
but potentially abundant coverage by macroalgae in shallow areas
· Benthic communities likely those expected for systems with reduced levels of DO, food
chain dependent on heterotrophs with localized areas dependent on both heteroLrophs and
autotrophs
Moorings Bay
· Redox layer typically deeper than 20 em, indicating sufficient DO levels in sediments
· Macroa1gae common, but little to no seagrass
· Benthic communities likely those expected for systems with adequate levels of DO in
sediments, food chain dependent upon both heterotrophs and autotrophs
PBSI
32
Clam Say System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Water Quality Discussion and Recommend'atltmsf 133
As relates to the analysis of existing water quality, it should be noted that Florida Administrative
Code (62-40.540) clearly states that, "All local governments, water management districts, and
state agencies are directed by Section 373.026(2), F.S., to cooperate with the Department in
making available to the Department such scientific or factual data as they may possess." Further,
" The Department's FLORIDA STORET water quality data base shall be the central repository
of the state's water quality data. To assure that it is readily available to the public and for use in
the Department's watershed management program, all appropriate water quality data collected
by the Department, Districts, local governments, and state agencies shall be placed in the
FLORIDA STORET system within one year of collection."
The absence of Clam Bay data sets in the STORET system is inconsistent with Florida
Administrative Code, and efforts should be made to ensure that appropriate water quality data
are provided to FDEP for uploading into STORET.
It is also evident that the dissolved oxygen (DO) data collected to-date in Clam Bay would result
in classification of Clam Bay as impaired using guidance contained within FDEP's Impaired
Waters Rule (IWR). Guidance within the IWR could also likely result in the classification of
portions of Clam Bay as impaired for chlorophyll a, pW1icularly in Upper Clam Bay.
However, it is important to note that IWR guidance on DO and chlorophyll a can be locally
inappropriate, particnlarly in subtropical systems. In their study of dissolved oxygen levels in
the Everglades, McCormick ct al. (1997) studied both nutrient-impacted sites and reference sites.
The reference sites all had levels of total phosphorus below adopted guidance for Everglades
restoration efforts, and were characterized by healthy assemblages of emergent plant
communities. McCormick et al. (1997) found that".. .even at reference sites, O2 was less than
the 5 mg r' water quality standard for other water bodies (State of Florida Class III Standards)
from 40-70% of time."
Reference sites used in the Everglades study by McCormick et al. (1997) and also in the Gordon
River TMDL rcport (FDEP 2008) failed the State of Florida's DO standards for both freshwater
and marine waterbodies. Collier County should consider working with FDEP to develop locally-
appropriate site-specific alternative criteria (SSAC) for both DO and chlorophyll a for the Clam
Bay and Moorings Bay systems.
The need for SSACs for DO and chlorophyll a is further highlighted due in part to the
discrepancy between actual water quality and "anticipated" water quality. For example, the very
low levels of DO throughout the Clam Bay system, both from the review of historical water
quality data and as infcrred based on Redox depths, is not necessarily indicative of a nutrient-
enriched water body. While chlorophyll a levels wcre not uncommonly above the impairment
threshold level of 1 I ug/l, only the Upper Clam Bay system would be declared impaired based
on annual averages (the requirement for an impairment determination). Also, levels of TN and
TP are frequently higher than the median value for Florida estuaries (40 to 80% of TN values
exceed the Florida median, and I () to 80% of TP values exceed the Florida median), the highest
values w'e typically found in Upper Clam Bay, rather than the more urbanized location of the
Seagate Drive station. These findings suggest that circulation, perhaps more than nutrient
loading, might be responsible for spatial patlcrns of water quality in the Clam Bay system.
PBSI
33
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item No. 10F
December 15, 2009
Water Quality Discussion and Recommend'atltfAsf 133
The finding that Redox layers are almost uniformly deeper in Moorings Bay than in Clam Bay
further suggests that the more well flushed Moorings Bay system (see circulation results) is
better able to accommodate nutrient enrichment than the less well flushed Clam Bay system.
The pollutant loading model for Clam And Moorings Bays produced by PBS&J (2008) further
demonstrates that the more "pollnting" Moorings Bay watershed does not seem to result in a
more degraded benthic community composition (based on Redox depths). And the finding that
the net flow of water in the vicinity of Seagate Drive is north to south suggests that the shallow
Redox depths of Clam Bay cannot likely be blamed on a pollutant load imported to Clam Bay
waters from the Moorings Bay watershed.
Collier County should enact a water quality monitoring program for the entirety of the Clam Bay
system, in coordination with the City of Naples ongoing efforts in Moorings Bay. Current
monitoring efforts are not adequate for the purposes of ambient water quality monitoring and
state requirements for the TMDL program. Such and eff011 needs to be consistent with state
certifications and standard operation procedures required by FDEP. Suggested sampling
locations are shown in Fignre 4.1, and a suggested sampling parameter list is shown in Table 4.1.
PHSI
34
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item No. 10F
December 15, 2009
Water Quality Discussion and Recommend'atltmsf 133
Figure 4.1. Recommended Sampling Locations for Upper, Inner and Outer Clam
Bay.
These sa~pTing sites should be visited on a monthly basis, as close in time to data collection
efforts by the City of Naples as possible. In addition, the following parameter list is
recommended (Table 4. I) to ensnre adequate parameters are collected for any reasonable
characterization efforts and/or TMDL-related issues.
PBSl
35
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item No. 10F
December 15, 2009
Water Quality Discussion and Recommend'atkfflsf 133
Table 4.1. Recommended Parameter List for Ambient Water Quality Monitoring
Program for Clam and Moorings Bays.
Water Qualit
lChlorophylJ a
!Phaeophytin
Nitrate-Nitrite
'Total Kjeldahl Nitrogen
,Total Nitrogen
1-
LOPhosp~:te _ __I
iTotal Phosphorus
IDissolved oxygen I
------ L____~~__~__
jFeCal Coliform I
IBOD 1
jColor -~~~1~--~-m ------~----:----~--_--~---
I ' I
'Enterococci i- -- - --- - ~----------;-- ---~
ITurbiilitY------+-------~---~--- -- - - -- ------------
Isalinity -~-i -~--- ---------- --;--~ ~
ICOndUCtiVity -f----------------+ --------- ---~
IpH ---- ------1-- __u_ ---- ~ __ - 1- __ __ ___ _ ______~
I + I ~
:Temperatur~-------- ! .------------.----'-------~---;----~----~ I
I------+------------~-_L-- .._________~__j
Secchi , I
I '
___1__..._.__ .-------.--______ ________ --~__J
Photosynthetically I I
i::~t:e R:diatio: (PARl_1 . -----___-1
L ___---.J .m. --_ ,-----____J
PHSI
36
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Page 59 of 133
5.0 Model Review
5.1 Review of RMA2 model of Clam Bay, Humiston & Moore (2003)
Summary
The Humiston & Moore study modeled the Clam Bay estuary system to determine the effects of
varying freshwater inflow on water levels in Clam Bay, and concluded that a more healthy
system can be achieved by diverting freshwater runoff into Vanderbilt Lagoon instead of Upper
Clam Bay, as well as promoting flushing and exchange within the system via channel dredging.
These measures would reduce mean water levcls and crcate more transient wet/dry regions, but
could reduce the tidal prism through Clam Pass and possibly affect inlet stability.
The H&M model was sufficient for its original purpose, but a new effort is necessary if a
comprehensive model of circulation within the system is desired. Limitations of the H&M
model include:
. The model does not encompass Moorings Bay or account for the exchange between Clam
Bay and Moorings Bay.
. The model domain does not include the transient wet/dry mangrove forests in Clam Bay.
. Only one freshwater inf10w is accounted for as a boundary condition.
. The offshore tidal boundary condition was limited in amplitude as well as duration.
. The model was calibrated for tidal range only, with no assessment of phase lag or flow
velocities.
A modeling effort sufficient to properly recreate the hydrodynamics of the Clam Bay / Moorings
Bay system would require a near total reboot of the H&M RMA2 model; it is recommended that
an updated model be developed using a more comprehensive model, such as Delft3D.
Model Report Overview
In 2003, Humiston & Moore Engineers (H&M) developed a circulation model of the Clam Bay
estuary system for the Pelican Bay Services Division (PBSD). The intent of the modeling effort
was to evaluate the effects of varying freshwater inf10w into Upper Clam Bay on water surface
elevations in the system and the resulting health/recovery of the mangrove population.
The modeling effort utilized RMA2, a finite-element, 2D depth-averaged model. The model grid
extended from the culverts at Seagate Drive north to Upper Clam Bay, bounded by the mangrove
border and the opening of Clam Pass. The boundary conditions forcing the model
hydrodynamics were (I) a varying water surface elevation at the Gulf of Mexico (Clam Pass),
and (2) freshwater inf10w at the northern end of Upper Clam Bay. The water surface elevation
boundary condition varied in time, while the freshwater inf10w was held constant during each
individual model run. The model was calibrated according to measured tidal ranges using a 2.5
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Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Model Rwl'eWf 133
ft tidal range for 24 hr at the Gulf boundary, and verified using a 2 ft tidal range boundary
condition. After this process, the freshwater inflow into Upper Clam Bay was varied to
determine the resulting effects on water levels in the system.
According to the model results, diverting freshwater inflow from Upper Clam Bay into
Vanderbilt Lagoon during the rainy season would reduce the mean water level in stressed
mangrove areas by 0.15 ft to 0.20 ft, or 40% of the mean tidal range. This diversion would allow
mangrove areas that are largely flooded during rainy season to alternatively flood and dry, and
this water would have higher salinity than without the Vanderbilt connection. This situation
would have a positive impact on mangrove health as well as benthic and marine organisms in the
system. A potential drawback to the Vanderbilt diversion is the reduction of the tidal prism
through Clam Pass by 10%, which could negatively affect the stability of the inlet. In light of
evidence that improved/increased flushing positively impacts mangrove and overall system
health, the report recommends that freshwater inflow be diverted from Upper Clam Bay into
Vanderbilt Lagoon and the dredging of shallow 'areas in the meanders between bays be
continued; in addition, it also suggests that the connections between each bay could be
straightened to further improve flushing and exchange within the system.
Model Restrictions and Limitations
While the H&M model was sufficient and effective for its original intended purpose, there are
several limitations that preclude it from being used in a comprehensive study of circulation
within and between Clam Bay and MOOlings Bay, even if the model bathymetry were to be
updated with the most recent collected data.
The first limitation is that of model extent; the model encompasses Clam Bay only, and does not
incInde Moorings Bay and Doctors Pass. Based on data collected in August 2009, measurable
volumes of water are exchanged between the two bodies of water through the culverts at Seagate
Drive. Head (water level) differences during the period of August 14,2009 to August 23, 2009
ranged from -0.44 ft (north < south) to + 1.54 ft, with the Moorings Bay side of the culverts
reaching low tide approximately 1.5 hI' before Outer Clam Bay. Flow velocities from Moorings
Bay to Clam Bay were observed on the order of 0.33 ft/s, while velocities from Clam Bay into
Moorings Bay reached 3 ft/s; the net flow between the basins thus appears to be southward.
From these observations, it is apparent that the two systems are physically intertwined, and the
hydrodynamics of Outer Clam Bay are at least partially affected by conditions in Moorings Bay.
Second, the model's domain is limited to the bays and channels within the mangrove extent;
alternately wet and dry regions of mangrove forest are not taken into account. Flow through the
mangroves is likely a significant physical process affecting flow and exchange within the system.
During the August 2009 data collection period, flow at the bridge north of Clam Pass was
observed to be in the range of 2 ft/s when water levels dropped below -0.6 ft NA VD88, during
both incoming and outgoing tides. At higher water levels, velocity magnitudes were reduced,
irrespective of flow direction. This indicates that at lower water levels, flow is constricted to
between mangrove banks and accelerates, while higher water levels allow flow to 'spread out' on
PBSl
38
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Model ~RMf 133
the flat mangrove forest, reducing velocities in the channel. Without taking into account the
large areas of low-lying, alternating wet/dry regions, modeled flow velocities may be inaccurate
at certain tidal stages, and it may be difficult to achieve a true assessment of flushing and tidal
exchange.
The model is also limited by its inclusion of only a single freshwater inflow at the north end of
Upper Clam Bay. While this may be the most significant input, it could be beneficial to include
all stormwater sources into Clam Bay, as well as Moorings Bay, as boundary conditions. In
addition, the offshore tidal boundary conditions were limited to a range of 2.0 ft to 2.5 ft. Spring
tides in the area can have a range in excess of 4 ft, which was observed during August 2009; the
model should be calibrated for all expected 'normal' tidal fluctuations. The model was limited to
24-hour run durations; longer time periods would encompass the mixed tidal characteristics of
the Gulf and give a more representative portrayal of net flows within the system.
Finally, the H&M model was calibrated for tidal range only, with n'o accounting for flow
velocities or phase lag between the bays. The phase lag represents the time necessary for the
tidal wave to propagate from one basin to the next, and is the driving force behind flow and
exchange. For e~ample, the phase lag observed in August 2009 between the north and south
sides of Seagate Drive result in flow through the culverts underneath the roadway. A more
accurate model calibration should achieve agreement in both phase and amplitude of modeled
parameters. Flow velocities are also an important calibration parameter, and as discussed above,
are highly dependent on the model domain boundaries.
Based on the limitations of the H&M model presented above, it is recommended that an updated
modeling effort be implemented if a comprehensive model of circulation within the system is
desired. This updated eff0l1 should encompass the entire estuary from Upper Clam Bay to
Doctors Pass, include wetting and drying of the mangrove flats, and undergo a more robust
calibration effort using both tide and velocity data. While RMA2 could be utilized for this task,
the effort necessary to adapt the H&M RMA2 model to the new requirements would be nearly
equal to the effort to start fresh with a more robust model, such as Delft3D.
Using a model such as Delft30 would also have a distinct advantage over RMA2. The initial
modeling effort could include only 2D hydrodynamics, but Delft3D is modular such that the
addition of new modeling parameters (3D dynamics, morphology, water quality, etc.) can be
added to the basic 20 model framework without the need to recreate a new model. This allows a
highly detailed modeling effort to be completed piecewise over time with a single integrated
system rather than using multiple disconnected models.
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Clam Bay System Data Collection and Analysis
October 2009
Agenda item NO.1 OF
December 15, 2009
Model ~;ewf 133
5.2 Review of Clam Bay hydrographic assessment report, Tackney &
Associates (1996)
Report Overview
The study by Tackney (l 996) was undertaken in response to an increasing rate of mangrove die-
off in Upper Clam Bay. Its purpose was to determine if the hydraulic characteristics of the Clam
Bay system could encourage periods of excessively high water levels in Upper and Inner Clam
Bay; also investigated were the Seagate Drive culverts and the stability of Clam Pass.
In general, the small depth of Upper and Inner Clam Bays compared to the Gulf tidal range, as
well as their distance from Clam Pass, result in diminished tidal ranges in these bays, as well as a
mean water surface elevation above that of the Gulf. Freshwater inflow from stormwater sources
also increases the mean water level in these bays.
Water levels and CUlTent velocities were measured within Clam Bay at 11 and 10 stations,
respectively, between May 3 and July 12, 1996. In addition, water levels on either side of
Seagate Dr, as well as flow velocity in the culverts below, were measured for a 4 day period. An
attempt was made to filter rainfall effects from the data by excluding data adjacent to such
events.
The field data collection confirmed that Upper and Inner Clam Bays exhibit an attenuated tidal
range compared to the Gulf of Mexico, and their mean water surface elevations were about 0.2 ft
higher than the mean Gulf level. On the south end of the system, a majority of the tidal
attenuation occurs between Clam Pass and the area between the middle and south boardwalks. A
bathymetric survey was also completed; it showed that shallow areas between the middle
boardwalk and Inner Clam Bay area likely cause of the significant tidal attenuation in the upper
reaches of the system.
At Seagate Dr, velocities in the culverts were measured to be around 2 to 4 fUs, with a maximum
value cif 5 ft/s. Assuming that flow rates are sinusoidal and uniform in both directions, this
results in 650,000 cf of water exchanged back and forth during each tide, with little to no net
flow.
Inlet stability is affected by its scouring capacity, and thus a function of the cun'ent magnitude
through the inlet. It is clear that Clam Pass is not particnlarly stable, since it has closed multiple
times since the 1970s. Increasing the tidal prism of the pass is the best way to increase its
stability; this can be accomplished by removing or reducing the flow restrictions within Clam
Bay and allowing for more effective flushing and water exchange. Actions detrimental to inlet
stability would include enlarging the opening at Seagate Dr and diverting flow to Vanderbilt
Lagoon.
PBSI
40
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item No. 10F
December 15, 2009
Model ~ie'wf 133
Report Review
In general, the basic principles of this rep0l1 are sound. Tidal attenuation and water
superelevation in the system is most likely caused by the flow restrictions due to meandering
passages and shallow water depths in the creeks between bays, with storm water runoff also a
contributing factor. The field data collection augments and supports the theoretical assertions.
The conjectures made on inlet stability are accurate in the context of a theoretical discussion.
While these basic concluding remarks are seemingly accurate, the report provides limited to no
analysis or calculations to support these findings. Basically we have to "take the authors word
for it" and while theoretical, these remarks are more opinion then fact. The report indicates that
a preliminary model is being developed, but no report or mode] could be located.
Furthermore, another point of concern with the findings is the section on flow velocities and
resulting estimations of volume exchange between Outer Clam Bay and Moorings Bay. It is
unclear how the velocities were measured, and if the directionality of flow was taken into
account. It is mentioned that tide data was recorded on either side of the culverts during the
current measurements, but these data are not discussed. The report appeared to assume that
current direction reached the same magnitude in both directions and for equal durations, resulting
in little net flow between the water bodies.
The field data collection effort of August 2009 showed that this scenario is clearly not in effect
today. The tidal range on the south side of Seagate Dr was 34% larger than that on the north side
(4.4 ft vs. 2.9 ft); furthermore, a significant phase lag between the two sides was such that on an
outgoing tide, the south side of the culvel1s was as much as 1.5 ft lower than the north side.
CUlTent velocities reached 3 ft/s in the southerly direction, but only 0.3 ft/s in the n0l1herly
direction. An estimate of volnme exchange for the study period yielded a net flow of 969,000 cf
from Outer Clam Bay into Moorings Bay per tidal cycle (l82,000 cf northerly, 1,] 51 ,000 cf
southerly). Studies by the USEPA (1975 & 1977) SUPP011 the conclusion of net southerly flow.
PBSJ
41
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Page 64 of 133
6.0 Hydrographic Data Collection
Morgan & Eklund, Inc. sent a survey crew to the Clam Pass Project Area a week before the field
data collection was to begin to set a network of horizontal and vertical control points in the
project area. These control points were referenced horizontally to the North American Datum of
1983 (NAD 83), Florida State Plane East, and vertically to the North American Vertical Datum
of 1988 (NA VD 88). The topographic and bathymetric survey would be based on these points,
as well as the elevations of the tide and current instruments.
Field data collection for the Clam Pass Tide and Cnrrent Study began on August 14, 2009. The
team consisting of members of Morgan & Eklund's survey crew and PBS&J's Coastal Group
met at Naples Landing Park. The seven Coastal Leasing MicroTide gauges were turned on and
set to record the pressure every 10 minutes (Figure 6. l).
Figure 6.1. Coastal Leasing MicroTide Gauge and concrete base.
The three Workhorse Sentinel Acoustic Doppler Current Profilers (ADeps) were also activated.
These instruments are self-contained with the power supply and data recorder in a water-tight
case. The team then split into three groups, one group to deploy the offshore/deeper tide gauges,
one crew to deploy the inshore/shallow water gauges, and one crew to survey/elevate the gauges.
The inshore crew left Clam Pass Park in a 16ft jon boat and wound their way north through the
mangroves to Upper Clam Bay. A 1-1/2 inch galvanized pipe was hammered into the bay
bottom and Tide Gauge #1 was strapped to the pipe with hose clamps in about 2 ft of water.
Tide Gauge #2 was deployed in Inner Clam Bay in about 3 ft of water and strapped with hose
clamps to an existing PYC pipe that looked to be part of an old stilling well water level gauge.
The location and elevation of these gauges was recorded using Real-Time Kinematic Global
Positioning System (RTK GPS; Figure 6.2).
PBSI
42
Clam Bay System Data Collection and Analysis
October 2009
...
Agenda Item NO.1 OF
December 15, 2009
Hydrographic Data Collfe~IGAf 133
The offshore crew left the Naples Landing boat ramp and ran out Gordon Pass in a 25 ft boat to
set Tide Gauge #3 on the gulf side of Clam Pass. Upon arriving at the designated position the
tide gauge was strapped to a concrete base and lowered to the bottom in about 14 feet of water.
An orange anchor buoy marked was attached to the concrete base and a Differential GPS point
was taken at the location for recovery. The survey crew shot in the gauges with a level, elevating
the gauge to the nearest DEP R-Monument. The process was repeated for Tide Gauge #4 on the
Gulf side of Doctor's Pass. It too was set in approximately ]4 ft of water. The offshore crew
then proceeded inside Doctor's Pass north to Venetian Bay to set the Tide Gauge #5 on the south
side of Seagate Drive in approximately 10 feet of water. The survey crew elevated the gauge to
a benchmark in the established control network.
Figure 6.2. Elevating Tide Gauge with RTK GPS.
The inshore crew then traveled south to Seagate Drive and set Tide Gauge #6 attached to a
concrete base on the north side of Seagate Drive in about 5 ft of water. The survey crew used a
level to elevate this gauge to a benchmark in the established control network. Tide Gauge #7
was set on a concrete base in Outcr Clam Bay in 3 ft of water and clevated with RTK GPS. The
inshore crew then set a Workhorse ADCP "BrdgS" in approximately 4 ft of water on a concrete
base at the trolley bridge in Clam Pass Park; this instrument was also elevated with RTK GPS.
A second Workhorse ADCP "ClamP" was attached with hose clamps to a 1-1/2 inch galvanized
pipe hammered into the bottom in about 4 ft of water inside Clam Pass just cast of the mouth.
The survey crew used a level to clevate this instrument from R-42 just south of Clam Pass. A
third Workhorse ADCP "BrdgN" was attached to a concrete base and dcployed in 4 ft of water at
the trolley bridge north of Clam Pass. RTK GPS was used to elevate this instrument.
The three crews then teamed up again to deploy the SonTek Shallow Water ADCPs in Moorings
and Venetian Bay. These instruments we not self-contained and had a data and power cable
attached to the unit that was fed along the bottom to a onshore battery. A Leve]ogger pressure
sensor was attached to the concrete base as well to rccord the water level independent of the
SonTek. The first SonTek ADCP/Levclogger was deployed on the north side of the Harbour Dr.
Bridge in approximately 15 ft of watcr. The second SonTek ADCP/Levelogger was deployed on
PBSJ
.,
43
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Hydrographic Data Colf~IGAf 133
the south side of Park Shore Dr. in about 9 ft of water. The third SonTek/Levelogger was
deployed on the south side of Seagate Drive in about 5 ft of water. All three SonTek ADCPs
were elevated to benchmarks in the established control network with a level (Figure 6.3).
On Monday August 17lh, Morgan & Eklund's crew continued with the topographic and
bathymetric surveys of Clam Pass, Clam Bays (Upper, Inner, and Outer), Venetian and Moorings
Bays, as well as profiles R- 38 through R-44 along the beach. Meanwhile the tide and current
instruments were collecting data. Unfortunately, the SonTek ADCP/Levelogger at Seagate
Drive was found vandalized on Monday morning. The battery was stolen and the power/data
cord was ripped out of the unit. A new power/data cord was sent overnight from SonTek and a
new battery was purchased. On Tuesday the SonTek ADCP/Levelogger was redeployed south of
Seagate Drive in about 4 ft of water. The battery box and cable was buried in the bushes along
the shoreline. On Wednesday moming, the SonTek ADCP/Levelogger at Harbour Dr. was
found to have its battery stolen. A new battery was purchased and the instrument was
redeployed on Wednesday morning. For the remainder of the week, all instruments were
constantly monitored by PBS&J and Morgan & Eklund staff and no vandalism was discovered.
Figure 6.3. SonTek ADCP on concrete base.
On Saturday, August 22, 2009, the team once again surveyed all of the instruments with a level
or RTK GPS prior to removal on Sunday, August 23. All of the mounting pipes and concrete
bases were also removed. The data was downloaded from the instruments and plotted in Excel
to convert the data from pressure to water level.
PBSI
44
Clam Bay System Data Collection and Anaiysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Page 67 of 133
7.0 Hydrographic Data Analysis
7.1 Introduction
The data collection effort yielded conCUlTent water level and flow velocity measurements for a
period of 8 days, from August 15 to August 23, 2009. All instruments were successful in
collecting data; however, severa] acts of vandalism resulted in the partial loss of flow velocity
data at South Seagate Dr and Harbour Dr. Figure 7.1 illustrates the locations of the deployed
instruments.
The data was processed using Matlab to synchronize each instrument to one another, create
graphs and animations of both water level and flow velocities, and estimate flow rates and
volume exchange using a combination of water level and flow velocity. The collected data and
derived quantities were useful in gaining insight into the circulation patterns and magnitudes
within both Clam Bay and Moorings Bay. including the exchange between the two through the
Seagate Drive culvel1s.
7.2 Water Levels
Figures 7.2 to 7.14 show the water surface elevation time series for 12 locations in Clam Bay and
Moorings Bay for the period of August ]5 to August 23, 2009. They are ordered roughly n0l1h
to south, starting with Upper Clam Bay and ending with Gulfside Doctor's Pass. The time axis
in each graph is marked in 6 hour increments. Table 7.1 outlines the minimum and maximum
observed water levels at each location. as well as the observed tidal range (simply the difference
between maximum and minimum levels).
It should be noted that the water level data from the Clam Pass gauge is of concern, with a range
less than expected and an overall elevation that appears to be too low. The data and instrument
has been checked multiple times and no problems were found, however it is not recommended to
use these data for anything other than phase lag comparisons; the Gulfside Clam Pass data was
substituted when determining velocities and flow rates, described in subsequent sections.
45
Clam Bay System Data Collection and Analysis
October 2009
PBSI
Agenda Item No. 10F
December 15, 2009
Hydrographic Data AR~Sf 133
Table 7.1. Water level parameters in Clam Bay; August 15 to August 23, 2009.
Locati on Minimum WSE Maximum WSE Mean WSE Range
(ft NA VD88) Cft NA VD88) (ft NA VD88) Cft)
Upper Clam Bay -0.3 0.8 0.21 1.0
Inner Clam Bay -0.3 0.6 0.20 0.9
North Bridge -1.2 1.7 0.06 2.9
Gulfside Clam Pass -2,6 1.8 -0.01 4.4
Clam Pass -3.3 -1.1 -2.31 2.2
South Bridge -1.3 1.7 0.14 3.0
Outer Clam Bay -1.3 1.5 0.02 2.8
North Seagate Dr -1.2 1.6 0.10 2.9
South Seagate Dr -2.6 1.9 -0.10 4.4
Park Shore Dr -2.0 1.8 0.08 3.8
Harbour Dr -2.2 2.3 0.23 4.5
Gulfside Doctor's Pass -2.4 2.1 0.10 4.4
PHS]
46
Clam Bay System Data Collection and Analysis
October 2009
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Agenda Item No.1 OF
December 15, 2009
Hydrographic Data AR~Sf 133
Examining the tide range attenuation and phase lags between the various paJ1s of the system can
lead to conclusions abont the main arteries of flow and circulation in Clam Bay and Moorings
Bay. The measured tidal range at both gauges in the Gulf was 4.4 ft; the data is consistent with
predicted tides in both elevation and phase (see Figure 7.14) for the period of study. The two
locations in the Gulf were almost perfectly in phase.
The phase lag between the Gulf and Clam Pass was about 15 minutes. There was negligible lag
between Clam Pass and North Bridge, and N0l1h Bridge had a range of only 2.9 ft compared to
the 4.4 ft range in the Gulf, a decrease of 34%. To the north, Inner Clam Bay lags North Bridge
by about 3.5 hours; this is likely due to friction and loss of momentum as the tide propagates
through the winding channels and flooded mangrove forests. The tidal range also drops to less
than I ft. As an unexpected observation, Upper Clam Bay appears to lead Inner Clam Bay by
approximately 2 hours. The tidal range is I ft, less than 25% of the Gulf tidal range. Both Upper
and Inner Bays have a mean tide level about 0.20 ft above the mean Gu]f level, likely due to
stormwater inflow forcing a head increase.
South of Clam Pass, the tide at South Bridge is 30 minutes behind the tide at North Bridge, due
io the farther distance from Clam Pass. Outer Clam Bay and North Seagate Dr are in phase with
South Bridge. In Moorings Bay, there is a lag of less than 30 minutes between the Gulf at
Doctor's Pass and South Seagate Dr. Dne to the wide opening at Doctor's Pass, as well as the
armored shorelines, the tide propagates throughout Moorings Bay with little lag and no reduction
in tidal range. South Seagate Dr and the Gulf both have a range of 4.4 ft. This suggests greater
flushing of Moorings Bay as compared to Clam Bay.
Since South Seagate Dr has a tidal range 1.5 ft larger than North Seagate Dr and the tide
propagates faster through Moorings Bay than Clam Bay, there are water ]evel differences
observed on either side of Seagate Dr during each tidal cycle; see Figure 7.]0. During incoming
tides, the south side has a higher water leve] than the north side, up to 0.25 ft in difference and
leading in phase by about 30 minutes. On the olltgoing tide, the south side leads the north by 1.5
hours, with a water level difference of up to 1.5 ft. The result is that water flows back and forth
between the two water bodies, with the majority of flow southward from Clam Bay into
Moorings Bay,
PB51
61
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item NO.1 OF
December 15, 2009
Hydrographic Data AR~Sf 133
7.3 Current Velocities and Flow Rates
Figures 7.15 to 7.26 illustrate the velocity data from the six ADCPs that were deployed in Clam
Bay and Moorings Bay for the period of August 15 to August 23, 2009. They are ordered
roughly north to south, starting with North Bridge and ending with Harbour Dr. The time axis in
each graph is marked in 6 hour increments. At Clam Pass and the two bridges, figures 7.15,
7.17, and 7.19 show the water snrface elevation and current profile over time, with the color of
each area scaled to the horizontal velocity magnitude. Figures 7.16, 7.18, and 7.20 show the
depth-averaged velocity magnitude with time. At South Seagate Dr, Park Shore Dr, and Harbour
Dr, Figures 7.21, 7.23, and 7.25 show both the n0l1hing and easting components of the depth-
averaged velocity, while Figures 7.22, 7.24, and 7.26 show the combined horizontal velocity
magnitude.
As mentioned before, the Gulfside Clam Pass water level was used with the Clam Pass current
meter due to a suspect data set. The gaps in the South Seagate Dr and Harbour Dr data were due
to acts of vandalism during the deployment. After the Harbour Dr gauge was redeployed, the
readings appear to be erroneous due to their small magnitude, but no discrepancies can be found
in the data files or instrument setup. For the purposes of calculating flow rates at Harbour Dr,
only the data before the vandalism occurred was used.
Table 7.2 outlines the current velocities and flow rates for each instrument location. Flow rates
were estimated as the depth-averaged velocity multiplied by cross-sectional area at each time
step. The cross-sectional area varied with depth corresponding to the tide level. The maximum
currents and flow rates were the largest value observed between August 15 and August 23. The
'average tidal prism' means the average volume of water passing the instrument site in either the
incoming or outgoing direction during a single tidal cycle (I high tide, 1 low tide). For example,
all water moving south at Harbor Dr would be included in the 'outgoing' volume, while all water
moving north is designated 'incoming'. The difference in the incoming and outgoing volumes at
each location is thus the net flow.
It is important to note that the field data was collected during spring tides, where the tidal range
is larger than normal (higher highs, lower lows). Also, there were several rainfall events during
the study period, which affect water levels in Clam Bay and Moorings Bay due to urban
drainage. Evidence of this rainfall can be seen in the water level graphs (Figures 7.2 and 7.3) of
Upper and Inner Clam Bay, where it appears the mean water level rises during the week as
storm water enters the system.
PHS;
62
Clam Bay System Data Collection and Analysis
October 2009
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Agenda Item No. 10F
. December 15, 2009
Hydrographic Data ARI!i1~Sf 133
At the North Bridge, the highest velocities appeared to occur when the water levels were lowest
(outgoing tide), as flow was constricted to within the main channel and not spread over the
mangrove forest. Outgoing velocities reached 1.8 ftis while incoming velocity peaked at 0.4 fUs,
The highest observed flow rate was outgoing at 291 cfs, and net flow per tidal cycle was
outgoing on the order of 3,68 million cf, In Clam Pass, peak incoming and outgoing velocities
were equal at 3,5 ft/s, with the peak incoming flow rate of 1451 cfs greater than the outgoing rate
of 1017 cfs, Accordingly, net flow was observed to be incoming at a rate of 2,93 million cf per
tidal cycle, At the South Bridge, incoming and outgoing velocities and flow rates were nearly
equal (1.7 to 1,9 ftis and 716 to 777 cfs, respectively), Net flow was slightly outgoing at 566,000
cf per tidal cycle; however, since velocities and fiow rates were similar in both directions, it is
very possible that at other times, net flow could be incoming at this location,
At Harbour Dr, the maximum outgoing current was 0,6 ftls faster than the maximum incoming
current, and outgoing peak flow rates were 14% higher than incoming, Net flow was outgoing,
on the order of 2.41 million cf per tidal cycle, The data at Park Shore Dr followed the same
pattern, with the outgoing direction being dominant, although lesser in magnitude,
As observed in the water level data, the relative responsiveness of Moorings Bay to the Gulf tide
in comparison to that of Clam Bay causes water level differences on either side of Seagate Dr of
up to 1.5 ft, with the largest differences during outgoing tide, where Clam Bay is perched higher
than Moorings Bay, This leads to water flow through the Seagate Dr culverts and exchange
between the two water bodies, The maximum nOliherly CUlTent during the study period was 0.3
ft/s (35 cfs), while the maximum southerly current was 3,0 ft/s (108 cfs), an order of magnitude
of difference, These conditions yield an average net flow volume of 969,000 cf of water to flow
from Clam Bay into Moorings Bay during each tidal cycle (182,000 cf flow from Moorings Bay
to Clam Bay; 1,151,000 cffiow from Clam Bay to Moorings Bay),
7.4 Conclusions
It is important to note that the flow calculations are based on the conditions during the study
period and the resultant trends may only be applicable to the study period, However, previous
studies have documented similar trends in tidal range, tidal phase lag, and flow, Relative tidal
ranges and phase lag trends in this study are comparable to data collected by Humiston & Moore
(2007), The USEP A (1977) performed an analysis of fiow through the Seagate Dr culverts, and
determined that net flow was southward,
Clam Bay and Moorings Bay are two very different bodies of water that form a single interactive
system, Due to channel meandering, constriction, and friction from mangrove forests, there is
significant phase lag and tidal range attenuation throughout the Clam Bay system, The tidal
range in Upper Clam Bay and Inner Clam Bay is reduced by 75% with respect to the Gulf of
Mexico, with a lag in phase of 3,5 hours, Likely due to stormwater drainage, their mean water
levels are 0,2 ft above the Gulf, Even in Outer Clam Bay, the tidal range is reduced by 34%, and
the phase lag is 30 to 45 minutes behind the Gulf,
PBSI
76
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item No.1 OF
December 15, 2009
Hydrographic Data Atl~sf 133
Moorings Bay, on the other hand, does not experience the tidal lag and attenuation found in
Clam Bay, On the south side of Seagate Dr, which is the northern terminus of Moorings Bay,
the tidal range is identical to that in the Gulf, and phase lag is negligible, This is due to the
hardened shore of Moorings Bay, which does not absorb as much tidal energy, as well as the
larger opening of Doctor's Pass encouraging flushing, At Seagate Dr, the combination of a full,
responsive tide on the south side and a lagging, attenuated tide on the north side leads to water
level differences at this location, which drives water flow and exchange through the culverts
beneath Seagate Dr.
Just south of the culverts, the peak southerly current is 3,0 fUs, while the peak northerly current
is only 0,3 fUs, Peak flow volume rates are 3 times higher in the southerly direction, Tn an
average tidal cycle during the field study, 182,000 cf of water moved from Moorings Bay to
Clam Bay, while 1,151,000 cf moved from Clam Bay to Moorings Bay, Net flow is thus
969,000 cf of water per tidal cycle from Clam Bay into Moorings Bay, Because net flow is
overwhelmingly southerly into Moorings Bay, Moorings Bay is more affected by conditions in
Clam Bay than vice-versa,
In order to analyze potential changes to the system to improve circulation and dissolved oxygen
(DO) within the Clam Bay system, a hydrodynamic model will need to be developed to
understand the interactions between Clam Bay (Upper, Inner and Outer), Clam Pass, Moorings
Bay, and Doctor's Pass,
PHSI
77
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item No, 10F
December 15, 2009
Page 100 of 133
8.0 References
Antonini, G" D,A, Fann, and p, Roat. 2002, A Historical Geography of Southwest Florida
Waterways: Volume Two: Placida Harbor to Marco Island, Florida Sea Grant FLSGP-
M-02-003,
Brown, T,R. and H,O, Hillestad, 1998, Clam Bay Restoration and Management Plan, pp, 216,
Collier County, 1997, Clam Bay Natural Resources Protection Area, Report, 85 pp,
Conservancy of Southwest FIOlida, 1997, Clam Bay Restoration and Management Plan: April 9,
1997, Position Statement.
Dawes, C" C. Lobban, and D, Tomasko, 1989, "A comparison of the physiological ecology of
Halophila decipiens and H. johnsonii in Florida," Aquatic Botany 33: 149-154.
FDEP, 1996, Water Quality Assessment for the State of Florida, Section 305(b} Main Report,
Humiston & Moore Engineers, 2003, Clam Bay Hydrodynamic Modeling and Analysis,
Humiston & Moore Engineers, 2007, Clam Pass Restoration and Management Plan-
Bathymetric Monitoring Report #8,
PBSJ, 2008, Clam Bay Seagrass Assessment. Submitted to Collier County Coastal Zone
Management Department,
McCormick, P,V" Chimney, MJ, and D,R, Swift. 1997, Diel oxygen profiles and water column
community metabolism in the Florida Everglades, U,S,A, Archives die Hyrobiologie,
140: 117-129,
Smith, S,V"Kimmerer, WJ" Laws, E,A" Brock, R.E" and T,W, Walsh, 1981. Kaneohe Bay
sewage diversion experiment: perspectives on ecosystem responses to nutritional
perturbation, Pacif. Sci, 35: 278-396,
Tackney & Associates, Inc, 1996, Preliminary Hydrographic Assessment - Clam Bay Systems,
Tomasko, D,A" D,L. Briston, and J,A, Ott. 2001, Assessment of Present and Future Nitrogen
Loads, Water Quality, and Seagrass (Thalassia testudillwn) Depth Distribution in Lemon
Bay, Florida, Estuaries 24(6A}: 926-938,
Tomasko, D,A. and B,E, Lapointe, 1991. Productivity and biomass of Thalassia testudillum as
related to water column nutrient availability and epiphyte levels: field observations and
experimental studies, Marine Ecology Progress Series 75: 9-17,
PBSI
78
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item No, 10F
December 15, 2009
Refl!jleh(5leSf 133
D,S, Environmental Protection Agency, 1975, Field Studies, Park shore and Clam Bay Systems,
Naples, FL. Region IV, D,S, EPA Surveillance and Analysis Division, Athens, GA
D,S, Environmental Protection Agency, 1977, Field Studies, Parkshore and Clam Bay Systems,
Naples, FL. Region IV, D,S, EPA Surveillance and Analysis Division, Athens, GA
Valiela, L, Costa, J" Foreman, K" Teal, ],M" Howes, B" and D, Aubrey, 1991. Transport of
groundwater-borne nutrients from watersheds and their effects on coastal waters,
Biogeochemistry 10: 177-197,
PBSI
79
Clam Bay System Data Collection and Analysis
October 2009
Agenda Item No. 10F
December 15, 2009
Page 102 of 133
Kathv Worlev Comments
Comments on PBS&J Report: Clam Bay System Data Collection and Analysis based on a
preliminary review, Note an in depth look at this report is put on hold until answers to the
questions that are raised in this missive are forthcoming, I apologize for the disjointed nature of
these comments - unfortunately I have been dealing with some health issues for the past 3 weeks
which have limited review of the report,
Note: Statements that are in red italics are directly from PBS&J report
Executive Summary: Page i section: Review Points 1 and 2:
The FDEP mandate to get data into STORET is important for achieving state-wide water quality
goals and initiatives, The County should definitely comply with this mandate, but this is not the
main reason to perform water quality monitoring, Water Quality monitoring is one of the
methods commonly used to find out what types of pollutants are in the water, can overtime
establish any trends, serve as an early warning system for potential developing problems, and can
give an indication of their possible source, The information provided by water quality monitoring
can help indicate what types of aquatic flora and fauna the estuary could support, given the
physical and nutrient water parameter levels present in the water overtime (Note: water quality is
not the only thing that dictates what species will reside or use a water body), It seems that there
are excessive concerns about getting a negative review by FDEP and triggering an investigation
towards a possible TMDL, and while it is nice to head off perceived problems, the TMDL
program is just a way to get Counties to address any water quality problems, which is a good
thing,
Dissolved Oxygen levels are perceived as a problem regarding State standards in Clam Bay,
However in order to trigger a TMDL, dissolved oxygen levels have to be below Standards in
concert with causative pollutants, Biological Oxygen Demand, Total Nitrogen and Total
Phosphorus also have to exceed State standards, Dissolved oxygen levels recorded in Clam Bay
have been below the State standard, typical of a lot of estuarine waterways in the County
including Rookery Bay (usually during the summer), This is not unusual and as long as the
levels are not constantly below the State standard or at anoxic levels that can precipitate fish kills
(given the wann water (d,o and temp have inverse relationship)), these levels are not surprising
and can be defended, Rookery Bay is an FDEP reference site (Water Body lD :# 3259M), This
site does have dissolved oxygen levels below State standards and Rookery Bay has not triggered
a TMDL by FDEP since it does not have a causative pollutant, nor has the Tamiami Canal
system (Water Body Id : 3261 B),
Water Quality monitoring programs are important and should be implemented for Clam Bay just
be sure you know the reason to do so is track water quality trends over time; what the water
quality means to the organisms that live in that water way; and for people who wish to use that
waterway for fishing, swimming or other recreational activities,
PBS&J's Critique of other studies
Agenda Item No, 10F
December 15, 2009
Page 103 of 133
I do not intend to comment extensively on these sections other than to say that it appears that the
context and purpose for doing past hydrology and water quality studies were not considered
when the review was written, Mr, Humiston's rebuttal to PBS&J's comments concerning their
report are valid, Similarly, the critique of the water quality studies done by Pelican Bay and the
Conservancy were performed for specific reasons, FYI - the physical parameters collected by the
Conservancy do meet the standards for use by FDEP STORET guidelines the data has just never
been entered on a regular basis, And as far as the nutrient parameters, it was stated up front by
the Conservancy that these data were not performed by a certified lab, but were performed in
accordance with acceptable methods, quality controlled with period split samples with a certified
lab, and that only a few key parameters were investigated for trends - all of which are standard in
most water quality studies, FYI "The most important nutrients in coastal estuaries are dissolved
inorganic nitrogen and phosphorus compounds" (Holmboe, et. aI., 2001), WHOOPS - Now I
am getting defensive so I'll stop!
, Statements Fom Introduction page I paragraphs I and 4:
Paragraph 1: "Clam Bo)' and Moorings Ba)' are important naturalfeatures in Collier County",
Paragraph 4 sentence 3: "Ill COllzrast, lJ/uch (~lthe shoreline q!,Afool'ings Bay lvas s;gll?flc([nl~V
altered through dredge and fill oetiFit.l', such that natural shoreline features in the northem
portions o{Moorings Bo)' were mostly a0sent hy the 1950s"
The statement in paragraph I contradicts the statement in Paragraph 2 as the entire Moorings
Bay today is unnatural. Moorings Bay is not a natural feature, It used to be natural in the 50s'
when the mangrove forest extended from Moorings through Vanderbilt. Additionally, although
Clam Bay is unarguably the most natural system of mangroves remaining in the urban Naples
landscape (discounting Rookery Bay) it is not entirely natural either given the encroaching
development and isolated state today,
Agenda Item No.1 OF
December 15, 2009
Page 104 of 133
,
~,.-
Source: USGS 1953, Outer (Lower) Clam Bay and Moorings 1953: Undeveloped Natural State
The PBS&J report, intended or not, gives the reader the impression that Moorings Bay is being
compared to Clam Bay and Clam Bay is coming off as being perceived as more impaired, These
2 systems should not be compared for estuarine health as Moorings Bay is no longer an estuary,
Dr, Bauer from the City stated as much at the last meeting, Collier County Pollution Control,
Save the Bays, the Conservancy and the City have for decades worked to improve the conditions
within Moorings Bay given that this is a hardened structural man-made system, For years all
have been pushing for rip-rap when seawalls fail and need to be replaced, fertilizer ordinances,
stormwater control, etc and under Dr. Bauer's guidance some strides have been made in these
areas to help improve the conditions of this man-made canal system, The only connection that
Moorings Bay and Clan1 Bay have at this point is the culvert,
Question: In the introduction please define what this report considers the boundaries of the
"Clam Bay Watershed" throughout this report to avoid confusion,
Statement from Page 4 last paragraph: "Instead, the cone/usion was reached that die-ojf was
likely dlle to excessil'efi-eslnniter inpllt to the svstem ./i-om the adjacent developed uplallds alld
an inadeqllate di,'peniOlI of the increased freslnl'ater inpnt dill' to severelv constricted tidal
dlUnnels in the mangruve'/()rCi';t. As ([ rc,vlllt, the mangrove/ore.,,'t becwne inundated with "vater
lel'els higher than the tops of the black mangl'Ol'C pneulllatophores, nil' duration of ill creased
water le\'els was sllffieient to kill the trecs by blocking o.ngell t'Xclwnge to tlze helow grolllld
tissues ".
While this statement is true it is important to also remember that impoundment of excessive
freshwater from unusually high rainfall amounts in 1992 and 1995 was the straw that tipped the
Agenda Item No, 10F
December 15, 2009
Page 105 of 133
scales in the northwest corner of the Clam Bay mangrove system and that by all indications was
stressed to begin with most likely due to development on the borders of this forest. A lot of
emphasis is being placed on improving flushing within the Clam Bay system as a solution to
problems that have developed within the mangroves in the past. While flushing is essential to
mangrove systems and usually occurs naturally, any excessive anthropogenic freshwater inflows
into Clam Bay should be dealt with at the source instead of flushing the excessive freshwater and
anthropogenic introduced pollutants to the Gulf, This in itself should be perceived as a problem
as in effect we are just contributing to polluting the Gulf and although the levels are probably
small in comparison to other inputs it is time we start to address the Gulf instead of treating it
like a septic tank throughout the Gulf States, Additionally, improving the flushing of Clam Bay
seems to be perceived as some sort of cureall, which is not accurate, Too much flushing is just as
much a problem as too little in an estuary, as the habitats and species that use these environments
are adapted to shallow, low energy environments, Also, given that estuaries are shallow and the
land features typically are at low elevation, very little rise in water levels is needed to flood the
mangroves for tidal flushing as long as no impediments that impound the water exist.
Additionally, the usual way to improve flushing is through dredging which can alter the detritus-
based system of a mangrove estuary by stirring up and/or removing sediment and disrupting the
nutrient sources necessary to the organisms that rely on detritus for food and cover, and can also
interfere with the natural decomposition process by bacteria and other organisms, Therefore,
dredging to improve flushing should be tempered and used sparingly in order to keep the balance
of the system in check,
Statemelltji-om Page 5 ],2: "/n re,'pO/lSe to eOlleems relaled 10 Ihe isslles of water qualily alld
r;irelllatioll ill the Clam Bav and lv/oorillgs Bay .ITstellls, Collier Count)' reqllested PBS&J
prepare a proposal to cOllduct a cirC1llatiolllllld 11'llter qualilv stlldv to de/ermine thefhl/owillg:
. What is the extelll ami relative health of the nlltllml reSllllrees ill Clalll Bay Illld lv/oorings
BIlY?"
While water quality and hydrology are important components without biological studies it will
not be possible to determine the extent and relative health of the natural resources,
." What do historical data sllggest, ill terllls olstatlls alld trcnd,., abollt the health of Clalll HIlY
alld Moorillgs Bay?"
Historical biological data also needs to be addressed prior to hypothesizing about the health of
the system,
. "J-foH'do drclIlatiol7 patterns and }/utrient dclivClT ill/eract to create spatial patterns' ql'
miler quality ill Clal1l Hay alld AIoorillgs Hal., Illld hm,. these pal/ems Il/feet the estllarille
flora alldfilullll! "
Some inferences can be made from the water quality concerning what species could possibly
survive in that particular water but it can't tell you population dynamics and trends,
Agenda Item No, 10F
December 15, 2009
Page 106 of 133
. "How will challges in circulation within Clam Bay and between Clam Bay and Moorings Bay
affect the overall estuwy (as defilled in Figure J,5)?"
This will only answer definitively the effect on the hydrology and not the biology,
Question Regarding 2,0 Methods 2,3 page 7
Please specify the number of sediment samples were taken in the system and were any replicates
taken? Additionally what were the weather conditions during the 2 day period of sampling?
What method was used to classify the soil conditions based on color? Muliers? Were hue, value
and color intensity evaluated? What were the ranges?
StatementFom 2,0 Methods 2.4 page 8
"n1is task consisted of completing a bathymetric survey of a portioll of the project area, The
bathymetric survey of'the project area illcluded Clam Pass (;'ncluding thc ebb shoal complexj,
Upper, Jllner, and Outer Clam Ray, and Moorings Ray",
Please provide the bathymetry map
Regarding Statements from 2,0 Methods page 8 Currents/Water Levels: page 8:
"Currellt and water lel'elmcasurcmcllIs were taken with ill the project arca O1'er a period of'8
daysji)r use in a planning lel'eI circulaTion allalysis, This data call also be IIsed/or the
caUhrafioJ1 (?( a potential hydrodynamic llllmcricu! mode!. CurrellL\' and It'uter levels lveTe
measured at jive alld sewn locutions withillthe project area, respectively",
And Statements from 7,J
"The data collection effiJrt yielded concurrent water level andj/ow velocity measurementsjiJr a
period oj'8 days,fi'om August J5 to August 23, 2009, All illStl1lments were success/it! in
collecting data; hOlvever, ,\'(!ver(t! act.\' qfvandalism "
"it should be noted {hat the water level dataFom the Clam Pass gauge is of concern, with a
range less than eJ.pec{ed and an overall ele1'(/tioll that appears to be too low"
And Statements from Hydrographic Data Analysis 7,3 Current Velocities and Flow Rates page
62:
"The gaps in the South Seagate Dr and Harbour Dr data Here due to acts of1'(/lIdalism during
the deployment, A/ier the Harbour Dr gauge lvas redeployed, the readillgs appear to be
erroneous due to their small magllitude, but no diserepaucies ean bejinllld ill the datajiles or
instrument setup, For the purposes of' calculaling.flow rotes al Harbour Dr,
only the data befiJre Ihe vandalism occurred ,.vas used",
Equipment malfunctions do occur within the field, however not repeating the experiment given
the unexpected data; readings that appear erroneous; and only using data prior to incidents given
Agenda Item No.1 OF
December 15. 2009
Page 107 of 133
that the period of observation is so short does not give confidence in using these data for model
calibration, I have often endured equipment failures that cause the experiment to be repeated
otherwise there would have been no confidence in the data, Even when I did some surface water
level studies in the past where a gap in the data was caused by equipment vandalism I was able
to eliminate this data as I had a year worth oflevels and a two week gap was within the realm of
acceptable loss, However in this case where the period was 8 days the loss of half the data at
some of the sites is too great a percentage to discount.
I have a great deal of concern and would not be able to trust any modeling done with the
readings that were collected over such a short time span; that were fraught with problems,
readings that appeared to be erroneous at Clam Pass (which is one of the focal points
hydrologically) and the time frame of only using a "spring tide" where only the extremes and not
the norms are used,
Most hydrologic data sets today that arc used in conjunction with biological components (which
is necessary to develop any sort of management plan that has validity) in estuaries typically rely
on a time series water level and velocity for a month covering neap and spring tides, For
example, Van Santen, et. al. , 2007 collected time series water level, velocity and sediment
accumulation for a month covering neap and spring tides in order to ensure that a complete
hydrographic picture could be inferred, Ji, et. aI., 2001 measured data for tidal calibration that
included tidal elevation, salinity, temperature, current velocity at various locations throughout
the estuary for 31 days in order to ensure accuracy,
Two independent data sets are required for calibration and subsequent validation of a
hydrodynamic model. The observation times should be divided into two separate components I
month for calibration and I month for validation is sufficient and model sensitivity studies are
essential (Huang, 2007), Various year's wOlth of this kind of data is available from other sources
that could be vetted to complete a better hydrologic picture for use in modeling this estuary,
Granted that past hydrologic investigations over the years had different goals, their data is more
robust and more suited to model calibration and verification, which at the moment would make
these past modeling efforts more useful than an updated more sophisticated model whose
calibration and validation is suspect.
"Handling model complexity and reliability is a key area of research today" (Raick, et., aI.,
2006), Currently in marine ecosystem modeling the idea is to include an ecological component
in conjunction with a general circulation model. What ever strategy is undertaken the key is
assessment, as the biology must be linked to the hydrology and physical environment
characteristics (Raick, et., al. 2006),
Regarding Statementfi-om the executive summary:
"In order to onaly::e potential changes to the .\y.r;,tem to improl'c circulation and dis'Soh'cd (uygen
(DO) ,vi/hill the ClalJ/ Ba)' S]'.I/elll, a hydmd1'l1illllic lJ/odel will need /0 he dCl'eloped to
unders/alld the illterac/ions he/ween Clam Bar (UPPCl'. IIIIICI' and Oll/er), Clam Pass, A100rings
Bay, and Doc/or '.I' Pass"
Agenda Item No. 10F
December 15, 2009
Page 108 of 133
This statement concludes that there is a need to improve circulation and dissolved oxygen within
Clam Bay neither or which has been adequately substantiated or established at this time,
particularly in reference to the ecology,
Statement from Hydrographic Data Analysis page 61
"As an une'pected observation, Upper Clam Bay appears to lead Inner Clam Bay by
approximate(y] hours. 771e tidal range is Ifi, less than 25% of the Gulf tidal range, Both Upper
and Inner Bays have a mean tide level about 0,20 fi above the mean Gulf level, likely dlle to
stormwater i1!flo1'l'forcillg a head increase ".
Given the unexpected results alluded to by the author it is prudent to repeat this experiment to
confirm whether the results are an anomaly, Additionally, the time lag could and probably does
change during the wet and dry seasons,
StatementFom Hydrographic Data Analysis 7,3 Current Velocities and Flow Rates page 62:
It is important to note that the field data was collected during spring tides, 1-1'here the tidal range
i.-.j larger than normal (higher highs, Im,vcr IOv,}....:J. Al.s'o, there were several rah~f(dl events during
the study period, which affiy't water levels in Clam Ba\' and Moorings Bay due to urban
drainage, Evidence of this rainfiill can be seen in the water level graphs (Figures 7,2 and 7,3) of
[Jpper and 111ner Clam Ba.v, 1vl1ere it appear:')' the mean 1vater /cl'el rise.s' during the week as
s'tornHvater enters the .\ystem.
What were the extent of the rainfall events and when did the events occur in comparison to when
the inflows show up?
The choice of using higher and lower than normal tides can skew the data and should cover an
entire spectrum of tides to accurately come up with net values although the time when the
readings occurred does give some insight (0 extreme conditions as stated in the reports
conclusion (page 74), It is importunt to note thut theflow calculations are based on the
conditiollS during the studv pcriod and the resultaut trends may on(v be applicuble to the study
period.
Given the lack of confidence in the data set (data gaps), any results and conclusions about the
hydrology would also be suspect and thus any comments on actual values relating to tidal cycles
and currents reported in this report would be moot.
In regard to the Water Quality Component of the PBS&J report:
This is part of the report is geared at a review of past data and basically reinforced the basic
information that was already apparent such as:
· There were erroneous values in the data set from Collier County,
· The ends of the Clam Bay system appeared to have more instances lower dissolved
oxygen levels and/or nutrient levels which is typical of any system that has deadends -
the farther the distance from the pass",,"
Agenda Item No, 10F
December 15, 2009
Page 109 of 133
I would have liked to see statistics broken out by season as this is an important driver in water
quality and could explain some of the readings that are shown in the graphs, For example, did the
instances of low dissolved oxygen occur primarily during the summer months and how does the
dissolved oxygen correlate to water temperature values? What were the depths at the various
stations in comparison to levels that were reported - is the higher nutrient levels and lower
dissolved oxygen recorded in concert with very shallow depths and could sediment resuspension
possibly interfered during sampling? Were nutrients and chlorophyll levels higher during the
2005-2007? If so, resuspension of nutrients caused by hurricanes could result in algal blooms as
seen in southern estuaries in Florida in 2005, Chlorophyll a levels increased with algal blooms
and the majority ofregions that Boyer, et. aI., 2009 assessed in 2006, CHLA was higher than the
median at their sites, but did not appear to indicate negative trends in southern estuaries,
Mangrove interfaces with the Gulf had higher chlorophyll a levels in 2006 than in 2005, likely
the result of the hurricanes that hit south Florida in 2005 and likely does not indicate long-term
trends (Boyer, et. al. 2009)..
Were low dissolved oxygen levels and/or higher nutrient levels persistent over time or just
isolated incidents? Were low dissolved oxygen levels primarily between 3 - 4 mg/I or lower and
if so how long did the condition last? Any relationship to precipitation events? Were any tables
generated that detailed the data and statistics that could clear up some of these questions?
Discounting obvious outliers - are dissolved oxygen or nutrient values that were lower/higher
than the ambient levels correlated to weather events such as storm events or episodic algal
blooms that appear in the Gulf'? (see next paragraphs for the context of this question),
The Gulf coast of Florida receives discharges from a lot of rivers in the northern and central parts
of the west coast. Runoff from these rivers affects the chemistry and biology of estuaries with
maximum discharges tending to occur in the spring and fall. The southern movement of the
waters in the Gulf could affect the southern parts of SWFL waters, An episodic event during the
spring occurred when elevated pigment concentrations persisted of 1-6 weeks extending 250 km
along the Florida shelf. Plume formation was associated with discharge from local rivers in NW
Florida; seasonal changes in height between the shelf and the Gulf of Mexico waters; Loop
current circulation and upwellings in the Gulf of Mexico off De Soto; and discharge from the
Mississippi and Mobile rivers, On the FI01ida Shelf in the Gulf of Mexico toxic dinoflagellates
have episodic blooms that are suspected of adding to the total nutrient production, These blooms
tend to occur in the summer or fall but can occur at any time, The semi-regular occurrences of
this bloom indicates that energy levels to higher tropic levels could be seasonal. In May of 1992
a particularly high chlorophyll a bloom occurred (Gilbes, et.al. 1996), Do the high chlorophyll a
levels that were found in Clam Bay con"espond to the semi regular events in the Gulf shelf
particularly in 1992? The impact that nutrients from the Gulf on local estuaries is poorly
understood but should be considered as possible explanation of local nutrient and chlorophyll
spikes during episodic blooms (Gilbes, et. al. 1996),
In general, from a cursory inspection of the figures presented in the report it is no surprise that
the upper regions of the Clam Bay system are higher in nutrients given that the system has been
cut off from its natural connections to the north, This is found in both manmade canal systems
including Moorings Bay and natural systems that lack river inflows, Additionally, when
Agenda Item No, 10F
December 15, 2009
Page 110 of 133
analyzing the data efforts should be made to explain possible elevated levels such as those
discussed above if applicable,
Regarding section 3,2 Dissolved Oxygen page 14 in the report:
"E1,'tremely e1e1'ated concelltrations of DO were observed between August 20()] and August
2002; these data must have been reported illaecurately, alld cannot be representative of the
ambiell/ DO readillgs at that time, To accommodate this data problem, Figure 3,5 was created,
where the yaxis was trullcated at a more realistic maximum DO level of10 mg/l",
It would be more appropriate to omit the erroneous data from the set rather that trying to
visualize it in truncated form, Suggest including a table of the outliers and stating that these
values were not included in analysis of the data set as the values reported were suspect and to
include them when making analysis could skew the data set. It is not clear whether or not these
suspect values that the authors "truncated" to "10 mg/l" were used in any of the statistics
presented in Figure 3,6, If they were they should be removed as given the obvious erroneous
level of those values it is not appropriate to include in the statistics and could lead to erroneous
conclusion given that there is no way to arbitrarily assign a value to these particular values with
any degree of certainty,
Regarding section 3,2 Chlorophyll page 17 in the report:
"1so/uted elevated cOllccntratiollS of chlorophyll a h",'c been observed at the W-n and W-1 sites,
however, the conco/tration observcd on Septcmber 1996 at the W-6 site (299 J1.g/L) is unlike~v in
the marine waters, and so the data are displayed (Figure 3,8) II'ith a truncated y-axis ",
Again, as with the dissolved oxygen, it would be more appropriate to omit the erroneous
chlorophyll a data from the set rather that trying to visualize it in truncated form, Suggest
including a table of the outliers and stating that these values were not included in analysis of the
data set as the values reported were suspect and to include them when making analysis could
skew the data set. It is not clear whether or not these suspect values that the authors "truncated"
to 50? mg/l" were used in any of the statistics presented in Figure 3,9, If they were they should
be removed as given the obvious erroneous level of those values it is not appropriate to include
in the statistics and could lead to erroneous conclusion given that there is no way to arbitrarily
assign a value to these particular values,
Regarding on Page 20 on the report:
While certain facts presented in the PBS&J's report regarding TMDL's are correct, the
interpretation of what actually triggers a TMDL does not appear to be in accordance with
FDEP's guidelines.
"Site W-7 exceeded an anllual average Chi-a concentration (if 11 J1.g/L during both 2005 and
2007, Based upon existing criteria ji-OI/1 FDEP, Clam Bay would likely be declared verified
impaired due to elevated chlorophyll a cOllcentratiollS"
Agenda Item No, 10F
December 15, 2009
Page 111 of 133
According to FDEP's current Impaired Waters Rule 10% of the samples have to exceed annual
averages of II ug/l for the Water Body, Given the bar chart values from the Figure 3,9 in the
report - it does not appear that 10% of the annual averages for chlorophyll a are impaired as all
of the sites would be looked at together. As on the chart only W -7 has instances were the annual
average is above I I ug/I and the rest of the stations appear to be within FDEP's criteria it is
unlikely that Clam Bay (WBID) by itself would be classified as verified impaired, Also there are
a minimum number of samples needed to put a water body on the Verified list (with at least a
90% confidence), Within the data set (discounting any suspect samples) - How many total
samples were there? - And how many were impaired? Were confidence intervals generated for
the data?
Regarding the Nutrient Analysis:
When trying to understand and analyze nutrient cycling dynamics it is important to take into
account that estuarine wetlands act as a f1lter as they tend to sequester or recycle nutrients, It is
important to remember that mangrove systems are a sink for nutrients and bind large amounts of
N and P for production, Ignoring the uptake and release of nutrients, particularly from minerals
that occur naturally in mangrove swamps, can cause errors in determining the nutrient balance
necessary to sustain the estuary (Wosten, ct. aI., 2(03), Calculations based entirely on hydrology
and water quality which vary considerably in time and space without considering the natural
biological and nutrient cycling within the estuary is questionable, While these elements are
important relying on them alone for management of the estuary could lead to erroneous
conclusions about the estuary dynamics (Wosten, et. aI., 2(03), The dynamics of an estuary have
to be taken into account when evaluating an estuary like Clam Bay versus evaluating a man-
made canal system like Moorings, For example: Shallow water estuaries (like Clam Bay) should
. accumulate substantial amounts of organic matter that becomes incorporated into the benthos
where it degrades and is modified by microbes, Microbial communities employ complex
anaerobic and aerobic transformations that result in the amount of organic and inorganic
nutrients within and above the sediment. Tide and wind indirectly influence microbial
communities and thus nutrient concentrations within the sediment through resuspension activity
that arise from these forces (Seymour, et. aI., 2(07), Naturally nutrients could be higher in Clam
Bay due to natural interactions, whereas in Moorings Bay there is a lack of natural nutrient
cycling due to the lack of detritus buildup which is necessary to an estuary, "Resource
management strategies must take into account system-specific factors" (Tomasko, et. aI., 2005),
Regarding - Sediment and Biological Health Characteristics
The survey conducted by PBS&J only provides a cursory look at the sediment and any attempt at
using this qualitative data to describing redox conditions and benthic communities is fraught
with assumptions that could lead to erroneous conclusions, As the visibility in Clam Bay is
generally low, any characterizations derived from the survey are anecdotal at best since very
little of the surrounding habitats would be visible to the observer, Biological assessments have to
encompass the whole spectrum of the food web and not just a visual interpretation of a few of the
lower level organisms mentioned in this study, without looking at the community from the top
down also, Due to the scope of this study there was no possibility of characterizing the health of
Agenda Item No.1 OF
December 15, 2009
Page 112 of 133
the benthic community with any degree of certainty with the methods that this survey employed,
as typically indices are used to describe benthic populations,
Regarding Sediments and Redox in Mangrove Estuaries
Mangrove soils have been described as highly anaerobic, sulphidic, reduced inundated muds,
whose physicochemical properties vary with elevation and forest type (Alongi and Sasekumar,
1992), The most significant effect of inundation is depletion of soil oxygen, Biological and
chemical reactions are largely controlled by oxidation-reduction processes, which are necessary
to cycle nutrients within the air, water, and soil. Transformations of nitrogen, sulfur, iron,
manganese and carbon occur under anaerobic conditions, where nitrate (N 03 "), manganese oxide
(Mn02), iron hydroxides (Fe(OHh), sulfate (S04"2), and carbon dioxide (C02), in this order, act
as electron acceptors in the absence of oxygen (Vespraskas and Faulkner, 200 I), Redox
potential, expressed and measured as Eh, is a useful indicator of what types of reduced elements
one can expect to find in soil solution It is an electrical measurement that shows the tendency of
a soil solution to transfer electrons to or from a reference electrode, From this measurement,
estimates can be made to as to whether the soil is aerobic or anaerobic, and whether or not
chemical compounds including iron oxides or nitrate have been chemically reduced or are
present in their oxidized forms.. Interactions between soil redox potential and availability of
essential nutrients are extremely complex (Clough, 1992) and are influenced by a variety of
factors including surface water and groundwater inflows, oxygen availability, plankton
productivity, pH, and moisture content (Alongi, et. aI., 1992),
Color is an obvious cue to soil processes as the color of soil is often determined by the various
compounds within it, mineral grains, biological activity, and natural pigments like iron and other
oxides, Seasonal variations in precipitation and evapotranspiration rates lead to water table
fluctuations causing alternating reduction and oxidation with respect to iron oxides, Mobilization
of ferrous iron during periods of reduction can cause segregation in soil zones, However
sometimes in areas of high water tables these conditions don't develop leading to anomalous
conclusions about color inferences about redox (Rabenhorst and Parikh, 2000), At best in
mangrove estuaries color can give a rough idea of the types of minerals that could be present in
the substrate, but inference to redox potential of these soils is not recommended, Redox potential
should be measured and even then it describes what oxygen-reduction reactions are likely to be
occurring in the sediment in that localized area as redox potentials tend to fluctuate, For
example, the brown to green color variation in marine sediments marks the depth where nitrate
has been reduced to Fe3+ to FE 2+, The color change can be reversed due to the oxidation
properties of iron, The depth to the brown - green transition provides a rapid way to estimate
redox conditions in sediments however this depth transition cannot be related to productivity
(Rabenhorst and Parikh, 2000), Thus the Statement Fom the executive summwy point 6: "As a
result, A100rillgs Bay, althollgh suhjCCI 10 cxtensivc IIrhall slorl11walcr rUllo(f, appears 10 have
waleI' ecology cOlldilions helieI' Ihall Ihose(imnd ill Clal11 Bay: Ihis is supported by Ihe resulls of
Ihe Redox layer illvesligalion" should be suspect. Although most mangrove sediments are
characterized by negative redox potentials and anoxic conditions that can persist to the surface,
some of the surficial sediments near the landward margins are aerobic in nature, possibly due to
burrowing fauna, Mangrove sediments near the surface often have highly variable redox, which
Agenda Item No.1 OF
December 15, 2009
Page 113 of 133
result in various colors in the soil and rapid changes in redox potential (Eh) over small distances
(Clark, et. aI., 1998),
Regarding Statements made in the executive summmy #2 and #3:
"Afine-gruillcd sedimenllava wasfiilll1d in llIosllocalions ofDlllcr Clalll Bav, 77!is
sediment depth was approximalelv 5(cel inlhe area o(lhe Seagall' callais, was not
prel'l1lent in AJoorings Bav, and varied ill deplh in Outer, lillieI' alld Upper Cll1m Bl1vs',
"It is nO! known 111 this tillle if"thefine-grained sedilllem lava is nalllra!!v occurring, or
occurring as a rc..ult (~rman-made changes to file Clam Boy system. It is, hrHt:evcr,
kllownlhal the sediment layer in Ihe Seagale cwwls has I1CClllllllll1led since the canals
were dug in the I 950s ",
Fine sediments are not uncommon and occur naturally in mangrove estuaries (Alfaro, 2005; Van
Santen, et., aI., 2007; Bala Krishna Prasad and Ramanathan, 2005; Alongi, et. aI., 2005; Schmid,
et., aI., 2006) often in the upper reaches of the estuary (Van Santen et., aI., 2007), Therefore it is
not unusual or even unexpected that the PBS& J found evidences of these types of sediments
within the Clam Bay system as there is often an active capture of fine cohesive sediments by
mangroves (Van Santen, et., aI., 2007), "Manb'TOVe sediment can provide a sink for trace metals
since the mangroves create a baffle that promotes the accumulation of fine-grained organic
matter-rich sediment which is usually sulphidic due to the presence of sulphate- reducing
bacteria in the sediment" (Clark, et. aI., 1998),
Sediment accumulation is commonly a by-product of man-made narrow canal systems like
Seagate and Aqualane Shores, Additionally, previous investigations by Dr, Aswani Volety
(FGCU) that were performed for Save the Bays revealed that in Moorings Bay bottom conditions
in Moorings Bay varied from sandy, rock, shell rubble to muddy hypoxic sediments, Rock
bottoms particularly in those areas that are dredged would limit any sediment inferences,
Regarding StatementFom 3,3 Task 3 - Sediment and Biological Health Characterization
General Biological Survey Results page 28
"Redox laycrs wac al or close 10 the surfuce t< ]0 elll) ill bmh Uppcr I1l1d OUla Clam Ba)'. In
cOlltrast. Redox layers' lI'ere (lp;c(1/~v deeper rhall ]() em i1/ Inlier Clam Bo.r ul1d A{oorings Bay.
i7/(!sc dala sllgge."l//zat hen/hie C0ll11111ll1irics 1\'Ould he e.rpccfcd 10 ne (~j'hn\'e,. diren.;;ty (i{no!
I1bllndl1nee) in bOlh Uppa alld Outer Clam BI1Ys"
Benthic Communities
Benthic communities arc not composed of just seagrass, and macroalgae that are mentioned in
this report and given the low sample size (albeit cost driven) and the lack of stringent survey
protocols (visual only), and no repetitions overtime, there is no way to quantify the benthic
communities, The macrobenthic community alone covers a diverse spectrum of species
including but not limited to sponges, mollusks, wom1S, crabs, lobsters, prawns, etc, (Ellison,
2008) which are not able to be quantified by the cursory inspection performed during this study,
Agenda Item No, 10F
December 15, 2009
Page 114 of 133
Thus statements such as those made in the executive summwy #6 and 7 reiterated below do not
represent the "benthic communities" nor the inferences or comparisons made between the "redox
layer" and the diversity of these communities (given the methodology used, limited sampling,
and lack ofEh measurements, etc,) in Clam Bay and Moorings Bay
"The shallow Redox laver depths ill most of Clam Bav, ill combillation with the fillegrained
sedimelltsfi!llnd ill most locatiolls, suggest that henthie (i,e" "hottoIlHhFellillg") commullities in
Clam Bay would he expectcd to he less diverse thall ill ,~foorings Bay",
" Combilled, these results indicate that despite the more modified shoreline and greater
po/lutallt loading potential, Moorings Ba)' would appeal' to IW1'e a more diverse and
healthy benthic ecology than Clam Bay. Differellces in the ecologicalfimctioning between Clam
Bay and Moorillgs Bay could be due to differences ill tidal circulation alld
residence time ".
The relationship between the ecological function and sediment properties in inter-tidal mangrove
forests is poorly understood due to the complex interactions between the abiotic and biotic
elements (Chapman and Tolhurst, 2004), , Soft sediments are complex, having different physical
properties, different degrees of microbes, fauna and trace metals that vary spatially and
temporally (Chapman and Tolhurst, 2007), Studies performed by Chapman and Tolhurst (2004)
revealed that variation in the benthos did not correlate to bio-dependant properties of the
sediment at any scale nor the properties of the sediment relate to any habitat. Their data
indicated that properties of the sediment were not related to the properties and processes that
drive the benthos, since there was a very large variation in benthos within small sites, These
results emphasize the necessity of sampling at a hierarchy of scales to make any definitive
statements concerning the benthos as it relates to sediment (Chapman and Tolhurst, 2004),
Biogeomical sediment properties can change depending upon the biota directly through
consumption and indirectly by excretion, Benthos can change their local distribution patterns as
they move to find food, There is no neat correlation between grain size, sediment color and
benthic diversity as patchy distributions are common in soft sediments, Since mangrove forests
live in complex environments that have different habitats and substrates with diverse
macrobenthic fauna living on the sediment in different abundances it is necessary to examine
relationships between the sediment and benthic macrofauna at multiple scales as direct
correlations are often inadequate as benthos has differed among the same habitats in multiple
mangrove estuaries and even among replicates within the same habitat (Chapman and Tolhurst,
2007), Thus while some sediment properties may be important in determining the structure of
macrofauna they are not consistent. Alternatively some organisms may have similar effects upon
sediments in different places while the same species may affect the sediment differently from
place to place, One problem with many of the studies that compare sediments and benthos is that
there is little replication and the need to carry out experiments at multiple scales across multiple
habitats, without replication there is a strong possibility that can lead to erroneous conclusions
(Chapman and Tolhurst, 2007), The sil,,'uificance of trophic interactions and the mangrove
sediments should not be underestimated or ignored in understanding ecosystem health, The
unexpected diversity in patterns of resource use in mangrove systems (as described by Bouillon,
et.al. 2008) emphasizes the complex and highly dynamic environment of these estuaries which
complicates interpretation of trophic interactions necessary to promote faunal health (Bouillon,
et., aI., 2008), Thus the lack of apparent resources in Moorings Bay might not support a diverse
Agenda Item NO.1 OF
December 15, 2009
Page 115 of 133
benthic community regardless of the sediment characteristics, Macro and micro benthic
organisms vary in scales of em to km and on temporal scales of minutes to years due to the
complex interactions between many biological and physical variables such as tides, erosion,
deposition, shore height, nutrients, grazing, settlement, migration and episodic events like storms
and human impacts, Patterns of variation in benthos and the relationship to the sediment begs the
question of does the sediment dictate the biota or does the biota dictate the sediment as the biota
can alter sediment porosity and grain size, organic content etc, (Chapman and Tolhurst, 2004),
Small scale variation in spatial patterns is not unusual in intertidal environments, Some studies
show little variation in the benthos among different habitat relative to the smaller scale variation
within habitats, Sediments themselves also can strongly exhibit variations in their properties
within sites and within habitats of sites thus compounding the problems of identifying simple
relationships and the ability to make judgments on the types of benthos associated with a
particular sediment type (Chapman and Tolhurst, 2004), Mangrove areas in paIiicular may differ
significantly in their benthic community compositions and interactions, Seagrass areas tend to
have higher numbers than mangroves which tend to have lower numbers - although some
estuaries have a high degree of macro-invertebrate diversity across habitat. Some estuaries show
seasonal variation in faunal assemblages, Higher diversity of benthic habitats were found in
Rookery Bay's mangroves than in the adjacent seagrass beds and unvegetated areas, although
other areas in Florida this was reversed (Alfaro" 2005), This begs the question of localized site
specific differences and the difficulty in making assumptions about the benthic community based
on sediment characteristics and the ephemeral nature of the habitat.
References
Alfaro, AC, 2005, Benthic macro-invertebrate community composition within a
mangrove/seagrass estuary in northern New Zealand, Estuarine Coastal Shelf Science,
66:97=110,
Alongi, D,M" Boto, K,G, and Robertson, A,I. 1992, Nitrogen and Phosphorus Cycles, In:
Tropical Mangrove Ecosystems, Robertson, AI. and Alongi, D,M, (Eds,), American
Geophysican Union, Washington D,C. 251-292,
Alongi, D, M, and Sasekumar, A 1992, Benthic Communities, In: Tropical Mangrove
Ecosystems, Robertson, A,I. and Alongi, D,M, (Eds,), American Geophysican Union,
Washington D,C. 137-171
Alongi, D,M, Pfitzner, .I" Trott, L.A, Tirendi, F" Dixon, p" and Klumpp, D,W, 2005, Estuarine,
Coastal and Shelf Science, 63: 605-618,
Bala Krishna Prasad, M, and Ramanathan, A,L. 2008, Sedimentary nutrient dynamics in tropical
estuarine mangrove ecosystem, Estuarine, Coastal and Shelf Science, 80: 60-66,
Agenda Item NO.1 OF
December 15, 2009
Page 116 of 133
Boyer, J,N" Kelble, C.R" Ortner, P,B, and Rudnick, D,T, 2009, Phytoplankton bloom status:
Chlorophyll a biomass as an indicator of water quality condition in the southern estuaries of
Florida, Ecological Indicators, 95: 56-67,
Chapman, M,J, and Tolhurst, TJ, 2004, The relationship between invertebrate assemblages and
bio-dependant properties of sediment in urbanized and temperate mangrove forests, Journal of
Experimental Marine Biology and Ecology, 304:51-73,
Chapman, M,G, and Tolhurst, T,J, 2007, Relationships between benthic macrofauna and
biogeochemical properties of sediments at different spatial scales and among different habitats in
mangrove forests, Journal of Experimental Marine Biology and Ecology, 343: 96-100,
Clark, M, W., McConchie, D" Lewis, D,W, and Saenger, p, 1998, Redox stratification and
heavy metal partitioning in Avicennia-dominated mangrove sediments: a geochemical model.
Chemical Geology 149: 147-171.
Clough, B.F, 1992 Primary Productivity and Growth of Mangrove Forests, In: Tropical
Mangrove Ecosystems, Robertson, A,1. and Alongi, D,M, (Eds,), American Oeophysican Union,
Washington D,C. 225-249,
Ellison, A.M, 2008, Managing mangroves with benthic biodiversity in mind: Moving beyond
roving banditry, Journal of Sea Research, 50:2-15,
Gilbes, F" Tomas, C, and Walsh, J,J, 1996, An episodic chlorophyll plume on the west Florida
shelf. Continental Shelf Research, 16(9): 1201-1224,
Huang, W, 2007, Hydrodynamic modeling of~shing time in a small estuary of North Bay
Florida, Estuarine, Coastal and Shelf Science,l'!r"i22-731,
Holmboe, N" Kristensen, E, and Anderson, F,O, 2001. Anoxic Deposition in Sediments from a
tropical Mangrove Forset and the Temperate Wadden Sea: Implications ofN and P addition
Experiments, Estuarine, Coastal and Shelf Science, 53:125-140,
Ji, Z,O" Morton, M,R, and Hamrick, J,M, 2001. Wetting and Drying Simulation of Estuarine
Processes, Estuarine, Coastal and Shelf Science, 53:683-700,
Rabenhorst, M,C, and Parikh, S, 2000, Propensity of soils to develop redoximorphic color
changes, Soil Sci, Soc, Am, J, 64:1904-1910,
Raick, C" Soetaert, K, and Gregoire, M, 2006, Model complexity and performance: How Far
can we Simplify, Progress in Oceanography, 70: 27-57,
Sclunid, J,R" Worley, K, and Addison, D,S, 2006, Naples Bay Past and Present: A chronology
of disturbance to an Estuary, Conservancy of Southwest Florida, 37-57,
Agenda Item NO.1 OF
December 15, 2009
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Seymour, J,R" Seuront, L., and Mitchell, J,G, 2007, Microscale gradients of planktonic
microbial communities above the sediment in a mangrove estuary, Estuarine, Coastal and Shelf
Science, 71: 651-666,
Tomasko, D,A., Corbett, c.A., Greening, H,S.. and Raulerson, G,E, 2005, Spatial and temporal
variation in seagrass coverage in Southwest Florida: assessing the relative effects of
anthropogenic nutrient load reductions and rainfall in four contiguous estuaries, Marine Pollution
Bulletin, 50: 797-805,
Van Santen, P,V, Augustinus, P,G,E,F" Janssen-Stelder, Quartel, S, And Tri, N,H, 2007,
Sedimentation in an estuarine mangrove system, Journal of Asian Earth Science, 29: 566-575,
Vespraskas, M.J, and Faulkner, S,P, 2001. Redox Chemistry of Hydric Soils, In: Wetland Soils,
Richardson, 1. L. and Vespraskas, M.J, (eds), CRC Press LLC. Boca Raton, 85-105,
Wosten, J,H,M" DeWilligen, p" Tri, N,H" Lien, T,V" and Smith, S,V, 2003, Nutrient dynamics
in mangrove areas of the Red River Estuary in Vietnam, Estuarine, Coastal and Shelf Science,
57: 65- 72,
David Roellig Comments
I, Pagel, first paragraph, 1st line delete the word "natural", 3'd line, delete the word
"perhaps", Second paragraph, second line. after the word "inflow", add "along with sea
water by the tides, delete the words, "most ,ikely", 4th line, delete "Additionally, it was
likely that", 6th line, delete the word, "likely", 7th line, delete the words "tropical", The
purpose of this comment is to show the need for editing which is a problem throughout
this report,"
2, Page 3, last paragraph, 3'd line, delete" significant modification" and insert "elimination
of the mangrove forest and artificial armoring of the shoreline,",
3, Page 5, I" paragraph, item I "delete the word "retrofitting" and insert the words,
"Replaced the culverts under Seagate Drive with three 36' culverts"
4, The report lacks any information on the existing Seagate culverts sueh as: number,
length, diameter and elevation, It should also be noted that the flap gates on the north
side of the culverts were removed some years ago,
5, The report mentions the weather during the data collection period, but includes no
information whether weather events had any impact on the collected data,
6, The calculations should be provided to show how the culvert flow rates and speeds were
developed,
Agenda Item No.1 OF
December 15, 2009
Page 118 of 133
7, The Seagate flap gates were removed many years ago with the concurrence ofFDEP and
the City of Naples, At the time, the general opinion was that the flap gates were not
providing any real benefits due to lack of significant flow, It is hard to believe now that
the flow is ten times greater in the southward direction, The reinstallation of new flap
gates or structures should be investigated,
8, Fresh water inflows to Moorings Bay must be investigated with an inventory of outfalls
and sources of discharge,
9, Any water quality concerns should be addressed at their source, The impression is given
that tidal flushing can solve any possible problems, For more than 50 years, the concept
of "Dilution is the Solution to Pollution" has been discredited and will not be an
alternative for either Clam or Moorings bays,
I 0, A primary goal of any model study should be sizing Clam Pass with its tidal prism to
maximize the ability of the pass to be self-flushing,
II, The Executive Summary is too long, It should be condensed to a page or two,
Ron Glah Comments
First I have no agenda regarding Hummiston and Moore or others, My issues are the wording
and the accuracy of the wording in the executive summary,
In item I and 2 they raise the STORET issue and make the lack of reporting sound very onerous,
I thought I remember an earlier discussion that this was not as serious an issue at the time, but all
future data collection needed to be in added to the STORET. Again item 4 raises the question of
water quality collection by PBSD,Again the wording concerns me vs, just stating the need for
additional data collection, Item 5 They state that Clam Bay is Verified Impaired for water
quality, Do we really have enough data to make that statement in an executive summary? Item 7
is comparing apples and oranges, but if you read the beginning you get an impression that
Moorings Bay is better maintained! Item I on page iii needs to underline the word sufficient.
Item 3 should add" Due to it limited scope that was specified at the time,"
-3.2 used very appropriate wording
-I agree with paragraph 2 on page 34
-Paragraph 3 Page 38, I agree with those words, New technology will always improve findings
and make prior knowledge seem primitive,
-Para 3 and 4 Page 39 reasonable words that do not find their way into the executive summary
-Para I page 4 I Well stated and bettcr sounding vs, Executive summary
Bottom line: new gauging technology, a more complete study and a better understanding of dat
in a grassy estuary requires the need for further testing and comparing the data to other estuaries
with similar attributes, Clam bay and Mooring are very different in make up and are not
appropriate for comparison,
Agenda Item No.1 OF
December 15, 2009
Page 119 of 133
Also what consultant worth their salt would trash another consultants work and recommend
further work!
My objective is to let data identify the problems vs, community emotions,
PBS&J Report
Remarks on Executive Summary and Detail Report
By Linda Roth
earlier 10/28/09
Introduction:
The Clam Bay System Data Collection & Analysis Report dated October, 2009 by PBS&J can be
easily misinterpreted at first glance, However, if one spends enough time exan1ining it, one will
uncover the following points,
The Executive Summary has a number of assertions and omissions that create false impressions
of information reported in the Detail Analysis, Furthermore, the Detail Analysis makes a number
of statements that are implied as facts, but are just conjectures based on little or no evidence,
Examples are listed below, together with a number of questions about the report itself,
List of Comments:
I, The monitoring equipments used to estimate flow rates and volume exchange were vandalized
at two critical locations (one at South Seagate Dr" and the other at Harbour Dr. near Doctor's
Pass), Additionally, the data collected at Clam Pass was deemed unreliable; it was not used, and
substituted with data collected at a location in the Gulf (Gulfside Clam Pass, p, 47), At these
locations, 4 days of data were collected instead of 8 days, in August. Even though this
equipment for collecting data for water level and flow capacity was broken or deemed unreliable,
and only 4 days of data could be used, this data was utilized to estimate flow rates and volume
exchange between Clam Bay and Moorings Bay, and to reach the conclusion that "the net flow is
overwhelmingly southerly into Moorings Bay, and Moorings Bay is more affected by conditions
in Clam Bay than vice versa" (pp, 44, 45, 62, 76, 77), This scarcity of data is not stated in the
Summary,
2, Even if the data collected is assumed accurate, it only applies to conditions present during
these 4 days, On page 62, it states "It is important to note that the tide data was collected during
"spring tides" where the tidal range is larger than normal (higher highs, lower lows), Also there
were several rainfall events during the study period which affect water levels"," It seems that
wind directions would also have a significant effect. This is not stated in the Summary,
The report states, "During incoming tides, the south side has a higher water level than the north
side, up to 0,25 ft in difference, and leading in phase by about 30 minutes, On the outgoing tide,
the south side leads the north by 1.5 hours, with a water level difference of up to 1.5 ft, The
Agenda Item No, 10F
December 15, 2009
Page 120 of 133
result is water flows back and forth between the two bodies, with the majority of flow southward
from Clam Bay into Moorings Bay", This is just an intelpretation of what happened during these
4 days of data collection, This is not applicable to any other time, (p, 61)
3, The important information, on page 33, that Impaired Water Rules (IWR) guidance on
Dissolved Oxygen (DO), and chlorophyll G can be locally inappropriate, particularly in
subtropical systems, is not stated in the Executive Summary,
4, There is a discrepancy between actual water quality and "anticipated" water quality, The low
level of DO is not necessarily indicative of nutrient-enriched water body, This is stated in the
Detail report, but not in the Summary, (p, 33)
5, In regards to Chlorophyll G, the report on page 33 asserts that only Upper Clam Bay would be
declared impaired, (This may not be the case if the more recent data of 200S cited in the
references were used instead of leaning on old data, See pages IS-20, The ones in 200S were all
below the median level for Florida estuaries,)
6, The report does not state that the removal in 1997 of the one way flap gates which directed the
water flow from Moorings Bay to Clam Bay was due to concerns that the causation of the
problems in Clam Bay being largely the result of 27" of additional water which resulted in the
drowning of the mangroves, (pp, iv in the Summary & p, 3 in the Report) (City Council
Workshop, Aug, 3, 1995)
7, The report does not show the City of Naples having 4 water quality monitoring locations
immediately south of Clam Bay as stated in the first sentence on page 7, It shows 4 monitoring
stations widely spread throughout Moorings Bay with one station south of Doctors Pass, (p,ll)
S, On Pages 40 and 41, doubt is cast about the Tackney & Associates' report as being
"theoretical assertions", Then, the PBS&J report proceeds to make its own theoretical assertions
about "effective flushing", "water exchange" and "inlet stability",
9, Interestingly, water color is tested, but not fecal coliform which is required by the Florida's
TMDL program, (p, 12) Why? There is considerable data on Moorings Bay's water quality
collected by "Save the Bay", and other agencies, Why is it not presented in the report?
10, The Water Quality Review and Analysis of 5 stations in Clam Bay were presented. There
was none presented for Venetian and Moorings Bay; yet conditions in all 3 Bays are the subject
of speculation, (pp, 14-25)
11, The report states there is no seagrass in Moorings Bay, and lots of macroalgae, Are these not
indicators of poor water quality from increased nutrients? (p, 32)
12, In Outer Clam Bay, Dr, Tomasko of PBS&J in 2007 reported that there were numerous
seagrass beds, This report found only one seagrass bed, and the explanation for this is the
Agenda Item No.1 OF
December 15, 2009
Page 121 of 133
ephemeral nature of this species, Could they have been destroyed by motorboat and jet ski
traffic? If not, the seagrass should grow back in the near future, (P,29)
13, Adequate DO in sediments cannot be interpreted that Moorings Bay has a more diverse
benthic community, Is there not more DO in sediments just offshore? Some of these areas have
very limited benthic communities, (p, 29)
14, Clam Bay Estuary is a wetland comprised of"mudtlats" at low tides and during dry periods,
Sediment made of mud naturally holds less DO than more porous sediments such as sand, But
these mudtlats are teeming with micro-organisms and invertebrates that support juvenile fish,
birds and other wildlife,
15, The criteria for the locations of an ambient monitoring program are not described, But the
report declares that the site locations chosen by PBSD & the Conservancy were inappropriate, (p,
40),
16, The report omits the fact that the Seagate canals & Moorings Bay are no longer a natural
estuary, Their shorelines are comprised of man-made canals with cement walls embedded with
stonnwater run-off drainage pipes emptying into Outer Clam Bay and Moorings Bay, Moorings
Bay is not an estuarine habitat.
17, Numerous scientists (Drs, Bauer & Tomasko and others) have stated that the nutrient loading
in Clam Bay very likely comes from Moorings Bay and Seagate, All the lawn drainage pipes
emptying directly into the water of Outer Clrnn Bay & Moorings Bay are clear indications of this
likelihood, (City Council meetings, May & Sept 2008) (FDER a,k,a, FDEP ] 981 report)
(Tomasko Seagrass Report, 2007)
18, The water circulation and tlushing in Moorings Bay has basically remained the same since
the removal of the one way tlap gates at the Seagate culverts in 1997, The amount of nutrient
loading into Moorings Bay has not decreased, and may have increased due to more housing,
boats and docks since] 997, All available data shows that Moorings Bay's water is distressed,
These conditions have not changed significantly, Yet, based on this report, we are to believe that
the water quality has miraculously become better,
Conclusion:
As can be seen from the many examples cited above, this report is inconclusive at best. Hence,
its assertions, conclusions and recommendations cannot be taken seriously, At worse, it is
incompetent and fraudulent; no knowledgeable person should condone or validate it.
The report's Conclusion that "",the net tlow is overwhelmingly southerly into Moorings Bay,
Moorings Bay is more affected by conditions in Clam Bay than vice versa" is an unsubstantiated
assertion, Broken equipments, substitution of data at one location for another, and data collected
over a short four-day period during special weather conditions cannot be used to extrapolate
what took place or will take place between the two water bodies, Previous scientific studies
Agenda Item No, 10F
December 15, 2009
Page 122 of 133
(with the exception of the 1977 USEPA analysis mentioned by PBS&J), and II years of
anecdotal and empirical evidence indicate that the exchange of water in the culverts under
Seagate Drive goes back and forth depending on the tides, cWTents, water levels, weather
conditions, seasons, etc, In other words, the direction of water flow is inconsistent and
controlled by Mother Nature, Unnecessary human interference is dangerous and extremely
expensive, The Clam Bay estuary, the Natural Resource Protection Area from Vanderbilt Beach
Road to Seagate Drive, is a complex and sensitive ecosystem, This coastal wetland is just like the
mangroves, it needs wet and dry periods, When it is continuously inundated with water,
unpredictable bad things will happen (e,g" mangrove die-offs), Who will be responsible, and
how much more of taxpayers' money will be spent on restoration? Billions of tax dollars are
needed to restore the "Field of Grass" in the Everglades because of human misconception,
The report ends by calling for a hydrodynamic model in order to understand and improve
circulation and dissolved oxygen (DO) within the Clam Bay system, According to this report,
the DO in Moorings Bay is good, and that the low level of DO throughout the Clam Bay system
inferred based 'on Redox depths (dissolved oxygen in sediment), is not necessarily indicative of a
nutrient-enriched body (p, 33), Then why is the County wasting our tax dollars, and for whom?
Furthermore, a scientific model is something one produces on a computer by in-putting certain
parameters, It is not representational of what will happen in reality, It is what one thinks or
hopes might happen, and can be influenced by preset agendas,
Finally, in the field of environmental science, there are no definitive approaches, Whether an
approach works or not can only be verified by anecdotal and empirical evidence over a long
period of time, One can safely say that the approaches used by PBSD, H&M, and the
Conservancy have been well tested, The 50 acres of dying mangroves are recovering nicely,
The Clam Bay Estuary (mangrove forests, bays and wildlife) is healthy and thriving, It would
even be healthier when the Seagate and Moorings communities stop emptying their stormwater
run-off into the bays, Our tax dollars and energy should be spent on helping these communities
implement Best Management Practices (BMP), as well as oyster, clam, and mangrove restoration
programs, instead of trying some costly unproven methods of disturbing the balance of the
fragile Clam Pass/Clam Bay ecosystem,
Agenda Item No, 10F
December 15, 2009
Page 123 of 133
PBSJ
5300 West Cypress Street
Suite 200
Tampa, Florida 33607
Phone: (800) 477-7275
November 17, 2009
Response to Comments RE: Clam Bay System Data Collection & Analysis Report (October 2009)
To:
Gary McAlpin - Collier County
Clam Bay Advisory Committee
From:
Jeffrey R. Tabar, PE
Todd J, DeMunda, EI
There are several recurring themes that highlight the main concerns brou9ht forth regarding the Clam Bay
System Data Collection & Analysis Report, submitted by PBS&J to Collier County in October 2009, This
document is intended to address the issues related to the data collection and analysis effort.
1, The duration of the data collection was insufficient to either provide insight into the dominant
circulation patterns in Clam Bay and Moorings Bay or be useful for calibration of any future
hydrodynamic model,
The field data collection program was designed to capture an extensive amount of data over a period of
time to document circulation patterns through the entire system. Concurrent water level and flow velocity
data was collected for 8 days in August 2009 at 13 locations, encompassing the area between the Gulf of
Mexico, Upper Clam Bay and Doctor's Pass. Several instruments were paired with standalone tide
gauges for redundancy in case of malfunctions or other issues, for a total of 16 instruments deployed,
Therefore, a consistent 8 day record of water level exists for the entire system. While an 8 day period
may be considered short-term, the data is reflective of the long-term trends in the system and would be
sufficient for calibration of future hydrodynamic modeling efforts.
There have been other field studies in the past regarding Clam Bay and Moorings Bay (USEPA, 1975,
1977; FDER, 1981; Tackney, 1996; Humiston & Moore, 2003) that collected data; however, none of these
studies utilized the span and number of instruments used in the PBS&J effort. Ideally, it is preferred to
have these instruments in place over a long time period, but budget and time constraints force a tradeoff
between the number of instruments deployed and analyzed versus the length of time of the deployment.
In this study, it was determined that a comprehensive instrument deployment for a shorter period of time
was the best use of the available resources while still providing a sufficient view of the system dynamics;
the high resolution of the data shows important elements of circulation that would have been missed with
a lesser number of deployed instruments, regardless of any gain in deployment duration,
2, Data was collected during a period of above-average tidal range, rendering any conclusions or
insight regarding circulation useless for any other period of time,
Tides in the eastern Gulf of Mexico are mixed semidiurnal, with 2 highs and 2 lows of varying magnitude
per day, During the August 2009 data collection effort, the maximum tidal range was 4.0 It, compared to
the long-term average of 2.0 It (the difference between MHW and MLW at Naples). The highest observed
Agenda Item No, 10F
December 15, 2009
Page 124 of 133
water level at Doctor's Pass was 2.0 ft NAVD88, while MHW at Naples is 0,3 It NAVD88, The lowest
water level at Doctor's Pass was -2,3 ft NAVD88, while MLW at Naples is -1,7 It NAVD88. This time
period, while exhibiting a more pronounced tide range than 'normal', was chosen for several reasons. In
order to acquire a complete perspective on the system at a single time period, the data collection effort
was performed in conjunction with a comprehensive bathymetry survey of Clam Bay and Moorings Bay,
Higher water levels were necessary in order to move the survey vessel and equipment into the upper
reaches of Clam Bay, as well as the shallow regions throughout the system,
Further, the time period of the collection effort was during a segment of the mixed tide cycle that
contained high and low tides varying significantly in magnitude; see Figure 7.14 on page 60 of the report,
which shows the predicted and measured water level in the Gulf at Doctor's Pass, High tides ranged in
elevation from 0.5 It to 2.1 It NAVD88, while low tides ranged from -2.4 It to -0,1 It NAVD88. Successive
high and low tides varied by differences from 0,7 It to 4.0 It, Therefore, during the 8 days of concurrent
data, the tidal range varied to such an extent that tides greater than, equal to, and lesser than the long-
term average were observed.
For an example of how different tidal ranges affect the system dynamics, see Figure 7.21 on page 69 of
the report, which illustrates the current velocity magnitudes immediately south of Sea gate Dr. The peak
southerly velocity of 2.5 ft/s at approximately 6:00pm on August 18 corresponds to an outgoing tide with a
range of 4.0 It (see Figure 7.14 on page 60 of the report), The next southerly peak, at around 6:00am on
August 19, corresponds to an outgoing tide with a range of 1,5 ft. At Seagate Dr, it is apparent that the
southerly velocity peaks correspond to outgoing tides, and the magnitude of, the velocity is proportional to
the magnitude of the corresponding tidal change. On incoming tides, velocity at Seagate Dr is northward,
but its magnitude does not appear to correlate with the magnitude of the tidal change.
In conclusion, a variety of tidal ranges, greater than, equal to, and lesser than the long-term average,
were observed within the 8 day study period, Further, while the magnitude of the system dynamics may
be scaled to the magnitude of the tidal range, the overall patterns and trends remain the same, Barring
an extreme event such as a storm surge, there is no compelling reason to expect normal fluctuations in
tidal range over the lunar cycle to drastically alter circulation trends within the system,
3, Equipment malfunctions and vandalism resulted in several gaps in the data, rendering the entire
data set suspect and of little value,
Concurrent data was collected for a period of 8 days, and as mentioned in Item 1, several instruments
were outfitted with redundant tide gauges in case of issues like those experienced. During the 8 day
period, the batteries powering the South Seagate Dr and Harbour Dr ADCPs were stolen and the South
Seagate Dr instrument cable was destroyed, At South Seagate Dr, this vandalism resulted in the need
for removal and redeployment of the instrument and a loss of velocity data for 3.5 days, from August 15 to
noon on August 18, During this time, however, a separate tide gauge was continuously recording nearby,
so there is a complete set of water level data in the South Seagate Dr area. The 4.5 days that velocity
data exists covers a variety of tidal ranges from 1.5 ft ~ 4.1 It, and the flow direction and magnitude show
a definite correlation with the tide phase and amplitude, Given that the tidal fiuctuation during the 3.5
days of missing data is not radically different from the other 4.5 days, there is no reason to believe that
flow velocities and patterns were distinctly different, either, The data that exists is sufficient to gain insight
into how flow direction and magnitude at Seagate Dr vary with tidal fluctuations in Clam Bay and
Moorings Bay,
At Harbour Dr, the stolen battery resulted in the loss of about 18 hours of data from the night of August 18
to midday on August 19, Upon reconnection of a new battery and a reset of the instrument, data was
collected but appears to be unreliable, The deployment log and instrument have been thoroughly
checked for errors, but to no avail. Taking these issues into account, there are about 3.75 days of usable
velocity data at Harbour Dr; see Figure 7.25 on page 73 of the report. However, since the instrument did
not need to be removed from the water during this time, the redundant tide gauge at this location
recorded a full 8 days of water level data. As at Seagate Dr, there is no reason to expect that the flow
Agenda Item NO.1 OF
December 15, 2009
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patterns during the missing time span were drastically different than the recorded data, given the similar
water level variations during both periods.
It should be noted that for any future hydrodynamic model calibration, the water level data serves as the
most important parameter, as flow patterns and magnitudes are driven by the differences in water level
across the water body, Calibration for flow velocity is important as well, but can be approached in a
different manner, During the calibration process, it is desirable for measured and modeled water levels to
be consistent over time; this is feasible due to the generally smooth variations that occur with water level
over time. Calibrating for velocity in the same manner would be difficult to impossible, given the much
greater variability and scatter of the measured velocity data over shorter time periods, Instead of
attempting to get a high correlation between measured and modeled velocity for the entire time series,
the modeler can first calibrate for water level, and once that is sufficiently matched, the velocity data can
be used as a 'check' to make sure that the general direction, magnitude, and phase of the modeled
velocities are in line with the measured data.
At the Clam Pass ADCP, there is a continuous velocity data set for the 8 day span; however, after
analysis, we are suspect of the water surface elevation data. The range appears to be too small, and the
overall elevation appears too low, Multiple checks of the instrument log, setup, and survey data did not
provide answers to this issue, and two identical instruments with identical setups did not have this
problem. As such, we did not use this water level data for any analysis, When estimates of flow rates
and volumes were developed, the measured Gulf tide at Clam Pass was used instead, given that gauge's
proximity to the gauge in Clam Pass. This substitution was clearly stated with caveats in the report.
While the loss of this water level data is unfortunate, there is still a multitude of other measured tide data
in this study, with several (Gulfside Clam Pass, North Bridge) in close proximity to Clam Pass. The
velocity data in the pass is reliable, and the amount of water level data at other locations still provides an
extensive view of the circulation within the system.
In conclusion, at both Seagate Dr and Harbour Dr, despite the data gaps, there is sufficient velocity data
to both gain an understanding of the flow patterns and magnitudes as well as serve as a useful data set
for any future model calibration. Given that the flow rate exercise was a cursory estimate, the substitution
of water level data from the Gulf to calculate flow rates at Clam Pass is a reasonable approximation. The
absence of water level data at Clam Pass is regrettable, but the large amount of gauges at other locations
in the system nonetheiess allows an extensive look at the system circulation.
4, The report needs to provide more information about the Seagate Dr culverts and flap gates, It is
hard to believe that the flap gates were removed due to a lack of flow, but now flow Is lOx greater
in the southerly direction than the northerly direction. ,
The flap gates on the culverts, removed in 1997, were installed such that flow to the north was allowed,
while southward flow was blocked. The data collected in August 2009, in the absence of flap gates,
exhibited peak velocities 10x greater in the southerly direction than the northerly direction. Peak flow
rates were 3x greater in the southerly direction, and the estimated average volume exchange was 6x
greater in the southerly direction. The magnitude of the southerly flow is proportional to the concurrent
fluctuation in water level. See Item 2 for more details. These findings are consistent with the flap gate
removal; the collected data demonstrates relatively low flow from Moorings Bay into Clam Bay (seemingly
regardless of the concurrent magnitude of change in water level), which may be too weak to have opened
the flap gates while they were installed. Any water that 'piled up' in Clam Bay due to the restriction on
southward flow would have only exacerbated thiS scenario.
Furthermore, the conclusion of dominant southward flow through the Seagate Dr culverts, with the
magnitude dependent on the range of tidal fluctuation, has been documented several times in the past.
In 1977, the USEPA performed a dye study and concluded that there existed a net southerly flux from
Clam Bay to Moorings Bay after the installation of the Seagate Dr culverts. In 1981, the Florida
Department of Environmental Regulation measured flow with dye tracer and current meters, concluding
that southerly flow is 50-60% greater in the southerly direction at Seagate Dr. In discussions with local
Agenda Item No, 10F
December 15, 2009
Page 126 of 133
citizens, the consensus is that while flow does indeed move in both directions, it is much stronger when
flowing southward from Clam Bay into Moorings Bay, To our knowledge, the only source that mentions
equal flow in both directions is that of the 1996 report by Tackney & Associates. In this report, however, it
appears that it was merely assumed that the flow varied uniformly back and forth through the culverts,
without directional current data to support this assertion.
In light of the multiple current measurements, dye tracer studies, and anecdotal evidence pointing
towards dominant southward flow, the observations made in August 2009 are not the result of
intermittent, exceptional conditions. Due to the differences in water levels and the speed of tidal
propagation in Clam Bay and Moorings Bay, flow rates at Seagate Dr are significantly higher in the
southerly direction on an ebb tide than they are in the northerly direction during a flood tide, The
evidence is very supportive of the conclusion that net water exchange through the Seagate Dr culverts is
predominantly southward,
5, The report needs to provide details on the flow calculations presented in Section 7.3,
Flow rates were estimated as the depth-averaged velocity multiplied by cross-sectional area at each time.
step. The cross-sectional area varied with depth corresponding to the tide level. Equations 1 and 2 show
the procedure for calculating flow rates and volumes for each data time step; total volumes are found by
adding together the volumes in either direction, and the net volume is the difference between the total
volumes,
Equation 1. Flow rate (ft3/s) over time.
Q(t) = v(t)W[d + 1'J(t)]
Equation 2. Flow volume (fe) per time step.
Vet) = Q(t)dt
In the above equations, Q(t) (1I3/s) is the flow rate over time, vet) (IUs) is the depth-averaged velocity over
time, W (II) is the width of the channel in which flow was measured, d (II) is the depth of the channel
relative to the NAVD88, I}(t) (II) is the water surface elevation relative to NAVD88 over time, Vet) (113) is
the volume exchange during each time step, and dt (s) is the length of the data time step, Table 1 below
outlines the channel width and depth values used for the flow rate estimations, Channel widths were
estimated from aerial imagery; the width at Seagate Dr is an estimation of the effective width of the area
with the majority of water flow, since the instrument was located south of the culverts rather than inside
the culverts. It should be reiterated that these estimations of flow rates were a cursory exercise, and do
not account for changes in the channel width caused by the rising and falling tide.
Table 1. Channel parameters used at each location to estimate flow rates and volumes.
Location W(II) d(lI)
North Bridee 35 5.5
Clam Pass 80 3.5
South Bridge 90 4.3
South Seagate Dr 15 4.5
Park Shore Dr 80 8.6
Harbour Dr 70 13
Agenda Item No.1 OF
December 15, 2009
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6, What were the weather conditions during the data collection effort?
Table 2 outlines the weather conditions during the data collection effort. Information was taken from the
Weather Underground website (www.wunderqround.com); the source is the National Weather Service
daily summary for Naples Municipal Airport (KAPF).
Table 2. Weather conditions durinn Aunust 2009 data collection effort.
Rainfall Sea Level Wind Speed Wind Max, Max.
Date Pressure Wind Speed Wind Gust
(in) (in) (mph) Direction (mph) (mph)
August 13 0.41 29.98 5 S 17 25
August 14 0.00 30.00 7 E 31 37
August 15 0.63 29,98 9 ESE 28 35
August 16 0,24 30.03 7 ESE 16 22
August 17 0.51 30.03 7 ENE 17 24
August 18 0.07 30.03 6 NE 12 --
August 19 0.00 30.00 7 SE 13 --
August 20 0.06 3002 5 ESE 12 16
August 21 trace 3001 6 NE 16 21
August 22 0.00 29.95 4 WNW 16 21
August 23 0.00 29.92 5 WSW 12 15
August 24 0.23 29.97 5 I ESE 24 33
August 25 0.98 29.97 6 ENE 23 29
It should be noted that the rainfall events experienced during the field study were of the transient
afternoon thunderstorm variety, and the ephemeral nature of these storms is such that rainfall within the
Clam Bay watershed may be different from the rainfall at Naples Municipal Airport, approximately 6 mi
south of Clam Bay.
The only significant rainfall events within the 8 day data span were those of August 15,16, and 17, where
a total of 1.38 in fell. This rainfall is likely a contributing factor to the slight (< 0.5 ft) increase in apparent
mean water levels in Upper and Inner Clam Bays. The other likely factor is the increasing range of the
'smaller' tide each day as the study progresses. Wind speeds are somewhat gusty, but the dominant
direction is largely easterly; this likely precludes wind setup as a major factor in the system circulation,
since the major axes of Clam Bay and Moorings Bay are aligned in a north-south manner.
References
Florida Department of Environmental Regulation. 1981. Diagnostic i Feasibility Study for Moorings Bay,
Collier County, FL.
Humiston & Moore Engineers, 2003, Clam Bay Hydrodynamic Modeling and Analysis.
Tackney & Associates, Inc. 1996. Preliminary Hydrographic Assessment - Clam Bay Systems.
U.S. Environmental Protection Agency. 1975. Field Studies, Parkshore and Clam Bay Systems, Naples,
FL. Region IV, U.S. EPA Surveillance and Analysis Division, Athens, GA
U,S, Environmental Protection Agency, 1977. Field Studies, Parkshore and Clam Bay Systems, Naples,
FL. Region IV, US. EPA Surveillance and Analysis Division, Athens, GA
Agenda Item No.1 OF
December 15, 2009
Page 128 of 133
Response to Criticisms
Most ofthe comments on the PBS&J report were related to water quality and the natural systems
characteristics of both Moorings Bay and Clam Bay, In particular, most comments relate to the
perception that the two systems were being compared to each other, particularly in terms that were
unfavorable toward Clam Bay's water quality, without due consideration of its broader ecological
health, This is an unfortunate conclusion perhaps due in part to the somewhat simplistically-worded
Executive Summary, While Moorings Bay was referred to as a "natural system" in one part of the
report, and such a choice of words is problematic, the text of the report clearly refers to the loss of
natural shoreline features in Moorings Bay, and in fact includes two aerial photographs to highlight that
impact. We believe that the text is very clear in noting that Clam Bay has retained most of its natural
shoreline features, while Moorings Bay has not, However, a natural systems inventory was not the
primary purpose of this effort, and the scope of work (reviewed and approved by the Clam Bay Technical
Advisory Committee) did not include the time or funds necessary for such an effort, This project was
focused on water quality, specifically as it relates to the Impaired Waters Rule (IWR) and the Total
Maximum Daily Loads (TMDL) program, The following text will attempt to address concerns that appear
to underlie the majority of comments received on this report,
Water Qualitv "impairments" for dissolved oxvgen aren't problematic
The data set for Clam Bay that was reviewed by the authors contains a number of erroneous readings
for dissolved oxygen (DO), but these values are on the high end of the scale, While it could be argued
that all DO data are suspect, we believe that only the extremely high values are problematic, For the
sites examined, between 20 to 50% of DO readings (by site) fell below the IWR standard of 4 mg / liter,
This finding is not proof in and of itself that these low DO readings are due to human activities, as the
report clearly states, In fact, the report states that a number of locations, including the reference sites
for the Gordon River TMDL report and reference sites throughout the Everglades also fail DO standards,
The authors do not see how our text could be construed as suggesting that the likelihood of "failing" of
DO standards (that are discussed as being problematic) would be suggestive that Clam Bay is in trouble,
ecologically,
However, Clam Bay sites also have levels of TN and TP that would, in conjunction with the DO readings,
most likely result in the bay being declared impaired by FDEP, Data are presented throughout the
report that show levels of nutrients in Clam Bay, Based on guidance obtained by FDEP, "screening"
levels of TN are exceeded at Clam Bay sites between 21 and 73 percent of the time, Levels of TP used by
FDEP to screen for a possible nutrient link for DO violations are exceeded between 2 and 11 percent of
the time for Clam Bay sites, For both TN and TP, the lowest frequency of exceedance for screening
levels were at the Seagate Drive site,
Staff from FDEP have confirmed that it is likely, based on data collected by the Pelican Bay Services
Division, that Clam Bay would be declared "impaired" for DO, This impairment status decision could be
problematic, as the report clearly states, In particular, the report cites the example of Rookery Bay,
which has been listed by FDEP as "Verified Impaired" despite the fact that the authors of this report
Agenda Item NO.1 OF
December 15, 2009
Page 129 of 133
(and at least one reviewer as well) regard Rookery Bay as mostly an unimpaired system, An additional
specific example of the unrealistic nature of IWR's default DO targets for the western Everglades is
outlined in the report,
Interestingly, within Moorings Bay, data provided by the City of Naples show that just under 6 % of all
DO readings were under the IWR standard of 4 mg / liter. For TN, 2 percent of Moorings Bay samples
exceeded the IWR screening level, while no TP values exceeded the IWR screening level. These more
recent data from Moorings Bay could represent an improvement in water quality conditions, compared
to those noted in a 1981 study by the Florida Department of Environmental Regulation, That study
(FDER 1981) suggested that the apparently improving water quality conditions in the late 1970s in
Mooring Bay were perhaps associated with reduced rates of development of the watershed,
While wildlife utilization by birds, fish, etc, may in fact be higher in Clam Bay, compared to Moorings
Bay, the IWR and the TMDL programs do not allow for the luxury of claiming systems to be "pristine"
due to an abundance of wildlife sitings, Somewhat paradoxically, one of the most impacted lakes in
Florida (Lake Hancock), which has incredibly poor water quality and a TMDL calling for more than 70
percent reductions in TN and TP loads, is also home to thousands of alligators, and has a significant
number of bald eagles along its shoreline, Wildlife utilization and water quality do not always "match"
in terms of characterization efforts,
Water qualitv "impairments" for chlorophvll-a aren't problematic
In general, this argument is a more plausible one to make, The report clearly shows that the only station
within Clam Bay that exceeds the 111lg / liter standard for chlorophyll-a is located in the far northern
reach of Upper Clam Bay, But water quality sampling locations aren't in ideal locations for an ambient
monitoring program, and the IWR allows for "impairment" to be determined not only based on
exceeding a set level, but also by the trend, if any, between "historic" and "verified" time periods,
PBS&J has recently worked with FDEP to delist water quality impairment in Roberts Bay and Blackburn
Bay (within Sarasota Bay), as seagrass coverage increased over the past 20 years in these "impaired"
systems, If Clam Bay was to be lumped together such that water quality in Upper, Inner and Outer Clam
Bay were combined, it would likely be that the lower levels of chlorophyll-a, TN and TP, and the higher
levels of DO in the areas further south would cancel out (to an extent) the higher levels found in areas
north of Clam Pass,
Moorings Bay and Clam Bay are different systems, and their ecological values are different
This contention is not at odds with our report, It is noted in the report that Moorings Bay has none of
the natural shoreline features of Clam Bay, But the focus of this report, based on a scope of work
reviewed and approved by the Clam Bay Advisory Committee, did not include assessments of shellfish
and finfish or bird abundance, Nor do there appear to be ongoing assessments of a similar nature for
these two systems, to our knowledge,
The wording used in Section 4.0 in the PBS&J report does not suggest that Clam Bay's ecology is
"impaired", only that existing state guidance would likely result in its water quality being determined to
Agenda Item No, 10F
December 15, 2009
Page 130 of 133
be impaired, The numerous criticisms received that the PBS&J report suggests Clam Bay is ecologically
unbalanced are without merit, in the authors' opinion,
The shallow Redox layer and fine<grained sediments noted in Outer Clam Bay are "natural"
The shallow Redox layer found throughout Upper Clam Bay could in fact be a completely natural
feature, as most mangrove-lined, semi-isolated systems have thick organic layers that are associated
with low levels of DO and a heterotrophy-dominated food web (note language used in Section 4,0, and
bullet points in the Executive Summary), However, the fine layer of silt and silty clay found in Outer
Clam Bay may (or may not) be related to human activity, The report clearly states that further work is
needed to determine if this layer of silt - which appears to have created a shallow Redox layer - is (for
example) 5,000 years old, or 50 years old, That assessment is key to understanding if this sediment layer
is natural or problematic, and the report clearly makes this statement,
Interestingly, the 1975 EPA study on Clam Bay and Moorings Bay (called Parkshore in that study)
concluded that reduced numbers oltaxa (I.e" species of benthic organisms) in portions of the Clam and
Moorings Bay systems were likely associated with the increased amount of fine-grained sediments (I.e"
silt) in those same locations,
Agenda Item No, 10F
December 15, 2009
Page 131 of 133
COLLIER COUN1Y GOVERNMENT
Pelican Bay Services Division
801 Laurel Oak Drive. Suite 605. Naples, Florida 34108. (239) 597-1749. Fax (239) 597-4502
December 3, 2009
Mr, Leo Ochs, County Manager
Office of the County Manager
Collier County Government Center
3301 S" Tamiami Trail
Naples, Florida 34104
RE: Clam Bay Data Analysis, Prepared by Post, Buckley
Dear Mr, Ochs,
This will confirm your request of Mr. Dorrill and our offer to provide an alternative to
resolve a dispute over the release of the above referenced report, As you are aware there
is concern within Pelican Bay that the recent Clam Bay water quality analysis may have
inaccurate conclusions that would cast the system or historical data in a negative manner,
I understand that you share our concern that all work performed in Clam Bay be both
accurate and focused on improving this critical environmental resource, For this reason
our board voted at its meeting on December 2nd to authorize the following proposal:
. That a joint selection of outside peer review be undertaken for all work performed
to date. This will require that an acceptable scope of services be developed to
include historical water quality collection methods, lab analysis and modeling
in addition to the recent work prepared by Post, Buckley.
· We would propose that the cost ofthis effort and any future phased peer review
be split between the Pelican Bay Services and Public Service divisions in your
agency,
.)
. We would prefer that both our Board and the county participate in the selection of
this individual who would be a recognized expert in the field and based in a
university setting not directly involved with any consulting firm,
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Agenda Item No. 10F
December 15, 2009
Page 132 of 133
Page Two
Clam Bay Data Analysis,
Prepared by Post Buckley
I want to thank you for your leadership and desire to move these efforts forward and
allow the County Commission to address this matter at its meeting on December 15,
2009, I am willing to assist you and would be happy to answer any questions that you
may have on this effort to resolve our concerns,
Sincerely,
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Mary Anne Womble, Chairwoman
Pelican Bay Services Division
Cc: Pelican Bay Services Division Board
Mr. Neil Dorrill
file
Agenda Item No.1 OF
December 15, 2009
Page 133 of 133
: Neil DorrHI [mailto:neil@dmgfl.com]
Sent: Friday, December 04, 2009 3:44 PM
To: McAlpinGary; michaelsheffielod@coliiergov,net
Subject: RE: Pelican Bay Letter
Gary: I have reviewed the Executive Summary and Mrs Womble's letter of December 3" concerning
the Post, Buckley report, Both are consistent with The Pelican Bay Advisory Board's discussion of this
matter earlier this week. Our desire is to have a critical review of scientific or technical data that has
been performed to date or will be undertaken in the future. Our proposal is not intended to delay any
work that may be contemplated by the Board of County Commissioners at their meeting on December
1S'h Neil Dorrill, Division Administrator
From: McAlpinGary [mailto:GaryMcAlpin@colliergov,net]
Sent: Friday, December 04, 2009 10:03 AM
To: ochsJ; brock_m; Neil Dorrill; ramsey-m; GreeneColleen
Subject: FW: Pelican Bay Letter
<<CBAC Update Report ES Rev 8.docx>>
Leo,
Relative to the letter from the Chairwoman of the PBSD concerning the peer review, please see
the highlighted paragraph in the executive summary, The key item that is not mentioned in the
Chairwoman's letter is timing, We agreed with Neil that his peer review would not hold up the
circulation/modeling study and that it would be accomplished early in the execution of the
modeling program, Other than that, we are in agreement with what the chairwoman addresses
in her letter.
I have talked to Neil and he will email me something to that effect that will also be included as
backup to the Executive Summary, John Arceri, was very strong on this point feeling that
additional clarification is needed to avoid issues in the future,
From: brock_m
Sent: Friday, December 04, 2009 9:06 AM
To: ramsey_m; McAipinGary
Subject: Pelican Bay Letter
<<Ietter.pdf>>
Good morning, Please see attached, Gary-Leo has suggested you include this with your 12/15
executive summary, Thanks, MJ for Leo