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CBAC Agenda 11/19/2009 MEETING AGENDA CLAM BA Y ADVISORY COMMITTEE WEDNESDA Y, NOVEMBER 19,2009 -- 1 :00 P.M. North Collier Regional Park, 15000 Livingston Road, Administration Building, Room A, Naples. I. Call to Order II. Pledge of Allegiance III. Roll Call IV. Changes and Approval of Agenda V. Public Comment VI. Approval of Minutes I. September 24, 2009 2. October 8, 2009 3. October 28, 2009 VII. Chairman's Comments VIII. Staff Reports IX. New Business I. PBS&J Data Analysis Report and Findings a. PBS&J Report b. Comments c. Response to Comments X. Old Business XI. Announcements XII. Committee Member Discussion XIII. Next Meeting Date/Location December 17, 2009 - North Collier Regional Park, 15000 Livingston Road, Administration Building, Room A, Naples. XIV. Adjournment All interested partied are invited to attend. and to register to speak and to submit their obJections, If any, in writing, to the board prior to the meeting if applicable For more information, pkase contact Gail 0 llambright Oit (239) 252-2966 If you UTe a person with a disability who needs any accommodation in order to participate in this proceeding, you are entitled. at no l:Ost to you, to the provision of certain assist::mce Pleas!.' contact the Collin County Facilities Management Department loented at 3301 l:usl Tamiami Trail, Naples, FL 34112, (239) 252-~n!W CBAC November 19. 2009 IX-1 New Business 1 of 1 EXECUTIVE SUMMARY Review and address comments on the PBS&J Data Analysis Report and Findings for the Clam Bay Estuary and approve the recommendations listed below. OBJECTIVE: Review and address comments on the PBS&J Data Analysis Report and Findings for the Clam Bay Estuary and approve the recommendations listed below. CONSIDERATIONS: The Board of County Commissioners based on recommendations from the Clam Bay Advisory Committee directed that an existing data review and analysis along with the collection of hydrographic data for the Clam Bay system be performed. This study was concluded by PBS&J and Turrell-Hall & Associates and is presented for review and comment. Comments and questions from members of the CBAC are attached for discussion. ADVISORY COMMITTEE RECOMMENDATIONS: Staff is recommending approval of the following recommendations: 1. Approve moving forward with a water monitoring program as outlined in the report. 2. Approve moving forward with additional sediment toxicology and aging data collection/analysis. 3. Approve the water circulation/flushing modeling program. FISCAL IMPACT: This study is an analysis of existing data along with the collection of hydrographic data to better understand the issues surrounding the Clam Bay system. Funding requirements will be addressed based on recommendations selected. GROWTH MANAGEMENT IMPACT: This is only a study. There are no Growth Management Impacts resulting from this study. LEGAL CONSIDERATIONS: The County Attorney's office has not reviewed this report. Approval of this report requires a majority vote. RECOMMENDATION: Review and address comments on the PBS&J Data Analysis Report and Findings for the Clam Bay Estuary and approve the recommendations outlined in this Executive Summary. PREPARED BY: Gary McAlpin, CZM Director CBAC November 19, 2009 IX~1a New Business 2 of 89 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 circulation models for Clam Bay, and the collection and analysis of hydrodynamic data from Clam Bay and Moorings 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 quality 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 "Verified 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 chlorophyll-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 PBSJ Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 3 of 89 Executive Summary to actual water quality problems, without diluting its efforts by pursuing "fixes" to impairments that are naturally occurring. 5. ChIorophyll-a is an indicator of phytoplankton abundance 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 orgamsms. A general biological survey of Clam Bay and Moorings Bay found that: 1. 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 area of the Seagate canals, was not prevalent in Moorings Bay, and varied in depth in Outer, Inner and Upper Clam Bays. 3. It is not known at this time if the tine-grained sediment layer is naturally occurring, or occurring as a result of man-made changes to the Clam Bay system. It is, however, known that the sediment layer in the Sea gate 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 recommended 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 result of reduced circulation. 5. These same sediments appear to create conditions that limit the diffusion of dissolved oxygen into the bottom. PHSJ Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-la New Business 4 of 89 Executive Summary 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 would be expected to be less diverse than in Moorings Bay. 7. Clam Bay and Moorings Bay are functionally different systems, and it is ncither possible nor appropriate to expect these two systems to havc 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: I. The previous circulation model was completed in 2003 by Humiston 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 modcl to improve tidal flushing for the health of the entirc 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 function as a comprehensive model will essentially require starting from scratch with the model development. 4. If starting 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. P8SI iii Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 5 of 89 Executive Summary 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 report 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: I. 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 I980s, 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-oft's, 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. PHS1 iv Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 6 of 89 Executive Summary 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 1.5 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. PBSJ v Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 7 of 89 Table of Contents 1.0 Introduction ................................................................... ...... ........................................... ..............1 1.1 Clam Bay and Moorings Bay Issues ......................... .........................................1 1.2 Outline of Presenf 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 CurrentslWater 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......... .............. ................................................. ...................... .AO Report Review....................... .............. ..........................A 1 6.0 Hydrographic Data Collection .............. ............A2 7.0 Hydrographic Data Analysis 7.1 Introduction ............... ................. 7.2 Water levels ...... ................. 7.3 Current Velocities and Flow Rates. ........................................................ 7.4 Conclusions..... .............................. ............A5 .........A5 ................... . ........... .......A5 .........62 ....... .................. ...... .................. 76 8.0 References ......................... ..................78 PBSJ Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 8 of 89 List of Figures Figure I. I. Aerial Photo (circa I940s) 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 aI., 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 aI., 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. ........................ .......................................................................... I] 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 mg/L, 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). Thc Percent of DO Values Lower Than the lWR Thrcsho1d 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 Pcriod of Record in Clam Bay With the y-axis Truncated (the orange line denotes 36 Ilg/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 I I Ilg/L, the threshold for impairment from FDEP's IWR; the red line indicates the median value for Florida estuaries; 9 mg/L)............................................... 20 Figure 3. I O. TN:TP Ratios for Clam Bay from January 2005 to May 2009 (the sbaded area indicates the range for a co-limited system). ...................................................................21 Figure 3. I I. Relationship Between Chlorophyll a and Total Nitrogen in Clam Bay (figure from PBS&J [2008]). .................. ...................................................................................... 22 Figure 3. I 2. Relationship Between Chlorophyll a and Total Phosphorus in Clam Bay (figure from PBS&J [2008J). ................... ............................................................................ 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/L]). .................. .............................................................................24 Figure 3.14. Mean and Median TN concentrations (left axis). Percent of TN Values Grcater than the Median for Florida estuaries (0.8 mg/L; right axis). .......................................... 25 Figure 3.15. Total Phosphorus Levc1s 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 P8SJ Clam Bay System Data Collection and Analysis October 2009 CBAC November 19. 2009 JX-1a New Business 9 of 89 List of Figures 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. I 7. 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 cm, Green symbols represent Redox layer> 20 cm. ......................................................................... 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. I. 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 August 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; August 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 GuIfside 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 7.1 I. Water surface elevations at South Seagate Dr; August 15 to August 23, 2009. ....57 Figure 7.12. Water surface elevations at Park Shore Dr; August 15 to 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. Current velocity at North Bridge; August 15 to August 23,2009..........................64 Figure 7.17. Current velocity and water surface elevation at Clam Pass: August 15 to August 23, 2009. ................................ ............................................................................... 65 Figure 7.18. Current velocity at Clam Pass: August 15 to August 23, 2009. ............................ 66 Figure 7.19. Current velocity and water surface elcvation 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 components 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 ii Clam Bay System Data Collection and Analysis October 2009 PHSJ CBAC November 19, 2009 IX-1a New Business 10 of 89 List of Tables Table 3.1. Water Quality Parameter List for Various Monitoring Programs, Compared to Data Requirements for the Stale of Florida's TMDL Program. ............................................... 12 Table 4.1. Recommended Parameter List for Ambient Water 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 P8SJ Clam Bay System Data Collection and Analysis October 2009 CBAC November 19. 2009 IX-1 a New Business 11of89 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 focus of much activity to keep it open since at least the 1970s (Collier County, 1997). In the late I990s, 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 1.1). 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). PHSJ Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 12 of 89 Introduction 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 at, 2003). PBSJ 2 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 13 of 89 Introduction In its pre-development condition, both Doctor's Pass and Clam Pass were small natural tidal inlets, and both were subject to migration and closure (Antonini et aI., 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 I950s by construction of two roads; Vanderbilt Beach Road to the north and Seagate Drivc to the south. As it was originally configured, Seagate Drive c10scd 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 occur in both directions (Collier County, 1997). In the I980s, the tidal connection between Upper Clam Bay and Vanderbilt Lagoon was severed due to development activities (Collier County, 1997). Although Clam Bay's watershed had been developed rather extensively, the shoreline features 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 1970s (Figure 1.4). Figure 1.3. Aerial photograph (2006) of Clam Bay and immediate watershed PHSJ 3 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 14 of 89 Introduction Figure 1.4. Aerial photograph (1970s) of Moorings Bay and immediate watershed (photo from Antonini et at, 2003). Prior studies in similar lagoonal systems in Southwest Florida suggest that increased urbanization brings about increased freshwater intlows 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- I 990s, 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 PBSJ 4 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 15 of 89 Introduction 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: I. 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 storm water 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 quality 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 terms of status and trends, about the health of Clam Bay and Moorings Bayo . How do circulation patterns and nutrient delivery interact to create spatial patterns of water quality in Clam Bay and Moorings Bay. and how thesc 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)'> 5 Clam Bay System Data Collection and Analysis October 2009 PBSJ CBAC November 19. 2009 lX-1a New Business 16 of 89 Introduction Figure 1.5. Project Area and Location Names for Clam and Moorings Bays. This report summarizes results obtained to-date on these questions. P8SJ 6 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 17 of 89 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 macroalga1 coverage throughout the Clam and Moorings Bays system. Field sampling occurred 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, Le. dead-end channels, shallow vegetated areas, shoal locations, navigation canals, tidal canals, etc. Samples were collected by inserting 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 macroaIga1 abundance, etc.). PHS, 7 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 18 of 89 Methods 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 up-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 YD88) 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 Current 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. Currents and water levels were measured at five and seven locations within thc 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) Gu1fside 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: (1) 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 Dri ve bridge Key issues to be addressed using the results include: . Velocities and !low rates through Clam Pass . Flow exchange volume and direction between Clam Bay and Venetian Bay through the Seagate Drive culvert PBSj 8 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 lX-1a New Business 19 of 89 Methods . 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. PHS1 9 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 20 of 89 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. CilY of Naples . PBSJ # PHSt) - S()u,hw~sl ConscrvlIncy (Clam Hay) . S()ulhw~sl Conservancy (Moorings Bay) ~- ,.. ........ .... ......... ... ... ............................ Nov-81 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. PBSl 10 Clam Bay Sysfem Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 21 of 89 Water Quality Review and Analysis 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 the entire Clam and Moorings Bays system. The Pelican Bay monitoring program, which was originaJly designed to answer 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 the focus of trend analysis efforts. In contrast, stations used by the Conservancy for its monitoring efforts tend to be located in more open-water locations, and are, on the whole, appropriately sited for a monitoring effort. 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. 11 Clam Bay System Data Collection and Analysis October 2009 PHSj CBAC November 19, 2009 IX-1a New Business 22 of 89 Water Quality Review and Analysis 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. ~ ater,g\la1itJ [Chlorophyll " i:p~<leophytin [Nitrate INitritc l. .,., ~_ . IN i~I'<t_~~_:N. i_t~_i~c. ITota] Kje]dah] Nitrogen rrotal Nitrogen Orthophmphate :Total Ph()sphorus rDis~?_~Yc.~-S'_~yg~n iFecal Coliform lAmmonia :Arsenic !BOD l~alcium Chloride 'Color Copper _ 'Enterococci Hardness- Calculated M'-lgnesium Total Organic Carbon Total Su~p~c.nded Solids _Turbi~i~y' Y{)latile Suspended Solids Total Dissolved Solids ;Silicate !Salinity !C-'~,~,~~~~iyity J'H ,'I~I!1P~~ature Secchi ;P-hotosynthc(ically Active 'Radiatioo (PAR) 'Depth . , i IPelican Bay ISouthwest iServices ,J~~I1ser:':cl!I1c~J l~!\,isi()ll '" ' ..~. PBSJ 12 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 23 of 89 Water Quality Review and Analysis Of all the water quality monitoring programs, past and current, 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 reporting 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, Valie1a et al. 1990, Tomasko and Lapointe 1991). 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 I with water samples continuing to be sampled monthly. A large suite of water quality parameters are analyzed including: total Kjeldahl nitrogen (TKN), nitrate (NO}), nitrite (NO,), 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 northernmost portions of Upper Clam Bay, along the shoreline) W-7 (at the northern trolley bridge), W-6 (at the trolley bridge north of Clam Pass), W-I (at the canoe ramp at the park), and Seagate (at Seagate Drive). Clam Bay System Data Collection and Analysis October 2009 P8Sl 13 CBAC November 19. 2009 IX-1a New Business 24 of 89 Water Quality Review and Analysis 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/I. PBSJ 14 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 25 of 89 Water Quality Review and Analysis Figure 3.4. Dissolved Oxygen over the period of record in Clam Bay. Erroneous Values are Evident between August 2001 and August 2002. 100 -+-W G ___W 1 W 1 - UCBkl< d.~<)Cilg;)tc 80 "- 1;,0 60 S o . " > . o '0 . > "0 ~ .10 o t j2 j , 20 ij , ~.. \j~~..",~~I\.~ i", ,..' '~..J.. /~ . .,.1 .. ....".,. 'lI.. '" ~" , .., ~ ~ ' o <)cp81 Mar 8~ AUf188 JiJn'J2 Jul9S Dee ':J8 Jun 02 Nov OS Apr 0',) PBSJ 15 Clam Bay System Data Coliection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 26 of 89 Water Quality Review and Analysis 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. -+-\11/ L ___IN i \V 1 -UCl:>RI< ~'~'&';.eaf;Jt(' 10 It 'hi 1 I '), ~ ........~ , I . I ry I I g t:~H r ~ Ij :1 I J j , 1 I :'~i 1 '" I n J " (, I tI .E- o 5 I . t' " . > . 0 " . > T ~ 4 is '" . . . . 0 ':lcp 81 Mclr 8~, Aug 1'.:8 Jan 92 Jul':J'i Dc( 91:\ lUll 01 Nov U~) Apr U9 P8Sl 16 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 27 of 89 Water Quality Review and Analysis 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). '" " G .s o . " > x o 'C . > ~ 4 o 10 g 2 WI . Average \'V b .Median Wi "/0 Va I Lit'S <: 4,0 f'1f,/1 Seilgatc 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. o UC1:3f{K Chlorophyll a Chlorophyll a data are available from January 1996 until May 2009 at the W-J, W-6 and W-7 sites (Figure 3.7). Sampling for the Seagate sites began in January ZOOI 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-I sites, however, the concentration observed on September 1996 at the W-6 site (299 ~g/L) is unlikely in the marine waters, and so the data are displayed (Figure 3.8) with a truncated y-axis. PBSl 17 Clam Bay System Data Collection and Analysis October 2009 GO 50 "0 . v o . 'C 30 ~ v x w '" 20 10 o CBAC November 19, 2009 IX-1a New Business 28 of 89 Water Quality Review and Analysis Figure 3.7. Chlorophyll a Concentration over the Period of Record in Clam Bay. 3S0 ~W.G ~.w / IN I --UCI:lKK wh~,~,"t'ilgatf.' 300 2:10 '" ~ 200 .:. , .. ~ ~ 0 <; ISO ;;; v 100 '0 lit o,.r,;;,* , ~ ..~~';;M".-&~. Oct 9~) L)c.: cJ~J ),In()' l-cb Uti Figure 3.8 compares the Chl-a data to the median and 90% value for all Florida estuaries (FDEP 1996; 9 and 36 Ilg/L, respectively). Values were consistently greater than the median with occasional spikes above the upper 90% value of 36 ug/I. Upon displaying the data as annual average values, the UCBRK site was excluded due to a lack of recent data (Figure 3.9). P8SJ 18 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 29 of 89 Water Quality Review and Analysis Figure 3.8. Chlorophyll a Concentration Over the Period of Record in Clam Bay With the y-axis Truncated (the orange line denotes 36 1J9/L, the upper 90% value for Florida estuaries; the red line indicates the median value for Florida estuaries; 9 mg/L). ')0 I) ~.w J W 1 -lJU3KK..--'.-l'd11ate 40 I "- 3D " if '" . >- ~ 0. 0 <; :c 20 I u ~. \ ,K I !I' r 10 , o Oct 9'.'> Dee 99 Jiln04 Feb OOS PHSJ 19 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 30 of 89 Water Quality Review and Analysis Figure 3.9. Annual Average Chlorophyll a Concentration for 2005, 2006, 2007 and 2008 (the black line denotes 11 Ilg/L, the threshold for impairment from FDEP's IWR; the red line indicates the median value for Florida estuaries; 9 mg/L). _2I)U~. _-,om, qWi! ZOUI 12 " "- " 2- 0 " .. 0. 0 0; :;; v , o WI we _lUOe: -Mcdidn -Iluf]/L )t' ~1 ~;d t ,~' Site W-7 exceeded an annual average Chl-a concentration of I] ~g/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 Station Wi Multiple techniques 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-Iimitcd system. In Clam Bay, overall the TN:TP ratio indicate a co-limited system with periods of both nitrogen 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. I I and 3.12, respectively). PHS1 20 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 31 of 89 Water Quality Review and Analysis 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). BO -4-W.6 -ll-W I W 1 -UCBRK -...Seagatc /0 UlI so 0- ~ '" 4U L z I \" ~ t, IlIr ~l ,0 , I I i , , I ' " '\ I II; ~ i I '^ I , 111 ,. , , , 'I {''t I ,I{ !i \y '< !I I ' L /~~ !j~ , 20 y}\1 h \ rjt~' " \ 100~ I I " V ~ ~ I J V v' 0 Jall'O~; Jan 06 Jdn 07 Jan 08 0('(.013 P8SJ 21 Clam Bay System Data Colleclion and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 32 of 89 Water Quality Review and Analysis Figure 3.11. Relationship Between Chlorophyll a and Total Nitrogen in Clam Bay (figure from PBS&J [2008]). 16 Chl.a ~ 4.33 +5.03(TN); R' ~ 0.13; P ~ 0.045 . 14 . . 12 ~ . . . ~ 10 g: . . .1 . 8 . . >, . .c 0. 0 6 . .Q .c . 0 4 . . . . .. 2 0 0.0 0.2 0.4 0.6 0.8 1.0 1.2 TN (mg filter) P8SJ 22 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX~ 1 a New Business 33 of 89 Water Quality Review and Analysis 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 Ol . .6 !1l . ...!. 8 . >- .<:: 0. 0 6 . ~ 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 correlation 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, NO, and N02 (Figure 3.13). Total nitrogen data are available for sites W-6, W-7 and W-l 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 mg/L, respectively). The greatest TN concentration was found at the UCBRK site with concentrations decreasing the further south in the watershed sampled (Figure 3.14). PBSJ 23 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 34 of 89 Water Quality Review and Analysis 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). lU -"-W (, ......\'1/ J WI -U(BKK ~~~~l'~lCJtl' " '" G ~ -S c . ~ g z jj Ii! 4 2 t . U ~l'11 81 Mdr i5~ /l.ugtlt\ Jdl1';J2 Jul ~:\ Dec ':.18 Jun U2 Nov US Apr U':J PHSJ 24 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 35 of 89 Water Quality Review and Analysis 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). "- " E- o . g 08 'z jj >= l.G 1.2 04 o UU:lI{K Total Phosphorus WI 90 . Average .Median % Values > O,~ mg/I 80 IU GU :,0 ~ 0 , ~ . ~ 40 ~ "- JO 20 10 0 we WI )C>d[;dte Total phosphorus data are available from November 198 I to May 2009 at the W - I, 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. I 5). 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%. PBSJ 25 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 !X~ 1 a New Business 36 of 89 Water Quality Review and Analysis 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]). ~w L ___\.'1// \'II 1 --U([1Ri< ""0~~(',lgate U8 ;;:::, O,b E . , i5 "' " o "' .. "2 0.4 11 0,2 TI h I LJ I" J I u )CP 81 M:+f 8'-, /\Ul: 88 !elnq2 J u I '::l~; Dee 98 Jun U2 Nav U:, Apr O':J 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. I 6). PBSS 26 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19. 2009 IX-1 a New Business 37 of 89 Water Quality Review and Analysis 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). <:. ~ .E- , <; ~ ~ o ~ 0. ~ ,2 012 U,U~ U.U4 o \\'/ . ^ver<l!~,-' Wl, .rv1cdiM\ WI '% Volues:> UUI Mf~/I Sl'<l f~d t C' 90 ,u 10 60 . ')0 ~ . " . . o . .::u ~ 30 20 10 o P8SI UCtjRK 27 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 38 of 89 Water Quality Review and Analysis 3.3 Task 3 - Sediment and Biological Health Characterization General Biological Survey Results Figure 3.17 summarizes the results of the Redox depth survey undertaken 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 cm, Green symbols represent Redox layer> 20 cm. Redox layers were at or close to the surface (< 20 cm) in both Upper and Outer Clam Bay. In contrast, Redox layers were typically deeper than 20 cm in Inner Clam Bay and Moorings Bay. P8SI 26 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 39 of 89 Water Quality Review and Analysis 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 macroaIgae 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, Haloohi1a decipiens. This species, as opposed to shoal grass P8Sl 29 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 40 of 89 Water Quality Review and Analysis (HaloduIe 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, macroa1gae were commonly encountered in all regions surveyed except for Upper and Outer Clam Bays (Figure 3.19). PBSJ 30 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 41 of 89 Water Quality Review and Analysis 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). PBSJ 31 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19. 2009 IX-1a New Business 42 of 89 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 macroalgae 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 cm, 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 cm), indicating reduced DO levels in sediments . Limited and/or coverage by seagrasses, mostly Haloohila decioiens with likely ephemeral but potentially abundant coverage by macroaIgae 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 heterotrophs and autotrophs Moorings Bay · Redox layer typically deeper than 20 cm, indicating sufficient DO levels in sediments . MacroaIgae 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 PHS] 32 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 43 of 89 Water Quality Discussion and Recommendations As relates to the analysis of existing water quality, it should be noted that Florida Administrative Code (62-40.540) clearly states that, "AII 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, particularly in Upper Clam Bay. However, it is important to note that IWR guidance on DO and chlorophyll a can be locally inappropriate, particularly in subtropical systems. In their study of dissolved oxygen levels in the Everglades, McCormick et 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, 0, 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 report (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 inferred based on Redox depths, is not necessarily indicative of a nutrient- enriched water body. While chlorophyll a levels were not uncommonly above the impairment threshold level of II 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 10 to 80% of TP values exceed the Florida median), the highest values are 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 patterns of water quality in the Clam Bay system. PBSJ 33 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 44 of 89 Water Quality Discussion and Recommendations The finding that Redox layers are almost uniformly deeper in Moorings Bay than in Clam Bay further suggests that the more weJl flushed Moorings Bay system (see circulation results) is better able to accommodate nutrient enrichment than the less well flushed Clam Bay system. The poJlutant loading model for Clam And Moorings Bays produced by PBS&J (2008) further demonstrates that the more "polluting" 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 shaJlow 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 effort needs to be consistent with state certifications and standard operation procedures required by FDEP. Suggested sampling locations are shown in Figure 4.1, and a suggested sampling parameter list is shown in Table 4.1. PHSJ 34 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 45 of 89 Water Quality Discussion and Recommendations Figure 4.1. Recommended Sampling Locations for Upper, Inner and Outer Clam Bay. These sampling 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 4.1) to ensure adequate parameters are collected for any reasonable characterization efforts and/or TMDL-related issues. P8S1 35 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 46 of 89 Water Quality Discussion and Recommendations Table 4.1. Recommended Parameter List for Ambient Water Quality Monitoring Program for Clam and Moorings Bays. Water Quality I l'ChloroPhYll a Phaeophytin [Nitrate-Nitrite i I. Proposed for Collier Count!.. r. --.- - - . , i , Total Kjeldahl Nitrogen Total Nitrogen 'Orthophosphate iTotal Phosphorus , [Dissolved oxygen i IFeca1 Coliform , BOD Color :Enterococci Turbidity Salinity ,Conductivity pH Temperature Secchi Photosynthetically Active Radiation (PAR) Depth PBSJ 36 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 47 of 89 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 intlow 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 tlushing and exchange within the system via channel dredging. These measures would reduce mean water levels and create 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 intlow 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 tlow 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 intlow 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 (l) a varying water surface elevation at the Gulf of Mexico (Clam Pass), and (2) freshwater intlow at the northern end of Upper Clam Bay. The water surface elevation boundary condition varied in time, while the freshwater intlow was held constant during each individual model run. The model was calibrated according to measured tidal ranges using a 2.5 PBSl 37 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19. 2009 lX-1a New Business 48 of 89 Model Review 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 Moorings 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 include 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 rt (north < south) to + 1.54 ft, with the Moorings Bay side of the culverts reaching low tide approximately 1.5 hr 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 rt/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 PBSJ 38 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 49 of 89 Model Review 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 stonnwater 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 no 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 example, 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 effort 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 Delft3D would also have a distinct advantage over RMA2. The initial modeling effort could include only 2D hydrodynamics, but De1ft3D is modular such that the addition of new modeling parameters (3D dynamics, morphology, water quality, etc.) can be added to the basic 2D 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 disconnectcd models. PHSJ 39 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 50 of 89 Model Review 5.2 Review of Clam Bay hydrographic assessment report, Tackney & Associates (1996) Report Overview The study by Tackney (1996) 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 storm water sources also increases the mean water level in these bays. Water levels and current velocities were measured within Clam Bay at I I 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 ft/s, with a maximum value of 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 current magnitude through the inlet. It is clear that Clam Pass is not particularly 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 thc 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. PHSJ 40 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19. 2009 IX-1 a New Business 51 of 89 Model Review Report Review In general, the basic principles of this report are sound. Tidal attenuation and water supere1evation 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 j(Jr 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 model 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 culverts was as much as 1.5 ft lower than the north side. Current velocities reached 3 ft/s in the southerly direction, but only 0.3 fI/s in the northerly direction. An estimate of volume exchange for the study period yielded a net flow of 969,000 cf from Outer Clam Bay into Moorings Bay per tidal cycle (182,000 cf northerly. 1,151,000 cf southerly). Studies by the USEPA (1975 & 1977) support the conclusion of net southerly flow. ms, 41 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 52 of 89 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 Current 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 6.1). Figure 6.1. Coastal Leasing MicroTide Gauge and concrete base. The three Workhorse Sentinel Acoustic Doppler Current Profilers (ADCPs) 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 16 ft 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 PVC 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). P8SJ 42 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19. 2009 IX-1 a New Business 53 of 89 Hydrographic Data Collection 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', Pass. It too was set in approximately 14 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 Outer Clam Bay in 3 ft of water and elevated 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 east of the mouth. The survey crew used a level to elevate this instrument from R-42 just south of Clam Pass. A third Workhorse ADCP "BrdgN" was attached to a concrete base and deployed 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 Levelogger pressure sensor was attached to the concrete base as well to record the water level independent of the SonTek. The first SonTek ADCP/Levelogger was deployed on the north side of the Harbour Dr. Bridge in approximately 15 ft of water. The second SonTek ADCP/Levelogger was deployed on PBSJ 43 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 54 of 89 Hydrographic Data Collection 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 17th, 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/LeveIogger 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 morning, 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. PBSJ 44 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 55 of 89 7.0 Hydrographic Data Analysis 7.1 Introduction The data collection effort yielded concurrent water level and llow velocity measurements for a period of 8 days, from August 15 to August 23, 2009. All instruments were successful in collecting data; however, several acts of vandalism resulted in the partial loss of llow velocity data at South Seagate Dr and Harbour Dr. Figure 7.1 illustrates the locations of the deployed instruments. The data was processed using MatIab 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 culverts. 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 15 to August 23, 2009. They are ordered roughly north 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. PBSJ 45 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 a New Business 56 of 89 Hydrographic Data Analysis Table 7.1. Water level parameters in Clam Bay; August 15 to August 23, 2009. Location Minimum WSE Maximum WSE Mean WSE Range (ft NA V088) (ft NA V088) (ft NA V088) (ft) 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 SeaQate Dr -1.2 1.6 0.10 2.9 South Seagale 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 P8SJ 46 Clam Bay System Data Collection and Analysis October 2009 g <II : ~ .~ . c;; H l: ,W ocl ~~~.! u '" _ co ~~~C " :c Q, E Cl o i :I: .~ ~~ ~1J " 0 q; ;0 0 ~ + 0 0 . \ . 0 E " i ~3 m w > '" . m i G ~ :;; ~ . X .,; e c N C N X .; e. N ... ~ w '" ~ .. .9 on i: "'" .9 Z t; "" .!! - '8 .... ... ~ q ;; 'C - >- ~ ~ '" "" E Q ~ c:; "'" .9 Z m "" 0 ::; .9 ~ ;.... 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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 North 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 1 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 Gulf 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 to 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. Due 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 level differences observed on either side of Seagate Dr during each tidal cycle; see Figure 7.10. 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 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, PBSJ 61 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 72 of 89 Hydrographic Data Analysis 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 surface elevation and current profile over time, with the color of each area scaled to the horizontal velocity magnitude. Figures 7.16, 7. I 8, 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 northing 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 !low 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 !low 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, ] 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 !low. 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. 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Il.) ~ 0 o ~ e., ,,0 ~ w ~ o:l~~E~~Q:l~ 0 -~ " E e:: $2 s:: E Eo: " "'0: E ~ ""0 3 u 1;; ..::g~Q:lOea...co!:~ ~.<: 0 0 u U U.<: " E.<: U [/) [/)[/)..0 (:) 0 t 1-0 t::-s ~ '5 ;; ~ .<:-",t;l " ....l o...ltiOVJUo_t:: ~ t;l:r: '0 c..aZ':= 1;1180 ge., ~ ::J _::J Z [/) :; 0 0 CBAC November 19, 2009 IX-1a New Business 86 of 89 Hydrographic Data Analysis 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 ft/s while incoming velocity peaked at 0.4 ft/s. The highest observed now rate was outgoing at 29 I 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 now rate of 1451 cfs greater than the outgoing rate of 1017 cfs. Accordingly, net now 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 ft/s and 716 to 777 cfs, respectively). Net now was slightly outgoing at 566,000 cf per tidal cycle; however, since velocities and flow 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 ft/s faster than the maximum incoming current, and outgoing peak now rates were 14% higher than incoming. Net flow was outgoing, on the order of 2.4 I 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 northerly current 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 cf flow 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 USEPA (1977) performed an analysis of flow through the Seagate Dr culverts, and determined that net now 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. PBSJ 76 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19. 2009 lX-1 a New Business 87 of 89 Hydrographic Data Analysis 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 ftls, while the peak northerly current is only 0.3 ft/s. Peak flow volume rates are 3 times higher in the southerly direction. In 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. P8Sl 77 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19. 2009 IX-1a New Business 66 of 69 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 Florida. 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, M.J. and D.R. Swift. 1997. Die1 oxygen profiles and water column community metabolism in the Florida Everglades, USA. Archives die Hyrobiologie. 140: 117-129. Smith, S.V., Kimmerer, W.J., Laws, E.A., Brock, R.E., and T.W. Walsh. 1981. Kaneohe Bay sewage diversion experiment: perspectives on ecosystem responses to nutritional perturbation. Pac if. Sci. 35: 278-396. Tackney & Associates, Inc. 1996. Preliminary Hydrographic Assessment - Clam Bay Systems. Tomasko, D.A., D.L. Briston, and J.A. Otto 2001. Assessment of Present and Future Nitrogen Loads, Water Quality, and Seagrass (Thalassia testudinum) Depth Distribution in Lemon Bay, Florida. Estuaries 24(6A): 926-938. Tomasko, D.A. and B.E. Lapointe. 1991. Productivity and biomass of Thalassia tesrudinum as related to water column nutrient availability and epiphyte levels: field observations and experimental studies. Marine Ecology Progress Series 75: 9-17. PBSJ 78 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1a New Business 89 of 89 References 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, U.S. EPA Surveillance and Analysis Division, Athens, GA ValieIa, I., Costa, J., Foreman, K., Teal, J.M., Howes, B., and D. Aubrey. 1991. Transport of groundwater-borne nutrients from watersheds and their effects on coastal waters. Biogeochemistry 10: 177-197. P8S1 79 Clam Bay System Data Collection and Analysis October 2009 CBAC November 19, 2009 IX-1 b New Business 10f21 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 ofthe report. Note: Statements that are in red italics are directly from PBS&J report Executive Summary: Page i section: Review Points J 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 llora 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 warm 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 ID :# 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. P BS&J 's Critique olother studies CBAC November 19, 2009 IX-1 b New Business 2 of 21 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 certif\ed 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., 200]). WHOOPS - Now I am getting defensive so I'll stop! Statements from Introduction page 1 paragraphs 1 and 4: Paragraph 1: "Clam B((I' and AI/ooring.,,' Ba\' are important natllra/features in ('o/lier ('Olll1ly Paragraph -I sentence 3: "In conlras/, mlfch oflhe shoreline <?l Aloorings Bay was signlliconlly allered Ihrollgh dredge and .Jill activitl,'. stich thaI nalura! shorelin!' ji.:ullIres in Ihe northern /,OI'IIOI1S o(Moortf/gs lI"v ,,'er(' mosll)' "bsen! bv 1h(' /950.," 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. CBAC November 19. 2009 IX-1b New Business 3of21 , '1 ..........~... ...J;.:..~l!'.'" ..1,..... .. .. ':. .<< , .;"ni" i. . .'t!.: .~.~. 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, storm water 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 Clam 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: "Ins/cad. /he conclulloll was reached Ihal dic-ojt I['{/.\' like/v due {() e.rcnsi\'(' fresfll1'(/tcr ill/JUt to the .\:.I'.\'tel1l from the adjacent developed uplands and an jYUUh'(jU{ftf dispersion oj' flw iI/creased fj'('slll1'utcf' inpul due to sevt'f'('ly cOf/slric/ed lida! channels ill the tl!{lf!grove ji)/'{iSI. /1s (/ resull. the J/umgrOl'(' /()re.\t he('anle inundaled H'ilh H'oler !eve!s highe/' Ihon the lOpS (l the hlock IIlWl.f!.rure rmeUf!1({tol,llOres, The durotiull 0/ illcreased wuler hTCl\ \VOS ,,"lIl/iclen! 10 kill Ihe /J'('L'S h)' hlocking OXl'gt'11 ext-!wflgt 10 the helow ground lissue,',>' " 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 CBAC November 19, 2009 IX-1 b New Business 4 of 21 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. Statement from Page 5 1.2: 'In response /() ('on('crns related 10 the ISSlles otwalcr 'lllahlV "nd (';rculot;on in the ('10m B((v and .Hoorings IJcn/ s\;,s{ems, ('oilier ('Ollr/tv rt'qlle.\/ed !)1J5;&.1 prepare a /wo/)(),\'{f/lu C'(mdUCl u circulal;oll (fnd I\'aler (/lIo!iry Sfllt~l'IO dc/ermine {he/hI/owing: . Ulnl! is Il1e ex{en! ond /,e/alh'e' h('(/Ilh of Ihe nafural reWHll'c(,s ill Clam Bay and /l4uorings Ba(' .. 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 d" hi.\loricul dala sUKKcsl. in Icrms o/sl"lIIS "lfd Irelflls. "bolltlhe health ot ('/am B"r and ,Uoorings Bar:) "' Historical biological data also needs to be addressed prior to hypothesizing about the health of the system. . "HOlt' do circulation pallerns and rlutrieI1l delivery inferw:tlo create spalial pa!ferns (~l water quality in Clam Bay and A100rings B(~v, and how Ihes'e pallel'rl.\; lffj(>CI {he estuarine .flora <mll/auna) .. 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. CBAC November 19, 2009 lX-1b New Business 5 of 21 . "HO\I' will c1ll11lg~s ill circulalion within Clam Ba)' and betw~~n Clam Ba)' and Moorings Ba)' atteclth~ overall ~stuarv (as detined in Figur~ 1.5p" 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') Statementf/'om 2.0 Methods 2.4 page 8 "This lask COl1sisled (~r('()m[Jl(!tinp, (( huth.vllu'lric survt'.v (~l({ portion (~lthe projecl arell. The halhymelric surve,F oj/he pl'o/eel area included ClulIlPass rindlHlin,g lhe chh shoal complex), {;/J!}(!l'. inner. (lml (Juler ('lam Bo)', lInd i\lo()l'ing.<i Bo)' ". Please provide the bathymetry map Regarding Stalementsjrom 2.0 Methods page 8 Currents/Water Levels: page 8: "Curre11l and waler level meaSlfl'ellH.!nls l.-rere laken wilhin (he pro/eel area Ol'er a period (~l8 da)"lill' us~ in a planning lel'e/ circulalion anal)'sis. This dala can also be usedlor Ihe calihralioJ1 q/a potential hydn){~\'n(/mic numerical model. ('lfrrents and waleI' lel'els were measured at.!i\'(' ond 5,'f'Vel1 lo('alions l1'ilhinlhe pny"ec/ area, respectively". And Statements from 7. I "rhe data co/lcC/ion e/tol'l vielded concurrenl wal~r level amlflow velocilv measuremenfsjor a period 0111 davs,from AugusI /510 AU?;lIsl 23. ]O(N. All instrumellls w~re successful ill (.'ol/ecling da!a: }uH1'('l'er, ,\'everal ({cIs oj"\'awlalism" "It should he noled Ihal (he ~r(}(er level do!ujl'om !he ('Iarn I'as.'\" gauge is (~j'conc('rn, wi/h a rouge less Ihun e"tpecl('(1 and un 01'(,/,(111 ('Ievulion Ihot ap/Jew's 10 he 100 low" And Statements./i'om Hydrographic Data Analysis 7.3 Current Velocilies and Flow Rales page 62. "The gill'S in Ihe Sowh ,Yeagat" Or IIl1d /larhour 01' daw were dlle to 1I('ls ot vandalism during Ihe d~I'lovl1lelll. .l/icl' Ihe /larhour Dr gauge was rcdcp/oj'cd Ihe rcodings ol'peal' 10 h~ erroneous due to rheil' sl1lolllllagniuf{!e, bul no discrepancies can hefiwnd in the du/uflles or ;'ls1rument selllp. For !11(' purpo.'\'es ol'co/culoling)lol1' rales al!farholll' Dr, 011/).' the datu htdi)/,e the \'(:{fula/ism O{'CUlTed IFas lIsed". Equipment malfunctions do occur within thc field, however not repeating the experiment given the unexpected data; readings that appear erroneous; and only using data prior to incidents given CBAC November 19, 2009 IX~ 1 b New Business 6of21 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 of' levels 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 are 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 3 I 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 1 month for calibration and I month for validation is sufficient and model sensitivity studies are essential (Huang, 2007). Various year's worth 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 Statement from the executive summary: "Ill order /0 (/1}(//I'::(' jHJlenlhll changes 10 Ih(' srslem 10 itlll)f'(FVC circulation {lnd dissoh'ed ()~vgen iDO) "itlul'! fhe ClulII Buy s\.\lelll. a hn//'lldVl'!ulllic IIIlIdel 11'111 need /II he de\.elllped III unden,land the iJ1/i//'acfiolls helween CI(lJ}] nUl' rippcl', Inlier und ()lIler;, ('lam Pass. :\1oorings Bay. oHd Doctor 's I 'ass " CBAC November 19, 2009 IX-1 b New Business 7of21 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 "AI (Ill lInn/lc('led oh"'I"'1I1 ion, Lj'l}('r ('1011I Bo)' oPIJew.1 10 Icod Inner ('1011I Bar hy oppl'Oxllllolt'''' 2 hOllrl. /he 1,,/01 mnge ill/I. Ins Ihon 25:'<, 0/ Ihe (;111(11.101 rungi'. lir)/h Upper and Inna /JU)'I' have a IIIcon Iidc Ic,'e/ oholll OJ!! II obo,,'e Ihe mean C;ul( level. IIke/)' due to S[()f'flnva(er if?flOli'j()}'l'mg (l hcud 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. Statementfrom Hydrographic Data Analysis 7.3 Current Velocities and Flow Rates page 62: /1 II IlIIpOrlol1/ 10 no Ie that Ihe.fle/d dala was col/e('led during spring IIdel. where Ihe IIdol range is largeI' than normal (higher highs, lower loH's). Also, Ihere were s('\'el'(/ll'aif~l{f1l event.\' during Ihe Sll(((r period. ~vhich af/i'l'l H'are!' leFels in Clam B(~\) and A100rings Bay due to urban drainage, fvidence (~lfhis rai1?fitll ('011 he see17 in Ihe waler lel'(!lg/'ul'h'l (Figlll'e,\' -:,1 and 7,3) (~/ LJJper and Inflt!r ('jam flay. whcre il appear,\" {he mean H'afer lel'el rises during fhe lreek as slOrnnl'Clfer enters Ihe syslem. What were the extent ofthe 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 to extreme conditions as stated in the reports conclusion (page 74). II II ll/lporlonl to note Ihallhef/o\1' ('ol('ulollons IIrc hOlcd on the ('ondltlollS during Ihe Ilnd)' period and Ihe ,.e.mllonllrend, mo)' on/)' be apl'//('()ble lolhe sllldy 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 10 the WaleI' Quality Component o/Ihe 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...... CBAC November 19. 2009 IX-1 b New Business 8 of 21 I would have liked to see statistics broken out by season as this is an important driver in water quality and could explain some ofthe 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 2005-2007'1 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 of regions that Boyer, et. al., 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. aI. 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 ofthis question). The Gulf coast of Florida receives discharges from a lot ofrivers 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 Florida 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 correspond to the semi regular events in the Gulf shelf particularly in 1992'1 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, Irom 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 CBAC November 19, 2009 IX-1b New Business 9of21 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: 'Extremel), elevated concentratiollS oj DO were observed between August 2001 and August ]00]: these data must have been reported inaccurately, and cannot he representat h'e o( the ambient DO r(!(/dings at/ho/time. T() accommodate this data proh/t'/I/, Figure 3.5 lI'as crcated. where the I 'axis \1'as trulJcated at a more realistic maximum DO level oj I 0 1IIg/1" It would be more appropriate to omit the erroneous data trom 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: "Isolated elel'uted concel1lmtiollS ojchlorophl'il u huve heen obse/'1'('(1 utthe W-6 alld 11'-1 sites, hown'er, the concelllratioll observed Oil September 1996 atlhe 11'-6 sile 099 IlgL) iSllnlikelv ilJ the rnarine walers, amI so the dOla ore displa.'ved (Figure 3.N) with a IrllnC((fedy-axi,)' ", 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, ",,",'ile J;r~"7 ('-,,('cedcd all (11111/1(" avef'a,Il,'t' CI'1I..{l conu'nlration (~lll 1I,\!,'L during holh ]{)()5 and ]()(F, !3used OI)()1J niltillg cri/erlll from FDD', t 'fam !3ay ll'Ould likel) be declared l'erified impaired dUi.' 10 del'a/cd chlorophyll (l COf/ccl7lraliof/.\'" CBAC November 19, 2009 IX-1b New Business 10of21 According to FDEP's current Impaired Waters Rule 10% of the samples have to exceed annual averages of II ugll for the Water Body, Given the bar chart values from the Figure 3,9 in the report - it does not appear that J 0% 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 II ug/l 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 filter 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 Nand 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, et. a!., 2003), 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. a!.. 2003), 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 examplc: Shallow water cstuaries (like Clam Bay) should accumulate substantial amounts of organic matter that becomes incorporated into the benthos where it degrades and is moditied by microbes, Microbial communitics employ complcx anaerobic and aerobic transformations that result in thc 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 horn these forces (Seymour, et. a!., 2007), 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. a!., 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 ofa few of the lower level organisms mentioned in this study, without looking at the community horn the top down also, Due to the scope of this study there was no possibility of characterizing the health of CBAC November 19, 2009 IX-1 b New Business 11of21 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 (N03-), manganese oxide (MnO,), iron hydroxides (Fe(Ollh), sulfate (S04-'), and carbon dioxide (CO,) in this order, act as electron acceptors in the absence of oxygen (Vespraskas and Faolkner, 2001), Redox potential, expressed and measured as Eh, is a useful indicator of what types of reduced elements one can expect to tind in soil solution It is an electrical measurement that shows the tendency of a soil solution to transfer electrons to or trom 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. a!., 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 Fe]' to FE ", 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 Statementjrom the executive summary point 6: "As If result, ,Hooting", B(~v, although slff~je(J 10 e.rh'f1S11'f !Arhat! stornnr(Th'l' f'lll7otl appears to !Jm'e water ecology condltiolls be tier fhan tl/(/Iejhllml in Clam Bav: fhis is slIpporled bv the reslIlls oj Ihe Redox layer inl'cstigation" 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 CBAC November 19, 2009 IX-1b New Business 12of21 result in various colors in the soil and rapid changes in redox potential (Eh) over small distances (Clark, et, a!., 1998), Regarding Statements made in the executive summary #2 and #3: 'A fine-grained see/hl/enl l(in'l' w(lslound ill lJ1o:-;1locolion',' o{( }zller ('lam 80.1'. This sediment depth l1'as opfJl'uximalely 5/,'C'1 fJ! Ihe an'tJ o/Ihe Seagotc canals. l1'a,\' not !,rendent in ,\1ooriJ1,!.!.'l Bay, dnd nll'icd in depth in ()u/er, Inner and l/fJfJer ('lal1l Bar,\': '. .'11 is nol known al tIllS lime ijlhcline-graillcd s{'di"'{'ntl(~)'{'r is nalllral(l' occurring, or occurring as a resull oj'nwfl-l1lade chan,l.!,es 10 the ('10m Bay syslem. It is, however, knOll'n thal/he .'iedime11f la.-vel' ill the 5,'eagate canals has accumulaled since lhe cana/.\ were dug ill the 1950s", Fine sediments are not uncommon and occur naturally in mangrove estuaries (Alfaro, 2005; Van Santen, et" a!., 2007; Bala Krishna Prasad and Ramanathan, 2005; Alongi, et. a!., 2005; Schmid, et., a!., 2006) often in the upper reaches of the estuary (Van Santen et., a!., 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., a!., 2007), "Mangrove 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. a!., 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 V olety (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 Statement from 3,3 Task 3 - Sediment and Biological Health Characterization General Biological Survey Results page 28 "Redox lavers IVere at O/' close to the slIrti":,, (< 20 em) ill both Upper and Ollter Clam Bav, In eOl1fl'lJst, Redox lavers were l.l'liiCil/!)' deeper !111m 20 elll ill IIlner Clalll /Ja)' alld Moorings Bay. These dOlO slIggesl Ihat henthic con1lrJuni/ies \1'ould be expee/ed to he (~llovF(!r divers;!.v (ffnot alnwdance) in both Upper and (Jater C'fam /JiH'S" Benthic Communities Benthic communities are 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 macrobcnthic community alone covers a diverse spectrum of species including but not limited to sponges, mollusks, worms, crabs, lobsters, prawns, etc, (Ellison, 2008) which are not able to be quantified by the cursory inspection pertormed during this study, CBAC November 19, 2009 IX-1 b New Business 130121 Thus statements such as those made in the executive summary #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 of Eh measurements, etc,) in Clam Bay and Moorings Bay "The ,I'hol/ow Redox lm'('/' delJths ill IIWI/ or Clam lio)', ill coII/billalion with the fineg/'ained sedimefllsjiJund in I}/()sl jocallofls. suggest Iha/ ht'}l!!Jic (i.t'., .'hol/om-dwelling") communities ill ('lam !3l(l' l1'Ollhl he expecled 10 he If!sS diverse Ihan in j\!ool'ings B(~v ". " ('amhined these resulls indicote Ihill despite [he mo/'e madllied shoreline and greiller poUutant loading potentia!. Aloorings Bl~V H'(w!d appear Lo have a more diver.'it' and health" benthic ecology than ('lam B01' Oilliorellces in the ecologicalfunclioning helweal ClolI/ Iia)' (lnd Moorings Bo)' could he due to difjerences illtidol circulolion and residencf! lime ". The relationship between the ecological timction 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, ditTerent 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 atTect the sediment ditTerently 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 significance of trophic interactions and the mangrove sediments should not be underestimated or ignored in understanding ecosystem health, The unexpected diversity in patterns ofresource 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 CBAC November 19. 2009 IX-1 b New Business 14 of 21 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 particular 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 un vegetated 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, A,C, 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,J. 1992, Nitrogen and Phosphorus Cycles, In: Tropical Mangrove Eco~ystems, Robertson, A,J. 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,J. and Alongi, D,M, (Eds,), American Geophysican Union, Washington D,C. 137-171 Alongi, D,M, Pfitzner, J" 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, CBAC November 19, 2009 IX-1b New Business 150f21 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, MJ, 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, TJ, 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- J 00, Clark, M, W" McConchie, D" Lewis. D,W, and Saenger, p, 1998, Redox stratitication and heavy metal partitioning in A vicennia-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 Geophysican 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 flushing time in a small estuary of North Bay Florida, Estuarine, Coastal and Shelf Science, 74: 722-731, Holmboe, N" Kristensen, E, and Anderson, F,O, 2001. Anoxic Deposition in Sediments trom 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,G" 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, Schmid, 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, CBAC November 19. 2009 IX-1b New Business 16 of 21 Seymour, J,R" Seuront, L., and Mitchell, lG, 2007, Microscale gradients of planktonic microbial communities above the sediment in a mangrove estuary, Estuarine, Coastal and Shelf Science, 71: 65 I -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, MJ, and Faulkner, S,P, 200}, Redox Chemistry of Hydric Soils, In: Wetland Soils, Richardson, J, L, and Vespraskas, MJ, (eds), CRC Press LLC. Boca Raton, 85-105, Wosten, lH,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 Roellil!. Comments I, Page I, first paragraph, 1st line delete the word "natural", 3" line, delete the word "perhaps", Second paragraph, second line, after the word "innow", add "'along with sea water by the tides, delete the words, "most likely", 4th line, delete "Additionally, it was likely that", 6th line, delete the word, "likely", 7'h 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, 3d line, delete" significant modification" and insert "elimination of the mangrove forest and artificial armoring of the shoreline,", 3, Page 5, I st paragraph, item ] "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 such as: number, length, diameter and elevation, It should also be noted that the nap gates on the north side ofthe 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 now rates and speeds were developed, CBAC November 19, 2009 IX-1 b New Business 17 of21 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 intlows 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, 1 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, I I, 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 1 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 suflicient. 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 41 Well stated and better 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, CBAC November 19, 2009 IX-1b New Business 18 of 21 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 examining 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 arc 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 affcct 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 [,5 It, The CBAC November 19, 2009 IX-1 b New Business 19 of 21 result is water flows back and forth between the two bodies, with the majority of flow southward from Clam Bay into Moorings Bay", This isjust an interpretation of what happened during these 4 days of data collection, This is not applicable to any other time, (p, 6 I) 3, The important information, on page 33, that Impaired Water Rules (IWR) guidance on Dissolved Oxygen (DO), and chlorophyll a 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 a, 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 of2008 cited in the references were used instead of leaning on old data, See pages 18-20, The ones in 2008 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 of27" of additional water which resulted in the drowning ofthe mangroves, (pp, iv in the Summary & p, 3 in the Report) (City Council Workshop, Aug, 3, 1998) 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, I I) 8, 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 tecal 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) II, 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 ofPBS&J in 2007 reported that there were numerous seagrass beds, This report found only one seagrass bed, and the explanation for this is the CBAC November 19, 2009 IX-1 b New Business 200f21 ephemeral nature ofthis species, Could they have been destroyed by motorboat and jet ski traffic? Ifnot, 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 "mudflats" at low tides and during dry periods, Sediment made of mud naturally holds less DO than more porous sediments such as sand, But these mudflats 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 storm water 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 Clam Bay & Moorings Bay are clear indications of this likelihood, (City Council meetings, May & Sept 2008) (FDER a,k,a, FDEP 198 I report) (Tomasko Sea grass 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 1997, 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 !low 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 CBAC November 19, 2009 IX-1 b New Business 21 of 21 (with the exception of the 1977 USEPA analysis mentioned by PBS&J). and 11 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, currents, 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-off;;), Who will be responsible, and how much more oftaxpayers' 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 storm water run-off into the bays, Our tax dollars and energy should be spent on helping these communities implement Best Management Practices (I3MP). as well as oyster, clam, and mangrove restoration programs, instead of trying some costly unproven methods of disturbing the balance of the tragi Ie Clam Pass/Clam Bay ecosystem, CAC November 19, 2009 IX-1 c New Business 1 of 8 P8SJ 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) --~---^-'~ , , There are several recurring themes that highlight the main concerns brought 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 resolullon 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 ft, compared to the long-term average of 2,0 ft (the difference between MHW and MLW at Naples). The highest observed PBSJ CAC November 19, 2009 IX-1 c New Business 2 of 8 water level at Doctor's Pass was 2.0 ft NAVD88, while MHW at Naples is 0.3 ft NAVD88, The lowest water level at Doctor's Pass was -2.3 ft NAVD88, while MLW at Naples is -1,7 ft 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 ft to 2.1 ft NAVD88, while low tides ranged from -2.4 ft to -0,1 ft NAVD88. Successive high and low tides varied by differences from 0,7 ft to 4,0 ft. Therefore, during the 8 days of concurrent data, the tidal range vaned 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 Seagate Dr. The peak southerly velocity of 2.5 ftls at approximately 6:00pm on August 18 corresponds to an outgoing tide with a range of 4,0 ft (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 matfunctions 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 Sea gate 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 to 4.1 ft, and the flow direction and magnitude show a definite correlation with the tide phase and amplitude. Given that the tidal fluctuation 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 PBSJ 2 CAC November 19, 2009 IX-1 c New Business 3 of 8 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 ievel 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 nonetheless 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 10x 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 Sea gate 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 P8SI 3 CAC November 19, 2009 IX-1 c New Business 4 of B 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 ffow 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 (fe/s) over time Q(t) = v(t)W[d + 7)(t)] Equation 2. Flow volume (fe) per time step. Vet) = Q(t)dt In the above equations, Q(t} (ft3ts) is the fiow rate over time, viti (ftts) is the depth-averaged velocity over time, W (ft) is the width of the channel in which flow was measured, d (ft) is the depth of the channel relative to the NAVD88, fI(t} (ft) is the water surface elevation relative to NAVD88 over time, Viti (ft') 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(ft\ d(ft) North Bridne 35 5,5 Clam Pass 80 3,5 South BridCe 90 4.3 South Seaoate Dr 15 4.5 Park Shore Dr 80 86 __ Harbour Dr 70 13 PBSJ 4 CAC November 19. 2009 IX-1 c New Business 5 of 8 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 durinq Auaust 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 3003 7 ESE 16 22 August 17 0.51 3003 7 ENE 17 24 August 18 0,07 3003 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 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 t 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, U,S, EPA Surveillance and Analysis Division, Athens, GA PBSJ 5 CAC November 19, 2009 IX-1 c New Business 6 of 8 Response to Criticisms Most of the 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 aualitv lIimoairments" for dissolved oxve:en aren1t oroblematic 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 SO% of DO readings (by site) fell below the IWR standard of 4 mg I 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 FOEP, "screening" levels of TN are exceeded at Clam Bay sites between 21 and 73 percent of the time, levels of TP used by FOEP 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 FOEP 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 CAC November 19. 2009 lX-1 c New Business 7 of 8 (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 I 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 llllg I 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 Bav and Clam Bav are different svstems, 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 qualitv being determined to CAC November 19, 2009 IX-1c New Business 8 of 8 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 laver and fine-grained sediments noted in Outer Clam Bav are "natural" The shallow Redox iayer 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 SO 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 of taxa (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,