Site-Specific Information 

in Support of Establishing Numeric 

Nutrient Criteria in Suwannee 

Estuary/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, 2010 
Draft ii August 2010

Table of Contents

Executive Summary ............................................................................................................... 1

Geographic and Physical Description ..................................................................................... 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 Closures........................................................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 Estuary .................................................................................................................90

Methodology for Criteria Development.........................................................................................90

Summary of the Proposed Criteria................................................................................................. 92

References .......................................................................................................................... 95
Draft 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 bold 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-corrected 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 Quinlan 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)...............................................66
Draft iv August 2010

Table 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 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 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. .........................................................................................................................................94
Draft 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 saltwater 

marshes along the shores............................................................................................................10

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 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 aerial 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.................................. 29
Draft 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 Wildlife 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/trip) 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 trichromatic 

method. .......................................................................................................................................44

Figure 30. Mean total nitrogen (μg/L) across all sample years (approx. 1997-2009) and all 

estuary sites (excludes 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)......................................................50
Draft 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 estuarine sites. .....................................56

Figure 46. Stations 1 and 2 excluded for Suwannee, Station 1 excluded for Waccasassa, and 

Stations 2 and 3 excluded for Withlacoochee. R2

= 0.84 for Suwannee, R2= 0.36 for 

Waccasassa, R2

= 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. R2

= 0.87 for Suwannee, R2= 0.40 for 

Waccasassa, R2

= 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 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 exceeded only 1% of all dates from 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). ...................................................................................................................................68
Draft viii 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 McKinney, 

who indicated confidence in those data points (especially for earlier years). Data are 

from 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 75th and 90th 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 75th and 90th 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 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 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 Withlacoochee-6. ..............................................................................82
Draft 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. ...........................................................85
Draft 1 August 2010

Executive Summary

This report was prepared by the Florida Department of Environmental Protection (FDEP), in cooperation 

with local scientists, to support the development of numeric nutrient criteria for the Suwannee, 

Waccasassa, and Withlacoochee Estuaries. 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 Withlacoochee 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 coastal 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 nonchlorophyll particulates are the major contributors to light limitation, except at times of very low river 

flow. During low flow periods, the river is dominated by Floridan Aquifer spring flow, and water clarity 

and anthropogenic nitrate concentrations are high. 

Submersed 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). The 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 anthropogenic activity in the basin. The nutrient inputs are associated with the high 

percentage of wetlands in the watershed and the shallow nature of the estuary, 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 Estuary has been hydrologically modified by the Inglis Dam, the Cross Florida Barge 

Canal, and the Crystal River Power Plant. The Withlacoochee River, which originates 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 Inglis 
Draft 2 August 2010

dam actually prevents some of the natural 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 there 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 nutrient 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 report 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 1a. Checklist of nutrient enrichment symptoms in the Suwannee, Waccasassa, and Withlacoochee 

Estuaries

Response 

Variable

Observed 

Historically

or 

Currently?

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 phenomenon.

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 community 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 for 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 Withlacoochee 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 

drain 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 arises 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 Georgia. 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 throughout the watershed, the region contains fewer lakes than other 

areas of the state, but wetlands are plentiful. There are 98 known springs that discharge within the 

Suwannee River coastal drainage area; 4 are 1st magnitude and 39 are 2nd magnitude. The River flow is 

highly influenced by springs during periods of low rainfall. During normal to high flows, the 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 silviculture and agriculture (Table 

1). Large timber 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 urbanized 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, and 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 FDEP 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 (km2

) 

Suwannee Sound – 

70 km2 Horseshoe 

Cove – 140 km2

40 km2 (EPA), 

49,749 acres or 

201 km2

 (DACS)

52,000 acres (DACS 

report)

Carlson et al. 

2010

Watershed area 

(km2

) 

26,000 km2

Coastal drainage area 

(Lower Suwannee 

HUC)- 4568 km2 and 

includes Levy, Dixie, 

Taylor, Gilchrist, 

Columbia, Suwannee, 

Madison Counties

CDA =2,128 km2

and includes 

Gilchrist, Alachua, 

Levy, and Marion 

Counties

CDA = watershed = 

5133 km2 and 

includes Citrus, 

Sumter, Marion, 

Hernando, Polk, 

and Lake Counties.

NOAA 2007

Charbonneau

HUC Area (km2) Lower Suwannee HUC 

= 4,088 

2,334 5,332 FDEP ArcGIS 

HUC coverage

Mean depth (m) 2.24 m 1.69 m 2.24 m Project COAST 

sampling, 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 

Withlacoochee 

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 associated 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 10.00
Draft 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 southeasterly 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 

propel 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 prevailing 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 River 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 maximum 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 fishing 

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 Ecological 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).

Aquaculture 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), seagrass 

coverage (continuous, discontinuous), 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 that 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 potentially

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 interpolated when cloud cover obscured retrieval (from Jolliff et al. 2003). 
Draft 12 August 2010

Figure 5. MODIS satellite 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.

Waccasassa 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 

Waccasassa 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 (CDA). 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. Wetlands 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

Wind-driven resuspension of organic materials in the estuary contributes 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 km2 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 (predominantly 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, originating from the Floridan 

Aquifer-fed Rainbow Springs. 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. The 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 north. 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, and 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, including 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 watershed. 

Public land ownership is significant 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 bay 

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 Withlacoochee 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 rate 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, personal 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 report 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 nitrate, 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 the 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 facilities 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 very 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 elevated 
Draft 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 Basin 

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 (Harrington 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. Wildlife also likely contributes 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 Network (2001-2006) from Harrington 

et al. (2010). 
Draft 21 August 2010

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

Waccasassa 

There are several domestic wastewater facilities that discharge in the watershed, with three facilities 

that discharge to percolation ponds, two facilities that discharge to surface water outfalls, and three 

facilities that discharge to land application (Charbonneau 2010; Table 5). Percolation ponds and land 

application sites likely contribute nutrients 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 wastewater. Stormwater 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 likely 

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 watershed 

include cattle ranching, row crops, sod, pasture, pine plantation, and cypress harvesting. The primary 

industrial 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 wetlands 

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. Historically, 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 rural 
Draft 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 increased 

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 loads 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 businesses 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 Withlacoochee 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

FLG110651 CEMEX Construct Materials FL LLC - Belleview 

Ready Mix Plant

CBP 0.00 Marion

Biological Summary

SAV and Species Composition

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 macroalgae. 

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). Carlson 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 clarity 
Draft 25 August 2010

was due to excessive color, turbidity, or chlorophyll a. Preliminary results from a 2004-2009 optical 

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 River, 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, FWRI, 

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 potentially 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). There 

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 

seagrass, 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 Aquatic 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, totaling 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 m2 “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 =heavy), 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 Key. Overall, preserve staff monitor 100 seagrass stations from Crystal River to 

St. Marks. The database is relevant for comparing parameters like species composition, blade lengths, 

total coverage and sediment types along the entire Big Bend coastline. 

The 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 attributed to the patchiness of seagrass 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 is 
Draft 28 August 2010

the only green marcoalgae 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 River. 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 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.
Draft 30 August 2010

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. 

Phytoplankton Species Composition

Putnam (1967) studied algal production and photosynthesis in the Waccasassa Estuary and found that, 

93% of the time, production in the Waccasassa Bay 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 concluded that “the land 

apparently is infertile and following heavy rains nutrients leach out of the soil in insufficient amounts to 

alter productivity 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 marine portions (E. Quinlan, personal communication). She suggests that the Suwannee River’s 

low salinity outflow precludes the maintenance of K. brevis blooms (Quinlan and Phlips 2007).

Macroalgal Species Composition and Biomass (Including 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 distribution 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 levels 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

AugNov

Feb

May

AugNov

Feb

May

AugNov

Feb

1999 2000 2001

Ulva lactuca, Enteromorpha intestinalis, Laurencia spp.

Ulva lactuca, Gracilaria spp., Ectocarpus spp.

Maximum Dry Weight (grams m-2)

Quantitative Samples Collected
Draft 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 Production and Frequency/Duration of Bed Closures

There are five monitored shellfishing areas within the region covered in this summary: Horseshoe Beach, 

Suwannee Sound, Cedar Key, Waccasassa Bay, and Withlacoochee Bay. Information can be accessed 

through the Florida Department 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, 2004b, 2004c, Kuhnman 2004, 2007). There are 

open, closed, and conditionally approved shellfish harvesting areas within those regions, and those 

assignments are dependent 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 levels 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 of 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 seasonal changes in community composition were observed, due to 

recruitment of young of year fish (YOY). 

 

<5

45
Draft 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. The 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. Fish species spatial distribution was driven primarily by salinity (Tukey 

and Dehaven 2006). The authors commented that maintenance of healthy seagrasses is critical to 

fisheries support in this area. The results of Tukey and Dehaven’s (2006) study were similar 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 

Independent Monitoring (FIM) Program operated by the FWCC (Figure 24). FWCC produces 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). The FIM program has been sampling in the Cedar 

Keys/Suwannee Sound area for 10 years, but no long 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 Independent Monitoring 

program stratified random sample areas, 2008. Totals in bold represent total of top 10 dominant, 

total recreationally important species, and grand total. 
Draft 36 August 2010

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.

Table 8. Number of recreationally important species (Selected Taxa) collected in the Fisheries 

Independent Monitoring program stratified random sample areas, 2008.
Draft 37 August 2010

Quantification of Landings from Commercial/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 

Counties (Figures 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

2008
Draft 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

2008
Draft 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 become 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 until 

January 2006, in Dixie and Levy counties, resulting in temporary closures of the Cedar Key, Suwannee 

Sound, Horseshoe Beach and Waccasassa Bay shellfish harvesting areas. This event affected essentially 

all of the Florida Gulf Coast with no previous event of this magnitude recorded in this region (Kuhnman 

2007). From 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 (DeHaven 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 January 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 for 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 fish. 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 the 
Draft 40 August 2010

Caloosahatchee River 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. brevis blooms, a combination of sources 

is required to maintain a high biomass blooms (>106 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 reports or 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 studies included:

• 1964 study of Waccasassa Bay (Putnam 1967); 

• Mote Marine Lab study of the Waccasassa and Withlacoochee Rivers 1984-1985; 

• Project COAST, Dr. Tom Frazer, UF IFAS. Monthly monitoring at ten sites at each of these 

three estuary systems monthly since 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 projects 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 Suwannee Estuary sites 1997-2009, data 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 Study 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/m3

), 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 higher 

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 Study 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 determination. 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. Metered 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 authors’ 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 dependent 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 Waccasassa. 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 chlorophyll 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 lower 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 available 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 1984-1985 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, 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.

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/m3

) 

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 Data Analysis 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). 

Uncorrected 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 1984-1985 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 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)

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

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

Project COAST, 1997–Present 

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 depth, 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 FDEP 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 available. 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 nitrogen, 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 Niño 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 estuary 

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

700

TN (ug/L)

Mean Total Nitrogen (μg/L) by System

0

10

20

30

40

50

60

TP (ug/L)

Mean Total Phosphorus (μg/L) by System
Draft 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

12

CHL (ug/L)

Mean Chlorophyll-a (μg/L) by System
Draft 48 August 2010

Figure 33. Long term average data for the Suwannee Estuary, including all estuary sites (excludes 

freshwater sites) (from 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-08

TN (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-08

TP (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-08

CHL-a (ug/L)

Suwannee Average Chlorophyll-a (CHL-a)

1997 through 2008 Estuarine Stations 
Draft 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-08

TN (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-08

TP (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-08

CHL-a (ug/L)

Waccasassa Average Chlorophyll-a (CHL-a)

1997 through 2008 Estuarine Stations 
Draft 50 August 2010

Figure 35. Long term average data for the Withlacoochee Estuary, including all estuary sites (excludes 

freshwater sites). From Frazer and Jacoby (2010). 

Data Analyses by FDEP

Project COAST data 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 12). Annual geometric means of total nitrogen, total phosphorus, and 

chlorophyll a (uncorrected) were calculated and plotted for each station each year (Figures 37-45). The 

following sites were excluded from calculation of geometric means due to predominantly fresh 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 37 and 40). 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 from 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-08

TN (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-08

TP (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-08

CHL-a (ug/L)

Withlacoochee Average Chlorophyll-a (CHL-a)

1996 through 2008 Estuarine Stations 
Draft 51 August 2010

The zonation was more gradual in the Waccasassa, with geometric means ranging from 400-700 μg/L for 

TN and 20-60 μg/L for TP (Figures 38 and 41). Zonation in the Withlacoochee was also gradual, with 

geometric means ranging from 250-500 μg/L for TN and 20-40 μg/L for TP (Figures 39 and 42). The 

geographic zonation is different for chlorophyll a due to the interaction with color, described below. 

There is a clear negative relationship between salinity and TN and between salinity and TP for all three 

systems, though the relationship is weakest for the Waccasassa (Figure 46 and 47). The strength of 

these relationships can likely be explained by the level to which the estuaries are dominated by the 

rivers that feed them or the locations of the sites (Figure 36). 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 49) 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 bay (Figure 50).

For chlorophyll a, there is a peak in concentration (~10-12 μg/L) at mid-salinity (see Suwannee example 

in Figure 48 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 riverdriven 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 shown for the Suwannee in Figure 48. These data suggest 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 available
Draft 52 August 2010

Figure 36. Project COAST sampling sites in the Suwannee, Waccasassa, and Withlacoochee estuaries.

Figure 37. Mean TN at Project COAST Suwannee estuarine sites.
Draft 53 August 2010

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

Figure 39. Mean TN at Project COAST Withlacoochee estuarine sites.
Draft 54 August 2010

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

Figure 41. Mean TP at Project COAST Waccasassa estuarine sites.
Draft 55 August 2010

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

Figure 43. Mean chlorophyll a at Project COAST Suwannee estuarine sites.
Draft 56 August 2010

Figure 44. 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 46. Stations 1 and 2 excluded for Suwannee, Station 1 excluded for Waccasassa, and Stations 2 

and 3 excluded for Withlacoochee. R2

= 0.84 for Suwannee, R2= 0.36 for Waccasassa, R2= 0.70 for 

Withlacoochee. 

Figure 47. Stations 1 and 2 excluded for Suwannee, Station 1 excluded for Waccasassa, and Stations 2 

and 3 excluded for Withlacoochee. R2

= 0.87 for Suwannee, R2= 0.40 for Waccasassa, R2= 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 10
Draft 59 August 2010

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.

0

200

400

600

800

1000

1200

1400

0 5 10 15 20 25 30 35

Geometric 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 35

Geometric 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 35

Geometric 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

2007
Draft 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 51 and 52), and the geometric means were typically within 1 μg/L of each other (Table 14). This 

comparison is important because FDEP prefers to use phaeophytin-corrected values for assessment 

purposes. 

0

200

400

600

800

1000

1200

1400

0 50 100 150 200

Geometric 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 35

Annual 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

2007
Draft 61 August 2010

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.

Table 14. 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 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.

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 Estuary, 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 analyses: chlorophyll, 

bacteria, TP, SRP, TN, NO3, NO2, NH4, Silica, and nutrient limitation experiments. She 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 methods. 

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-limiting in the nearshore region. An example of this limitation can be 

seen in the chlorophyll a estimates of 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 seasonal 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 plume may play a significant role in defining the abundance and 

distribution of microalgae in the sediment of the Suwannee River estuary. 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 dominated 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 

exceeded only 1% of all dates from 1960-2001. Figure from 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 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). 

The 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). 

Only during very low flow periods was 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 productive 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 (oyster 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 salinity as the most important factor (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). During 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 portions (E. Quinlan, personal communication). She suggested that the Suwannee River’s low 

salinity outflow precludes the maintenance of K. brevis blooms (Quinlan and Phlips 2007).

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). 
Draft 67 August 2010

Suwannee River Water Management District Monitoring 

The Suwannee River Water Management District (SRWMD) has sampled four estuary sites bimonthly in 

the Suwannee Estuary from 1995-present (Figure 56). Robbie McKinney of the SRWMD analyzed these 

long term data using Lowess regression, and found no significant trends for TKN, NO2+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 hypothesized 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 detection 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 57. Location of SRWMD sampling sites in the Suwannee River Estuary (SRE) and Cedar Keys 

(CKF). 

FDEP Analysis of SRWMD Data

FDEP analyzed 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 17 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 data qualified with “J” and “Q” remark codes 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 data points for which the MDL 

was not reported (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 detect) for TKN at both Cedar Keys sites on 1/14/99 and 3/10/99 

were checked with SRWMD and it was determined that they were values in their database. Early 1999 

was a period of very low water. On June 11, 1998 at station CKF020C1 a corrected chlorophyll a of 54.2 

μg/L and an uncorrected value of 22.3 μg/L were 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. 

The geometric means for TN, TP, and chlorophyll a (uncorrected and phaeophytin-corrected) were

calculated for each site and each year for which there were at least four data points. There is a negative 

relationship between TN concentrations and salinity (Figure 58). It was 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 

geometric 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 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. 

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 0 
Draft 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 McKinney, who indicated confidence in those data 

points (especially for earlier years). Data are from sites as in Figure 38.

Figure 59. Annual geometric means for TN at four Suwannee Estuary sites.
Draft 71 August 2010

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

Figure 61. Annual geometric means for chlorophyll a at four Suwannee Estuary sites.
Draft 72 August 2010

Cedar Keys Water Quality

The SRWMD data for Cedar Keys were analyzed in the same manner as the Suwannee estuary data. 

There was not a strong relationship between salinity and total nitrogen as was observed at Cedar Keys 

sites (Figure 62), 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 

(Figures 63-65). 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 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). 
Draft 73 August 2010

Figure 63. Annual geometric mean Total Nitrogen for Cedar Keys SRWMD sites, 1996-2006. The 

dashed and dotted lines indicates the 75th and 90th 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 indicates the 75th and 90th 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 for Cedar Keys SRWMD 

sites, 1996-2006. 

Random Sampling by IMAP Program through FWRI

Florida’s Inshore Marine Monitoring and Assessment Program (IMAP) was 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 Withlacoochee Bays in 2001, and Big Bend in 2002 (including Horseshoe 

Cove, north of Suwannee). Table 18 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 salinity value (Table 18). 
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 depth 

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 findings, 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 temperature. 

Results are only available for a limited number of years to date, but Figures 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 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.
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 River (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 deviation, 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 Time between Sampling Entities

This section summarizes the annual geometric means calculated by FDEP for TN, TP, and chlorophyll 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 organizations, and to look for trends through time at 

geographically comparable sites. Table 19 compares such pairs of sites (circled in Figure 73) through 

time. Data are also shown in Figures 74-76 for sites sampled during the same time periods. At these 

sites, 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 74), and chlorophyll a 

values from COAST tended to be higher than from SRWMD (Figure 76). 

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 remains. For a given salinity, 

the COAST TN values are lower than the SRWMD values (Figure 77). 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 the FDEP lab in Tallahassee and the LakeWatch Lab to determine 

comparability of results.
Draft 80 August 2010

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. 

- = 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 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. 

- = 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 56 
Draft 81 August 2010

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. 

- = 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 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. 
Draft 83 August 2010

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. 

 

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. 
Draft 84 August 2010

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).
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) List 

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 assessment 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 aquatic life use.
Draft 86 August 2010

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

IIIM = Class III Marine

WBID Waterbody

Segment 

Name 

Waterbody 

Type

Waterbody 

Class

Parameters 

Assessed 

under 2007 

IWR 

Concentration 

Causing 

Impairment 

Priority for 

TMDL 

Development

Comments 

3422D LOWER 

SUWANNEE 

ESTUARY 

ESTUARY IIIM Nutrients 

(Chlorophylla)

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. 

The 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 the 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 Waterbody

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 IIIM Nutrients 

(Chlorophylla)

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 IIIM Nutrients 

(Chlorophylla)

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 

verified 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 priorities of the 

Gulf of Mexico Alliance (GOMA) is the need to improve microbial source tracking and pathogendetection methods for use under Gulf of Mexico conditions (GOMA 2009). The GOMA Pathogens 

Workgroup recently submitted comments regarding the status of EPA recreational water quality criteria 

(GOMA 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 primarily 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 large amount of organic detritus 

material and/or colored dissolved organic matter (CDOM; GOMA 2009). Boehm et al. (2009) express 

similar concern about the current and proposed recreational criteria, and specifically call attention to 

the need for further research and revision in tropical waters and waters adversely impacted by urban 

runoff and animal feces. This is not to say that fecal coliform and Enterococci bacteria cannot indicate 

human sources or cannot co-occur with nutrient inputs; this suggests that there is ample evidence to 

caution against making the assumption that the presence of these bacteria automatically indicates 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 many 

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 

assumption 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, 

contamination 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 to 
Draft 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 

reintroduction 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 nutrients, 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. Subsequently, 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 possibly 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 preliminary results of FWRI studies 

suggest that chlorophyll a and turbidity play a greater role in light limitation in the Big Bend region as a 

whole (Paul Carlson, personal communication). During a period of low flow, when the river was more 

dominated by anthropogenic loading of nitrate-nitrite, increased macroalgal growth was 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 impacts thus far on 

the estuary. FDEP is confident that once the TMDL for the Suwannee 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 bay 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 the 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 the 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 is 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 magnitude 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 distribution 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 part 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 consistent 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 and 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 highly 
Draft 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 parameter represents an insignificant departure from the 

historical condition, known as a de minimus change (US Sixth Circuit Court 2008). Therefore, the longterm geometric mean limit was derived to allow for up to a ten percent increase in the long-term 

geometric 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 endpoint. 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 shortterm response cannot be demonstrated, or there is no indication 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 magnitude 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 annual 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 target 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 multi-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 assessment period, FDEP derived criteria expressed as an annual geometric mean by 

using the 75th 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 during 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 annual 
Draft 92 August 2010

geometric means, while the single site magnitude was calculated 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 

homogeneous. 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

FDEP 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 geometric 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 than 3 ppt. The following COAST sites were excluded due to their predominantly fresh 

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 22a. Proposed numeric nutrient criteria for all segments of the Suwannee 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

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 To be 

determined

Offshore 422 464 560 600 - 

Chla - - - - - 

Nearshore 4.60 5.06 7.25 9.84 To be 

determined

Offshore 5.27 5.79 7.40 7.83

 

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. 

- = 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 5.78
Draft 94 August 2010

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. 

- = 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 9.4
Draft 95 August 2010

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