# Site

- Specific Information in Support of Establishing Numeric Nutrient Criteria in Suwannee E stuary/Suwannee Sound/Cedar Keys, Waccasassa Bay, and Withlacoochee Bay

Division of Environmental Assessment and Restoration Standards and Assessment Section Florida Department of Environmental Protection Tallahassee, FL 32399

August 25, 2010Draft ii August 2010 

### Table of Contents Executive Summary

............................................................................................................... 1 Geographic and Physical De scription

..................................................................................... 4
Suwannee Watershed

..................................................................................................................... 5 Suwannee Estuary

.......................................................................................................................... 9 Waccasassa Bay

........................................................................................................................... 12
Withlacoochee Watershed

............................................................................................................ 14 Withlacoochee Estuary

................................................................................................................. 14


### Sources of Nutrients

............................................................................................................ 17

Suwannee

................................................................................................ .................................... 17

Waccasassa

................................................................................................ ................................ . 21
Withlacoochee

............................................................................................................................. 22 

### Biological Summary

............................................................................................................. 24

SAV and Species Composition

....................................................................................................... 24 Phytoplankton Species Composition

.............................................................................................. 30 Macroalgal Species Composition and Biomass (Including Calcareous Forms)

.................................. 32 Shellfish Production and Frequency/Duration of Bed Clo sures
........................................................ 33 Fish Community Studies

................................................................................................................ 33 Quantification of Landings from Commercial/Recreational Fisheries

.............................................. 37 Harmful Algal Blooms

................................................................................................................... 39 Hypoxia

................................................................................................ ....................................... 40


### Water Quality Studies

......................................................................................................... 40 Putnam 1967 Study of Waccasassa Bay

......................................................................................... 40

1984

– 85 Mote Marine Lab Study of Selected Rivers

....................................................................... 41 Project COAST, 1997

– Present

........................................................................................................ 45 Suwannee River Water Management District Monitoring

.............................................................. 67 Random Sampling by IMAP Program through FWRI

...................................................................... 74 YSI data from FDEP Aquatic Preserves Dataloggers

....................................................................... 76 Comparison of Nutrient Levels through Time between Sampling Entities

........................................ 79 

### Waters on the 303(d) List

..................................................................................................... 85 Impairment for Bacteria

............................................................................................................... 88 

### Proposed Numeric Nutrient Criteria

..................................................................................... 89

Suwannee Estuary

........................................................................................................................ 89 Waccasassa Bay

........................................................................................................................... 89
Withlacoochee Estu ary
................................................................................................................. 90 Methodology for Criteria Development

......................................................................................... 90 Summary of the Proposed Criteria

................................................................................................ . 92


### References

.......................................................................................................................... 95Draft iii August 2010 

### List of Tables

Table 1. Land use distribution in the Suwannee, Waccasassa, and Withlacoochee Coastal Drainage Areas, based on 2004 land uses. Parks and zoos were included in the upland forest classification rather than in urban, and pastures were included in shrub, range, and pasture rather than agriculture.

............................................................................................. 6 Table 2. Physical properties of the estuaries of the Suwannee, Waccasassa, and Withlacoochee Rivers.

................................................................................................ ............................................ 7 Table 3. Energy coefficients associated with land uses, as described for the LDI (Brown and Vivas 2004). Higher values indicate greater intensity of human land use.

............................................ 8 Table 4. Permitted facilities in the Suwannee Basin (from Hallas and Magley 2008).

.............................. 18 Table 5. Permitted facilities in the Waccasassa River watershed (from FDEP WAFR database).

.............. 22 Table 6. Permitted facilities that discharge to surface waters in the Withlacoochee River watershed (from FDEP WAFR database).

.................................................................................... 24 Table 7. The top 10 numerically dominant fish taxa collected in the Fisheries Independent Monitoring program stratified random sample areas, 2008. Totals in bo ld represent total of top 10 dominant, total recreationally important species, and grand total.

................... 35 Table 8. Number of recreationally important species (Selected Taxa) collected in the Fisheries Independent Monitoring program stratified random sample areas, 2008.

................................ 36 Table 9. Physical and chemical characteristics of Waccasassa Estuary, as reported in Table 1 of Putnam (1967).

............................................................................................................................ 41 Table 10. Summary of water clarity data for estuarine sites off the Waccasassa and Withlacoochee Rivers, from the 1984

- 85 study by Mote Marine Lab. Values are means and standard deviations, from Tables 48, 49, and 50 of Dixon (1986). Negative river miles indicate distance from the mouth of the river to the estuary sampling point.

.................. 43 Table 11. Annual geometric means of chlorophyll a (uncorrected) and total nitrogen for 1984

- 1985 study of Waccasassa and Withlacoochee River sites by Mote Marine Lab. Number of samples per year in parentheses.

............................................................................................ 45 Table 12. Number of times each of 10 stations were sampled in each estuary system each year for Project COAST, directed by Dr. Tom Frazer at UF.

................................................................ . 51 Table 13. Average, minimum, and maximum salinity values (parts per thousand) for Suwannee Estuary sites sampled by Project COAST for each year and all data for each site. Sample sizes as in Table 10.

........................................................................................................ 58 Table 14. Comparison between station geometric means for the first 9 months of 2007 (n = 9 monthly samples) uncorrected and phaeophytin

- corre cted chlorophyll a (μg/L) measurements for the Waccasassa and Suwannee Estuaries.

................................................... 61 Table 15. Mean annual values for phytoplankton abundance (chlorophyll a) in the “reef” and “nearshore” regions of the Suwannee River estuary, and discharge

- weighted nutrient loading rates (g s -1 of TN and TP) from the Suwannee River. Standard errors are in parentheses (Table 2

- 1 of Quinl an 2003).

................................................................................... 63 Table 16. Light extinction coefficient (Kd) and Pearson correlation coefficients for three major components of light absorption: Tripton, CDOM, and phytoplankton chlorophyll a in the Suwannee River and its estuary. Table from Quinlan (2003).

.............................................. 66Draft iv August 2010 Ta ble 17. Range of sample sizes used in this analysis for TN, TP, and chlorophyll a data for each site and year. Annual geometric mean not calculated if n<4. Data points could be missing due to availability or exclusion of J or Q qualified data.

................................................ 69 Table 18. Mean values by area and year for IMAP sampling in the regions of the Suwannee, Waccasassa, and Withlacoochee Estuaries (data from FDEP IWR Run 40). Cedar Keys and Horseshoe Cove were part of the Suwannee Sound sampling unit. Samples for chlorophyll a were depth integrated, others were surface grabs.

.............................................. 75 Table 19a. Annual geometric means for TN (mg/L) for estuarine sites in the Suwannee, Waccasassa, and Withlacoochee estuaries. Site pairs and sampling entities as in Figure
73.

................................................................................................ ................................................ 80 Table 19b. Annual geometric means for TP (mg/L) for estuarine sites in the Suwannee, Waccasassa, and Withlacoochee estuaries. Site pairs and sampling entities as in Figure
73.

................................................................................................ ................................................ 80 Table 19c. Annual geometric means for chlorophyll a for estuarine sites in the Suwannee, Waccasassa, and Withlacoochee estuaries. Site pairs and sampling entities as in Figure 73. All chlorophyll a means shown are not phaeophytin

- corrected.

.......................................... 81 Table 20. Cycle 2 Verified List of impaired waters – Lower Suwannee Planning Unit.

............................... 86 Table 21. Cycle 2 Verified List of Impaired Waters

– Waccasassa Planning Unit.

....................................... 87 Table 22a. Proposed numeric nutrient criteria for all segments of the Suwannee Es tuary for TP, TN, and chlorophyll a. For compliance purposes, the long term geometric mean shall not exceed the long term limit nor shall the average of all stations in a segment exceed the network average more than twice in a 5 year period. The last column shows the value which single station shall not exceed, by segment, more than twice in a 5 year period.

................................................................................................ ......................................... 93 Table 22b. Proposed numeric nutrient criteria for all segments of the Withlacoochee Estuary for TP, TN, and chlorophyll a. For compliance purposes, the long term geometric mean shall not exceed the long term limit nor shall the average of all stations in a segment exceed the network average more than twice in a 5 year period. The last column shows the value which single station shall not exceed, by segment, more than twice in a 5 year period.

............................................................................................................................ 93 Table 22c. Proposed numeric nutrient criteria for all segments of the Waccasassa Estuary for TP, TN, and chlorophyll a. For compliance purposes, the long term geometric mean shall not exceed the long term limit nor shall the average of all stations in a segment exceed the network average more than twice in a 5 year period. The last column shows the value which single station shall not exceed, by segment, more than twice in a 5 year period.

................................................................................................ ......................................... 94Draft v August 2010 

### List of Figures

Figure 1. Study area of the Suwannee, Waccasassa, and Withlacoochee (South) watersheds. This region has numerous karst features, and here the springs are noted as blue points.

........... 5 Figure 2. Landscape Development Intensity coefficients of land uses within the Florida portion of the Suwannee Watershed, based on 2005

- 2008 aerial photos. LDI coefficients as in Table 3.

................................................................................................ .......................................... 9 Figure 3. Coast of Dixie and Levy Counties, estuaries of the Suwannee, Waccasassa, and Withlacoochee Rivers. Shown are conservation areas (federal, state, local, and private), seagrass coverage (continuous, discontinuous), and coverage of sa ltwater marshes along the shores.

........................................................................................................... 10 Figure 4. The average surface CDOM absorption over the West Florida Shelf for the period 1
Ju ne 98

- 17 July 98 shows the southward dispersal of the Suwannee River plume. At right, a time series (5 May 98 – 29 July 98) for locations along a transect through the river plume shows the variability in the modeled surface CDOM normalized by the highest value modeled for that location during the time period (red). Similarly, 7

- day composite SeaWiFS chlorophyll

- a values for the corresponding pixel locations are presented (black) as values normalized by the highest value observed during that time period. Values were interpolated when cloud cover obscured retrieval (from Jolliff et al. 2003).

................................................................................................ ...................................... 11 Figure 5. MODIS sattelite imagery from 4/22/2009 of the Big Bend and Springs Coast, showing abundance of colored dissolved organic matter (CDOM) from the Suwannee River surrounding Cedar Keys to the south and extending north to Horseshoe Beach.

....................... 12 Figure 6. Landscape Development Intensity coefficients of land uses within the Waccasassa watershed, based on 2005

- 2008 aerial photos. LDI coefficients as in Table 3.

.......................... 13 Figure 7. Landscape Development Intensity coefficients of land uses within the Withlacoochee watershed, based on 2005

- 2008 aeri al photos. LDI coefficients as in Table 3.

.......................... 16 Figure 8. Median concentrations of nitrate+nitrite in the Spring Network, 2001

– 06 ( from Harrington et al. 2010).

............................................................................................................... 19 Figure 9. Median orthophosphate concentrations in the Spring Network (2001

- 2006) from Harrington et al. (2010).

.............................................................................................................. 20 Figure 10. Aquifer vulnerability in spring areas, Figure 16 from Harrington et al. (2010).

........................ 21 Figure 11. Big Bend seagrass cover in 1984, 2001, and 2006. Of note for this report is the apparent decline in seagrass coverage north of Suwannee Sound potentially due to effects from the Suwannee River (from Carlson et al. 2010).

..................................................... 25 Figure 12. Distribution map for Thalassia testudinum, showing comparison of 1984 and 2000 surveys (from Hale et al. 2004).

.................................................................................................. 26 Figure 13. Distribution map for Syringodium filiforme, showing comparison of 1984 and 2000 surveys (from Hale et al. 2004).

.................................................................................................. 26 Figure 14. Distribution map for Halodule wrightii, showing comparison of 1984 and 2000 surveys (from Hale et al. 2004).

............................................................................................................... 27 Figure 15. FDEP Aquatic Preserves SAV sampling sites at Cedar Keys, Levy County, Florida.

................... 28 Figure 16. Frequency of occurrence of seagrass species at Cedar Keys, 2006

- 2009.

................................ . 29Draft vi August 2010 Figure 17. Average total grass coverage, Cedar Keys, 2006

- 2009. AVG B&B represents the average Braun

- Blanquet ranking assigned at each of 100 sampling quadrats per year. Ranks are abundance codes ranging from 1

- 5.

........................................................................... 29 Figure 18. Average epiphyte ranking, St. Martins Marsh Aquatic Preserve ,2004

- 2009. Shown are average epiphyte rankings of 100 sampled quadrats. Possible epiphyte ranks range from 1

- 4.

................................................................................................ ...................................... 30 Figure 19. Variation in productivity pattern in Waccasassa Bay (from Putnam 1967). Larger circles indicate higher primary productivity.

............................................................................... 31 Figure 20. Variation of chlorophyll a in estuarine surface water in Waccasassa Bay (Figure 7 from Putnam 1967).

............................................................................................................................. 31 Figure 21. Observed macroalgal succession on a subset of oyster reef at the mouth of the Suwannee River, 1999

- 2001 (from Quinlan 2010).

..................................................................... 32 Figure 22. Macroalgal biomass and SAV species distribution in Suwannee Sound, measured in Spring 2000 and Spring 2001 (from Quinlan 2010).

.................................................................... 33 Figure 23. Sampling sites for the 1997

- 1999 fish community study by Tukey and Dehaven (2006) (figure from Tukey and Dehaven 2006).

...................................................................................... 35 Figure 24. Map of Cedar Key sampling area of the Fisheries Independent Monitoring Program. Zones are labeled B, C, and F. Grids containing portions of Zones B and F are labeled B/F.

................................................................................................ .............................................. 36 Figure 25. Total commercial blue crab and oyster catch (pounds/trip) for Dixie and Levy Counties from 1995

- 2008. Data from the Florida Fish and Wi ldlife Conservation Commission.

.............. 37 Figure 26. Total commercial shrimp catch (pounds/trip) for Dixie and Levy Counties from 1995

- 2008. Data from the Florida Fish and Wildlife Conservation Commission.

................................ 38 Figure 27. Total commercial finfish catch (pounds/t rip) for Dixie and Levy Counties from 1995

- 2008. Data from the Florida Fish and Wildlife Conservation Commission.

................................ 38 Figure 28. Locations of sampling sites for which data were analyzed from the 1984

- 1985 Mote Marine Lab study in the Waccasassa and Withlacoochee estuaries.

.......................................... 42 Figure 29. Total nitrogen and chlorophyll a data collected 1984

- 1985 by Mote Marine Lab for SWFWMD minimum flows and levels studies. Sites as in Figure 72. Chlorophyll a values are not phaeophytin

- corrected and were analyzed with the trich romatic method.

................................................................................................ ....................................... 44 Figure 30. Mean total nitrogen (μg/L) across all sample years (approx. 1997

- 2009) and all estuary sites (exclud es freshwater sites). From Frazer and Jacoby (2010).

............................... 46 Figure 31. Mean total phosphorus (μg/L) across all sample years (approx. 1997

- 2009) and all estuary sites (excludes freshwater sites). From Frazer and Jacoby (2010).

............................... 46 Figure 32. Mean chlorophyll a (μg/L) across all sample years (approx. 1997

- 2009) and all estuary sites (excludes freshwater sites). From Frazer and Jacoby (2010).

............................................ 47 Figure 33. Long term average data for the Suwannee Estuary, including all estuary sites (excludes freshwater sites) (from Frazer and Jacoby 2010).

....................................................... 48 Figure 34. Long term average data for the Waccasassa Estuary, including all estuary sites (excludes freshwater sites). From Frazer and Jacoby (2010).

..................................................... 49 Figure 35. Long term average data for the Withlacoochee Estuary, including all estuary sites (excludes freshwater sites). From Frazer and Jacoby (2010).

..................................................... 50Draft vii August 2010 Figure 36. Project COAST sampling sites in the Suwannee, Waccasassa, and Withlacoochee estuaries.

................................................................................................ ..................................... 52 Figure 37. Mean TN at Project COAST Suwannee estuarine sites.

............................................................. 52 Figure 38. Mean TN at Project COAST Wacasassa estuarine sites.

........................................................... 53 Figure 39. Mean TN at Project COAST Withlacoochee estuarine sites.

..................................................... 53 Figure 40. Mean TP at Project COAST Suwannee estuarine sites.

............................................................. 54 Figure 41. Mean TP at Project COAST Waccasassa estuarine sites.

.......................................................... 54 Figure 42. Mean TP at Project COAST Withlacoochee estuarine sites.

...................................................... 55 Figure 43. Mean chlorophyll a at Project COAST Suwannee estuarine sites.

............................................. 55 Figure 44. Mean chlorophyll a at Project COAST Waccasassa estuarine sites.

.......................................... 56 Figure 45. Mean chlorophyll a at Project COAST Withlacoochee estuarin e sites.

..................................... 56 Figure 46. Stations 1 and 2 excluded for Suwannee, Station 1 excluded for Waccasassa, and Stations 2 and 3 excluded for Withlacoochee. R 2 = 0.84 for Suwannee, R 2 = 0.36 for Waccasassa, R 2 = 0.70 for Withlacoochee.

.................................................................................. 57 Figure 47. Stations 1 and 2 excluded for Suwannee, Station 1 excluded for Waccasassa, and Stations 2 and 3 excluded for Withlacoochee. R 2 = 0.87 for Suwannee, R 2 = 0.40 for Waccasassa, R 2 = 0.76 for Withlacoochee.

.................................................................................. 57 Figure 48. Average annual salinity for each site plotted against the annual geometric means for total nitrogen, total phosphorus, and chlorophyll a for each site sampled for Project
Coast 1997

- 2007.

........................................................................................................................ 59 Figure 49. Color vs. TN in the Suwannee estuary.

...................................................................................... 60 Figure 50. Salinity vs. TN in Waccasassa Bay.

............................................................................................ 60 Figure 51. Comparison of uncorrected and phaeophytin

- corrected chlorophyll a (μg/L) for 10 sites in the Waccasassa Estuary for the first nine months of 2007.

............................................ 61 Figure 52. Comparison of uncorrected and phaeophytin

- corrected chlorophyll a (μg/L) for 10 sites in the Suwannee Estuary for the first nine months of 2007.

............................................... 62 Figure 53. Sampling sites used by Quinlan and Phlips, 1996

- 2003.

........................................................... 63 Figure 54. Flow rates in the Suwannee River at the Wilcox gauging station. (A) Long

- term mean monthly flow rates from 1932 to 1999. (B) Mean monthly flow rates f rom 1998

- 2001. The dashed line (

--- ) indicated median flow rate for the Suwannee River. The gray line represents the flow rate exceeded 99% of the time from 1960

- 2001, and the asterisk (***) line represents the flow rate exceeded only 1% of all dates fro m 1960

- 2001. Figure from Quinlan (2003).

........................................................................................................ 64 Figure 55. Flushing rates in the reef region of the Suwannee River estuary. (A) Calculated flushing rate (d -1 ) of the reef region compared to riverine flow from April 1998 to April 2001. The points are the flushing rates, and the line is the least squares fit of the estimated flushing rates based on riverine flow. (B) Flushing rate (d -1 ) in the reef region from 1998

- 2001 (mean 3.4 ± 1.4 days, n=35). Figure from Quinlan (2003).

............................. 65 Figure 56. SRWMD long term sampling sites within the Suwannee Estuary (from McKinney 2010).

................................................................................................ .......................................... 67 Figure 57. Location of SRWMD sampling sites in the Suwannee River Estuary (SRE) and Cedar Keys (CKF).

................................................................................................ ................................... 68Draft viii August 2010 Figure 58. Annual mean salinity vs. annual geometric mean TN for 4 sites in the Suwannee
Es tuary, sampled by SRWMD or their contractors. Only site

- years with four or more data points were used. Salinity data include “0” data points from Robbie McKinney, who indicated confidence in those data points (especially for earlier years). Data are fro m sites as in Figure 38.

............................................................................................................ 70 Figure 59. Annual geometric means for TN at four Suwannee Estuary sites.

........................................... 70 Figure 60. Annual geometric means for TP at four Suwannee Estuary sites.

............................................ 71 Figure 61. Annual geometric means for chlorophyll a at four Suwannee Estuary sites.

............................ 71 Figure 62. Annual average salinity versus annual geometric mean total nitrogen for sites CKF020C1 and CKF030C1 at Cedar Keys collected by the SRWMD from 1996

- 2006 (n = 22 site

- years).

.............................................................................................................................. 72 Figure 63. Annual geometric mean Total Nitrogen for Cedar Keys SRWMD sites, 1996

- 2006. The dashed and dotted lines indicates the 75 th and 90 th percentile of all annual geometric means, respectively (from both sites, n=22 annual geometric means, calculated with lognormal distribution function).

................................................................................................ 73 Figure 64. Annual geometric mean Total Phosphorus for Cedar Keys SRWMD sites, 1996

- 2006. The dashed and dotted lines indicates the 75 th and 90 th percentile of all annual geometric means, respectively (from both sites, n=22 annual geometric means, calculated with lognormal distribution function).

....................................................................... 73 Figure 65. Annual geometric mean corrected and uncorrected chlorophyll a for Cedar Keys SRWMD sites, 1996

- 2006.

........................................................................................................... 74 Figure 66. Monthly mean, standard deviation, and ranges of salinity from an o n- site YSI probe datalogger at Seahorse Key, near Cedar Key (from Charbonneau 2010). Zeros indicate missing data due to lag in monitoring effort.

............................................................................. 76 Figure 67. Monthly mean, standard deviation, and ranges of water temperature from an on

- site YSI probe datalogger at Seahorse Key, near Cedar Key (from Charbonneau 2010). Zeros indicate missing data due to lag in monitoring effort.

................................................................ 76 Figure 68. Monthly mean, standard deviation, and ranges of dissolved oxygen from an on

- site YSI probe datalogger at Seahorse Key, near Cedar Key (from Charbonneau 2010). Zeros indicate missing data due to lag in monitoring effort.

................................................................ 77 Figure 69. Monthly mean, standard deviation, and ranges of water temperature from an on

- site YSI probe datalogger at the mouth of the Suwannee River (from Charbonneau 2010).

............ 77 Figure 70. Monthly mean, standard deviation, and ranges of salinity from an on

- site YSI probe datalogger at the mouth of the Suwannee River (from Charbonneau 2010).

............................ 78 Figure 71. Monthly mean, standard deviation, and ranges of water temperature from an on

- site YSI probe datalogger at the mouth of the Withlacoochee River (from Charbonneau 2010).

................................................................................................ .......................................... 78 Figure 72. Monthly mean, standard deviation, and ranges of salinity from an on

- site YSI probe datalogger at the mouth of the Withlacoochee River (from Charbonneau 2010).

..................... 79 Figure 73. All study sites for which FDEP analyzed data within this report. Circled areas indicate pairs of sites sufficiently close enough in space for data comparison. 1 – COAST Suwannee

- 4 = SRWMD SRE070C1; 2 – COAST Suwannee

- 5 = SRWMD SRE040C1; 3 – MML WACC

- 10 = COAST Waccasassa

- 8; 4 – MML WITH

- 10 = COAST Withlacoochee

- 7; 5 - MML WITH

- 7 = COAST With lacoochee

- 6.

.............................................................................. 82Draft ix August 2010 Figure 74. Comparison of annual geometric mean total nitrogen at 2 pairs of sites in the Suwannee Estuary in which the members of each pair are located fairly close to one another. Site pairs as in Figure 73.

............................................................................................. 82 Figure 75. Comparison of annual geometric mean total phosphorus at 2 pairs of sites in the Suwannee Estuary in which the members of each pair are located fairly close to one another. Site pairs as in Figure 73.

............................................................................................. 83 Figure 76. Comparison of annual geometric mean chlorophyll a (uncorrected) at 2 pairs of sites in the Suwannee Estuary in which the members of each pair are located fairly close to one another. Site pairs as in Figure 73.

...................................................................................... 83 Figure 77. The relationship between mean annual salinity and annual geometric mean total nitrogen for two sites located fairly close together in the Suwannee Estuary (sites shown in Figure 73).

.................................................................................................................... 84 Figure 78. WBIDs in the Suwannee, Waccasassa, and Withlacoochee Estuary regions, and sampling stations from Project COAST and the SRWMD.

........................................................... 85Draft 1 August 2010 

### Executive Summary

This report was prepared by the Florida Dep artment of Environmental Protection (F DEP ), in cooperation with local scientists, to support the development of numeric nutrient criteria for the Suwannee,
Waccasassa , and Withlacoochee E stuaries. The primary purpose of the proposed numeric nutrient criteria is to protect healthy

, well

- balanced natural populations of flora and fauna from the effects of excess nutrient enrichment.

The Suwannee, Waccasassa, and Withla coochee Estuaries are open , shallow estuaries in Florida’s Big Bend. These estuaries are fed by rivers with a high percentage of wetlands in their watersheds, so color and organic matter concentrations are high, which suppresses algal productivity in the rivers but naturally fuels it in the estuary. This portion of Florida’s coast contains many conservation lands, therefore wide expanses of swamps and coastal marshes remain intact to support the ecosystem and provide a filter between uplands and the coast al areas.

The Suwannee Estuary is a dynamic system because it is dominated by river flow

, and the biological communities in the estuary are highly influenced by these freshwater inputs

. During high river flow, swamp water (originating from the Okeefenokee Swamp) dominates, and color and organic nutrient concentrations are relatively high, but inorganic nutrient concentrations are very low . Color and non

chlorophyll particulates are the major contributors to light limitation, except at times of very low ri ver flow. During low flow periods, the river is dominated by Floridan Aquifer spring flow, and water clarity and anthropogenic nitrate concentrations are high

.

S ubmersed aquatic vegetation (SAV) beds are abundant along this part of the coast, but not quite as dense when compared with adjacent regions such as Apalachee Bay

. Reductions in SAV have been observed north of the Suwannee River mouth and have been linked to high river flows during years of abnormally high rainfall (1998, 2004

– 05) . T h e reduction in light is strongly influenced by water color, turbidity , and chlorophyll a , and it is unclear which of these factors may be linked to SAV loss and if that loss is to be expected after extreme high

- flow periods. The Suwannee River is impaired for excess nitrate concentrations, but data indicate that the nitrate is diminished to background levels at the estuary interface

. Some increased benthic algal growth was observed during very low river flow periods

, possibly related to the excess nitrate . Phytoplankton, zooplankton, and fish communities are healthy, as determined by qualitative interpretation of research studies. Concentrations of total nitrogen and total phosphorus are strongly linked to salinity in this system.

Waccasassa Bay has the highest nutrient and chlorophyll a concentrations of the region , despite the extremely minimal a nthropogenic activity in the basin

. The nutrient inputs are associated with the high percentage of wetlands in the watershed and the shallow nature of the est uary , which results in frequent resuspension of estuarine sediments

. With the high color inputs from the extensive swamp systems, Waccasassa Bay naturally has lower water clarity than coastal areas to the north and to the south ; therefore the SAV communities are not as well developed or as well studied . However, evidence gathered shows that conditions have not changed in this estuary since the 1960s, when there was nearly no development and no point source discharges into the basin, so it follows that the existing condition protects the aquatic life use in the estuary

.

The Withlacoochee E stuary has been hydrologically modified by the Inglis Dam

, the Cross Florida Barge Canal , and the Crystal River Power Plant. The Withlacooch e e River, which origi nates in the Green Swamp, experiences low levels of disturbance and has been used by FDEP and EPA as a minimally disturbed reference system for freshwater nutrient criteria development. It is possible that the InglisDraft 2 August 2010 dam actually prevents some of the natu ral nutrient loading from reaching the estuary by holding back much of the natural flow

. The discharge from the Crystal River Power Plant does not contribute an additional nutrient load to the estuary , but has dikes that alter the exchange of water in the estuary

. No nutrient data are available from before dam construction, which occurred in 1969. TN and chlorophyll a concentrations have not changed in this estuary since the 1980s

, and t here is no evidence of other impairment in the estuary. There is a strong relationship between nutrient concentrations and salinity due to the dominance of the Withlacoochee River in the estuary

.
The evidence gathered by FDEP and presented in this document shows that aquatic life use in the
Waccasassa and Withlacoochee estuaries is fully supported

, and will be fully supported in the Suwannee estuary pursuant to the Suwannee River TMDL implementation. FDEP therefore proposes that the numeric nutrient criteria be crafted to maintain the existing nutrien t regime
, except for reduction in total nitrate loading into the Suwannee Estuary, commensurate with the established TMDL for nitrate in the Suwannee River

.

Contributors to this r eport include:

Thomas K. Frazer, University of Florida, Paul Carlson, FWCC

, Melissa Charbonneau, Big Bend Seagrasses and St. Martin Marsh Aquatic Preserves

, Erin Quinlan, (UF) Georgia Gwinnett College

, Jason Hale, Pandion Technology, Ltd.

, Robbie McKinney, SRWMD , and Nia Wellendorf, FDEP

.Draft 3 August 2010 Table 1 a

. Checklist of n utrient e nrichment s ymptoms in the Suwannee, Waccasassa, and Withlacoochee Estuaries

Response V ariable Observed
H istorically

or C urrently ? Explanation Source

Low DO (hypoxia/anoxia) No No impairments for dissolved oxygen in this region. One researcher noted low oxygen in the early morning hours when there was abundant macroalgal growth on oyster beds in the Suwannee Estuary during a period of low

water. Quinlan
2010

Reduced clarity No There is reduced water clarity in this region when high rainfall causes colored water discharge from the rivers (especially the Suwannee) to be high. This colored water can extend from Horseshoe Cove and down the Springs Coast, and is a natural phenomeno n. Carlson et al. 2010 ; Jolliff et al.
2004

Increased chlorophyll a concentrations Yes The Suwannee Estuary is on the 303(d) list for increase in chlorophyll a compared to historic concentrations. This effect was localized to the mouth of the river, and is addressed through the Suwannee River TMDL. Chlorophyll a values vary through time, but the FDEP analysis in this report did not indicate an upward trend. Hallas and Magley
2008

Phytoplankton blooms (nuisance or toxic) No - -

Problematic epiphyte growth No - -

Problematic macroalgal growth No One researcher documented increased seasonal macroalgal growth on the oyster beds in Suwannee Sound during low river flow period, but it was temporary and there is no indication that it was problematic. Quinlan
2010

SAV community changes or loss Yes Some SAV loss north of the Suwannee River, and some SAV comm unity change in the deep edge of SAV beds south of this region, both after record rainfall years

. Reduced water clarity is the likely cause in both cases, and evidence suggests that color (of natural origin) is the agent. Carlson et al. 2010 ; Hale et al.
2004 ; Quinlan
2003 Emergent or shoreline vegetation community changes or loss No - -

Coral/hardbottom community changes or loss N/A No confirmed record of hardbottom communities in this region. -

Impacts to benthic community Yes Very little information on benthic community, but one researcher documented a “plume” of benthic algae that followed the Suwannee River plume, during very low

- flow conditions. Quinlan
2010

Fish kills No -Draft 4 August 2010 Table 1b. Checklist of additional factors fo r the Suwannee, Waccasassa, and Withlacoochee Estuaries

- = Empty cell/no data Nutrient Factors Observed? Explanation Source Increased nutrient loading or concentrations Yes Increased nitrate loading has been documented for the Suwannee River, and a
TMDL has been established for nitrate in the river to address the negative biological
responses. Phosphorus loading has significantly decreased. Some increased concentrations during the wet season were detected over time by Jacoby et al. (2008) for some Withl acoochee sites

. Hallas and Magley 2008 ; Jacoby et al.
2008

Difference between nearshore and offshore levels Yes These river

- dominated estuaries show strong negative relationships between salinity and TN and salinity and TP. Figures 46 and 47

Mitigating factors that could prevent nutrient expression Yes High color suppresses phytoplankton growth in the Suwannee and Waccasassa systems Quinlan 2003 ; Putnam 1967 Other significant stressors to biological communities No

- -

Natural high nutrient episodes (e.g., seasonal or event driven) Yes Nutrient concentrations increase with increases in rainfall and river flow. -



### Geographic and Physical Description

The Suwannee, Waccasassa, and Withlacoochee (south) rivers are all large

, tannin

- stained rivers that d rain watersheds containing a high percentage of wetlands. They are considered together in this document because of the similar water chemistry of their estuaries. Figure 1 shows the extent of their watersheds ( the Florida portion of the Suwannee). Table 1 contains land use information for the watersheds, and Table 2 contains physical descriptions of the estuaries.Draft 5 August 2010 Figure 1. Study area of the Suwannee, Waccasassa, and Withlacoochee (South) watersheds. This region has numerous karst features, and here the springs are noted as blue points.

Suwannee Watershed

The Suwannee River a rises in the Okefenokee Swamp, emerging at Fargo, Georgia. It flows southwest into Florida, dropping in elevation through limestone and marine clay layers (Hawthorne Formation)

, resulting in Class II whitewater rapids, which are rare in Florida

. The river then turns west near White Springs, Florida, receiving the waters of the Alapaha and Withlacoochee (north) Rivers, which together drain portions of south

- central Geo rgia. The watershed contains a rich assortment of rivers and streams, springs, cypress ponds, swamps, and estuaries. The Florida portion of the watershed is divided into units of the Upper and Lower Suwannee , and tributaries (Figure 1) ( www.protectingourwater.org and Charbonneau 2010)

. The Gulf of Mexico lies along the southwestern edge of the watershed.Draft 6 August 2010 Because of the region's flat topography, the entire low

- energy shoreline is one large estuarine complex composed of river and tidal systems. Extensive seagrass beds stretch from these estuaries for miles into the open Gulf.

Although lakes are scattered th roughout the watershed, the region contains fewer lakes than other areas of the state , but wetlands are plentiful

. There are 98 known springs that discha r ge within the Suwannee River coastal drainage area; 4 are 1 st magnitude and 39 are 2 nd magnitude. The River flow is highly influenced by springs during periods of low rainfall. During normal to high flows, t he Suwannee is typically a highly colored river. River flow and discharge is heavily influenced by wetlands during high rainfall periods, resulting in an extensive plume of colored water into the Gulf during much of the year (Figure 5 ).

Growth and development along the watershed's rivers has been limited, largely because of floodplain management ordinances, land use plans, and land acquisition programs at state, regional, and local levels. To the west of the Suwannee River, the dominant land uses are si lviculture and agriculture (Table 1)

. Large t imber companies , following applicable forestry Best Management Practices, hold most of the coastal lowlands in large tracts of planted pine. Vast tracts of timber are also found in the wet flatwoods to the east of the Alapaha River and uppermost Suwannee River. East of the Suwannee River, silviculture and agriculture continue to dominate, but the amount of ur banized land is markedly greater than west of the river. The watershed has farms that combine row crops with livestock, large corporate dairies, and irrigated row crop and forage operations. Other land uses include poultry production, phosphate mining, a nd aquaculture. Phosphate mining in southeastern Hamilton County has altered a large part of the original landscape.

Table 1. Land use distribution in the Suwannee, Waccasassa, and Withlacoochee Coastal Drainage
Areas , based on 2004 land uses

. Parks and zoos were included in the upland forest classification rather than in urban , and pastures were included in shrub , range , and pasture rather than agriculture

.

Sources: Information for the Suwannee and Waccasassa from land use coverages in F DEP GIS system ; information for Withlacoochee from
SWFWMD. Land Use Suwannee (lower basin only, HUC 25) Waccasassa (HUC 32) Withlacoochee (HUC 34)

Urban 7% 6% 20% Agriculture 12% 6% 5% Shrub, range , and pasture 16% 10% 25% Upland forests 48% 45% 23%
Water 1% 2% 2% Wetlands 15% 30 % 23% Other 1% 1% 2%Draft 7 August 2010 Table 2. Physical properties of the estuaries of the Suwannee, Waccasassa, and Withlacoochee Rivers.

CDA = Coastal drainage area, defined by NOAA. Property Suwannee Waccasassa Withlacoochee Source Estuarine surface area (km 2 ) Suwannee Sound – 70 km 2 Horseshoe
Cove – 140 km 2 40 km 2 (EPA), 49,749 acres or 201 km 2 (DACS) 52,000 acres (DACS report) Carlson et al. 2010

Watershed area (km 2 ) 26,000 km 2 Coastal drainage area (Lower Suwannee HUC) - 4568 km 2 and includes Levy, Dixie, Taylor, Gilchrist, Columbia, Suwannee, Madison Counties CDA =2
, 128 km 2
and includes Gilchrist, Alachua, Levy, and Marion Counties CDA = watershed = 5133 km 2 and includes Citrus, Sumter, Marion, Hernando, Polk, and Lake Counties. NOAA 2007 Charbonneau

HUC Area (km 2 ) Lower Suwannee HUC = 4,088 2,334 5,332 FDEP ArcGIS HUC coverage

Mean dep th (m) 2.24 m 1.69 m 2.24 m Project COAST

sam p ling, UF Tidal range (m) 1.8 m – tides are mixed semidiurnal and typically two unequal high and low tides each day. Average 3.5 ft. Tides are mixed and semi

- diurnal, typically with two unequal high and two unequal low tides occurring each day. average 3.5 ft./
1.0668 m - semidiurnal, two tide cycles Charbonneau presentation

Tidal freshwater inflow (cfs) Average Daily Freshwater Inflow USGS station – 02323592 = 7599 cfs Average Daily Freshwater Inflow USGS station 02313700 = 250.52 cfs By Pass Channel Average - 423 cfs Withlacooch ee Inglis Dam Average – 1020.86 cfs USGS

Mean water residence time (days) 0.5 (50% of volume is exchanged twice daily) 0.5 (50% of volume is exchanged twice daily) 0.5 (50% of volume is exchanged twice daily) DACS

The landscape development intensity index (LDI) is an index that was developed to estimate the intensity of human land use based on nonrenewable energy flow (Brown and Vivas 2004). For the LDI, each land use was assigned a coefficient of energy use associa ted with that land use (Table 3). The agricultural land uses in the Suwannee Basin appear as widespread yellow areas, with urban centers in orange and red (Figure 2).Draft 8 August 2010 Table 3

. Energy coefficients associated with land uses, as described for the LDI (Brown and Vivas 2004). Higher values indicate greater intensity of human land use.

Land use LDI value

Natural Open water 1.00

Pine Plantation 1.58

Woodland Pasture 2.02

Pasture 2.77

Recreational / Open Space (Low

- intensity) 2.77

Low Intensity Pasture (with livestock) 3.41

Citrus 3.68

High Intensity Pasture (with livestock) 3.74

Row crops 4.54

Single Family Residential (Low

- density) 6.79

Recreational / Open Space (High

- intensity) 6.92

High Intensity Agriculture 7.00

Single Family Residential (Med

- density) 7.47

Single Family Residential (High

- density) 7.55

Low Intensity Highway 7.81

Low Intensity Commercial 8.00

Institutional 8.07

High Intensity Highway 8.28

Industrial 8.32

Low Intensity Multi

- family residential 8.66

High intensity commercial 9.18

High Intensity Multi

- family residential 9.19

Low Intensity Central Business District 9.42

High Intensity Central Business District 10.00Draft 9 August 2010 Figure 2. Landscape Development Intensity coefficients of land uses within the Florida portion of the Suwannee Watershed, based on 2005

- 2008 aerial photos. LDI coefficients as in Table 3.

Suwannee Estuary During the spring/summer season, prevailing southeasterl y winds bring warm humid air onshore from the Gulf, resulting in frequent summer convection storms. These thunderstorms are typically of high intensity, short duration, and limited aerial extent. In winter, prevailing northwesterly winds frequently
prope l frontal systems through the area. Suwannee Sound, an area of low energy Gulf Coast, is about six miles wide and 15 miles long, covering approximately 80 square miles. The broad shallow submerged shelf off the coast (up to 160 km wide), coupled with pre vailing storm winds from the north and east, results in low wave and wind energy effects on the shoreline. The average depth of the Sound is about 6 feet, and the maximum depths are associated with the river channels (to about 24 feet). There are no barrier islands or peninsulas stretching from the mainland to form an embayment. Shoals and oyster bars, many of which are exposed at low tide, act as permeable barriers and create a bay

- like system. The estuary is formed by freshwater from the Suwannee Rive r and numerous creeks mixing with Gulf water over a shallow limerock shelf (description from Kuhman 2007)

.
While the Suwannee River contributes the majority of freshwater inflow to Suwannee Sound, several other watersheds drain into coastal creeks along the shore. These include the California Swamp, Barnett Creek and the Black Point Swamp watersheds. Hydrography, with respect to tidal range, is complex. Daily tidal amplitude in the estuary may vary during a 30

- day period from one to four feet,Draft 10 August 2010 with a maxi mum range of over four feet and a mean range of 3.0 feet. The mean tidal prism results in an exchange of 50% of the areas volume twice daily (Kuhman 2007)

.
The Cedar Keys are located south of the Suwannee River in Levy County. They provide important fis hing grounds and shellfish production grounds for this region, and the town of Cedar Key has become a popular tourist destination. Coastal waters surrounding Cedar Keys are heavily influenced by the freshwater content and volume of flow from the Suwannee River.

A major feature of the watershed is its many protected natural areas, which include three national wildlife refuges, ten state parks or preserves, other public lands, and the Big Bend Seagrasses Aquatic Preserve. The preserve, the largest in Florida, includes about 450,000 acres of seagrass beds and salt marsh that extend southward and eastward from the St. Marks River to the south Withlacoochee River. The Big Bend Seagrasses Aquatic Preserve is the second largest contiguous area of seagrass habitat in the eastern Gulf of Mexico, making it an important resource not only to Florida but also nationally and internationally. The Big Bend area is also designated as an Outstanding Florida Water (OFW) and a U.S. Environmental Protection Agency Gulf Ecologi cal Management Site (GEMS). Other preserved areas in this region include the 53,000 acre Lower Suwannee National Wildlife Refuge, the 10,000 acre Jena Unit Big Bend Wildlife Management Area, and the Cedar Keys National Wildlife Refuge (Figure 3).

Aquacult ure is increasing along the coast, particularly in Levy County (the Cedar Key area), following a reduction in other fisheries resulting from the constitutional ban of gill nets. Submerged leases offshore from Cedar Key are used to raise littleneck clams for local, national, and international markets.

Figure 3. Coast of Dixie and Levy Counties, estuaries of the Suwannee, Waccasassa, and Withlacoochee Rivers. Shown are conservation areas (federal, state, local, and private), seagr ass coverage (continuou s, disco ntinuous), and coverage of saltwater marshes along the shores.Draft 11 August 2010 The plume of fresh water from the Suwannee River can be far

- reaching, especially during major storm
events. During the heavy rainfall El Niño event from October 1997 to June 1998, the freshwater discharge from the Suwannee River was nearly three times the long term average (Carlson et al. 2010). Modeling of the Suwannee River plume or colored dissolved organic matter (CDOM) for portions of 1998 showed tha t the CDOM of the river stretched from the Big Bend to the Charlotte Harbor area ( Figure 4 ; Jolliff et al. 2003). Jolliff et al. (2003) estimated the maximum amount of nitrogen potential ly made available to phytoplankton by the photochemical degradation of CDOM, and concluded that the nitrogen made available would, at most, support 5% of the nitrogen demand on primary production. This plume of CDOM from the Suwannee River plume does not normally reach this far south. The occurrence in 1998 was the result of several hydrologic conditions in the Gulf (Jolliff et al. 2003). However, the Suwannee River commonly influences areas to its north and south (Figure 5 ).

Figure 4. The average surface CDOM absorption over the West Florida Shelf for the period 1 June 98

- 17 July 98 shows the southward dispersal of the Suwannee River plume. At right, a time series (5 May
98 – 29 July 98) for locations along a transect through the river plume shows the variability in the modeled surface CDOM normalized by the highest value modeled for that location during the time period (red). Similarly, 7

- day composite SeaWiFS chlorophyll

- a values for the corresponding pixel locations are presented (black) as values normalized by the highest value observed during that time period. Values were interpolate d when cloud cover obscured retrieval (from Jolliff et al. 2003).Draft 12 August 2010 Figure 5. MODIS sa te l lite imagery from 4/22/2009 of the Big Bend and Springs Coast , showing abundance of colored dissolved organic matter (CDOM) from the Suwannee River surrounding Cedar Keys to the south and extending north to Horseshoe Beach.

W

accasassa Bay
The Waccasassa Bay Estuary is a small

, shallow estuary at the mouth of the Waccasassa River. The Waccasassa River drains forest and wetlands of Waccasassa Flats and is characterized as a blackwater river that begins as a small stream in Devils Hammock. The river’s headwaters arise at Blue Spring (Levy County ) and then run through Gulf Hammock for 29 miles to Waccasassa Bay (Charbonneau 2010)

. The
Waccasass a River is the largest tributary to the Waccasassa Bay. Otter Creek, Cow Creek, Ten Mile Creek, and the Wekiva River are three of the larger tributaries to the Waccasassa River. There are a total of seven known springs within the coastal drainage area ( C DA ) . There is no major commercial or residential development along the river (Charbonneau 2010)

. Several small towns are located along the tributaries in the northern extreme of the basin and include: Gulf Hammock, Otter Creek, and Lebanon Station. Wetl ands and silviculture are the dominant land use, followed by agriculture (Table 1). The land uses that surround the river and line the coastal areas are very benign in terms of energy intensity (Figure 6). The estuary is very shallow and broad, and is separated from land by vast salt marshes.Draft 13 August 2010 W ind

- driven resuspension of o rganic materials in the estuary contribute s to its productivity (Putnam 1967).

Figure 6. Landscape Development Intensity coefficients of land uses within the Waccasassa watershed, based on 2005

- 2008 aerial photos. LDI coefficients as in Table 3

.Draft 14 August 2010 Withlacoochee Watershed

The 157

- mile

- long Withlacoochee River originates in the 2,250 km 2 Green Swamp in northern Polk County , draining 80% of this protected swamp (Wolfe 1990)

. From there, it meanders northwest and then west, discharging into the Withlacoochee Bay Estuary in the Gulf of Mexico near Yankeetown. The river's waters are tea colored from tannins and other humic acid substances produced by decaying organic material (predomi nantly leaf litter in Florida swamps)

.

The 5.7

- mile

- long Rainbow River in western Marion County is a spring

- fed tributary to the Withlacoochee River. The Rainbow River's waters are exceptionally clear, originatin g from the Floridan Aquifer

- fed Rainbow Spri ngs. This system of 18 springs is the largest in the watershed, containing Florida's fourth largest spring, and the tenth largest freshwater spring in the world. It contributes up to 462 million gallons of fresh water daily to the Withlacoochee River. T he river feeds Lake Rousseau, a 3,657

- acre reservoir that was created in 1909 when the Florida Power Corporation completed the construction of the Inglis Dam (now the Inglis Lock) across the Withlacoochee River

,

The channel of the lower Withlacoochee River from Inglis to the river mouth was dramatically altered by the construction of the now

- deactivated Cross

- Florida Barge Canal in the 1960s. The canal bisected the lower river two miles below the dam. Numerous control structures regulate flows in both the river and its surrounding tributaries and wetlands, affecting flows to the Withlacoochee Bay Estuary. The estuary is part of a large complex of estuaries and bays that extend from Tarpon Springs in the south to the Big Bend / Apalachee Bay region in the nor th. These areas contain diverse fish and wildlife habitat and are extremely important for commercial and recreational fisheries and other wildlife.

The watershed's natural communities form an extensive and diverse ecosystem, ranging from river floodplain forests, cypress domes, pine flatwoods, a nd sandhills in the Green Swamp, to extensive lake systems and marshes in the middle of the watershed

, to salt marshes and the estuary at the river mouth. This ecosystem supports nearly 500 vertebrate species, incl uding freshwater and saltwater fish, amphibians, reptiles, birds, and mammals. In addition to a wide range of common vertebrate species, a number of state and federally protected species inhabit the Withlacoochee w atershed

.
Public land ownership is signif icant in the watershed. The Withlacoochee State Forest is currently the second largest state forest in Florida. It covers more than 140,000 acres in eastern Citrus and Hernando Counties. The Withlacoochee River and Little Withlacoochee River flow through it.

The land use within the Withlacoochee watershed is nearly evenly divided between natural land uses (forests, wetlands) and human impact land uses (urban and agriculture) (Table 1; Figure 7). The natural land use within the watershed , especially the wide buffer around the river, and the reservoir at Lake
Rousseau mitigate effects of the human land uses on the water quality in the Estuary. The majority of the agricultural land use is low intensity rangeland, which contributes relatively little in terms of nutrient load to the river. Urban centers are concentrated on the fringes of the watershed , while the headwaters are largely natural and protected (the Green Swamp).

Withlacoochee Estuary
The Withlacoochee Bay system is a large, shallow, wind

- driven estuary at the mouth of the Withlacoochee River, opening to the Gulf of Mexico to the southwest

. The bay system covers approximately 52,000 acres between South Mangrove Point and the Cross

- Florida Barge Canal. The b ay averages less than 3 feet at mean low tide, and the maximum depth is 20 feet at mean low tide within the Cross

- Florida Barge Canal (DeHaven 2004a)

.Draft 15 August 2010 The hydrology of Withlacooche e Bay has been altered by the dam at the Lake Rousseau reservoir and the canal that was built as part of the halted Cross Florida Barge Canal. These alterations limit the maximum flow rate of the lower river channel to a level that was the average flow ra te before the alterations (Wolfe 1990). The flow from north to south in the coastal area is also somewhat restricted by the canals and berms created for inflow and outflow of cooling water for the Crystal River Nuclear Power Plant (Charles Kovach, persona l communication).Draft 16 August 2010 Figure 7. Landscape Development Intensity coefficients of land uses within the Withlacoochee watershed, based on 2005

- 2008 aerial photos. LDI coefficients as in Table 3

.Draft 17 August 2010 

### Sources of Nutrients

Suwannee

FDEP ’s TMDL r eport by on the Middle and Lower Suwannee River ( Hallas and Magley 2008) describes various nutrient sources on the river , as follows:

**•** Beef, poultry, and dairy production and processing;

**•** Pastures and row crops ;

**•** Estimated 9,000 – 10,000 septic tanks in the Middle and Lower Suwannee basins ;

**•** Atmospheric deposition; and

**•** Permitted facilities

.

Estimated nonpoint source inputs of total nitrogen for 2007 were 66,005,375 lbs for the Middle Suwannee and 24,381,502 lbs for the Lower Suwannee, with the largest contributions from fertilizer, followed by dairy, beef, and poultry, and atmospheric sources. Excess ni trate, leached primarily from agricultural activities ( row and forage crops and dairy and poultry production ) contaminates ground water in the watershed

. In 2000, the Suwannee River Water Management District (SRWMD) staff calculated that 78 % of the nitrate load carried by the Suwannee River to the Gulf of Mexico was introduced into the river from the middle Suwannee watershed and the bottom section of th e Santa Fe watershed. Virtually all the nitrate load comes from ground water discharge via springs.

Other sources of nutrients to the basin include permitted facilities that discharge treated effluent to surface waters (Table 4).Draft 18 August 2010 Table 4. Permitted fa cilities in the Suwannee Basin (from Hallas and Magley 2008)

.

- = Empty cell/no data
IW - Industrial Wastewater ; DW – Domestic ; CFO - Concentrated Animal Feeding Operation ; CBP - Concrete Batch ; PET - Petroleum Cleanup GP (long term) ; WWTP ISW - Individual Stormwater

FACILITY ID FACILITY NAME Facility Type DESIGN Capacity (MGD) COUNTY

FL0000051 EI Dupont De Nemours Trailridge Mine IW 30.0 Bradford

FL0000183 Progress Energy FL - Suwannee River Power Plant IW 342.0 Suwannee

FL0001465 Pilgrim's Pride Processing Plant IW 1.5 Suwannee

FL0028126 Starke, City of WWTF DW 1.65 Bradford

FL0038300 Mead Westvaco Corp IW 0.0482 Columbia

FL0043567 Cochran Forest Products IW 0.05 Columbia

FL0189120 High Springs Commercial Park WWTF DW 0.03 Alachua

FLA011323 IFAS - Dairy Research Unit CFO 0.151 Alachua

FLA116173 Dairy Production Systems - Branford Farm CFO 0.175 Gilchrist

FLA116190 Piedmont Dairy CFO 0.045 Gilchrist

FLA116521 Alliance Dairies CFO 0.37 Levy

FLA161977 Oak Grove Dairy, Inc CFO 0.11 Dixie

FLA184047 Lafayette Dairy CFO - Lafayette

FLA184993 Hill Top Dairy CFO - Gilchrist

FLA282821 North Florida Holsteins CFO - Gilchrist

FLA285331 Bell Farm (FKA Aurora 1) CFO - Gilchrist

FLA362778 Shenandoah Dairy CFO - Suwannee

FLA371912 Full Circle Dairy, LLC CFO - Madison

FLA470031 Suwannee Farms Inc CFO - Suwannee

FLG110015 A Materials Group Inc - Plant #11 CBP - Columbia

FLG110073 Florida Rock Industries Inc - High Springs CBP CBP - Alachua

FLG110190 Florida Rock Industries - Starke CBP CBP - Bradford

FLG110278 Bell Concrete Products CBP - Gilchrist

FLG110304 Columbia Ready Mix Concrete Inc CBP - Columbia

FLG110369 A Materials Group Inc - Plant #12 CBP - Levy

FLG110370 Bell Concrete CBP - Levy

FLG110374 Columbia Ready Mix Concrete Inc CBP - Suwannee

FLG110450 Mayo Ready Mix Concrete CBP - Lafayette

FLG110558 Mayo Ready Mix Concrete CBP - Lafayette

FLG911679 Badcock Live Oak Warehouse PET - Suwannee

FLS000062 Lake City, City of - WWTF WWTP ISW - Columbia

FLS000062 Lake City, City of

- WWTF WWTP ISW - Columbia

According to the Springs Initiative 2010 Monitoring Report, springs in the Suwannee Basin have some of the highest nitrate concentrations in the state (Harrington et al. 2010). Groundwater nitrate concentrations are ver y high due to a significant percentage of agricultural land use over very vulnerable groundwater resource due to the karst geology

. Springs in the Suwannee Basin also have elevatedDraft 19 August 2010 orthophosphate concentrations, when compared with springs statewide, although this observation could be related to the phosphorus leaching from the surrounding Hawthorne Formation (a high phosphate marine clay complex). Harrington et al. (2010) also reported that the Suwannee B asin springs have elevated potassium concentrations that are potentially due to human sources, likely agriculture. They reported that most of the nitrate in Troy springs was from inorganic fertilizers and poultry manure. For Fanning and Manatee Springs, the likely sources of nitrate are fertilizer use and dairy operations. The springsheds of Troy, Fanning, and Manatee Springs contain numerous groundwater wells with nitrate concentrations greater than 10 mg/L, and some with greater than 50 mg/L (Harringto n et al. 2010). Inorganic fertilizer is also thought to be the primary contributor of nitrate in Rainbow Springs in the Withlacoochee basin (Harrington et al. 2010).

Reports of the Shellfish Harvesting Areas of the Suwannee Sound (Kuhman 2007) and Horseshoe Cove (Kuhman 2004) identify wildlife as a major source of fecal coliforms along the coastline, due to the abundance of conservation areas and wildlife preserves. W ildlife also likely contribut es some nutrients to the coastal area.

Figure 8. Median concentrations of nitrate+nitrite in the Spring Network , 2001

– 06 ( from Harrington et al. 2010)

.Draft 20 August 2010 Figure 9. Median orthophosphate concentrations in the Spring Netw ork (2001

- 2006) from Harrington et al. (2010)

.Draft 21 August 2010 Figure 10

. Aquifer vulnerability in s pring area s , Figure 16 from Harrington et al. (2010).

Waccasassa

There are several domestic w astewater facilities that discharge in the watershed , with three facilities that discharge to percolation p onds, two facilities that discharge to surface water o utfalls

, and three facilities that discharge to land a pplication (Charbonneau 2010 ; Table 5 ). Percolation ponds and land application sites likely contribute nu trients to the groundwater, which may seep to the estuary in this karst landscape (Harrington et al. 2010). There are also dairy farms and mines that discharge to surface waters (Table 5 ).Draft 22 August 2010 Table 5. Permitted facilities in the Waccasassa River watershed (from FDEP WAFR database)

.

FACILITY ID FACILITY NAME FACILITY
TYPE DESIGN CAPACITY

(MGD) COUNTY
NAME

FLA017396 Watson Farms Dairy AFO 0 Gilchrist

FLA011647 Levy County Jail WWTF DW 0.024 Levy

FLA317659 Bronson, Town of WWTF DW 0.083 Levy

FLA011656 Levy Forestry Work Camp WWTF DW 0.035 Levy

FLA011292 Newberry, City of WWTF DW 0.415 Alachua

FLG110540 A Materials Group Inc - Plant #13 CBP 0 Alachua

FLA178322 Florida Rock - Newberry Mine IW 0 Alachua

FL0633275 PEF Levy County Nuclear Plant Units 1 & 2 IW 0 Levy

FLA663492 Tarmac America - King Road Mine IW 0 Levy

FLA016620 Forestry Youth Training Center WWTF DW 0.01 Levy

FLA285757 Southeast Dairy Company AFO 0 Levy

FL0031216 Cedar Key WRF DW 0.18 Levy

Individual residences and businesses not served by WWTF’s dispose of domestic waste in septic systems. The soils within close proximity to Waccasassa River and tributaries are limited in terms of their condition for disposal of domestic waste water. Stormw ater runoff from urban, agricultural, and silviculture operations is a source of nutrients within the Waccasassa coastal drainage area

. Many rural areas have a lack of stormwater infiltration/catch basins. Wildlife in coastal conservation areas are likel y contributing some nutrients to the coastal area.

Withlacoochee
The dominant land uses and land coverage in the Withlacoochee Watershed are wetlands, upland forest, rangeland, agriculture, mining, and urban (Table 1). Agricultural activities in the waters hed include cattle ranching, row crops, sod, pasture, pine plantation, and cypress harvesting. The primary industri al land use is limerock mining. Other types of mining include the extraction of sand and horticultural peat. Although residential and commercial development in the region is increasing, the watershed as a whole remains largely undeveloped (FDEP 2006)

.
The Withlacoochee River's headwaters in the Green Swamp are mostly surrounded by rural areas and wetlands. Farther downstream, land use is more urbanized near Dade City in Pasco County, but low intensity agriculture (e.g., pasture) and wetlands still predominate. From the area around Lake Tsala Apopka downstream to Dunnellon, more land is developed, but low intensity agriculture and wetlan ds remain a dominant part of the landscape. Currently, there are no large urban centers on the Withlacoochee River.

Human activities over the last 150 years have significantly altered the character of the Rainbow River, especially in its lower reaches. H istorically, the major land uses along the river and surrounding areas were agriculture and mining. The construction of Lake Rousseau in 1909 raised water levels in the lower reaches of the Rainbow River, altering the river's flow and floodplain habitat. Land use immediately surrounding the Rainbow River has slowly shifted from mining and agriculture to mostly residential. Although most of the 73

- square

- mile watershed is still largely rural, portions are rapidly losing their ruralDraft 23 August 2010 character. Within a ten

- mile radius of Dunnellon, the population increased 37.5 percent between 1994 and 2004, however, population in Florida has leveled out during the past 2 years

.
Nitrate concentrations in the ground water discharging from Rainbow Springs have steadily increa sed over the last 30 years. The spring recharge area covers 650 square miles in Marion, Levy, and Alachua Counties. In western Marion County, residential and commercial growth has occurred at a rapid rate, and with it, potential sources and increased lo ads of nitrates and other contaminants.

Of the wastewater treatment plants in the watershed, disposal methods are: 90 Percolation Ponds, 11 Outfalls, and 63 Land Application Sites (Charbonneau 2010 ). There is very little discharge to surface waters, according to the FDEP WAFR database (Table 6). Percolation ponds and land application sites likely contribute nutrients to the groundwater, which may seep to the estuary in karst areas of the watershed (Harrington et al. 2010). Individual residences and busi nesses not served by WWTF’s in the towns of Yankee Town and Inglis (near the mouth of the river) dispose of domestic waste in septic systems. Stormwater runoff from urban, agricultural, and silviculture operations is a source of nutrients within the Withl acoochee Watershed. Yankee Town and Inglis lack stormwater infiltration/catch basins.

The 30,784 acre Waccasassa Bay State Preserve and the 24,625 acre Gulf Hammock Wildlife Management Area, which border the estuary (Figure 3) , contribute fecal coliforms from wildlife sources (DeHaven 2004a), and wildlife may also contribute nutrients.Draft 24 August 2010 Table 6. Permitted facilities that discharge to surface waters in the Withlacoochee River watershed (from FDEP WAFR database)

. Facility ID Facility Name Facility Type Design Capacity County

FLA128538 Cal

- Maine Foods, Inc. - Dade City, 88 CFO 0.00 Pasco
FLA135381 CAL MAINE FOODS INC

- BUSHNELL FACILITY CFO 0.00 Sumter
FL0025569 Dixie Lime & Stone Company IW 0.00 Sumter
FLG110559 Dublin Investments LLC CBP 0.00 Sumter
FLG110686 Prestige AB Management Co LLC

- Coleman CBP CBP 0.00 Sumter
FLG110790 Paleen Ready Mix LLC CBP CBP 0.00 Citrus
FLG110379 CEMEX LLC - Oxford Ready

- Mix Plant CBP 0.00 Sumter
FLG110317 Florida Rock Industries Inc - Holder Plant CBP 0.00 Citrus
FLG110676 Prestige AB Management Co LLC

- Hernando CBP CBP 0.00 Citrus
FLG110507 CEMEX LLC - Cobb Rd CBP CBP 0.00 Hernando
FLG110121 CEMEX LLC

- Wildwood Ready

- Mix Plant CBP 0.00 Sumter
FLG110237 Florida Rock Industries - Leesburg CBP CBP 0.00 Lake
FLG110222 CEMEX LLC - Brooksville Plant CBP 0.00 Hernando
FLG110711 CEMEX LLC - Bushnell RM Plant CBP 0.00 Sumter
FLG110321 Bower Enterprises Inc CBP 0.00 Polk
FL0322890 Mazak Limerock Mine IW 0.00 Sumter
FLG110397 Prestige AB Ready Mix, LLC CBP 0.00 Marion
FL0135372 CEMEX Construction Materials Florida LLC - St Catherine Mine IW 0.00 Sumter

FL0707686 Dumont Chemical IW 0.00 Sumter
FL0031895 CEMEX Construction Materials Florida LLC - Center Hill Mine IW 0.00 Sumter

FLG110761 Florida Rock Industries Inc

- Brooksville CBP CBP 0.00 Hernando
FLG110316 CEMEX LLC - Dunnellon Plant CBP 0.00 Marion
FLG110232 Evans Septic Tank & Ready Mix - Belleview CBP CBP 0.00 Marion
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### Biological Summary

SAV and S pecies C omposition
SAV beds along this portion of the coastline are substantial and relatively stable, due to the low energy coastline and the extensive marsh systems along the coastline that act as natural filters for sediment carried from upstream sources (Wolfe 1990). Seagrass species found along this part of the coast are Thalassia testudinum, Syringodium filiforme, Halodule wrightii, Ruppia maritime , and Halophila engelmannii (Iverson and Bittaker 1986)

. T. testudinum, S. filiforme, and H. wrightii were only found to
9 m depth , whereas H. engelmannii was found at greater depths in association with marine macro algae.

SAV mapping in this region from 1984, 2001, and 2006 imagery showed a decline in SAV in the area north of the Suwannee River (Carlson et al. 2010). Carlso n et al. (2010) attributed that loss to reduced clarity during high discharge periods of the Suwannee River; however, it is not clear if the reduced clarityDraft 25 August 2010 was due to excessive color, turbidity, or chlorophyll a

. Preliminary results from a 2004

- 2009 opti cal water quality study by the Florida Wildlife Research Institute (FWRI) of the Florida Fish and Wildlife Conservation Commission (FWCC) show that there is a gradient of chlorophyll a and turbidity along the coast, with higher values near the Suwannee Riv er, and declining concentrations along the Big Bend to St. Marks. Their preliminary analyses for the entire study area suggest that chlorophyll a and turbidity are more highly correlated with light attenuation than color (Paul Carlson and Laura Yarbro, FW RI, personal communication 7/31/10). SAV has not been mapped south of the Suwannee River.

Figure 11. Big Bend seagrass cover in 1984, 2001, and 2006. Of note for this report is the apparent decline in seagrass coverage north of Suwannee Sound poten tially due to effects from the Suwannee River (

from Carlson et al. 2010 ).

Field SAV surveys were conducted in 1974

- 1980 (Iverson and Bittaker 1986) and repeated in 2000 (Hale et al. 2004) in the Springs Coast and along the Big Bend Coast. Results showed some local species shifts but no overall trend of shift or SAV loss in the region from the Suwannee to the Withlacoochee Rivers (hypothesized species shift off Springs Coast discussed further in FDEP Springs Coast Summary). T here was some replacement of Thalassia with Halodule at sites just north of the Suwannee River between those time periods (Hale et al. 2004). Figures 12

- 14 show the location of the three dominant species of
seag rass, and increase or decrease from the 1974

- 80 study to the 2000 study.Draft 26 August 2010 Figure 12

. Distribution map for Thalassia testudinum, showing comparison of 1984 and 2000 surveys (from Hale et al. 2004).

Figure 13

. Distribution map for Syringodium filiforme, showing comparison of 1984 and 2000 surveys (from Hale et al. 2004).Draft 27 August 2010 Figure 14

. Distribution map for Halodule wrightii, showing comparison of 1984 and 2000 surveys (from Hale et al. 2004).

Staff from the Big Bend and St. Martin’s Marsh Aqu atic Preserves have been conducting seagrass surveys at 25 fixed sites around Cedar Keys since 2006 (Figure 15 )

. At each site

, 4 replicate quadrats are randomly selected, total ing 100 quadrats

. Coverage estimates of seagrass, rooted macroalgae, and drift algae are made using Braun

- Blanquet (B&B) sampling methods. This involves identifying percent coverage of all seagrass and algae species represented and within a 1 m 2 “quadrat.” The coverage abundance codes that the preserve uses are the following: 1 = <5% cover; 2 = 5

- 25% cover; 3 = 25

- 50%

cover; 4 = 50

- 75% cover; 5 = 75

- 100% cover. The type of data collected has been adjusted throughout the study period, but the site locations have remained the same. The Preserve continues to collect data on indicators that prove to be the most accessible and comparable and include : seagrass and macroalgae abundance, seagrass species composition, canopy height, epiphyte density (1 = clean, 2 = light, 3 = moderate, 4 =h eavy), water quality measurements (DO, pH, temp, salinity, turbidity, color, PAR), sediment type/grain size, and presence of other organisms present in the bed such as bay scallops and sea urchins. The monitoring program goals are to provide information to resource managers to assess the status of this resource within the aquatic preserve, and are not representative of the entire Springs Coast. The study area is located in Levy County around the waters of Seahorse Key, North Key, Atsena Otie
, and Snake Ke y. Overall, preserve staff monitor 100 seagrass stations from Crystal River to St. Marks. The database is relevant for comparing parameters like species compos i tion, blade lengths, total coverage and sediment types along the entire Big Bend coastline.

T he dominant seagrass species within the project area are Thalassia testudinum and Halodule wrightii (Figure 16 )

. Total seagrass coverage has ranged between 3.66 and 4.38 (Braun

- Blanquet scale ; Figure 17 ). The decline in total seagrass coverage could be at tributed to the patchiness of sea grass in the study sites. Total epiphyte coverage density has been stable throughout the study period (Figure 18 ). The study area may lack optimal growing conditions for green macroalgae . Since 2006 , Caulerpa prolifera isDraft 28 August 2010 the only green marcoalga e found within the study area. However, calcareous red algae are abundant in some of deeper Thalassia beds. This area of Florida coast is extremely shallow and is located approximately 20 km from the mouth of the Suwannee Rive r. Therefore, the waters around Cedar Key are characterized by a mixture of sand, silt and mud bottom types. The particulate matter in the water column attenuates light at shallow depths, partially limiting the overall growth of seagrass. Seagrass blade lengths tend to be shorter and percent coverage tends to be less dense when compared to other areas with better water clarity (Big Bend Seagrasses and St. Martins Marsh Aquatic Preserve staff)

.

Figure 15

. FDEP Aquatic Preserves SAV sampling sites at Cedar Keys, Levy County, Florida.Draft 29 August 2010 Figure 16. Frequency of occurrence of seagrass species at Cedar Keys , 2006

- 2009.

Figure 17. Average t otal g rass c overage , Cedar Keys , 2006

- 2009. AVG B&B represents the average
Braun

- Blanquet ranking assigned at each of 100 sampling quadrats per year. Ranks are abundance codes ranging from 1

- 5.Draft 30 August 2010 Figure 18. Average e piphyte r anking , St. Martins Marsh Aquatic Preserve , 2004

- 2009. Shown are average epiphyte rankin gs of 100 sampled quadrats. Possible epiphyte ranks range from 1

- 4.

Phytoplankton S pecies C omposition
Putnam (1967) studied algal production and photosynthesis in the Waccasassa Estuary and found that

, 93% of the time

, production in the Waccasassa B ay is likely to be higher than in either the river or the Gulf (Figures 19 and 20)

. He also conducted limiting nutrient bioassays, and concluded that nitrogen was the limiting nutrient. Interestingly, streamflow of the Waccasassa River was not correlated with productivity for any of the sampling stations in this study, and the author conclude d that “the land apparently is infertile and following heavy rains nutrients leach out of the soil in insufficient amounts to alter productiv ity in any immediate way in the estuary” (Putnam 1967). This study was conducted when Florida’s population was 6 million people. Putnam (1967) notes that “nutrients accumulate and are recycled metabolically within the system” such that added nutrients would not be exported readily out to the Gulf. Diatoms were the dominant phytoplankton group all year.Draft 31 August 2010 Figure 19

. Variation in productivity pattern in Waccasassa Bay (from Putnam 1967). Larger circles indicate higher primary productivity.

Figure 20. Variation of chlorophyll a in estuarine surface water in Waccasassa Bay (Figure 7 from
Putnam 1967)

.Draft 32 August 2010 Phytoplankton production in Suwannee Sound is relatively high, however, zooplankton production and food web assimilation is sufficient that excess chlorophyll is not observed . Quinlan et al. (2009) estimated that the resident microzooplankton could remove up to 83% of total daily primary production. The microzooplankton community was primarily composed of ciliates, dinoflagellates, and copepod nauplii, and ciliate densities were comparable to those reported for productive estuaries (Quinlan et al. 2009). The phytoplankton communities in the estuarine regions (reef and nearshore) of Suwannee Sound were dominated by diatoms. Studies of phytoplankton along the gradient from the river to the nearshore area revealed that salinity, light, and temperature play important roles in the distribution of phytoplankton species, with salinity as the most important factor (Quinlan and Phlips 2007). Riverine communities were light

- limited, especially during periods of typical or high flow, and nearshore communities are nutrient

- limited (Bledsoe and Phlips 2000, Quinlan and Phlips 2007). During periods of record low flow, phytoplankton biomass increased in the river due to increased residence time and water clarity (Quinlan and Phlips 2007). During the whole period of her study, Dr. Quinlan did not observe any traditional bloom species, including typical cyanobacteria in fresh portions or Karenia brevis in mar ine portion s (E. Quinlan, personal communi cation). She suggests that the Suwannee River’s low salinity outflow precludes the maintenance of K. brevis blooms (Quinlan and Phlips 2007).

Macroalgal S pecies C omposition and B ioma ss (I ncluding Calcareous Forms )
Seasonal periods of high macroalgae biomass were observed during the winter and spring from 1999 to 2001 (low flow years) at the mouth of the Suwannee River (Figure 21 ). Seasonal changes in water clarity and tidal cycles may affect the abundance and dist ribution of macroalgae in the Suwannee River Estuary. Benthic algal biomass was measured during 2000 and 2001 by Dr. Erin Quinlan, and spatial patterns indicated that benthic algal biomass is higher in the plume of the Suwannee River (Figure 22 ). The lev els of algae measured in these studies were not linked with any biological impairment.

Figure 21

. Observed macroalgal succession on a subset of oyster reef at the mouth of the Suwannee River, 1999

- 2001 (from Quinlan 2010 ). 0 100 200 300 400

May Aug Nov Feb May Aug Nov Feb May Aug Nov Feb

1999 2000 2001



### Ulva lactuca

, Enteromorpha intestinalis

, Laurencia spp

. Ulva lactuca

, Gracilaria spp

., Ectocarpus spp

.Maximum Dry Weight (grams m-2) Quantitative Samples CollectedDraft 33 August 2010 Figure 22

. Macroalgal biomass and SAV species distribution in Suwannee Sound, measured in Spring 2000 and Spring 2001 (from Quinlan 2010).

Shellfish P roduction and F requency /D uration o f Bed Closures

There are five monitored shellfish ing areas within the region covered in thi s summary: Horseshoe Beach, Suwannee Sound, Cedar Key, Waccasassa Bay, and Withlacoochee Bay. Information can be accessed through the Florida Dep artment of Agriculture and Consumer Services (DACS) Shellfish Environmental Assessment Section (SEAS) website http://www.floridaaquaculture.com/seas/seas_shamap.htm and in Shellfish Harvesting Area reports (DeHaven 2004a, 2004 b, 2004c, Kuhnman 2004, 2007). There are open, closed, and conditiona lly approved shellfish harvesting areas within those regions, and those assignments are dep endent upon season, freshwater flow from the rivers, and other ongoing monitoring parameters. Shellfish areas may be closed due to high levels of fecal coliforms in water samples, high density of Karenia brevis (see later section on HABs), or simply certain level s of freshwater discharge from rivers feeding the estuaries. Later sections in this report include discussions of the relevance of red tide and fecal coliforms to nutrient criteria development.

Fish Community Studies

Studies by Tukey and Dehaven (2006) of fish community composition in seagrass and tidal creek habitats in the Suwannee estuary (monthly sampling 1997

- 1999 ; Figure 23 ) showed clear support o f all age groups of fishes and high diversity in seagrass and tidal creek habitats. Thirty

- five species were unique to seagrass habitat

, and 35 species were unique to tidal creeks, with a total of 111 species found in the study altogether. Expected seaso nal changes in community composition were observed, due to recruitment of young of year fish ( YOY )

. 

## <5

45Draft 34 August 2010 Tukey and Dehaven (2006) found more species of fishes in the tidal creeks (80) than were found in studies of tidal creeks in other states and regions. Th e most common fish species found in seagrass habitats were Harengula jaguana, Anchoa hepsetus, Anchoa mitchilli, Membras martinica, Syngnathus floridae, Syngnathus scovelli, Eucinostomus spp ., Orthopristis chrysoptera, Lagodon rhomboides, Bairdiella chrysoura, Cynoscion nebulosus, and Menticirrhus americanus . The most common fish species found in tidal creek habitats were Brevoortia spp., Anchoa hepsetus, Anchoa mitchilli, Adinia xenica, Fundulus grandis, Fundulus majalis, Membras martinica, Menidia spp ., Oligoplites saurus, Eucinostomus harengulus, Eucinostomus spp ., Lagodon rhomboides, Bairdiella chrysoura, Cynoscion arenarius, Cynoscion nebulosus, Leiostomus xanthurus, Menticirrhus americanus, Sciaenops ocellatus, Mugil cephalus, and Gobiosoma bosc. Fis h species spatial distribution was driven primarily by salinity (Tukey and Dehaven 2006 ). The authors commented that m aintenance of healthy seagrasses is critical to fisheries support in this area. The results of Tukey and Dehaven’s (2006) study were simi lar to a study conducted at Cedar Key 50 years prior (Reid 1954).

Cedar Keys (including Suwannee Sound) is one of the intensive annual study areas for the Fisheries
In dep endent Monitoring (FIM) Program operated by the FWCC (Figure 24)

. FWCC produce s an annual report of sampling results

, summaries of the 2008 results suggest that this system is diverse and fully functioning ( Tables 7 and 8 ; from FIM 2009). T he FIM program has been sampling in the Cedar Keys/Suwannee Sound area for 10 years

, but n o lo ng term data analyses are available

.
Suwannee Sound is a designated critical habitat area for the federally threatened Gulf sturgeon (Federal Register Vol. 68, No. 53, 3/19/03). This designation was supported by Edwards et al. ( 2003 ), who studied the movements of adult Gulf Sturgeon in 1996 and 1998. Their study showed that adult fish that spawn up the Suwannee River spend 4

- 5 months of the year feeding in shallow marine waters off the mouth of the Suwannee River.Draft 35 August 2010 Figure 23

. Sampling sites for the 1997

- 1999 fish community study by Tukey and Dehaven (2006) (figure from Tukey and Dehaven 2006).

Table 7. The top 10 numerically dominant fish taxa collected in the Fisheries In dep endent Monitoring program stratified random sample areas, 2008. Totals in bold represent total of top 10 dominant, total recreationall y important species , and grand total

.Draft 36 August 2010 Figure 24

. Map of Cedar Key sampling area of the Fisheries In dep endent Monitoring Program. Zones are labeled B, C, and F. Grids containing portions of Zones B and F are labeled B/F.

Table 8. Number of recreationally important species (Selected Taxa) collected in the Fisheries
In dep endent Monitoring program stratified random sample areas, 2008.Draft 37 August 2010 Quantification of L andings from Co mmercial /

Recreational Fisheries
Fish landings data are available by county from the Florida Fish and Wildlife Conservation Commission. Shellfish, shrimp, and finfish landings have remained relatively constant over time for Dixie and Levy
Co unties ( Figure s 25

- 27 ). Missing bars indicate no landings for that year.

Figure 25

. Total commercial blue crab and oyster catch (pounds/trip) for Dixie and Levy Counties from
1995

- 2008. Data from the Florida Fish and Wildlife Conservation Commission. 0 100 200 300 400 500 600

Total Blue Crab Dixie County Total Blue Crab Levy County Oysters Dixie County Oysters Levy County 

# Commercial Landings (pounds/trip) of Selected Shellfish 1995

1996

1997

1998

1999

2000

2001

2002

2003

2004

2005

2006

2007

2008Draft 38 August 2010 Figure 26

. Total commercial shrimp catch (pounds/trip) for Dixie and Levy Counties from 1995

- 2008. Data from the Florida Fish and Wildlife Conservation Commission.

Figure 27

. Total commercial finfish catch (pounds/trip) for Dixie and Levy Counties from 1995

- 2008. Data from the Florida Fish and Wildlife Conservation Commission. 0 200 400 600 800 1000 1200

Total Food Shrimp Dixie County Total Food Shrimp Levy County Total Bait Shrimp Dixie County Total Bait Shrimp Levy County 

## Commercial Landings (pounds/trip) of Food and Bait Shrimp 1995

1996

1997

1998

1999

2000

2001

2002

2003

2004

2005

2006

2007

2008

0 100 200 300 400 500 600

Total Finfish Dixie County Total Finfish Levy County 

# Commercial Landings (pounds/trip) of Finfish, total of all species 1995

1996

1997

1998

1999

2000

2001

2002

2003

2004

2005

2006

2007

2008Draft 39 August 2010 Harmful Algal Blooms

Karenia brevis is a toxic dinoflagellate associated with Florida saltwater fish kills, neurotoxic shellfish poisoning, and an airborne irritant in seaspray that can cause respiratory discomfort in humans and other animals. This phenomenon, known as "red tide," occurs when K. brevis concentrations increase above normal background levels of 1,000 cells/ L (Kuhnman 2007)

. Red tide concentrations above 250,000 cells/ L can cause fish kills; however, concentrations as low as 5,000 cells/ L may cause shellfish to become toxic if the animals are exposed for a sufficent period

. Shellfish b ecome toxic by feeding on the dinoflagellates and absorbing toxin into their digestive tissues (Kuhnman 2007)

. Shellfish areas are closed to harvesting when concentrations in the vicinity exceed 5,000 cells/liter. Field studies indicated that shellfish may retain toxicity for two to four weeks; therefore, after concentrations return to normal in water, shellfish meats must be tested for toxicity before the area may be reopened to shellfish harvesting (Kuhnman 2007) . The Contingency Plan for Control of Shellfish Potentially Contaminated by Marine Biotoxins explains the procedure in more detail.

The latest red tide event in the general Suwannee Estuary area occurred from September 2005 un til January 2006, in Dixie and Levy counties
, resulting in temporary closures of the Cedar Key, Suwannee Sound, Horseshoe Beach and Waccasassa Bay s hellfish h arvesting a reas. This event affected essentially all of the Florida Gulf Coast with no previous event of this magnitude recorde d in this region (Kuhnman 2007)

. F rom December 18, 2003 to January 1, 2004, Dixie, Levy and Citrus counties also had temporary closures of the Cedar Key, Suwannee Sound and Citrus County Shellfish Harvesting Areas, as well as a precautionary closure of the Withlacoochee Bay Shellfish Harvesting Area due to red tide . In all cases

, Contingency Plan protocols were enacted. Following implementation of contingency plan protocols, all

areas were re

- opened. Prior to the aforementioned blooms, there had not been a Big Bend shellfish harvesting area closure due to red tide since 1979. Prevailing currents of the Big Bend coastal region typically hold blooms offshore ( Kuhnman 2007 ).

Two red tide occurrences have been recorded in the Withlacoochee Bay area (DeHave n 2004a)

. Levy County was closed for red tide in December 1979

, and the area had high red tide counts in June of 1980 but was not closed. The Citrus County Shellfish Harvesting Area, adjacent to and south of Withlacoochee Bay, was closed to red tide in J anuary 2004. Several rounds of water samples were analyzed from Withlacoochee Bay, but none of the samples contained the red tide organism (all samples 0 cells/liter). The shallow coastal shelf and the offshore current patterns, for the most part

, prevent red tides from reaching the Withlacoochee Bay.

The causes of red tide bloom and proliferation are still somewhat unknown, but the prevailing through is that the blooms begin offshore and can be supported closer to shore under certain conditions. Controls of bloom dynamics include physical parameters such as temperature and salinity, and nutrient form and availability. Evaluating the significance of a single factor is difficult (Vargo et al. 2008). Vargo (2009) reviewed the historic and current theories f or K. brevis initiation and maintenance, and identifies 24 hypotheses, falling into several main categories: 1) rainfall and/or riverine flux, 2) benthos or benthic flux, 3) water column hydrodynamics, and 4) chemical/allelopathy related.

Vargo et al. (2004

, 2008) evaluated many nutrient sources for their contributions to bloom initiation and maintenance: atmospheric deposition, estuarine flux, N

- fixation by the cyanobacteria Trichodesmium

, zooplankton excretion, benthic flux, and the decay of dead fis h. Atmospheric deposition and benthic flux were found to be minor sources to N and P fluxes, while zooplankton and dead fish were possibly significant contributors. The combined estuarine flux from Tampa Bay, Charlotte Harbor, and theDraft 40 August 2010 Caloosahatchee Rive r was found to supply varying, but sometimes adequate levels of N and P to support K. brevis populations at moderate, but not high biomass levels. Hu et al. (2006) studied riverine nutrient inputs for major estuaries on the central west Florida Coast (Peace, Caloosahatchee, Alafia, and Suwannee Rivers) and determined that estuarine nutrient flux, even in a high discharge period following hurricanes (when nutrient concentrations also were elevated), could not support significant blooms. They suggested that submarine groundwater discharge accounts for the necessary missing nutrients and can initiate and sustain major bloom events off the coast of central west Florida. In the recent studies examining the role of various nutrient sources in supporting K. brev is blooms, a combination of sources is required to maintain a high biomass blooms (>10 6 cells/L).

Hypoxia

No reports of hypoxia in this region were found , nor are any estuary WBIDs impaired for low dissolved
oxygen.



### Water Quality Studies

Several r eports o r data were available for the Suwannee, Waccasassa, and Withlacoochee area. If reports were available, they are summarized in this section. If data were available and additional analyses conducted by FDEP , they are also reported in this section. The stu dies included:

**•** 1964 study of Waccasassa Bay (Putnam 1967) ;

**•** Mote Marine Lab study of the Waccasassa and Withlacoochee R ivers 1984

- 1985 ;

**•** Project COAST, Dr. Tom Frazer, UF IFAS. Monthly monitoring at ten sites at each of these three estuary systems monthly si nce roughly 1997

. Some data were in Florida STORET, and

some were made available to FDEP from Aquatic Preserve staff ;

**•** Erin Quinlan (neé Bledsoe) dissertation work in the Suwannee Estuary. Conducted a series of research project s and monitoring, focused on phytoplankton and water quality, from 1996

- 2002. Results available in various publications. FDEP did not acquire these raw data ;

**•** Suwannee River Water Management District (SRWMD). Monthly or quarterly monitoring at several Suwa nnee Estuary sites 1997

- 2009, d ata available in Florida STORET; and

**•** FWRI IMAP program sampled the Suwannee Sound in 2000 and 2003, and Waccasassa Bay in 2001. These were one

- time probabilistic sampling programs that provide a snapshot of the water quality and biological communities.

Putnam 1967 S tudy of Waccasassa Bay
Hugh Putnam from the University of Florida conducted a 2

- year study of Waccasassa Bay in the 1960s. He described the system as a small shallow estuary with extensive salt marshes on the landward fringe. He describes the Waccasassa watershed as very minimally disturbed, with no industrial or domestic waste input. Mean chlorophyll a values (not phaeophytin

- corrected) for March, April, June, and July were between 15 and 20 μg/L (mg/m 3 )

, with lower concentrations during other months

. The mean chlorophyll a value he reported for all stations and all dates was 11.95 μg/L (Putnam 1967)

. He observed a productivity pattern of low phytoplankton production in the river and the open Gulf, and hi gher production where the river widens into an embayment. Table 9 contains summary information from the study.Draft 41 August 2010 Table 9

. Physical and chemical characteristics of Waccasassa Estuary, as reported in Table 1 of Putnam (1967).

1984

– 85 Mote Marine Lab St udy of Selected Rivers

Mote Marine Lab conducted a 2

- year study of water quality at river and estuary stations of the Waccasassa, Withlacoochee, Crystal, Weeki Wachee, and Aripeka rivers, under contract with the SWFWMD for minimum flows and levels determin ation. With the exception of the Aripeka sites, those data are in LEGACY STORET and in the IWR database . Data are reported and analyzed in Dixon (1986). Systems discussed here are Waccasassa and Withlacoochee. Meter ed parameters (salinity, pH, DO, and temperature) were recorded at 10 sites in both systems, with water chemistry (nutrients, turbidity, color, TSS, chlorophyll a, phaeophytin a , and transparency) collected at 5 stations. Withlacoochee River stations were sampled in 1984 and 1985, but Waccasassa was only sampled in 1985.

The author s’ interpretation of this study included the observation that dissolved oxygen levels were lowest in the Waccasassa River and Bay, of all the sampling sites from Waccasassa to Aripeka (Springs Coast) (Dixon 1986). They attribute these levels to the high organic matter and low photosynthetic activity. In their studies, they did not observe submersed vegetation in the Waccasassa River or Bay. The dissolved oxygen in Waccasassa Bay is dep endent upon seasonal fluctuations of flow and organic matter. Waccasassa River and Bay was the most colored system of the study, followed by Withlacoochee and then the Springs Coast systems. Suspended solids and turbidity were also highest for the Wacc asassa. The authors explain that this observation is likely due to turbulence within the Bay and release of organic particulate matter from the coastal marshes. In the Waccasassa system, there was a direct relationship between TSS and turbidity, and chlo rophyll a was not a driver of turbidity, though this system had the highest chlorophyll a values of the study , with means of 13.6 and 7.6 μg/L uncorrected chlorophyll a for sites seven and ten, respectively (Table 10 ) . Suspended solids and turbidity were l ower in the Withlacoochee, and authors hypothesize that wind

- driven resuspension was the main driver there. Water clarity data are summarized in Table 10

. Water quality data for Waccasassa station 10 and Withlacoochee stations 7 and 10 (Figure 28) were a vailable in LEGACY STORET and are described later in this report.Draft 42 August 2010 Figure 28

. Locations of sampling sites for which data were analyzed from the 1984

- 198 5 Mote Marine Lab study in the Waccasassa and Withlacoochee estuaries.Draft 43 August 2010 Table 10

. Summary of water clarity data for estuarine sites off the Waccasassa and Withlacoochee Rivers, from the 1984

- 85 study by Mote Marine Lab. Values are means and standard deviations, f rom Tables 48, 49, and 50 of Dixon (1986). Negative river miles indicate distance from th e mouth of the river to the estuary sampling point.

Data Type Waccasassa Waccasassa Withlacoochee Withlacoochee

Station 7 10 7 10

River Mile

- 0.16

- 2.37 0.00

- 4.73

Color (PCU) 45/18 27/9 34/22 11/6

TSS

- Surface (mg/L) 22/9 20/9 6/4 9/4

TSS

- Mid (mg/L) 36/29 21/10 8/3 10/5

TSS

- Bottom (mg/L) 34/23 25/10 8/3 14/12

Turbidity (NTU) 15.4/5.7 12.0/6.2 4.4/1.8 4.2/2.5

Chlorophyll a , uncorrected (mg/m 3 ) 13.6/5.5 7.6/2.9 4.9/2.3 5.2/3.1

Extinction Coefficient (m -1 ) 1.82/0.43 1.81/0.08 0.85/0.43 0.74/0.33

Depth receiving 20% light (m) 0.9 0.9 4.4 2.4

FDEP D ata A nalysis of the Mote Marine Lab Study
FDEP analyzed the data available in LEGACY STORET from the Mote Marine study

. FDEP calculated total nitrogen as the sum of nitrate+nitrite and TKN, if both data points were available. Total nitrogen ranged from 0.4 – 1.2 mg/L, with values for Waccasassa higher than for Withlacoochee (Figure 29; Table 11 ).
U ncorrected chlorophyll a values ranged from 1

- 12 μg/L (Figure 29; Table 11 ). Total phosphorus data from this study were not analyzed and are not presented here because the accuracy of those data is unknown at this time.Draft 44 August 2010 Figure 29

. Total nitrogen and chlorophyll a data collected 1984

- 198 5 by Mote Marine Lab for SWFWMD minimum fl ows and levels studies. Sites as in Figure 72. Chlorophyll a values are not phaeophytin

- corrected and were analyzed with the trichromatic method.Draft 45 August 2010 Table 11. Annual geometric means of chlorophyll a (uncorrected) and total nitrogen for 1984

- 1985 study of Waccasassa and Withlacoochee River sites by Mote Marine Lab. Number of samples per year in parentheses.

Site Total Nitrogen (mg/L) 1984 Total Nitrogen (mg/L) 1985 Chlorophyll a (μg/L) 1984 Chlorophyll a (μg/L) 1985
WACCA

- 10 n/a 0.834 (n=6) n/a 7.14 (n=6)

W ITH -7 0.629 (n=12) 0.588 (n=5) 4.58 (n=12) 3.88 (n=6)

W ITH

- 10 0.471 (n=10) 0.506 (n=6) 4.43 (n=12) 3.65 (n=5)

Project COAST, 1997 –P resent
Ten sites in each of the Suwannee, Waccasassa, and Withlacoochee estuaries have been sampled monthly since 1997 as part of project COAST led by Dr. Tom Frazer of the University of Florida (Figure
36 ). This project measures total nitrogen, total phosphorus, chlorophyll a , light extinction coefficient, Secchi dep th, color, salinity, dissolved oxygen, and temperature

. Water quality analyses are conducted at the University of Florida by the LAKEWATCH program. This is the most extensive and comprehensive dataset available for this region.

Project COAST data are summarized as mean concentrations for all estuary stations in Figures 30

- 32

. Results of F DEP analyses will be presented later in this report. The Withlacoochee estuary is included in reports of Project COAST results for Citrus County (see Jacoby et al. 2009 for most recent), but no published analyses of the Suwannee or Waccasassa data are availa ble. Dr. Tom Frazer presented some information from his dataset at the FDEP public meeting on 2/23/10, and that information is summarized here.

Overall, the Suwannee, Waccasassa, and Withlacoochee have higher TP and chlorophyll a values than the Springs Coast to the south or the Steinhatchee to the north (Figures 31 and 32 ).

Nutrient limitation studies conducted by Dr. Frazer on monthly samples collected from the Withlacoochee coastal system in 2000

- 2001 showed that 50% of samples were limited by nitro gen, 27% were limited by phosphorus, 15% were co

- limited, and 8% were undetermined (Frazer and Jacoby
2010 ).

High concentrations of total nitrogen, total phosphorus, and chlorophyll a were detected in 1998, 2004, and 2005 (Figures 33-35 ). 1998 was an El N iñ o year, with unusually high rainfall and heavy discharge from rivers along the Big Bend, while in 2004 and 2005 numerous hurricanes hit the Florida Big Bend.Draft 46 August 2010 Figure 30

. Mean total nitrogen (μg/L) across all sample years (approx. 1997

- 2009) and all est uary sites (excludes freshwater sites). From Frazer and Jacoby (2010)

.

Figure 31

. Mean total phosphorus (μg/L) across all sample years (approx. 1997

- 2009) and all estuary sites (excludes freshwater sites). From Frazer and Jacoby (2010)

. 0 100 200 300 400 500 600 700TN (ug/L) 

## Mean Total Nitrogen (μg/L) by System

0 10 20 30 40 50 60TP (ug/L) 

## Mean Total Phosphorus (μg/L) by SystemDraft 47 August 2010 Figure 32

. Mean chlorophyll a (μg/L) across all sample years (approx. 1997

- 2009) and all estuary sites (excludes freshwater sites). From Frazer and Jacoby (2010)

. 0 2 4 6 8 10 12CHL (ug/L) 

## Mean Chlorophyll

- a (μg/L) by SystemDraft 48 August 2010 Figure 33. Long term average data for the Suwannee Estuary, including all estuary sites (excludes freshwater sites ) (f rom Frazer and Jacoby 2010)

. 0 200 400 600 800 1000 1200

Mar

- 96 Aug

- 97 Dec

- 98 May

- 00 Sep

- 01 Jan

- 03 Jun

- 04 Oct

- 05 Mar

- 07 Jul

- 08TN (ug/L) Suwannee Monthly Average Total Nitrogen (TN) 1997 through 2008 Estuarine Stations

0 20 40 60 80 100 120 140 160

Mar

- 96 Aug

- 97 Dec

- 98 May

- 00 Sep

- 01 Jan

- 03 Jun

- 04 Oct

- 05 Mar

- 07 Jul

- 08TP (ug/L) Suwannee Monthly Average Total Phosphorus (TP) 1997 through 2008 Estuarine Stations

0 5 10 15 20 25 30 35 40

Mar

- 96 Aug

- 97 Dec

- 98 May

- 00 Sep

- 01 Jan

- 03 Jun

- 04 Oct

- 05 Mar

- 07 Jul

- 08CHL-a (ug/L) Suwannee Average Chlorophyll

- a (CHL

- a) 1997 through 2008 Estuarine StationsDraft 49 August 2010 Figure 34. Long term average data for the Waccasassa Estuary, including all estuary sites (excludes freshwater sites). From Frazer and Jacoby (2010)

. 0 200 400 600 800 1000 1200 1400 1600 1800

Mar

- 96 Aug

- 97 Dec

- 98 May

- 00 Sep

- 01 Jan

- 03 Jun

- 04 Oct

- 05 Mar

- 07 Jul

- 08TN (ug/L) Waccasassa Monthly Average Total Nitrogen (TN) 1997 through 2008 Estuarine Stations

0 20 40 60 80 100 120 140 160

Mar

- 96 Aug

- 97 Dec

- 98 May

- 00 Sep

- 01 Jan

- 03 Jun

- 04 Oct

- 05 Mar

- 07 Jul

- 08TP (ug/L) Waccasassa Monthly Average Total Phosphorus (TP) 1997 through 2008 Estuarine Stations

0 5 10 15 20 25 30 35 40

Mar

- 96 Aug

- 97 Dec

- 98 May

- 00 Sep

- 01 Jan

- 03 Jun

- 04 Oct

- 05 Mar

- 07 Jul

- 08CHL-a (ug/L) Waccasassa Average Chlorophyll

- a (CHL

- a) 1997 through 2008 Estuarine StationsDraft 50 August 2010 Figure 35. Long term average data for the Withla coochee Estuary, including all estuary sites (excludes freshwater sites). From Frazer and Jacoby (2010)

.

Data Analyses by FDEP
Project COAST d ata were available in STORET through 2006 for the Withlacoochee sites (with 2005 data absent), and datasets through 2007 for the Suwannee and Waccasassa sites were obtained from FDEP Aquatic Preserve staff (Table 1 2)

. Annual geometric means of total nitr ogen, total phosphorus, and chlorophyll a (uncorrected) were calculated and plotted for each station each year (Figures 37-4 5). The following sites were excluded from calculation of geometric means due to predominantly fres h nature (mean salinity < 3 ppt ) : Suwannee sites 1 and 2, Waccasassa site 1, and Withlacoochee sites 2 and 3. From these plots of annual geometric means through time, it is clear that the sites closest to the river mouths have highest nutrient concentrations. On the Suwannee, sites 3, 4, 5, and 6 have higher TN and TP concentrations than sites 7, 8, 9, and 10

, which are further offshore (Figures 3 7 and 4 0). Geometric mean TN ranged from 400

- 800 μg/L in nearshore sites and 250

- 400 μg/L in offshore sites, and geometric mean TP ranged fr om 40

- 80 μg/L in nearshore sites and 20

- 40 μg/L in offshore sites for the Suwannee. 0 200 400 600 800 1000 1200

Mar

- 96 Aug

- 97 Dec

- 98 May

- 00 Sep

- 01 Jan

- 03 Jun

- 04 Oct

- 05 Mar

- 07 Jul

- 08TN (ug/L) Withlacoochee Monthly Average Total Nitrogen (TN) 1996 through 2008 Estuarine Stations

0 20 40 60 80 100 120

Mar

- 96 Aug

- 97 Dec

- 98 May

- 00 Sep

- 01 Jan

- 03 Jun

- 04 Oct

- 05 Mar

- 07 Jul

- 08TP (ug/L) Withlacoochee Monthly Average Total Phosphorus (TP) 1996 through 2008 Estuarine Stations

0 5 10 15 20 25 30

Mar

- 96 Aug

- 97 Dec

- 98 May

- 00 Sep

- 01 Jan

- 03 Jun

- 04 Oct

- 05 Mar

- 07 Jul

- 08CHL-a (ug/L) Withlacoochee Average Chlorophyll

- a (CHL

- a) 1996 through 2008 Estuarine StationsDraft 51 August 2010 The zonation wa s more gradual in the Waccasassa , with geometric means ranging from 400

- 700 μg/L for TN and 20

- 60 μg/L for TP (Figures 3 8 and 4 1)

. Zonation in the Withlaco ochee was also gradual, with geometric means ranging from 250

- 500 μg/L for TN and 20

- 40 μg/L for TP (Figures 3 9 and 42). The geographic zonation is different for chlorophyll a due to the interaction with color, described below.

There is a clear negative relat ionship between salinity and TN and between salinity and TP for all three systems, though the relationship is weakest for the Waccasassa (Figure 4 6 and 4 7). The strength of these relationships can likely be explained by the level to which the estuar ies are dominat ed by the rivers that feed them or the locations of the sites (Figure 3 6). If the river is the dominant force in the estuary and there is a relatively short holding time, as for these systems, then the nutrient concentration is largely a function of dilution, as is salinity. The positive relationships between TN and color for these systems (shown for the Suwannee in Figure 4 9) also demonstrate that dilution.

Waccasassa Bay is somewhat more enclosed than the other two, and may be restricted by currents such that the residence time is longer. Waccasassa Bay is very shallow and wind driven circulation may also be a factor (Putnam 1967, Dixon 1986). TN concentrations are fairly consistent throughout the study area of Waccasassa Bay despite salinity levels, except for the high flow year of 1998, which brought unusually high nutrient concentrations into the b ay (Figure 5 0).

For chlorophyll a , there is a peak in concentration (~ 10

- 12 μg/L) at mid

- salinity (see Suwannee example in Figure 4 8 bottom panel) because that is the region in which phytoplankton are no longer limited by flow and tannins, but there are sufficient nutrients to sustain higher chlorophyll a levels than in the open nearshore area. This pattern is consistent with results of Quinlan (2003).

These relationships suggest that nutrient criteria could and should be linked to salinity in these river

driven systems. Salinity values at individual sites vary greatly within and between years (Table 13 ), such that it would not be appropriate to place geographic restrictions on salinity divisions for the purpose of assigned numeric criteria. However, relationships between nutrients and salinity are consistent from year to year, as sh own for the Suwannee in Figure 4 8. These data s uggest that a continuous salinity function may be appropriate for the Suwannee and Withlacoochee estuaries.

Table 12

. Number of times each of 10 stations were sampled in each estuary system each year for Project COAST, directed by Dr. Tom Frazer at UF.

Year Suwannee Waccasassa Withlacoochee
1996 Not sampled Not sampled 1
1997 6 7 12
1998 12 12 12
1999 12 12 12
2000 12 12 11
2001 12 12 12
2002 12 12 12
2003 12 12 12
2004 12 12 12
2005 12 12 Not available
2006 12 12 12
2007 9 9 Not availableDraft 52 August 2010 Figure 36

. Project COAST sampling sites in the Suwannee, Waccasassa, and Withlacoochee estuaries.

Figure 3 7. Mean TN at Project COAST Suwannee estuarine sites.Draft 53 August 2010 Figure 3 8. Mean TN at Project COAST Wacasassa estuarine sites.

Figure 3 9. Mean TN at Project COAST Withlacoochee estuarine sites.Draft 54 August 2010 Figure 4 0. Mean TP at Project COAST Suwannee estuarine sites.

Figure 4 1. Mean TP at Project COAST Waccasassa estuarine sites.Draft 55 August 2010 Figure 4 2. Mean TP at Project COAST Withlacoochee estuarine sites.

Figure 4 3. Mean chlorophyll a at Project COAST Suwannee estuarine sites.Draft 56 August 2010 Figure 4 4. Mean chlorophyll a at Project COAST Waccasassa estuarine sites.

Figure 45. Mean chlorophyll a at Project COAST Withlacoochee estuarine sites.Draft 57 August 2010 Figure 4 6. Stations 1 and 2 excluded for Suwannee, Station 1 excluded for Waccasassa, and Stations 2 and 3 excluded for Withlacoochee. R 2 = 0.84 for Suwannee, R 2 = 0.36 for Waccasassa, R 2 = 0.70 for Withlacoochee.

Figure 4 7. Stations 1 and 2 excluded for Suwannee, Station 1 excluded for Waccasassa, and Stations 2 and 3 excluded for Withlacoochee. R 2 = 0.87 for Suwannee, R 2 = 0.40 for Waccasassa, R 2 = 0.76 for Withlacoochee.Draft 58 August 2010 Table 13

. Average, minimum, and maximum salinity values (parts per thousand) for Suwannee Estuary sites sampled by Project COAST for each year and all data for each site. Sample sizes as in Table 10

.

Year Average Minimum Maximum Year Average Minimum Maximum Year Average Minimum Maximum Year Average Minimum Maximum 1997 18.50 8.00 26.00 1997 3.67 0.00 9.00 1997 10.67 7.00 15.00 1997 21.00 14.00 31.00 1998 14.22 2.00 26.30 1998 4.68 0.00 22.90 1998 13.70 0.00 25.70 1998 16.28 2.00 26.00 1999 22.47 14.40 34.30 1999 6.73 0.60 26.90 1999 21.77 10.30 30.60 1999 23.89 11.70 29.70 2000 24.28 16.20 28.60 2000 14.72 3.40 22.76 2000 20.54 13.80 26.80 2000 23.41 20.77 28.40 2001 23.46 9.46 29.79 2001 12.85 0.15 23.29 2001 20.96 14.02 28.17 2001 23.79 14.56 30.55 2002 23.30 13.33 25.50 2002 18.50 2.26 25.24 2002 22.75 13.52 26.46 2002 25.57 16.77 32.24 2003 18.86 10.41 28.70 2003 7.88 0.04 20.93 2003 14.69 0.30 29.61 2003 17.52 3.64 27.73 2004 18.51 5.50 24.31 2004 7.55 0.05 19.25 2004 15.72 0.52 25.27 2004 19.26 1.21 26.16 2005 16.08 0.09 30.14 2005 5.92 0.09 15.70 2005 14.48 0.04 26.85 2005 19.06 4.83 28.45 2006 18.98 3.06 29.26 2006 8.79 0.06 21.18 2006 17.42 9.02 27.80 2006 20.85 10.76 29.15 2007 25.91 21.66 29.77 2007 15.61 6.58 27.91 2007 22.63 15.49 29.24 2007 24.52 17.91 28.62 all data 20.42 0.09 34.30 all data 9.86 0.00 27.91 all data 18.02 0.00 30.60 all data 21.34 1.21 32.24

Year Average Minimum Maximum Year Average Minimum Maximum Year Average Minimum Maximum Year Average Minimum Maximum 1997 28.33 22.00 31.00 1997 27.67 23.00 33.00 1997 28.33 24.00 33.00 1997 28.50 22.00 35.00 1998 23.56 15.00 32.20 1998 23.67 8.00 31.40 1998 24.03 12.00 30.80 1998 25.07 10.00 32.00 1999 28.05 15.50 34.60 1999 28.18 15.40 34.00 1999 29.84 20.70 34.10 1999 30.38 20.00 34.50 2000 30.43 27.40 33.00 2000 30.14 26.80 32.40 2000 30.39 25.60 33.58 2000 31.00 27.03 34.30 2001 29.43 23.01 33.60 2001 28.46 22.26 32.72 2001 28.81 22.06 32.18 2001 29.61 26.02 32.36 2002 28.26 23.26 31.23 2002 28.84 21.10 31.65 2002 29.95 22.96 32.84 2002 30.18 24.54 33.13 2003 24.12 17.30 30.82 2003 23.20 14.72 31.41 2003 25.10 19.68 31.45 2003 26.91 21.99 31.51 2004 24.70 17.53 29.64 2004 24.96 10.00 30.48 2004 25.62 14.40 29.03 2004 25.49 8.49 30.26 2005 24.35 17.11 32.70 2005 25.50 16.74 30.90 2005 25.76 13.03 30.77 2005 26.50 9.29 31.41 2006 26.74 16.43 31.79 2006 26.20 19.32 31.05 2006 26.34 18.87 31.81 2006 27.31 20.27 33.03 2007 29.57 24.86 33.24 2007 29.67 25.89 32.73 2007 29.78 26.50 32.76 2007 30.66 27.12 32.90 all data 26.95 15.00 34.60 all data 26.85 8.00 34.00 all data 27.56 12.00 34.10 all data 28.28 8.49 35.00 Station 3 Station 4 Station 5 Station 6

Station 7 Station 8 Station 9 Station 10Draft 59 August 2010 Figure 4 8. Average annual salinity for each site plotted against the annual geometric means for tot al nitrogen, total phosphorus, and chlorophyll a for each site sampled for Project Coast 1997

- 2007. 0 200 400 600 800 1000 1200 1400

0 5 10 15 20 25 30 35Geometric Mean Total Nitrogen (μg/L)

Salinity (ppt) 

### Suwannee Estuary COAST Sites Mean Annual Salinity vs. Annual Geo Mean TN 1997

1998

1999

2000

2001

2002

2003

2004

2005

2006

2007

0 20 40 60 80 100 120 140

0 5 10 15 20 25 30 35Geometric Mean Total Phosphorus(μg/L)

Salinity (ppt) 

### Suwannee Estuary COAST Sites Annual Mean Salinity vs. Annual Geometric Mean TP 1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007

0 5 10 15 20 25

0 5 10 15 20 25 30 35Geometric Mean Chlorophyll a (μg/L)

Salinity (ppt) 

### Suwannee Estuary COAST Sites Mean Annual Salinity vs. Annual Geo Mean Chlorophyll a (uncorrected) 1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007Draft 60 August 2010 Figure 49

. Color vs. TN in the Suwannee estuary.

Figure 50

. Salinity vs. TN in Waccasassa Bay.

For most of the study period, only uncorrected chlorophyll a was analyzed. However, both uncorrected and phaeophytin

- corrected chlorophyll a were reported for 9 months of 2007 for the Suwannee and Waccasassa estuaries only . For both estuary systems, the two measurements are very highly correlated (Figures 5 1 and 5 2), and the geometric means were typically within 1 μg/L of each other (Table 1 4 ). This comparison is important because FDEP prefers to use phaeophytin

- corrected values for assessment
purposes. 0 200 400 600 800 1000 1200 1400

0 50 100 150 200Geometric Mean Total Nitrogen (μg/L)

Color (PCU) 

### Suwannee Estuary COAST Sites Mean Annual Color vs. Annual Geometric Mean TN 1999

2000

2001

2002

2003

2004

2005

2006

2007

0 200 400 600 800 1000

0 5 10 15 20 25 30 35Annual Geometric Mean TN (μg/L)

Mean Annual Salinity (ppt) 

## Waccasassa Bay COAST Sites Mean Annual Salinity vs. Annual Geometric Mean TN 1997

1998

1999

2000

2001

2002

2003

2004

2005

2006

2007Draft 61 August 2010 Figure 5 1. Comparison of uncorrected and phaeophytin

- corrected chlorophyll a (μg/L) for 10 sites in the Waccasassa Estuary for the first nine months of 2007.

Table 1 4

. Comparison between station geometric means for the first 9 months of 2007 (n = 9 monthly samples) uncorrected and phaeophytin

- corrected chlorophyll a (μg/L) measurements for the Waccasassa and Suwannee Estuaries.

Site Waccasassa Estuary Uncorrected Waccasassa Estuary Corrected Waccasassa Estuary % Difference Suwannee Estuary Uncorrected Suwannee Estuary Corrected Suwannee Estuary % Difference
1 4.71 3.73 21% 2.62 1.65 37%

2 4.95 3.81 23% 3.61 2.54 29%

3 7.07 5.41 23% 9.65 7.76 20%

4 6.50 4.86 25% 7.12 4.80 33%

5 6.61 5.18 22% 10.58 8.73 17%

6 4.54 3.73 18% 12.35 10.67 14%

7 1.50 1.05 30% 3.64 2.88 21%

8 5.86 4.92 16% 3.66 3.05 17%

9 4.46 3.77 16% 4.04 3.36 17%

10 3.27 2.69 18% 3.33 2.82 15%Draft 62 August 2010 Figure 5 2. Comparison of uncorrected and phaeophytin

- corrected chlorophyll a (μg/L) for 10 sites in the Suwannee Estuary for the first nine months of 2007.

Quinlan Dissertation on Water Quality and Phytoplankton in the Suwannee Estuary
For her dissertation work, Erin (Bledsoe) Quinlan conducted studies of water quality, phytoplankton, and zooplankton in the Suwannee Estuar y, and her results are available in various publications ( Bledsoe and Phlips 2000, Bledsoe et al. 2004, Quinlan 2003, Quinlan and Phlips 2007, Quinlan et al. 2009). She collected water quality samples via an integrated tube (3 m max) for the following ana lyses : chlorophyll, bacteria, TP, SRP, TN, NO3, NO2, NH4, Silica, and n utrient limitation experiments. S he measured salinity, temperature, DO , dissolved color, suspended solids, and flushing rates. She also sampled phytoplankton, zooplankton, macroalgae , and periphyton. These collections were made in various combinations at various time intervals and frequency throughout the study period 1996

- 2003. Water quality analyses were conducted in the NELAC

- certified lab of Dr. Phlips with FDEP and EPA

- approved analyses. For a short period in the beginning of her studies, Dr. Quinlan collected grab samples along with the integrated tube samples, and she said that most of the study area is so well

- mixed that results were comparable between the two collection met hods.

Her studies showed a clear gradient of phytoplankton community from the dark water river to the open estuary. She separated the study area into three regions: the river, reef, and nearshore regions (Figure
53 ).Draft 63 August 2010 Figure 53

. Sampling sites used by Quinlan and Phlips , 1996

- 2003.

The limiting nutrient varied by both the location and river flow. Nitrogen was the primary limiting nutrient in the reef region at all times. During periods of average riverine discharge, nitrogen was also limiting outside the oyster reefs in the nearshore region. During periods of low riverine discharge, phosphorus and nitrogen were co

- lim iting in the nearshore region. An example of this limitation can be seen in the chlorophyll a estimates o f phytoplankton biomass. The reef region typically had higher chlorophyll a values (>10 μg/L) than the nearshore region (<5 μg/L). The nearshore region experienced a significant increase in chlorophyll a to nearly 10 μg/L during the average

- high discharge season, in comparison to the low flow years in which levels are around 3 μg/L (Table 15 ). This contrast suggests that the nutrient rich riverine plume moving farther offshore during high discharge supplied additional nutrients for phytoplankton growth.

Table 15

. Mean annual values for phytoplankton abundance (chlorophyll a) in the “reef” and “nearshore” regions of the Suwannee River estuary, and discharge

- weighted nutrient loading rates (g

s -1 of TN and TP) from the Suwannee River. Standard errors are in parentheses (Table 2

- 1 of Quinlan 2003).Draft 64 August 2010 Seasonal periods of high macroalgae biomass were observed during the winter and spring at the mouth of the Suwannee River, probably due to natural s easonal changes in water clarity and tidal cycles. Algal and sediment samples were collected for biomass and species composition from 1999 to 2001. Nutrients from the Suwannee River p lume may play a significant role in defining the abundance and distribution of microalgae in the sediment of the Suwannee River estuar y. Results during 1999 and 2000

were from record low flow periods for the Suwannee River (Figure 54 ). Groundwater from the many springs along the Suwannee River dominate d the flow during periods of low rainfall, and it is well

- known that the nitrate levels in some springs are high enough to cause algal imbalances ( FDEP freshwater nutrient criteria documents)

.

Figure 54

. Flow rates in the Suwannee River at the Wilcox gauging station. ( A) Long

- term mean monthly flow rates from 1932 to 1999. ( B) Mean monthly flow rates from 1998

- 2001. The dashed line (

---

) indicated median flow rate for the Suwannee River. The gray line represents the flow rate exceeded 99% of the time from 1960

- 2001, and the asterisk (***) line represents the flow rate

excee ded only 1% of all dates from 1960

- 2001

. Figure f rom Quinlan ( 2003 ).Draft 65 August 2010 Figure 55

. Flushing rates in the reef region of the Suwannee River estuary. ( A) Calculated flushing rate (d -1 ) of the reef region compared to riverine flow from April 1998 to April 2 001. The points are the flushing rates, and the line is the least squares fit of the estimated flushing rates based on riverine flow. ( B) Flushing rate (d -1 ) in the reef region from 1998

- 2001 (mean 3.4 ± 1.4 days, n=35). Figure f

rom Quinlan ( 2003 ).

T he light extinction coefficient in the estuarine areas ( oyster reef and nearshore) was most strongly correlated with tripton (particulate organic matter) , followed by CDOM and chlorophyll a (Table 16 ). Onl y during very low flow periods wa s light extinction highly correlated with chlorophyll a

. These results indicate that phytoplankton biomass is not the major contributor to water clarity reductions, but rather the organic materials from swamp source waters (the Okeefenokee Swamp National Wildlife Refuge) in the Suwannee River.

Dr. Quinlan found that the Suwannee Estuary is a very product ive estuary, which commercial and sports fishers in the region have known for a long time. Phytoplankton production is high, and zooplankton production is high enough for food web assimilation to produce desirable fisheries biomass (fish, shrimp, and crabs) . Quinlan et al. (2009) estimated that the resident microzooplankton could remove up to 83% of total daily primary production. The microzooplankton community was primarily composed of ciliates, dinoflagellates, and copepod nauplii, and ciliate densities were comparable to those reported for highly productive estuaries (Quinlan et al. 2009).

The phytoplankton communities in the estuarine regions ( oyste r reef and nearshore) were dominated by diatoms. Studies of phytoplankton along the gradient from the river to the nearshore area revealed that salinity, light, and temperature play important roles in the distribution of phytoplankton species, with salini ty as the most important fac tor (Quinlan and Phlips 2007).Draft 66 August 2010 Riverine communities are light

- limited, especially during periods of typical or high flow, and nearshore communities are nutrient

- limited (Bledsoe and Phlips 2000, Quinlan and Phlips 2007). Duri ng periods of record low flow, phytoplankton biomass increased in the river due to increased residence time and water clarity ( Figure 55; Quinlan and Phlips 2007). During the period of study, Dr. Quinlan did not observe any traditional bloom species, including typical cyanobacteria in fresh portions and K. brevis in marine portion s (E. Quinlan, personal communi cation). She suggested that the Suwannee River’s low salinity outflow precludes the maintenance of K. brevis blooms (Quinlan and Phlips 2007).

Tabl e 16

. Light extinction coefficient (Kd) and Pearson correlation coefficients for three major components of light absorption: T ripton, CDOM, and phytoplankton chlorophyll a in the Suwannee
R iver and its estuary. Table from Quinlan (2003)

.Draft 67 August 2010 Suwannee River Water Management District M onitoring
The Suwannee River Water Management District (SRWMD) has sampled four estuary sites bimonthly in the Suwannee Estuary from 1995

- present (Figure 5 6 ). Robbie McKinney of the SRWMD analyzed these long term data using Lowess regression, and found no significant trends for TKN, NO 2+3 , or TP (McKinney 2010). He found an increase in ammonia at the four estuary sites, but FDEP workshop participants (2/23/10 in Crystal River) were surprised at the relationships and hypot hesized that the relationships were likely a function of salinity. Analysis of these data by FDEP revealed that the SRWMD detection limit for ammonia ranged from 0.02 to 0.099 mg/L, with the higher detection limit in more recent years. The change in det ection limit and plotting of non

- detect values as the detection limit is likely the reason for the perceived increase in ammonia in this time series.

Figure 56. SRWMD long term sampling sites within the Suwannee Estuary (from McKinney 2010 )

.

SRE030C1 – East Pass Channel, SRE050C1 – Alligator Pass, SRE070C1 – Wadley Pass, and SRE080C1 – Salt Creek.Draft 68 August 2010 Figure 5 7. Location of SRWMD sampling sites in the Suwannee River Estuary (SRE) and Cedar Keys (CKF).

FDEP A nalysis of SRWMD D ata
FDEP analyz ed the SRWMD data from the four Suwannee Estuary sites and two Cedar Keys sites (Figure
57 ). These data are available and were retrieved from STORET. Table 1 7 contains number sample dates per year for these sites. The SRWMD had additional sampling sites (SRE010C1, SRE020C1, SRE040C1, SRE060C1) that were sampled in a more limited number of years (1995

- 1999). Data were only analyzed from sites with the longest term record.

Data were screened prior to analysis , and d ata qualified with “J” and “Q” remark c odes were excluded. If there was more than one result for an analyte at a site on a given day, values were averaged for each site for each sampling date. Total nitrogen was only calculated if data were available for both nitrate/ nitrite and TKN. Results below detection were assigned a value at half the method detection limit (MDL). If the MDL was reported as zero (this occurred for chlorophyll a for SRE sites and for nitrate+nitrite for CKF sites), the value was assigned as half the average MDL of the dataset for that analyte. For chlorophyll a , the average MDL was 1 μg/ L. The detection limit for NO3/ NO2 was 0.2 or 0.1 mg/L in 1997

- 2000, and decreased to 0.0032 in 2005

- 2006, with many da ta points for which the MDL

wa s not repor ted (including all years in between those). A value of 0.005 was assigned for NO3/ NO2 data labeled as non

- detect but without a reported MDL, because that is half the value of the MDL for which a U was assigned (i.e., no samples were reported below detect with 0.2 as the detection limit.) The value of 0.003 mg/L was assigned to total phosphorus results labeled as non

- detect for which no MDL was reported because 0.006 mg/L was the only reported MDL for that analyte.Draft 69 August 2010 Apparent outliers of 0.04 mg/L (below d etect) for TKN at both Cedar Keys sites on 1/14/99 and 3/10/99 were checked with SRWMD and it was determined that the y were values in their database. Early 1999 was a period of very low water. On June 11, 19 98 at station CKF020C1 a corrected chlorophyll a of 54.2 μg/L and an uncorrected value of 22.3 μg/L w ere reported . A corrected value reported at that scale and more than double the uncorrected value suggests an analytical error, and although an error could not be verified with SRWMD

, those points were excluded from these analyses as probable erroneous data

.

T he geometric mean s for TN, TP, and chlorophyll a (uncorrected and phaeophytin

- corrected) w ere calculated for each site and each year for which there were at least four data points. There is a ne gative relationship between TN concentrations and salinity (Figure 58 ). It wa s not as strong as in the COAST dataset, and that is likely because the salinity range for these sites is narrower, there are fewer sites in this dataset, and they are all close to shore. Geometric mean TN ranged from 0.6

- 1.5 mg/L (Figure 59)

, geometric mean TP ranged from 0.04

- 0.13 mg/L (Figure 60) , and geometric mean chlorophyll a (corrected and uncorrected, as available) ranged from non

- detect to 6 μg/L ( Figures 61 ) . Annual
g eometric mean nutrient concentrations are somewhat higher at these sites than at the COAST sites overall, and that is likely due to the proximity of all of the SRWMD sites to freshwater sources (see Figure 73 for comparison of locations of COAST and SRWMD sites). The COAST dataset also contains more observations per year for nearly all years.

Table 1 7 . Range of sample sizes used in this analysis for TN, TP, and chlorophyll a data for each site and year. Annual geometric mean not calculated if n<4. Dat a points could be missing due to availability or exclusion of J or Q qualified data.

Note: Phaeophytin

- corrected chlorophyll a data only available 1995

- 2002. Year SRE030C1 SRE050C1 SRE070C1 SRE080C1 CKF020C1 CKF030C1

1995 0-3 0-3 0-3 0-3 3 3

1996 0- 12 0- 12 0- 12 8- 12 9 9

1997 8- 12 8- 12 6- 12 9- 12 11 11

1998 12 12 12 12 5 5

1999 7 7 7 7 7 7

2000 0 0 0 0 6 6

2001 2 2 2 2 6 6

2002 4-6 4-6 4-6 3-6 6 6

2003 5-6 5-6 5-6 5-6 6 6

2004 4-6 5-6 4-6 4-6 6 6

2005 4-6 3-6 5-6 4-6 6 6

2006 5-6 5-6 5-6 5-6 4 4

2007 3-4 4 2-4 4 0 0

2008 2 3 3-5 2 0 0

2009 2-5 2-5 2-5 2-5 0 0Draft 70 August 2010 Figure 58. Annual mean salinity vs. annual geometric mean TN for 4 sites in the Suwannee Estuary, sampled by SRWMD or their contractors. Only site

- years with four or more data points were used. Salinity data include “0” data points from Robbie McKi nney, who indicated confidence in those data points (especially for earlier y ears). Data are from sites as in Figure 38.

Figure 59

. Annu al geometric means for TN at four Suwannee Estuary sites.Draft 71 August 2010 Figure 6 0. Annual geometric means for TP at four Suwannee Estuary sites.

Figure 6 1. Annual geometric means for chlorophyll a at four Suwannee Estuary sites.Draft 72 August 2010 Cedar Keys Water Quality

T he SRWMD data for Cedar Keys were analyzed in the same manner as the Suwannee estuary data. There wa s not a strong relationship between salinity and total nitrogen as was observed at Cedar Keys sites (Figure 6 2 ), likely due to the lack of major freshwater inputs in the immediate vicinity of these sites. Annual geometric means of TN, TP, and chlorophyll a are similar to those of the Suwannee Estuary

. Geometric means range from 0.4

- 1.2 mg/L for TN, 0.04

- 0.09 mg/L for TP, and 2

- 14 μg/L for chlorophyll a ( Fi gures 6 3- 65). The apparent decreasing trend in chlorophyll a is more likely a function of an abnormally high year in 1998 than of a true downward trend.

Figure 6 2. Annual average salinity versus annual geometric mean total nitrogen for sites CKF020C1 and CKF030C1 at Cedar Keys collected by the SRWMD from 1996

- 2006 (n = 22 site

- years).Draft 73 August 2010 Figure 6 3 . Annual geometric mean Total Nitrogen for Cedar Keys SRWMD sites, 1996

- 2006. The dashed and dotted lines indicates the 75 th and 90 th percentile of all annual geometric means, respectively (from both sites, n=22 annual geometric means, calculated with lognormal distribution function).

Figure 64 . Annual geometric mean Total Phosphorus for Cedar Keys SRWMD sites, 1996

- 2006. The dashed and dotted lines ind icates the 75 th and 90 th percentile of all annual geometric means, respectively (from both sites, n=22 annual geometric means, calculated with lognormal distribution function).Draft 74 August 2010 Figure 65 . Annual geometric mean corrected and uncorrected chlorophyll a fo r Cedar Keys SRWMD sites, 1996

- 2006.

Random Sampling by IMAP Program through FWRI
Florida’s Inshore Marine Monitoring and Assessment Program (IMAP) wa s a probabilistic sampling program for Florida’s marine waters that sampled the whole state from 2000

- 2004. This program was conducted by the Florida Wildlife Research Institute (FWRI) in cooperation with EPA Gulf Breeze office. The areas considered in this report were sampled during the following years: Suwannee Sound in 2000 and 2003, Waccasassa and W ithlacoochee Bay s in 2001, and Big Bend in 2002 (including Horseshoe Cove, north of Suwannee)

. Table 1 8 contains summary water quality data from the IMAP program as reported in FDEP ’s IWR database Run 40 (2010). Although the IMAP reports indicate that TN was analyzed, only nitrate/ nitrite data were in the IWR

. Mean chlorophyll a ranged from 6.29

- 22.52 μg/L, mean color ranged from 20

- 167 PCU, and mean TP ranged from 0.053

- 0.093 mg/L. The lowest color and chlorophyll a means co

- occurred with the lowest sa linity value (Table 1 8 ).Draft 75 August 2010 Table 18 . Mean values by area and year for IMAP sampling in the regions of the Suwannee, Waccasassa, and Withlacoochee Estuaries (data from FDEP IWR Run 40). Cedar Keys and Horseshoe Cove were part of the Suwannee Sound sampling unit. Samples for chlorophyll a were dep th integrated, others were surface grabs.
Geographic
Area Year N Chlorophyll a (corrected, μg/L) Color (PCU) Nitrate + Nitrite (mg/L) Total Phosphorus (mg/L) Salinity (ppt )

Cedar Keys 2000 8 16.55 20 0.002 0.062 30.2

Cedar Keys 2003 1 9.75 35 0.009 0.093 20.0

Horseshoe Cove 2000 3 12.42 49 0.006 0.053 20.5

Horseshoe Cove 2002 1 19.94 53 0.002 0.068 21.2

Horseshoe Cove 2003 2 22.52 71 0.002 0.088 19.8

Suwannee Sound 2000 11 12.46 26 0.032 0.067 23.4

Suwannee Sound 2003 7 6.29 167 0.334 0.072 8.1

Waccasassa 2001 12 10.07 30 0.017 0.061 23.5

Withlacoochee 2001 9 12.33 47 0.015 0.057 22.0

IMAP reports from 2000 and 2003 include results for Suwannee Sound, including Cedar Keys and Horseshoe Cove. These reports do not include a qualitative assessment of the study findin gs, but rather just a report of the quantitative results.Draft 76 August 2010 YSI data from FDEP Aquatic Preserves Dataloggers

FDEP staff from the Big Bend Seagrass and St. Martins Marsh Aquatic Preserves maintain YSI dataloggers at three sites within this region , including the mouth of the Suwannee River, Seahorse Key of Cedar Keys, and in the Withlacoochee Estuary. They measure salinity, dissolved oxygen, and temp erature. Results are only available for a limited number of years to date , but F igures 66 – 72 provide a picture of the regime at these sites. Plots of dissolved oxygen were only available for Seahorse Key, and mean values were always greater than 5 mg/L

.

Figure 66. Monthly mean, standard deviation, and ranges of salinity from an on

- site YSI probe datalogger at Seahorse Key, near Cedar Key (from Charbonneau 2010). Zeros indicate missing data due to lag in monitoring effort.

Figure 67

. Monthly mean, standard deviation, and ranges of water temper a ture from an on

- site YSI probe datalogger at Seahorse Key, near Cedar Key (from Charbonneau 2010). Zeros indicate missing data due to lag in monitoring effort.Draft 77 August 2010 Figure 68

. Monthly mean, standard deviation, and ranges of dissolved oxygen from an on

- site YSI probe datalogger at Seahorse Key, near Cedar Key (from Charbonneau 2010). Zeros indicate missing data due to lag in monitoring effort.

Figure 69

. Monthly mean, standard deviation, and ranges of water temperature from an on

- site YSI probe datalogger at the mouth of the Suwannee River (from Charbonneau 2010).Draft 78 August 2010 Figure 70. Monthly mean, standard deviation, and ranges of salinity from an on

- site YSI probe datalogger at the mouth of the Suwannee Ri ver (from Charbonneau 2010).

Figure 71

. Monthly mean, standard deviation, and ranges of water temperature from an on

- site YSI probe datalogger at the mouth of the Withlacoochee River (from Charbonneau 2010).Draft 79 August 2010 Figure 72

. Monthly mean, standard dev iation, and ranges of salinity from an on

- site YSI probe datalogger at the mouth of the Withlacoochee River (from Charbonneau 2010).

Comparison of Nutrient Levels through T ime between Sampling Entities
This section summarizes the annual geometric means calculated by FDEP for TN, TP, and c hlorophyll a for areas that were sampled by more than one organization over various time periods. The purpose of this summary is to compare results by different organiz ations, and to look for trends through time at geographically comparable sites. Table 1 9 compares such pairs of sites (circled in Figure 7 3 ) through time. Data are also show n in Figures 7 4-76 for sites sampled during the same time periods. At these site s, sampling was conducted on different frequencies by different organizations, but all were sampled throughout the year, with > 4 samples used to calculate the geometric mean.

Total phosphorus data compare fairly well, but total nitrogen and chlorophyll a geometric means show some discrepancies. For SRE070C1 and Suwannee

- 4, for which there were eight sampling years in common, the TP values differed by an average of 15% (s.d. = 14%), TN values differed by an average of 27% (s.d. = 17%), and chlorophyll a values differed by an average of 39% (s.d. = 24%). TN values from the SRWMD sampling were always higher than from the COAST sampling (Figure 7 4 ), and chlorophyll a values from COAST tended to be higher than from SRWMD (Figure 7 6 ).

Annual geometric mean TN was plotted against annual mean salinity for SRWMD site SRE070C1 and COAST site Suwannee

- 4 to determine if the apparent bias is simply due to differences in salinity and influence from the river. Indeed, the salinities are different, but the bias remai ns. F or a given salinity, the COAST TN values are lower than the SRWMD values (Figure 7 7 ). It is unknown which values are closest to the true TN concentrations. Duplicate samples have been collected at a subset of COAST sites and are being analyzed by t he FDEP lab in Tallahassee and the LakeWatch Lab to determine comparability of results.Draft 80 August 2010 Table 1 9a. Annual geometric means for TN (mg/L) for estuarine sites in the Suwannee, Waccasassa, and Withlacoochee estuaries. Site pairs and sampling entities as in Figure 7 3.

- = Empty cell/no data Pair Site 1984 1985 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007

1 SRE070C1 - - - 0.85 0.95 0.75 - - 0.58 1.26 1.10 1.22 1.20 -
1 Suwannee -4 - - - 0.69 0.88 0.70 0.63 0.65 0.47 0.99 0.77 0.98 0.76 0.68

2 SRE040C1 - - - 0.87 0.92 0.81 - - - - - - - -
2 Suwannee -5 - - - 0.59 0.58 0.39 0.55 0.52 0.54 0.83 0.59 0.76 0.74 0.51

3 MML WACC -10 - 0.83 - - - - - - - - - - - -
3 Waccasassa -8 - - - 0.61 0.81 0.52 0.58 0.53 0.62 0.60 0.55 0.56 0.57 0.51

4 MML WITH -10 0.47 0.51 - - - - - - - - - - - -
4 Withlacoochee -7 - - - 0.30 0.49 0.33 0.28 0.29 0.26 0.34 0.36 - 0.33 -
5 MML WITH -7 0.63 0.59 - - - - - - - - - - - -
5 Withlacoochee -6 - - - 0.49 0.79 0.49 0.36 0.53 0.51 0.57 0.62 - 0.60 -

Table 1 9b

. Annual geometric means for TP (mg/L) for estuarine sites in the Suwannee, Waccasassa, and Withlacoochee estuaries. Site pair s and sampling entities as in Figure 73.

- = Empty cell/no data Pair Site 1984 1985 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007

1 SRE070C1 - - - 83 78 42 - - 62 103 102 108 49 -
1 Suwannee -4 - - - 77 87 68 62 65 63 93 87 109 76 72

2 SRE040C1 - - - 67 79 54 - - - - - - - -
2 Suwannee -5 - - - 70 67 43 51 52 70 82 64 84 63 56Draft 81 August 2010 Table 1 9c

. Annual geometric means for chlorophyll a for estuarine sites in the Suwannee, Waccasassa, and Withlacoochee estuaries. Site pairs and sampling entities as in Figure 73. All chlorophyll a means shown are not phaeophytin

- corrected.

- = Empty cell/no data Pair Site 1984 1985 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007

1 SRE070C1 - - 3.83 3.31 4.44 3.86 - - 2.21 1.12 2.33 2.76 3.13 2.98

1 Suwannee -4 - - - 2.57 2.85 4.57 5.60 4.92 5.07 4.77 4.00 2.88 4.75 7.12

2 SRE040C1 - - 5.78 4.62 4.17 6.67 - - - - - - - -
2 Suwannee -5 - - - 5.93 7.06 7.71 7.63 8.46 9.98 9.50 5.63 7.81 10.99 10.58

3 MML WACC -10 - 7.14 - - - - - - - - - - - -
3 Waccasassa -8 - - - 7.01 16.55 6.08 6.03 6.42 9.68 7.94 7.99 7.93 6.88 5.86

4 MML WITH -10 4.43 3.65 - - - - - - - - - - - -
4 Withlacoochee -7 - - - 3.78 8.18 3.61 2.21 3.29 2.97 6.34 5.96 3.50

5 MML WITH -7 4.58 3.88 - - - - - - - - - - - -
5 Withlacoochee -6 - - - 4.01 8.70 4.15 3.55 6.74 5.78 6.40 8.11 - 4.60 -Draft 82 August 2010 Figure 73. All study sites for which FDEP analyzed data within this report. Circled areas indicate pairs of sites sufficiently close enough in space for data comparison. 1 – COAST Suwannee

- 4 = SRWMD SRE070C1; 2 – COAST Suwannee

- 5 = SRWMD SRE040C1; 3 – MML WACC

- 10 = COAST Waccasassa

- 8; 4 – MML WITH

- 10 = COAST Withlacoochee

- 7; 5 - MML WITH

- 7 = COAST Withlacoochee

- 6.

Figure 7 4. Comparison of annual geometric mean total nitrogen at 2 pairs of sites in the Suwannee Estuary in which the members of each pair are located fairly close to one another. Site pairs as in Figure 7 3

.Draft 83 August 2010 Figure 7 5. Comparison of annual geometric mean total phosphorus at 2 pairs of sites in the Suwannee Estuary in which the members of each pair are located fairly close to one another. Site pairs as in Figure 7 3

.

Figure 7 6. Comparison of annual geometric mean chlorophyll a (uncorrected) at 2 pairs of sites in the Suwannee Estuary in which the members of each pair are located fairly close to one another. Site pairs as in Figure 7 3

.Draft 84 August 2010 Figure 7 7. The relationship between mean annual salinity and annual geometric mean total nitrogen for two sites located fairly close together in the Suwannee Estuary (sites shown in Figure 7 3

).Draft 85 August 2010 Figure 78

. WBIDs in the Suwannee, Waccasassa, and Withlacoochee Estuary regions, and sampling stations from Project COAST and the SRWMD.



### Waters on the 303(d) L ist

The Gulf of Mexico is listed as impaired for mercury, but FDEP does not believe that the impairment is related to nutrients

.

The Suwannee Estuary is listed as impaired for nutrients because the chlorophyll a concentration in 2004 and 2005 was more than 50% higher than the historic minimum concentration (Table 20 ). The only data available for this IWR a ssessment were from the SRWMD. The TMDL established for nitrate in the Suwannee River (Hallas and Magley 2008) is expected to address this increase

. It should be noted that there is no evidence to suggest that 6 mg/L chlorophyll a is detrimental to aquat ic life use.Draft 86 August 2010 Table 20

. Cycle 2 Verified List of i mpaired w aters – Lower Suwannee Planning Unit

.

IIIM = Class III Marine

WBID Water body Segment Name Waterbody Type Waterbody Class Parameters Assessed under 2007
IWR Concentration Causing Impairment Priority for
TMDL Development Comments

3422D LOWER SUWANNEE ESTUARY ESTUARY III M Nutrients (Chlorophyll

a) Median TN= 1.165 mg/L; Median TP= 0.0944 mg/L High Listed based on two consecutive years of annual average chlorophyll a values that exceeded the historical minimum of 4.0 ug/L by more than 50%. Annual averages: 1997 - 2.79 μg/L; 1998 - 4.63 μg/L; 2002 - 3.43 ug/L; 2004 - 6.14 ug/L; 2005 - 6.44 μg/L; 2006 - 5.06 μg/L.

T he COAST dataset analyzed in this report was not considered in the determination of impairment, and that the chlorophyll a values reported in the COAST study are not corrected for phaeophytin and cannot be directly compared with the early values in Table 16

.
Portions of the Waccasassa Estuary were listed on the 303(d) Verified List as impaired for chlorophyll a due to exceedances of the IWR’s 11 μg/L chlorophyll a threshold for impairment in estuaries (Table 21)

. These exceedances occurred primarily in years of abnormally high rainfall, as documented by Carlson et al. (2010). The data that led to impairment for WBID 8037 are the SRWMD data for Cedar Key, presented above (Figure 65)

. Although the mean chlorophyll a values exceed t he 11 μg/L threshold established in the Impaired Waters Rule, those values are similar to levels detected in studies of this estuary that took place prior to human disturbance ( Putnam 1967, Dixon 1986).Draft 87 August 2010 Table 21. Cycle 2 Verified List of Impaired Waters

– Waccasassa Planning Unit

.

- = Empty cell/no data
WBID Water body Segment Name Waterbody Type Waterbody Class Parameters Assessed under 2007
IWR Concentrati on Causing Impairment Priority for
TMDL Development Comments

3729 BLACK POINT SWAMP ESTUARY III M Nutrients (Chlorophyll

a) Median TN= 1.225 mg/L; Median TP= 0.108 mg/L Medium Annual averages for 1997, 1998, 2000, and 2005 exceeded the threshold of 11 μg/L for estuaries. Annual averages: 1997 - 12.78 μg/L; 1998 - 37.18 μg/L; 2000 - 12.72 μg/L;
2001 - 8.59 μg/L; 2002 - 6.99 μg/L; 2004 - 3.06 μg/L; 2005 - 19.78 μg/L. Based on TN/TP ratios of 3.45 to 28.82 with a median of 11.09 (n=52) over the verified period. Nitrogen and phosphorus are the limiting nutrients.
8037 WACCASASS ARIVER GULF 1 COASTAL III M Nutrients (Chlorophyll

a) Median TN= 0.83 mg/L; Median TP=
0.0643 mg/L Medium Annual averages for 1998 and 2005 exceeded the threshold of 11 μg/L for estuaries. Annual averages: 1997 - 9.94 μg/L; 1998 - 12.95 μg/L;
2000 - 7.93 μg/L; 2001 - 8.24 μg/L; 2002 - 4.90 μg/L; 2004 - 8.93 μg/L;
2005 - 15.45 μg/L. Based on TN/TP ratios of 4.56 to 106.7 with a median of 13.64 (n=98) over the

ver ified period. Nitrogen and phosphorus are the limiting nutrients.Draft 88 August 2010 Impairment for Bacteria

There are also waters in this region that are on the 303(d) list for bacteria (fecal coliforms). They are not listed above because FDEP has evidence that the presence of fecal coliforms does not necessarily indicate an anthropogenic nutrient source. The use of fecal coliforms as indicators of the presence of human pathogens has been under scrutiny in Florida for the past decade. One of the prioritie s of the Gulf of Mexico Alliance ( GO MA ) is the need to improve microbial source tracking and pathogen

detection methods for use under Gulf of Mexico conditions ( GO MA 2009). The GO MA Pathogens Workgroup recently submitted comments regarding the status of E PA recreational water quality criteria (GO MA 2009). They expressed concern that the EPA recreational criteria were derived in places that do not represent Gulf of Mexico conditions, and that the use of fecal indicators was not appropriate for waters prima rily influenced by animal sources. Areas in the Gulf of Mexico for which they thought the EPA criteria may not be appropriate included low population density coastal areas, areas of heavy rainfall, subtropical latitudes, and areas where waters contain a l arge amount of organic detritus material and/or colored dissolved organic matter (CDOM; GO MA 2009). Boehm et al. (2009) express similar concern about the current and proposed recreational criteria, and specifically call attention to the need for further r esearch and revision in tropical waters and waters adversely impacted by urban runoff and animal feces. This is not to say that fecal coliform and E nterococci bacteria cannot indicate human sources or cannot co

- occur with nutrient inputs; this suggests th at there is ample evidence to caution against making the assumption that the presence of these bacteria automatically indicate s the presence of anthropogenic nutrients.

The following text is from a review conducted by Dr. V. Jody Harwood of the University of South Florida as part of a microbial source tracking project she is conducting for FDEP :

The main groups of indicator bacteria for recreational water quality assessment in use today include fecal coliforms, or a specific member of that group, Escherichia coli, in fresh water and the genus Enterococcus in both fresh and estuarine/marine waters. However, in order for the indicator concept to work optimally there are m any assumptions that must hold true. One of the most important assumptions is that indicator bacteria must co

- occur with human pathogens when pathogens are present and pose a human health risk. Unfortunately, recent research has indicated that this

assum ption is often false by showing that the presence of indicator bacteria do not always correlate well with the presence of pathogens such as Salmonella, Campylobacter, Cryptosporidium, Giardia, or enteric viruses (Anderson et al. 2005, Bonadonna et al. 2002, Harwood et al. 2005, Lemarchand and Lebaron 2003, Lund 1996,
Rees et al. 1998).

One important reason for the lack of correlation between traditional fecal indicator bacteria and pathogens is that the indicator bacteria are not specific to humans, nor to other hosts known to shed human pathogens in their feces, but are present in the intestines of all warm

- blooded animals and some cold

- blooded animals (Souza et al. 1999). Because not all animals are equally likely to carry human pathogens, contaminati on from all sources does not represent an equal health risk. Thus, some sources of fecal contamination in water are of greater concern than others. Furthermore, there is increasing evidence of naturalized or environmentally adapted strains indicator bacteria (both coliforms and enterococci) that are capable of persisting in a culturable form for extended periods, or even growing, in a wide variety of environmental matrices, including terrestrial soils, aquatic sediments, and attached toDraft 89 August 2010 aquatic vegetation (Byappanahalli and Fujioka 1998, Byappanahalli et al. 2003, Ishii et al. 2006, Jeng et al. 2005, Ksoll et al. 2007, Solo

- Gabriele et al. 2000, Topp et al. 2003, Whitman et al. 2003). If indicator bacteria are persisting in environmental matrices their

re introduction into the water column, such as might occur during storms or high recreational activity, may lead to false positive indications regarding contamination and public health risk. As a result of these two confounding factors, it is now clear that simply measuring concentrations of waterborne indicator bacteria do not offer detailed enough information to properly determine health risks associated with recreational water use. Furthermore, this practice does not allow specific sources of contamination to be identified or targeted for remediation of water quality.



### Proposed Numeric Nutrient Criteria

The evidence gathered by FDEP and presented in this document demonstrates that the aquatic life use in the Waccasassa and Withlacoochee estuaries is fully supported , and that the aquatic life use in the Suwannee estuary will be fully supported after implementation of the nitrate TMDL

. FDEP therefore proposes that the numeric nutrient criteria be crafted to maintain the nutrient regime of the past 15 years for which data are available, to protect the healthy aquatic life use over that time period

, coupled with reductions of nitrate in the Suwannee that would correspond with implementation of the TMDL

. Due to the strong relationship between salinity and nutri ents, assessment areas should be delineated by salinity, and expected nutrient concentrations should reflect variation based on salinity.

Suwannee Estuary
Anthropogenic nitrate loading is known to be excessive in the Suwannee River . Su bsequently, there is a TMDL for nitrate and proposed nitrate limits for springs within the basin to address the imbalances of flora that have occurred due to the nitrate loading (Hallas and Magley 2008). Despite the riverine loading, the estuary has a healthy fishery, no impairments of dissolved oxygen, and no harmful algal blooms. Evidence shows that high flow events from the Suwannee River have contributed to losses and changes in the SAV community in Horseshoe Cove (Carlson et al. 2010) and possi bly the deep edges of Springs Coast seagrasses (Hale et al. 2004, Jolliff et al. 2003) . Studies by Quinlan (2003) showed color to be the chief factor in light limitation in the Suwannee Estuary

, but p reliminary results of FWRI studies suggest that chlorop hyll a and turbidity play a greater role in light limitation in the Big Bend region as a whole (Paul Carlson, personal communication). D uring a period of low flow, when the river wa s more dominated by anthropogenic loading of nitrate

- nitrite, increased ma croalgal growth wa s observed in the near shore oyster beds ( Quinlan 2010). Current nutrient loading to the estuary is higher than in years before human settlement, but it is unclear if there have been any long term negative impact s thus far on the estuary

. FDEP is confident that once the TMDL for the Suw annee River is met, the nutrient levels within the estuary will be fully protective of the designated aquatic life use.

Waccasassa Bay
Anthropogenic loading to Waccasassa Bay is extremely small, yet the b ay has the highest nutrient and chlorophyll a concentrations of the region. These levels are due to the high percentage of wetlands in the watershed and the shallow and turbid nature of the estuary. Waccasassa Bay naturally has lower water clarity than t he coastal areas to the north and to the south, so the SAV communities are not as well developed or studied . However, evidence gathered in this report demonstrates that conditions have not changed in this estuary since t he 1960s ( including chlorophyll a concentrations ) , so it is logical that the existing condition protects the aquatic life use in the estuary.Draft 90 August 2010 Withlacoochee Estuary

The Withlacoochee River is subject to some human development, but i s also characterized by an abundance of protected land

, and the river serves as a freshwater reference site . The estuary has been hydrologically modified by the Inglis Dam and the Cross Florida Barge Canal. It is possible that this modification actually prevents some of the nutrient loading from reaching the estuary. TN and chlorophyll a concentrations have not changed since the mid

- 1980s in this estuary, which suggests that anthropogenic activities are not having any measureable effect on the estuary.

[FDEP is seeking input on appropriate regionalization or separation by salinity in these estuaries ]

Methodology for Criteria Development
For consistent application and for providing an appropriate level of protection, water quality criteria need to include magnitude, frequency, and duration components. The mag nitude is a measure of how much of a pollutant may be present in the water without an unacceptable adverse effect. Duration is a measure of how long the pollutant may be above the magnitude, and frequency relates to how often the magnitude may be exceeded without adverse effects. It is preferred to derive the magnitude component of a criterion through a cause

- effect relationship (such as those measured through toxicity testing). The magnitude would then be set at a level that would protect a majority of the sensitive aquatic organisms inhabiting the system. Absent a demonstrated cause

- effect relationship, the magnitude may be set at a level designed to maintain the current data distribution, accounting for natural temporal variability, when the current conditions are protective of the designated uses of the waterbody. Since a criterion derived based on the existing data distribution has no direct link to any observed cause and effect relationship, it is assumed that maintaining the current data distribu tion will preserve the uses associated with that distribution.

The frequency and duration components of the criteria are best established as additional descriptors of the reference condition data distribution. Specifically, these components should be pa rt of a statistical test designed to determine whether the long

- term distribution of data has shifted upward ( or in some cases, downward) from the reference distribution. This test would then be used to determine whether future monitoring data are consis tent with the magnitude (long

- term average) defined by the reference dataset. It is critical to account for the natural variability surrounding the magnitude expression and to control for statistical errors.

The derivation of the magnitude, frequency an d duration components of the numeric nutrient criteria for Suwannee, Waccasassa, and Withlacoochee Estuaries is described briefly below. More details concerning the statistical approaches used can be found in the document “Overview of FDEP Approaches for Nutrient Criteria Development in Marine Waters” (FDEP 2010).

Magnitude
The magnitude component can be set at a variety of values based on the frequency and duration that will be used to determine compliance. For the “healthy existing conditions” approach , FDEP established the magnitude at: a) an adjusted long

- term central tendency (geometric mean) of the distribution, expressed as a long

- term geometric mean never to be exceeded; and b) an annual geometric mean, not to be exceeded more than two times over a five - year period. The long

- term average condition was adjusted to a level that represents an insignificant increase from the baseline. Allowing for an insignificant increase accounts for uncertainty in the estimate of the mean and partially addresses the fact that the reference based approach fails to identify a threshold of imbalance, and thus is highlyDraft 91 August 2010 prone to excessive Type I error. For the purpose of antidegradation evaluations, EPA has established that a ten percent change in a water quality pa rameter represents an insignificant departure from the historical condition, known as a de minimus change (US Sixth Circuit Court 2008). Therefore, the long

term geometric mean limit was derived to allow for up to a ten percent increase in the long

- term
g eometric mean, which was calculated as the geometric mean of the annual geometric means of the long

- term dataset for each segment of the waterbody.

Because it is not always practical to assess compliance with the criteria on the same long

- term basis,
FDEP also developed criteria expressed as an annual geometric mean so that estuaries could be assessed on an annual basis. It should be noted that the duration and frequency components of the criteria must be linked to the response timeframe of the sensitive e ndpoint. Short

- term averaging periods (e.g., 1 to 30 days) might be appropriate for nutrient criteria where a sufficiently robust cause

- effect relationship has demonstrated that a eutrophic response occurs over such timeframes. If however, such a short

t erm response cannot be demonstrated, or there is no indicati on of use impairment, longer averaging periods should be used.

Duration and Frequency
Since the duration and frequency components of the criteria must be consistent with the derivation of the ma gnitude component, the long

- term geometric mean target cannot simply be applied as an annual

mean. Doing so would result in an unacceptability high Type I failure rate (identifying a healthy system as being impaired) since approximately 50 percent of the individual yearly means are expected to be above the long

- term mean. Therefore, the long

- term target must be adjusted to allow for the application to a shorter duration with an acceptable Type I error rate of no more than a 10 percent.

An annual criterion with an approximate 10 percent Type I error rate for a given frequency was derived by appropriately accounting for the annual variability above the mean. This annual target concentration was derived as an upper percentile of the distribution of the annua l geometric mean concentrations. Previous proposals by EPA have utilized three

- year assessment periods to express the duration nutrient criteria components. Although it is possible to construct a test that achieves the 10 percent Type I error rate targe t over a 3

- year period, a slightly longer period (5 years) will provide better control for Type II error and will more fully capture climatic cycles ( e.g ., el nino, la nina), which tend to be longer than three years in Florida (and may actually be on a mul ti

- decadal scale). Furthermore, a five year period is more consistent with both the State’s five year 303(d) assessment and NPDES permit renewal cycles.

Given a five year a ssessment period, FDEP derived criteria expressed as an annual geometric mean by

us ing the 75 th percentile of the annual geometric means from the long

- term dataset. FDEP demonstrated that setting the criteria at this percentile results in a magnitude that, when expressed as an annual geometric mean not to be exceeded more than twice dur ing a five

- year period, will achieve the targeted 10 percent error rate

. The magnitude component of the criteria (not to be exceeded more than twice in a 5 year period) was established to allow for two separate assessments:

**•** As an annual geometric mean for a network of stations in a specified segment of the waterbody; and

**•** As an annual geometric mean for a single station in a given segment.

The two expressions of magnitude differ in the handling of within

- segment spatial variability. The network average magnitude was calculated based on the distribution of spatially averaged annualDraft 92 August 2010 geometric means, while the single site magnitude was calcula ted using the distribution of station annual geometric means. Use of the network average magnitude is appropriate for assessing overall segment
status. However, a network average is only representative of overall segment status if it is relatively homog eneous. If the segment is not well mixed, is very large, or contains localized nutrient sources, then there is a potential that isolated areas of enrichment may be masked in the network spatial
average. Therefore, the single station annual geometric mean has the benefit of assessing localized enrichment patterns. DEP has not decided whether both expressions of magnitude are needed in all cases, and we are seeking additional feedback from local experts and stakeholders.

Summary of the Proposed Criteria

FD EP proposes three sets of potential criteria: a) a long

- term geometric mean concentration; b) an annual geometric mean of values from a network of stations over a given area, not to be exceeded more than twice in a five

- year period; and c) an annual geome tric mean of values from a single location, not to be exceeded more than twice in a five

- year period.

The proposed long

- term concentrations for the protection of a healthy, well

- balanced aquatic community in Suwannee, Waccasassa, and Withlacoochee Estuaries, as well the annual limits for each segment, are provided in Table 22. Offshore values represent stations with annual average salinity greater than 25 ppt. Nearshore values represent stations with annual average salinity less than 25 ppt and greater th an 3 ppt. The following COAST sites were excluded due to their predominantly fres h nature (mean salinity < 3 ppt ): Suwannee sites 1 and 2, Waccasassa site 1, and Withlacoochee sites 2 and 3. Suwannee offshore sites were COAST sites 7, 8, 9, and 10, and two SRWMD stations at Cedar Keys. Suwannee COAST sites 3, 4, 5, and 6 , and six SRWMD Suwannee River Estuary (SRE) sites were used for the nearshore calculation. Waccasassa COAST sites 6, 7, 9, and 10 represent the offshore region, and sites 2, 3, 4, 5, and 8 comprised the nearshore. For the Withlacoochee, the offshore region includes COAST sites 4, 7, and 10, and the nearshore region includes COAST sites 1, 5, 6, 8, and 9. NOTE: Values proposed for nearshore Suwannee TN and chlorophyll a will be revised to take into account reductions in nitrate required for the Suwannee River TMDL. All COAST chlorophyll a data used are not corrected for phaeophytin.Draft 93 August 2010 Table 22 a
. Propos ed numeric nutrient criteria for all segments of the Suwannee Estuar y for TP, TN, and chlorophyll a. For compliance purposes, the long term geometric mean shall not exceed the long term limit nor shall the average of all stations in a segment exceed the network average more than twice in a 5 year period. The last column shows the value which single station shall not exceed, by segment, more than twice in a 5 year period.

- = Empty cell/no data

Segment LT_GM LT_Limit Network Average 2:5 Annual Limit Asse ssed as a Single Site
GM 2:5 Annual Limit Comments

TP - - - - - Nearshore 69.7 76.7 92.8 101.6 - Offshore 32.3 35.5 43.9 46.8 - TN - - - - - Nearshore 722 794 969 1075 T o be determined Offshore 422 464 560 600 - Chla - - - - - Nearshore 4.60 5.06 7.25 9.84 T o be determined Offshore 5.27 5.79 7.40 7.83

Table 22 b . Proposed numeric nutrient criteria for all segments of the Withlacoochee Estuary for TP, TN, and chlorophyll a. For compliance purposes, the long term geometric mean shall not exceed the long term limit nor shall the average of all stations in a segment exceed the network average more than twice in a 5 year period. The last column shows the value which single station shall not exceed, by segment, more than twice in a 5 year period.

- = Empty cell/no data Segment LT_GM LT_Limit Network Average 2:5 Annual Limit Assessed as a Single Site GM 2:5 Annual Limit
TP - - - - Nearshore 39.4 43.3 50.0 51.8

Offshore 25.6 28.2 33.5 34.0

TN - - - - Nearshore 427 470 536 546

Offshore 326 358 408 413

Chla - - - - Nearshore 5.31 5.84 7.46 7.68

Offshore 3.80 4.18 5.66 5.78Draft 94 August 2010 Table 22 c
. Proposed numeric nutrient criteria for all segments of the Waccasassa Estuary for TP, TN, and chlorophyll a. For compliance purposes, the long term geometric mean shall not exceed the long term limit nor shall the average of all stations in a segment exceed the network average more than twice in a 5 year period. The last column shows the value which single station shall not exceed, by segment, more than twice in a 5 year period.

- = Empty cell/no data Segment LT_GM LT_Limit Network Average 2:5 Annual Limit Assessed as a Single Site GM 2:5 Annual Limit
TP - - - - Nearshore 56 62 69 76
Offshore 35 38 47 55
TN - - - - Nearshore 627 690 772 835 Offshore 480 528 610 664
Chla - - - - Nearshore 6.3 7.0 8.8 10.8
Offshore 5.0 5.5 8.0 9.4Draft 95 August 2010 

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