Site-Specific Information 

in Support of 

Establishing Numeric Nutrient 

Criteria in Greater Apalachee Bay

Division of Environmental Assessment and Restoration

Standards and Assessment Section

Florida Department of Environmental Protection

Tallahassee, FL 32399

August 13, 2010 
Draft ii August 2010

Table of Contents 

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

Geographic and Physical Description ..................................................................................... 3

Sources and Fates of Nutrients .............................................................................................. 3

Point Sources ...................................................................................................................... 13

City of Tallahassee Nitrate Contribution........................................................................................14

Nonpoint Sources................................................................................................................ 14

Biological Summary............................................................................................................. 14

SAV in the Econfina/Fenholloway Systems....................................................................................17

Phytoplankton Density and Taxa in the Fenholloway/Econfina Systems.........................................22

SAV in the Steinhatchee Estuary ...................................................................................................22

Presence and Frequency of Harmful Algal Blooms (HABs) in the Econfina/Fenholloway 

Systems........................................................................................................................................27

Shellfish Production and Frequency/Duration of Bed Closures in Wakulla County...........................27

Water Quality Studies ......................................................................................................... 30

IMAP Probabilistic Sampling.........................................................................................................31

Preliminary Assessment of Optical Water Quality in Florida’s Big Bend Region–Carlson and 

Yarbro, FWRI................................................................................................................................35

LakeWatch Program.....................................................................................................................35

St. Marks/Wakulla Sampling ........................................................................................................37

City of Tallahassee Data on Nitrate Contributions .........................................................................44

Fenholloway/Econfina Studies......................................................................................................44

EPA 1999 Nutrient Study...............................................................................................................56

Steinhatchee Estuary Sampling, Project COAST, 1997–present.......................................................56

SRWMD Monitoring in the Steinhatchee Estuary........................................................................... 61

Existing Regional Nutrient Loading Models, HydroQual Inc. ................................................. 63

Waters on the 303(d) List..................................................................................................... 64

Impairment for Bacteria Not Necessarily Indicative of Anthropogenic Impact ................................65

Numeric Nutrient Criteria Recommendations ...................................................................... 67

References .......................................................................................................................... 71

Appendix A: Long-Term (1971–2004) Response of the Econfina and Fenholloway 

Drainages (Apalachee Bay) to the Discharge of Pulp Mill Effluents: Nutrient Loading, 

Limitation and Distribution.................................................................................................. 76

Appendix B: Rainfall and Seagrass Coverage Figures of the Fenholloway and Econfina 

Systems (from BVA Research for Buckeye Florida L.P.)......................................................... 77

Appendix C: Apalachee Bay Nutrient Criteria Support Analysis from HydroQual .................. 85
Draft iii August 2010

List of Tables

Table 1. Checklist of potential nutrient enrichment symptoms in greater Apalachee Bay 

(excluding the Fenholloway River).............................................................................................. 2

Table 2. Physical characteristics of Apalachee Bay...................................................................................... 9

Table 3. Land use percentages for the St. Marks and Wakulla River Basins................................................ 9

Table 4. 2001 and 2006 seagrass habitat, and the change that occurred, 2001–06, for the St. 

Marks, Aucilla, and Econfina Rivers (from Carlson, FWRI) .......................................................17

Table 5. Taxa-specific phytoplankton blooms in the Fenholloway and Econfina Estuaries, 2005–

09 (BVA data)............................................................................................................................28

Table 6. Occurrence of potentially harmful algal taxa in the Econfina and Fenholloway Rivers 

and Estuaries, 2005–09. ...........................................................................................................29

Table 7. Annual reported dockside commercial landings of shellfish for Wakulla County, Florida 

(FDACS data).............................................................................................................................30

Table 8. Summary statistics for the Big Bend area probabilistic sampling effort in July 2002 as 

part of the FMRI IMAP Program. The 75th and 90th percentiles are estimated based 

on a log normal distribution. ....................................................................................................31

Table 9. Mean values of chlorophyll a, TN, and TP for three water quality sampling events at 

nine LakeWatch coastal sites in Apalachee Bay, collected in 2001..........................................36

Table 10. Summary of selected water quality characteristics in the St. Marks and Wakulla River 

systems and Apalachee Bay (data from Florida STORET 2007) (Lewis et al. 2009)..................40

Table 11. Summary of selected water quality characteristics in the Wakulla River system (data 

from Florida STORET 2007) (Lewis et al. 2009).........................................................................40

Table 12. Latitudes and longitudes for discrete water quality stations for the Fenholloway and 

Econfina Estuaries (from BVA).................................................................................................. 48

Table 13. Comparison between station geometric means for 2007 (n = 11, or 12 monthly 

samples) and uncorrected and phaeophytin-corrected chlorophyll a (μg/L) 

measurements. .........................................................................................................................61

Table 14. Annual geometric mean concentrations of chlorophyll a (uncorrected), TN, and TP for 

Station STN060C1 in the Steinhatchee Estuary, sampled by SRWMD......................................63

Table 15. Impaired waters in the greater Apalachee Bay planning units..................................................65

Table 16. TN and TP loads and concentrations for the St. Marks, Aucilla, Econfina, and 

Steinhatchee Rivers. All loading numbers are based on annual geometric means.................68

Table A-1. Latitudes and longitudes for discrete water quality stations for the Fenholloway and 

Econfina Estuaries (from BVA data)..........................................................................................79

Table A-2. Data collected from 10 BVA monitoring stations listed in Table A-1........................................80
Draft iv August 2010

List of Figures

Figure 1. Greater Apalachee Bay region, including major rivers and conservation areas........................... 4

Figure 2. Composite map of the St. Marks River Planning Unit, including the 1998 303(d) list, 

Planning List, and Verified List waters, and potential pollution sources (FDEP 2003)................ 6

Figure 3. Composite map of the Aucilla/Wacissa, Econfina, Fenholloway, Steinhatchee, and 

Other Coastal Basin Planning Units, including the 1998 303(d) list, Planning List, and 

Verified List waters. .................................................................................................................... 8

Figure 4. Apalachee Bay Basin land use from FLUCCS. Agricultural = 849.05 km2 or 14.06% of 

land use, commercial and residential = 446.14 km2 or 7.39%, extraction = 9.52 km2 or 

0.158%, infrastructure = 66.44 km2 or 1.1%, natural = 888.41 km2 or 14.71%, 

silviculture = 2,121.23 km2 or 36.23%, and water and wetlands = 1,656.82 km2 or 

28.54% (Charbonneau 2010). ...................................................................................................10

Figure 5. Steinhatchee River Basin land use with FLUCCS. Agriculture = 36.85 km2 or 1.8% of 

land use, commercial residential = 29.67 km2 or 1.449%, extraction = 0.06 km2 or 

0.003%, infrastructure = 4.76 km2 or 0.233%, natural = 28.7 km2 or 1.402%, 

silviculture = 883.07 km2 or 43.140%, and water/wetlands = 1,063.89 km2 or 51.973% 

(Charbonneau 2010).................................................................................................................11

Figure 6. Conservation land in the Steinhatchee River Basin (Charbonneau 2010)...................................12

Figure 7. The major tributaries of the greater Apalachee Bay area and the drainage basins for 3 

of the major rivers and the Apalachee Bay CDA (Charbonneau 2010).....................................13

Figure 8. Seagrass habitat change for the St. Marks River to Ochlocknee River, 2001–06 (from 

Carlson, FWRI). .........................................................................................................................16

Figure 9. Seagrass habitat change for the Econfina River to St. Marks River, 2001–06 (from 

Carlson, FWRI). .........................................................................................................................16

Figure 10. Seagrass habitat change for the Fenholloway River to Econfina River, 2001–06 (from 

Carlson, FWRI). .........................................................................................................................17

Figure 11. Seagrass density for four taxa of seagrasses for Stations E08 and F10 (from BVA 

data). ........................................................................................................................................19

Figure 12. Seagrass density for five taxa of seagrasses for Stations EO9 and F16 (from BVA data).........20

Figure 13. Seagrass density (shoots/m2

) for each BVA discrete monitoring station, 2005–09 

(from BVA data)........................................................................................................................21

Figure 14. Seagrass and macroalgal biomass for the discrete water quality monitoring stations 

(2008 BVA data)........................................................................................................................23

Figure 15. Phytoplankton density for two cognate stations in the Econfina and Fenholloway 

Rivers. Each graph represents a given year from 2005 to 2009 (from BVA data)...................24

Figure 16. Phytoplankton taxa diversity (H) data for the Econfina and Fenholloway stations, 

2004–09 (from BVA data).........................................................................................................25

Figure 17. Locations of the 25 fixed sampling sites for the Steinhatchee Seagrass Monitoring 

Program (from Big Bend Seagrass Aquatic Preserve data). .....................................................26

Figure 18. Occurrence (%) of various seagrass species in the Steinhatchee Estuary, 2000–09 (Big 

Bend Seagrass Aquatic Preserve data). ....................................................................................26
Draft v August 2010

Figure 19. Average total seagrass coverage for the Steinhatchee Estuary, 2003–08 (Big Bend 

Seagrass Aquatic Preserve data). Braun-Blaunquet abundance codes: 1 = <5% cover; 

2 = 5%-25% cover; 3 = 25%-50% cover; 4 = 50%-75% cover; 5 = 75%-100% cover. .................27

Figure 20. Site locations and TN concentrations (μg/L) of Big Bend sites sampled in July 2002 as 

part of the FMRI IMAP probabilistic sampling. Note that the highest concentrations 

of N were found in the salt marshes.........................................................................................32

Figure 21. Location and chlorophyll a concentrations (μg/L) of all Apalachee Bay sites sampled 

as part of the FMRI IMAP probabilistic sampling. Sites were sampled once between 

2000 and 2004..........................................................................................................................33

Figure 22. Location and TN concentrations (μg/L) of all Apalachee Bay sites sampled as part of 

the FMRI IMAP probabilistic sampling. Sites were sampled once between 2000 and 

2004. .........................................................................................................................................34

Figure 23. Location and TP concentrations (μg/L) of all Apalachee Bay sites sampled as part of 

the FMRI IMAP probabilistic sampling. Sites were sampled once between 2000 and 

2004. .........................................................................................................................................35

Figure 24. LakeWatch 2001 site locations in Apalachee Bay.....................................................................36

Figure 25. Water quality stations in the Lower St. Marks River Basin and Apalachee Bay (boxes 

indicate station groups) (Lewis et al. 2009)..............................................................................38

Figure 26. Wakulla River water quality stations (boxes indicate station groups) (Lewis et al. 

2009).........................................................................................................................................39

Figure 27. (Top) N and (bottom) P concentrations in the St. Marks River (data from Florida 

STORET 2007) (Lewis et al 2009). .............................................................................................42

Figure 28. (Top) N and (bottom) P concentrations in the Wakulla River (data from Florida 

STORET 2007) (Lewis et al. 2009). ............................................................................................43

Figure 29. Map showing positions of sampling stations in the Econfina and Fenholloway River 

estuarine systems over the total sampling period. Additional charts indicate the 

sampling regimes associated with various field activities carried out during the 1970–

2004 sampling period (Livingston)............................................................................................45

Figure 30. Locations of BVA discrete water quality monitoring stations for the Econfina and 

Fenholloway Rivers. ..................................................................................................................47

Figure 31. Seagrass sample locations for the Econfina and Fenholloway Rivers, August 2009 

(from BVA). ...............................................................................................................................48

Figure 32. DO (mg/L) recorded at the Econfina and Fenholloway stations during the growing 

season from May through October (2004–09) (from BVA). .....................................................49

Figure 33. Top left graph shows particulate carbon at each station, top right graph shows 

particulate N at each station, and bottom graph shows particulate P for each station, 

2006–09 (from BVA). ................................................................................................................50

Figure 34. Graphs of TDN and TDP (mg/L) for each station during the growing season from May 

through October, 2006–09 (from BVA).....................................................................................51

Figure 35. Water color data summarized by cognate stations for the Buckeye Florida project, 

2004–09 (from BVA). ................................................................................................................52

Figure 36. Chlorophyll a (mg/L) for each station during the growing season from May through 

October, 2004–09 (from BVA). ................................................................................................. 52
Draft vi August 2010

Figure 37. Chlorophyll a data summarized by cognate stations, 2004–09, Buckeye Florida project 

(from BVA). ...............................................................................................................................53

Figure 38. Measured TP, TN, and chlorophyll a for the Econfina River area, Stations E06, E08, 

E09, E10, and E11 (annual calculations include May through October data only) (data 

from BVA; calculations by HydroQual). ....................................................................................54

Figure 39. Measured TP, TN, and chlorophyll a for the Fenholloway River area, Stations F06, F10, 

F11, and F16 (annual calculations include May–October data only) (data from BVA; 

calculations by HydroQual).......................................................................................................55

Figure 40. Locations of Project COAST sampling sites in the Steinhatchee Estuary. Sites 1 and 2 

are in the river channel but mean salinities at those sites are greater than 5 ppt 

(Charbonneau 2010).................................................................................................................57

Figure 41. Monthly average TN, TP, and uncorrected chlorophyll a for 10 estuarine stations in 

the Steinhatchee Estuary, collected by Project COAST, 1997–2008 (Frazer and Jacoby 

2010).........................................................................................................................................58

Figure 42. Annual average salinity plotted as a predictor of (1) annual geometric mean TN, (2) 

annual geometric mean TP, and (3) annual geometric mean uncorrected chlorophyll a 

at 10 sites in the Steinhatchee Estuary, 1997–2007. Linear trend lines fitted for TN 

and TP, and a 2nd-order polynomial fitted for chlorophyll a, for demonstration 

purposes....................................................................................................................................59

Figure 43. Relationship between individual sample analyses of uncorrected chlorophyll a and 

phaeophytin-corrected chlorophyll a for 10 sites sampled monthly in the Steinhatchee 

Estuary in 2007 and the first part of 2008................................................................................60

Figure 44. Location of the Steinhatchee Sound Station (STN060C1) sampled by the SRWMD..................62

Figure 45. TKN for the Steinhatchee station (2002–09) (from McKinney 2010)........................................62

Figure 46. All available TN and TP data for Steinhatchee Estuary Site STN060C1, sampled by the 

SRWMD.....................................................................................................................................63

Figure A-1. Seasonal rainfall for Perry, Florida, 1998–2009. Top graph shows 1998–2002 data, 

and bottom graph shows 2003–09 data (from BVA)................................................................78

Figure A-2. Discharge compared with 1977–2009 annual average for the Fenholloway and 

Econfina Rivers (from BVA).......................................................................................................79

Figure A-3. Distribution and abundance of seagrasses in the Econfina and Fenholloway Estuaries 

and Apalachee Bay, 1992 (from BVA).......................................................................................81

Figure A-3. Distribution and abundance of seagrasses in the Econfina and Fenholloway Estuaries 

and Apalachee Bay, 1992 (from BVA).......................................................................................82

Figure A-5. Percent coverage for the Econfina and Fenholloway Estuaries and Apalachee Bay, 

2005 (from BVA). ......................................................................................................................83

Figure A-6. Percent coverage for the Econfina and Fenholloway Estuaries and Apalachee Bay, 

2009 (from BVA). ......................................................................................................................84
Draft 1 August 2010

Executive Summary

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

with local scientists,1

Greater Apalachee Bay is a high-salinity, relatively shallow, wind-driven estuary in the Big Bend of 

Florida, adjacent to and contiguous with the Gulf of Mexico. The greater Apalachee Bay system extends 

from the area just east of Ochlockonee Bay to the Steinhatchee River, and also includes the Aucilla, 

Econfina, Fenholloway, and St. Marks Rivers. The coast is dominated by highly developed 

Spartina/Juncus saltwater marshes a with very high wetlands/open water ratio compared with the 

alluvial estuaries to the west (Livingston 2000). The inshore marine habitat of Apalachee Bay serves as a 

physically stressed but highly productive nursery for the developing stages of offshore forms, many of 

which form the basis of the region’s sports and commercial species. The bay’s extensive seagrass beds

are responsible for the high primary production of the bay and also serve as a dominant habitat feature. 

Phytoplankton productivity is relatively low in the largely oligotrophic offshore parts of Apalachee Bay. 

The highly complex, extremely productive food webs of the inshore marine systems of this area are 

principally driven by the seagrass beds and secondarily, by the Spartina/Juncus marshes. 

to support the development of site-specific numeric nutrient criteria for greater 

Apalachee Bay. 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. 

While the five major tributaries provide nutrients to the bay, the nutrients are primarily derived from 

natural sources (leaf litter and the Hawthorne geologic formation). Nutrient limitation experiments in 

the Fenholloway and Econfina systems indicate that inshore areas of both systems are generally limited 

by nitrogen (N), while farther offshore, experiments showed increased phosphorus (P) limitation. 

Seagrasses, which are the endpoint of concern in Apalachee Bay, remain relatively undisturbed by 

human activity, except for the nearshore Fenholloway system, which has been historically affected by 

pulp mill effluent but is currently undergoing restoration. Barry A. Vittor and Associates Inc. (BVA) 

analyzed the relationship between seagrass density, percent photosynthetically active radiation (PAR) 

on the bottom, water column chlorophyll a concentrations, and water color n the Fenholloway and 

Econfina systems. These relationships were described by a linked hydrodynamic water quality model,

and it was demonstrated that PAR of 15% light on the bottom and chlorophyll a of 6.1 micrograms per 

liter (μg/L) (not to be exceeded more than 10% of the time) would fully support a healthy, well-balanced 

seagrass community in the Fenholloway system. 

The Steinhatchee Estuary has been sampled monthly since 1997 as part of Project COAST, led by Tom 

Frazier of the University of Florida (UF). Data were available from the other tributaries as well. Based 

upon data extending from 1971 to the present (predominantly from Livingston), the greater Apalachee 

Bay is currently healthy and fully supports its designated use, except for a small area near the 

Fenholloway River (see Table 1). A Total Maximum Daily Load (TMDL) has been completed and 

approved by the U.S. Environmental Protection Agency (EPA) for the Fenholloway River, and it is 

expected to be implemented within the next five years, resulting in the full restoration of the 

Fenholloway system. Therefore, except for the Fenholloway, maintaining the current nutrient regime 

(which varies as a function of rainfall) is the recommended criterion for the bay. Since the bay has been 

demonstrated to be healthy, the existing nutrient load will be fully protective.

 

1 Contributors to this report included Dr. Skip Livingston, Dr. Carl Way, Tom Gallagher, Cristhian Mancilla, Melissa Charbonneau, Nia 

Wellendorf, and Randy Snipes.
Draft 2 August 2010

Table 1. Checklist of potential nutrient enrichment symptoms in greater Apalachee Bay (excluding the 

Fenholloway River). - = Empty cell/no data

Response Variable Observed 

Historically?

Observed 

Currently? 

Explanation Source

Low dissolved oxygen 

(DO) (hypoxia/anoxia)

In Certain 

Areas

In Certain 

Areas

DO concentrations are lower than the 4.0 milligrams 

per liter (mg/L) Class III marine water quality 

criterion in the minimally disturbed Econfina system 

due to natural phenomena associated with swamp 

inputs. The EPA is currently evaluating site-specific 

alternative criteria for DO in the area. The Econfina 

and Fenholloway both originate from backwater 

swamps and have natural low DO. There have not 

been adverse effects due to the low DO in the 

Econfina system. 

Livingston 2010;

EPA 1999;

Florida 303(d) 

list; 

BVA 2005–09

Reduced clarity No No A 1999 EPA study showed that water color for the 

Econfina Estuary averaged 160 platinum cobalt units 

(PCUs). Color varies naturally as a function of 

tannins from the extensive swamps. 

BVA 2005–09

Increased chlorophyll 

a concentrations

No No Chlorophyll a levels throughout the bay were 

consistently less than 6 mg/L found in the minimally 

disturbed Econfina system, which the EPA used as a 

reference system to derive the Fenholloway TMDL. 

BVA 2005–09; 

EPA 1999

Phytoplankton 

blooms (nuisance or 

toxic)

No No No adverse effects from potentially harmful algae, 

including the red tide–causing organism, Karenia

brevis has been observed. 

BVA 2005–09

Problematic epiphyte 

growth 

No No No problematic epiphyte growth has been reported 

for any of the greater Apalachee Bay systems. 

- 

Problematic 

macroalgal growth

No No No evidence was found of problematic macroalgal 

growth. 

BVA 2005–09

Submerged aquatic 

vegetation (SAV) 

community changes 

or loss

Yes No Other than historical losses near the mouth of the 

Fenholloway due to a pulp mill discharge (addressed 

by a TMDL), the loss and subsequent re-growth of 

SAV near the river mouths appears to be a natural 

phenomenon associated with hydrologic events, 

which reduce salinity and increase water color (from 

tannins). 

BVA 2005–09; 

Project COAST 

seagrass 

mapping 

Emergent or shoreline 

vegetation 

community changes 

or loss 

No No No change in this community was found in any 

reports or literature.

- 

Coral/hardbottom 

community changes 

or loss 

No No Hardbottom typically occurs approximately 20 miles 

from shore, and no change in this community was

found in any reports or literature.

- 

Impacts to benthic 

community

No No No evidence of impacts to benthic communities has

been found, except for the nearshore Fenholloway 

system, which will be addressed by an EPA approved 

TMDL. 

- 

Fish kills No No - - 
Draft 3 August 2010

Geographic and Physical Description

Greater Apalachee Bay is a high-salinity, relatively shallow, wind-driven estuary in the Big Bend of 

Florida, adjacent to and contiguous with the Gulf of Mexico. Table 2 lists the bay’s major physical 

characteristics. The greater Apalachee Bay system extends from the area just east of Ochlockonee Bay 

to the Steinhatchee River, and also includes the Aucilla, Econfina, Fenholloway, and St. Marks Rivers. 

The Apalachee Bay Coastal Drainage Area (CDA) includes nine Florida counties (Wakulla, Franklin, 

Liberty, Gadsden, Leon, Jefferson, Madison, Taylor, and Lafayette) and 4 Georgia counties (Decatur, 

Grady, Thomas, and Brooks). 

The surface area of Apalachee Bay comprises 85,112 acres, much of which is included in the Big Bend 

Seagrass Aquatic Preserve, which is also designated as an Outstanding Florida Water (OFW). The Big 

Bend Seagrass Aquatic Preserve includes most of the Wakulla and St. Marks Rivers southward toward 

the mouth of the Steinhatchee River. The net movement of water is from east to west, with the river 

inputs mixing with the more saline Gulf water. Figure 1 shows the greater Apalachee Bay region, 

including major rivers and conservation areas.

Figure 2 shows a composite map of the St. Marks River Planning Unit, including the 1998 303(d) list, 

Planning List, and Verified List waters, and potential pollution sources (FDEP 2003); Figure 3 provides the 

same information for the Aucilla/Waucissa, Econfina, Fenholloway, Steinhatchee, and Other Coastal 

Basin Planning Units. Table 3 shows the major land uses and percentages in the Wakulla River and St. 

Marks Basins. Figures 4 and 5 show land uses in the Apalachee Bay and Steinhatchee Basin, 

respectively, and Figure 6 shows conservation land in the Steinhatchee Basin. 

Sources and Fates of Nutrients 

The Apalachee Bay Estuary has five major tributaries: the St. Marks, Aucilla, Fenholloway, Econfina, and, 

Steinhatchee Rivers (Figure 7). While these contribute nutrients to the bay, the nutrients are primarily 

derived from natural sources (leaf litter and the Hawthorne geologic formation). Phytoplankton 

productivity in Apalachee Bay is generally low compared with the alluvial systems to the west

(Livingston 2010). 

Nutrient limitation experiments in the Fenholloway and Econfina systems indicate that the inshore areas 

of both systems are generally N limited, while farther offshore, experiments showed increased P 

limitation. Higher total inorganic nitrogen/total inorganic phosphorus (TIN/TIP) ratios indicated 

increased P limitation, showing the increasing importance of P to offshore areas of the Gulf.
Draft 4 August 2010

Figure 1. Greater Apalachee Bay region, including major rivers and conservation areas.
Draft 5 August 2010
Draft 6 August 2010

Figure 2. Composite map of the St. Marks River Basin shows cycle 2 impairments for Ammonia, DO, 

Nutrients, and other. (FDEP 2009). 
Draft 7 August 2010

 
Draft 8 August 2010

Figure 3. Composite map of the Suwannee Basin shows Aucilla/Wacissa, Econfina, Fenholloway, 

Steinhatchee Rivers and cycle 2 impairments for Ammonia, DO, Nutrients, and other. (FDEP 2009)
Draft 9 August 2010

Table 2. Physical characteristics of Apalachee Bay.

Data Values Source

Estuarine surface area 

(square kilometers [km2])

1,773 km2 Smith 2003; National Oceanic 

and Atmospheric 

Administration (NOAA) 

Watershed area (km2) 11,909.475 km2 EPA 1999

Land use See Figures 5 and 6 Suwannee River Water 

Management District (SRWMD) 

land use layers (Florida Land 

Use, Cover and Form 

Classification System [FLUCCS]) 

Mean depth (meters [m] ) 3.0 m EPA 1999

Volume (cubic meters [m3]) 3,398,212 m3 Smith 2003; NOAA

Tidal range (m) .75 m EPA 1999

Tidal freshwater inflow (1,000 

cubic meters per second [1,000 

m3s

-1])

150 m3/s EPA 1999

Mean water residence time 

(days)

3 days Charbonneau 2010

Table 3. Land use percentages for the St. Marks and Wakulla River Basins. 

Summary of Acres St. Marks (%)

Total

Wakulla (%)

Total 

Urban and built-up 6.68% 20.20%

Agriculture 13.02% 2.85%

Rangeland 1.11% 4.34%

Upland forest 57.26% 62.03%

Water 2.41% .67%

Wetlands 19.12% 8.54%

Barren land .01% .03%

Transportation, 

communications, and utilities 

.40% 1.33%

% TOTAL: 100% 100%
Draft 10 August 2010

Figure 4. Apalachee Bay Basin land use from FLUCCS. Agricultural = 849.05 km2 or 14.06% of land use, 

commercial and residential = 446.14 km2 or 7.39%, extraction = 9.52 km2 or 0.158%, infrastructure = 

66.44 km2 or 1.1%, natural = 888.41 km2 or 14.71%, silviculture = 2,121.23 km2 or 36.23%, and water 

and wetlands = 1,656.82 km2 or 28.54% (Charbonneau 2010).
Draft 11 August 2010

Figure 5. Steinhatchee River Basin land use with FLUCCS. Agriculture = 36.85 km2 or 1.8% of land use, 

commercial residential = 29.67 km2 or 1.449%, extraction = 0.06 km2 or 0.003%, infrastructure = 4.76

km2 or 0.233%, natural = 28.7 km2 or 1.402%, silviculture = 883.07 km2 or 43.140%, and 

water/wetlands = 1,063.89 km2 or 51.973% (Charbonneau 2010).
Draft 12 August 2010

Figure 6. Conservation land in the Steinhatchee River Basin (Charbonneau 2010).
Draft 13 August 2010

Figure 7. The major tributaries of the greater Apalachee Bay area and the drainage basins for 3 of the 

major rivers and the Apalachee Bay CDA (Charbonneau 2010).

Point Sources

There are several point sources in the lower St. Marks River (below St. Marks Spring rise). These include 

the city of Tallahassee Purdom Power Plant (Curtis 1997), the Murphy Oil Corporation tank farm, the St. 

Marks Refinery site, and the St. Marks domestic sewage treatment plant. The St. Marks sewage plant 

started piping treated domestic wastewater to the power plant for industrial reuse in 1999. The 

Tallahassee Southeast Farm, in the west central part of the planning unit, is a large, 2,163-acre 

wastewater reuse facility that uses sprayfields to treat most of the city’s municipal wastewater. The 

potential impact of this facility on nitrate-nitrogen concentrations in ground water and springs has been 

assessed by the Northwest Florida Water Management District (NWFWMD) (Chelette et al. 2002).

The Buckeye pulp mill is the major point source that discharges into Apalachee Bay via the Fenholloway 

River. The facility discharges into the Fenholloway River upstream of U.S. Highway 98, about 20 miles 

from the mouth of the river. Buckeye has a design flow of 43.8 MGD.
Draft 14 August 2010

City of Tallahassee Nitrate Contribution

City of Tallahassee Public Supply Wells

The city of Tallahassee provided nitrate nitrite (NO2+NO3-N) data for 29 Floridan aquifer public supply 

wells in its system. Due to their relatively long open-hole intervals, regular pumping, long periods of 

record, large zones of contribution, and high-discharge volumes, these wells are of particular interest. 

Specifically, the data represent the best available insight into the spatial distribution of NO2+NO3-N in 

the Floridan aquifer beneath the semiconfined portion of the study area. Data from the 29 city of 

Tallahassee wells were then aggregated into several subsets based on location. The semiconfined well 

dataset (716 values from 27 wells, excluding the 2 Woodville wells) showed no significant trend in 

NO2+NO3-N concentration over time. The median concentration from this set of wells was 0.33 mg-N/L 

(n=716, mean=0.35, standard deviation [stdev] =0.17). 

For the 20 city of Tallahassee wells south of Interstate 10, the median concentration was 0.36 mg-N/L 

(n=556, mean=0.38, stdev=0.16). Lastly, the 6 southernmost wells (south of Tram Road/Orange Avenue 

and adjacent to the Cody Scarp) had a median concentration of 0.48 mg-N/L (n=208, mean=0.48, 

stdev=0.16). These results show an increasing trend in NO2+NO3-N from north to south in Leon County 

under the semiconfining unit (NWFWMD 2002).

Wastewater Treatment Facilities

According to FDEP records, there are 69 wastewater treatment facilities (WWTFs) in Leon and Wakulla 

Counties. Of the 59 WWTFs within the semiconfined and unconfined areas, 21 are domestic and 38 are 

industrial. The total design capacity of the WWTFs, both domestic and industrial, is 38.05 million gallons 

per day (MGD). The majority of this capacity (32.06 MGD) is for domestic plants operated by the city of 

Tallahassee. The remaining facilities have a combined capacity of slightly less than 6 MGD (NWFWMD 

2002). 

Commercial Fertilizer Application

City of Tallahassee records indicate a 1999 application of 44,000 kg-N to 691 hectares (ha) at its facility. 

Since the Southeast Sprayfield (SESF) is the only area designated as pasture and cropland in the 

unconfined portion of Leon County, the N application to the SESF is assumed to represent all the

commercial fertilizer applied to this area (NWFWMD 2002).

Nonpoint Sources

The EPA (2009) states, “The vast majority of the nonpoint source runoff in the Econfina River Basin and 

Fenholloway River watershed are natural background levels of pollutants running off wetlands, forest 

and other non anthropogenic areas. Nonpoint source runoff in the basin is attributed to natural 

background loads and does not adversely impact natural water quality conditions.” 

Biological Summary

Seagrasses are important marine foundation species and are highly productive plants (Hughes et al.

2009). Their extensive root systems and dense, structured leaf canopies form habitat and provide food 

for a wide array of organisms, including commercially and recreationally important fish and 

invertebrates, wading birds, manatees, and sea turtles (Short and Wyllie-Echeverria 1996; Williams and 

Heck 2001; Wren 2009). Seagrasses enhance sediment stability, decrease wave energy, increase water 
Draft 15 August 2010

clarity, provide and stabilize habitats, and provide food and feeding pathways (see reviews by Phillips 

and McRoy 1980; McRoy and Helfferich 1977; Zieman and Zieman 1989). 

Adverse impacts to seagrasses come from a variety of sources, including reduced water quality and 

clarity, overgrazing, and physical damage from boats, dredging and development. Monitoring 

seagrasses has become one of the best methods for determining the overall condition of the nearshore 

aquatic environment because these plants are sensitive to environmental stressors. Seagrass 

communities have been proposed as “coastal canaries”—biological indicators of changing coastal 

conditions (Orth et al. 2006). 

Seagrasses are adversely impacted by anthropogenic nutrient enrichment (Orth and Moore 1983; 

Tomasko et al. 1996). Reduced underwater light penetration appears to be a primary driver of seagrass 

decline. The accepted thinking on this process is that increased inputs of N and P lead to the excess 

growth of phytoplankton and epiphytic algae, reducing available light to the seagrasses and causing 

decreased seagrass productivity and ultimately the large-scale loss of seagrasses (Duarte 1995). This 

explanation, while valid, does not give a complete picture of the synergistic factors controlling seagrass 

production. “Top-down” food web effects must also be considered. In controlled, in situ experimental 

studies in St. Joseph Bay, Florida, Heck et al. (2000), found that mesograzers (amphipods, caridean 

shrimp, gastropods, hermit crabs) controlled the effects of nutrient enrichment on the abundance of 

epiphytes. It is therefore critical to consider the role of “top-down” effects from overfishing or other 

food web disruptions in assessments of nutrient enrichment in Apalachee Bay. 

The Florida Fish and Wildlife Conservation Commission (FWCC) Fish and Wildlife Research Institute 

(FWRI) is currently involved in a project to assess water quality in Florida’s Big Bend region. Since 2002, 

FWRI scientists have conducted annual monitoring surveys of seagrass beds in this area. Although the 

data are collected only once a year, seven years of data provide some insight into the forces controlling 

water clarity and seagrass abundance in Florida’s Big Bend. Figures 8 through 10 show seagrass habitat 

change for three different coastal areas, and Table 4 shows 2001 and 2006 seagrass habitat, in acres, 

and the change that occurred from 2001 to 2006 for the St. Marks, Aucilla, and Econfina Rivers.
Draft 16 August 2010

Figure 8. Seagrass habitat change for the St. Marks River to Ochlocknee River, 2001–06 (from Carlson, 

FWRI). 

Figure 9. Seagrass habitat change for the Econfina River to St. Marks River, 2001–06 (from Carlson, 

FWRI). 
Draft 17 August 2010

Figure 10. Seagrass habitat change for the Fenholloway River to Econfina River, 2001–06 (from 

Carlson, FWRI). 

Table 4. 2001 and 2006 seagrass habitat, and the change that occurred, 2001–06, for the St. Marks, 

Aucilla, and Econfina Rivers (from Carlson, FWRI) 

- = Empty cell/no data

Note: Original table was in acres, converted to km2

. 

Habitat Type St. Marks

(West)

St. Marks

(East)

Aucilla Econfina All

Regions

2001 habitat area (km2) - - - - - 

Patchy seagrass 0.931 3.075 3.723 0.567 8.292

Continuous seagrass 63.576 63.171 99.350 115.375 341.473

All seagrass 64.506 66.247 103.073 115.942 349.765

2006 habitat area (km2) - - - - - 

Patchy seagrass 4.775 7.203 4.653 1.133 17.765

Continuous seagrass 56.332 59.205 98.581 114.890 329.009

All seagrass 61.107 66.408 103.235 116.023 346.775

Change 2001–06 (km2) - - - - - 

Patchy seagrass 3.844 4.127 0.890 0.566 9.473

Continuous seagrass -7.081 -3.965 -0.768 -0.485 -12.464

All seagrass -3.399 .161 0.121 0.080 -2.990

SAV in the Econfina/Fenholloway Systems

BVA Study of the Econfina and Fenholloway Systems, 2004–09
Draft 18 August 2010

BVA analyzed the relationship between seagrass density, % PAR on the bottom, water column 

chlorophyll a concentrations and water color for data collected from 10 monitoring stations in the 

Fenholloway and Econfina systems during 2006, 2007, 2008, and 2009 (BVA 2007, 2008, 2009). Seagrass 

densities showed a significant positive correlation with % PAR and significant inverse correlations with 

chlorophyll a and water color. Percent PAR was inversely correlated with both chlorophyll a and water 

color, indicating that these are the physical variables most responsible for determining the distribution 

and abundance of SAV. 

BVA also found that transparency and color in the Econfina and Fenholloway systems are greatly 

influenced by regional climatic factors, including seasonal rainfall and riverine discharge. Rainfall data 

from 1998 to 2009 for the Fenholloway River are shown in Figure C-11 in Appendix C, and river 

discharge data for 1977 to 2009 are compared with the 33-year annual average in Figure C-12 in 

Appendix C. The years 2003 and 2005 were extremely wet, with high rainfall and riverine discharge, 

while 2006, 2007, 2008, and 2009 were drier, with lower rainfall and riverine discharge. Drought 

conditions prevailed in the region during 2006 and 2007. During 2003, 2004 and 2005, water color was 

high and % PAR on the bottom was low compared with 2006 to 2009 (BVA 2005, 2006, 2007, 2008, 

2009). 

Seagrass data from the Econfina and Fenholloway systems indicate a gradual increase in the distribution 

and abundance of seagrasses from 2005 to 2009, coinciding with decreased water color and increased 

light availability (Figure 13). Figures 11 and 12 show taxa-specific seagrass densities for cognate Stations 

E09 and F16 from 2006 to 2009; both stations show a gradual shift in seagrass assemblage composition 

from a dominance of Halophila to a dominance of Syringodium. These data indicate a succession of 

seagrasses after the extremely wet conditions in the region from 2003 to 2005 that had reduced the 

distribution, abundance, and community composition of seagrasses. 
Draft 19 August 2010

Figure 11. Seagrass density for four taxa of seagrasses for Stations E08 and F10 (from BVA data).
Draft 20 August 2010

Figure 12. Seagrass density for five taxa of seagrasses for Stations EO9 and F16 (from BVA data).
Draft 21 August 2010

Figure 13. Seagrass density (shoots/m2

) for each BVA discrete monitoring station, 2005–09 (from BVA 

data). 

Historical seagrass coverage information is available for the Econfina and Fenholloway region from a 

1952 aerial photograph that depicts the area before the operation of the Buckeye Florida pulp mill, from 

1992 and 2001 seagrass surveys by Livingston (1994), and from 2005, 2007, 2008, and 2009 surveys by 

BVA. In the 1952 aerial photograph, there were no seagrasses in the mouth of the Fenholloway River, 

and no seagrasses have been found at this station in subsequent years because the flow and salinity 

regime of the Fenholloway Estuary was not optimal for seagrass settlement. However, at the remaining 

stations in both the Econfina and Fenholloway systems, there has been considerable year-to-year 

variation in seagrass abundance (note the change in distribution and abundance of seagrass from 1992, 

to 2001, to 2005, to 2009; Appendix C, Figures C-14 through C-17).

The distribution and abundance of seagrasses in the Econfina and Fenholloway systems have been 

quantitatively investigated at various intervals between 1972 and 2009 (Livingston 1994; BVA 2005, 

2006, 2007, 2008, 2009). The data indicate that there has been significant inter- and intra-annual 

variation in seagrass distribution and abundance in both systems. From 1972 to 1973, stations in the 

Fenholloway system had lower seagrass abundance than their Econfina cognates, with the lowest 

concentrations at the river mouths and with the highest abundances found in areas west of the Econfina 

mouth. In 1992 and 1993, seagrass abundances were very low in both systems, with the Econfina 
Draft 22 August 2010

system dominated by Syringodium, Thalassia, and Halodule, and the Fenholloway dominated by 

Halodule and Syringodium. 

From 1999 to 2001, there was a return of higher seagrass abundances in both systems. The highest 

biomass was found in the near offshore areas of the Econfina and the offshore, westernmost areas of 

the Fenholloway. In the Fenholloway, Syringodium dominated the assemblage with an increase in the 

abundance of Halophila englemannii. In 2005, seagrasses were present at only 5 of 142 stations in the 

Fenholloway system, while seagrasses were abundant in the Econfina system but in lower densities than 

in 2001. In 2006, seagrass abundances were high at the Econfina stations and along Fenholloway 

transects between Stations F10 and F11 to offshore Station F16. In 2007 and 2008, seagrass 

abundances were even higher than in 2006 at the Econfina stations, and seagrasses even appeared at 

Fenholloway Station F14 in 2008. The pattern of seagrass distribution and abundance in 2009 continued 

the pattern seen in 2007 and 2008.

For more seagrass information, see Dr. R. J. Livingston’s report on research from the Fenholloway and 

Econfina systems from 1970 to 2002 (Appendix A) and the results of BVA’s research (Appendix B). 

Phytoplankton Density and Taxa in the Fenholloway/Econfina Systems

Figures 15 and 16 show phytoplankton density and taxa diversity in the Fenholloway and Econfina 

systems. 

SAV in the Steinhatchee Estuary

FDEP’s Big Bend Seagrass Aquatic Preserve has been monitoring SAV (seagrass and macroalgae) at 25 

fixed sites (Figure 17) in the Steinhatchee area via Braun-Blaunquet species coverage estimates since 

2000, with estimates of total cover since 2003. At each site, 4 random 1 m2 quadrats are assessed. The 

coverage for each seagrass species, rooted macroalgae, and drift algae are assessed using the following

abundance codes: 1 = <5% cover; 2 = 5%-25% cover; 3 = 25%-50% cover; 4 = 50%-75% cover; and 

5 = 75%-100% cover. Also included in the sampling effort are sediment type, sediment depth, number 

of scallops and urchins, water quality parameters, horizontal Secchi, and presence of prop scars and 

blowout. Water quality parameters that are measured include temperature, salinity, pH, DO, light 

attenuation, nutrients, and total suspended solids (TSS) (Charbonneau 2010). The species composition 

of the seagrasses and proportion of macroalgae and bare ground remained constant over the 2000 to 

2009 sampling period (Figure 18). Total coverage within the 1 m2 quadrats was stable at approximately 

50% to 75% from 2003 to 2008 (Figure 19).
Draft 23 August 2010

Figure 14. Seagrass and macroalgal biomass for the discrete water quality monitoring stations (2008 BVA data). 
Draft 24 August 2010

Figure 15. Phytoplankton density for two cognate stations in the Econfina and Fenholloway Rivers. Each graph represents a given year from 

2005 to 2009 (from BVA data). 
Draft 25 August 2010

Figure 16. Phytoplankton taxa diversity (H) data for the Econfina and Fenholloway stations, 2004–09 (from BVA data). 
Draft 26 August 2010

Figure 17. Locations of the 25 fixed sampling sites for the Steinhatchee Seagrass Monitoring Program 

(from Big Bend Seagrass Aquatic Preserve data). 

Figure 18. Occurrence (%) of various seagrass species in the Steinhatchee Estuary, 2000–09 (Big Bend 

Seagrass Aquatic Preserve data). 
Draft 27 August 2010

Figure 19. Average total seagrass coverage for the Steinhatchee Estuary, 2003–08 (Big Bend Seagrass 

Aquatic Preserve data). Braun-Blaunquet abundance codes: 1 = <5% cover; 2 = 5%-25% cover; 3 = 

25%-50% cover; 4 = 50%-75% cover; 5 = 75%-100% cover. 

Presence and Frequency of Harmful Algal Blooms (HABs) in the Econfina/Fenholloway Systems

BVA (2009) identified specific phytoplankton taxa at the Econfina and Fenholloway Estuary monitoring 

stations between 2005 and 2009. Tables 5 and 6 show these data. The frequencies and magnitudes of 

specific taxa blooms were similar in both systems, with considerable intra- and interannual variation. 

Based on data collected from 2004 to 2009, it can be concluded that there is no difference in the 

occurrence of algal blooms between the Fenholloway and Econfina River Estuaries, and that the 

sporadic occurrence of the bloom taxa is a natural event. 

The K. brevis dinoflagellate has been historically found in Apalachee Bay, but very sporadically. It is 

believed that these blooms develop offshore, and easterly winds and incoming tides bring them closer 

to shore. The most recent K. brevis bloom in the Apalachee Bay area was transported from offshore 

waters to Wakulla County in November 2005, and yielded a peak concentration of 23,333 cells/L (Florida 

Department of Agriculture and Consumer Services [FDACS] 2009).

Shellfish Production and Frequency/Duration of Bed Closures in Wakulla County

From 1997 through 2007, the annual reported commercial landings of shellfish in Wakulla County 

averaged 38,335 pounds, with an annual dockside value of $64,321 (FDACS 2009). This accounted for 

1.9% of shellfish landings and 1.8% of shellfish value in Florida (FDACS). The primary species of shellfish 

harvested is the eastern oyster (Crassostrea virginica) (FDACS). The northern hard-shell clam or quahog 

(Mercenaria spp.) is also found in Apalachee Bay but not in commercially viable quantities (FDACS 2009). 

The winter oyster-harvesting season, currently defined for Wakulla County by the Marine Fisheries 

Commission, is September 1 through May 31 (FDACS 2009). 

Table 7 lists the annual dockside commercial landings of shellfish reported from 1997 through 2007 in 

Wakulla County by FDACS. There are currently no shellfish or aquaculture leases, shellfish nursery 

facilities, oyster resource enhancement projects, depuration facilities, or wet storage facilities in the 

area (FDACS 2009).
Draft 28 August 2010

Table 5. Taxa-specific phytoplankton blooms in the Fenholloway and Econfina Estuaries, 2005–09 

(BVA data).
Draft 29 August 2010

Table 6. Occurrence of potentially harmful algal taxa in the Econfina and Fenholloway Rivers and Estuaries, 2005–09. 

Note: Abundances shown in bold represent a bloom (defined as abundance greater than 1,000,000 cells/L). Blue represents Econfina stations, and green represents Fenholloway stations. 
Draft 30 August 2010

Table 7. Annual reported dockside commercial landings of shellfish for Wakulla County, Florida 

(FDACS data). - = Empty cell/no data

N/A = Not Available

Year Oysters 

(pounds)

Oysters 

($ value)

Clams 

(pounds) 

Clams 

($ value) 

Wakulla County - - - - 

1997 24,209 102,919 0 0 

1998 14,701 106,084 0 0 

1999 15,166 43,407 0 0

2000 24,567 31,092 0 0 

2001 71,155 51,625 0 0

2002 55,465 90,407 0 0 

2003 33,742 120,251 0 0 

2004 19,931 43,729 0 0 

2005 27,473 31,090 0 0 

2006 65,891 32,222 0 0

2007 70,013 54,712 0 0 

Wakulla County average 38,335 64,321 0 0

Florida average 2,049,991 3,632,782 N/A N/A

Water Quality Studies 

Several water quality studies have been conducted in greater Apalachee Bay. Each study is listed below 

and then described in more detail in subsequent sections: 

• The Florida Marine Research Institute (FMRI), now the FWRI, conducted an Inshore 

Marine Monitoring Assessment Program (IMAP) that sampled Apalachee Bay in 

2002. 

• The LakeWatch Program coordinated water quality sample collection at nine sites in 

Apalachee Bay, and each site was sampled three times: in January, March, and May 

2001. 

• Water quality data from a variety of sites representative of the St. Marks and 

Wakulla Rivers as well as adjacent areas of Apalachee Bay were retrieved from the 

Florida STORET database and are summarized. The data were collected by various 

agencies and organizations (e.g., FMRI, FDEP, LakeWatch) with varying 

characteristics, sampling procedures, and analytical methods.

• Dr. Robert J. Livingston of Florida State University (FSU) conducted a long-term 

water quality analysis in the Econfina/Fenholloway Estuaries from 1970 to 2004. 

• BVA performed a water quality study in the Econfina and Fenholloway Estuaries 

from 2004 to 2009. 
Draft 31 August 2010

• The EPA’s Ecological Assessment Branch in Athens, Georgia, conducted a nutrient 

study of the Econfina and Fenholloway systems for TMDL purposes. The EPA 

sampling periods were December 1998, March 1999, June 1999, and August–

September 1999. 

• Dr. Tom Frazer of UF studied the Steinhatchee Estuary (Project COAST) from 1997 to 

the present. 

• The SRWMD carried out monitoring at a site in the Steinhatchee Estuary from 1995 

to the present. 

IMAP Probabilistic Sampling

The FMRI sampled the Big Bend as part of its IMAP. IMAP is a probabilistic design sampling program in 

which 30 samples are collected to statistically represent the condition of an area at a given point in time. 

Thirty sites within the Big Bend, concentrated in Deadman’s Bay off the Steinhatchee River, were 

sampled from July 23 through 30, 2002 (Figure 20). Geometric mean concentrations of TN, TP, and 

chlorophyll a (phaeophytin-corrected) were calculated (Table 8). The geometric mean concentration for 

chlorophyll a was low, at 2.46 μg/L. Geometric means for TN and TP were moderate, at 660 and 28 

μg/L, respectively. All values were comparable to values reported for this area for longer periods (see 

Figure 41) and for other estuaries in the region that receive highly colored water and have intact coastal 

marshes (e.g., Econfina and Waccasassa). 

Table 8. Summary statistics for the Big Bend area probabilistic sampling effort in July 2002 as part of 

the FMRI IMAP Program. The 75th and 90th percentiles are estimated based on a log normal 

distribution.

Analyte Geometric Mean Log-estimated 75th

Percentile 

Log-estimated 90th

Percentile 

Chlorophyll a

(corrected, μg/L)

2.46 3.85 5.76

TN (μg/L) 660 765 874

TP (μg/L) 28 41 57

Other sites in Apalachee Bay were sampled for the IMAP Program in various years as part of statewide 

and regional sampling. Figures 20 through 23 present pictorial representations of the data distribution. 

Note that the highest nutrient concentrations were found immediately adjacent to the coastal fringe 

marshes. Values for TN were higher in the Steinhatchee Estuary compared with sites farther north in 

Apalachee Bay, and values for TP were similar throughout. Note that the interpretation of these data is 

limited because each site was only sampled once, and during different years in some cases.
Draft 32 August 2010

Figure 20. Site locations and TN concentrations (μg/L) of Big Bend sites sampled in July 2002 as part of 

the FMRI IMAP probabilistic sampling. Note that the highest concentrations of N were found in the 

salt marshes.
Draft 33 August 2010

Figure 21. Location and chlorophyll a concentrations (μg/L) of all Apalachee Bay sites sampled as part 

of the FMRI IMAP probabilistic sampling. Sites were sampled once between 2000 and 2004.
Draft 34 August 2010

Figure 22. Location and TN concentrations (μg/L) of all Apalachee Bay sites sampled as part of the 

FMRI IMAP probabilistic sampling. Sites were sampled once between 2000 and 2004.
Draft 35 August 2010

Figure 23. Location and TP concentrations (μg/L) of all Apalachee Bay sites sampled as part of the 

FMRI IMAP probabilistic sampling. Sites were sampled once between 2000 and 2004.

Preliminary Assessment of Optical Water Quality in Florida’s Big Bend Region–Carlson and Yarbro, 

FWRI

The FWRI has been monitoring seagrass at 100 random points along the Big Bend Coast, from St. Marks 

to Suwannee Sound, since 2002. From 2004 to 2009, it also collected optical water quality data at each 

site once during each summer. Salinity, Secchi depth, turbidity, TSS, color, chlorophyll a, and light 

attenuation in the water column were measured at each sampling point. Preliminary results show 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. Values for chlorophyll a are similar to values 

obtained from other data sources. Preliminary analyses for the entire study area suggest that 

chlorophyll a and turbidity are more highly correlated with light attenuation than color (P. Carlson and L. 

Yarbro, FWRI, pers. comm., July 31, 2010).

LakeWatch Program

The LakeWatch Program coordinated water quality sample collection at marine sites statewide during 

2001 (Hoyer et al. 2002). Nine sites were sampled in Apalachee Bay (Figure 24), and each site was 

sampled 3 times, on January 1, March 23, and May 17, 2001. Mean chlorophyll a per site ranged from 

0.93 to 2.90 μg/L, TN ranged from 190 to 287 μg/L, and TP ranged from 7.93 to 15.17 μg/L (Table 9). 
Draft 36 August 2010

Table 9. Mean values of chlorophyll a, TN, and TP for three water quality sampling events at nine 

LakeWatch coastal sites in Apalachee Bay, collected in 2001. 

Station Mean Chlorophyll a

(μg/L, uncorrected)

Mean TN 

(μg/L)

Mean TP 

(μg/L)

TAY1 1.00 190 7.93

TAY2 0.93 196 8.30

TAY3 0.93 233 10.00

WAK1 2.27 287 14.27

WAK2 1.70 213 12.23

WAK3 2.10 223 13.10

WAK4 2.90 280 15.17

WAK5 1.47 240 12.03

WAK6 1.33 233 10.87

 

Figure 24. LakeWatch 2001 site locations in Apalachee Bay.
Draft 37 August 2010

St. Marks/Wakulla Sampling

Water quality data from a variety of sites representative of the St. Marks and Wakulla Rivers as well as 

adjacent areas of Apalachee Bay were retrieved from the Florida STORET database and are summarized 

here. The data were collected by various agencies and organizations (e.g., FMRI, FDEP, LakeWatch)

using varying characteristics, sampling procedures, and analytical methods (Lewis et al. 2009). These are 

combined and presented here only to provide an overview of environmental characteristics in the 

various reaches of the system. 

Data were retrieved from 44 sites scattered throughout the Wakulla and St. Marks Rivers and the 

adjacent waters of Apalachee Bay. Twenty-nine sites were examined from the lower tidal reaches of 

both rivers along with sites in Apalachee Bay (Figure 25) to evaluate inputs to the estuarine portion of 

the system. Twenty-four sites were examined from the Wakulla River (Figure 26) to assess downstream 

water quality trends from the head springs to the confluence with the St. Marks. Nine sites were 

common to both analyses. Sites were chosen where collections spanned a range of sampling dates; 

single-sample collections were avoided when possible (Lewis et al. 2009). 

For the estuarine comparison, stations were combined into four groups representing the upper reach of 

tidal influence, the middle and lower reaches of the estuary, and Apalachee Bay (including adjacent

embayments such as Dickerson and Oyster Bays). Water quality characteristics varied spatially and

temporally throughout the collection sites, with specific conductance/salinity increasing and most of the 

other characteristics generally decreasing with movement downstream (Lewis et al. 2009). Table 10

summarizes water quality characteristics in the St. Marks and Wakulla River systems and Apalachee Bay, 

and Table 11 summarizes water quality characteristics in the Wakulla River system. 
Draft 38 August 2010

Figure 25. Water quality stations in the Lower St. Marks River Basin and Apalachee Bay (boxes 

indicate station groups) (Lewis et al. 2009).
Draft 39 August 2010

Figure 26. Wakulla River water quality stations (boxes indicate station groups) (Lewis et al. 2009).
Draft 40 August 2010

Table 10. Summary of selected water quality characteristics in the St. Marks and Wakulla River

systems and Apalachee Bay (data from Florida STORET 2007) (Lewis et al. 2009).

Table 11. Summary of selected water quality characteristics in the Wakulla River system (data from 

Florida STORET 2007) (Lewis et al. 2009).
Draft 41 August 2010

Nutrient concentrations (both N and P) were generally low throughout the St. Marks/Apalachee Bay 

system, except in the upper reach of the Wakulla River (i.e., Wakulla Springs, where higher levels of 

nitrates have resulted in an increased density of nuisance aquatic plants). Nitrate+nitrite concentrations 

in the upper tidal reach of the Wakulla River (U.S. Highway 98 Bridge) averaged 3 times greater than 

those observed on the St. Marks River at Newport (U.S. Highway 98 Bridge) (Table 10; Figure 27). 

Orthophosphate concentrations in the Wakulla, on the other hand, were only about half those noted for 

the St. Marks (Table 10). Ammonium values were low in the upper tidal reaches of both rivers. 

Ammonium and total Kjeldahl nitrogen (TKN) generally increased with distance downstream, while 

nitrate+nitrite and orthophosphate generally decreased (Table 10). TN and TP were lower in Apalachee 

Bay than in the rivers. Some seasonality was noted in levels of nitrate+nitrite in the upper tidal reaches 

of both rivers but not in orthophosphate. Chlorophyll concentrations were generally low throughout 

much of the system, with sporadic peaks in the rivers, particularly in the middle and lower tidal reaches 

(Table 8), where levels averaged 5.1 and 6.1 grams per liter (g/L), respectively. Values in these reaches 

were observed to exceed 10 g/L on several occasions. 

To examine downstream trends in water quality in the Wakulla River, stations were combined into four 

groups representing the head springs and the upper, middle, and lower reaches of the river, as shown in 

Figure 28. Water quality characteristics varied spatially and temporally throughout the collection sites, 

with specific conductance/salinity, DO, and chlorophyll generally increasing and most of the other 

characteristics decreasing with movement downstream (Table 11).
Draft 42 August 2010

Figure 27. (Top) N and (bottom) P concentrations in the St. Marks River (data from Florida STORET 

2007) (Lewis et al 2009). 
Draft 43 August 2010

Figure 28. (Top) N and (bottom) P concentrations in the Wakulla River (data from Florida STORET 

2007) (Lewis et al. 2009). 
Draft 44 August 2010

City of Tallahassee Data on Nitrate Contributions 

City of Tallahassee Public Supply Wells

The city of Tallahassee provided NO2+NO3-N data for 29 Floridan aquifer public supply wells in its

system (Appendix A, Table A-5, Figure A-43). Due to their relatively long open-hole intervals, regular 

pumping, long periods of record, large zones of contribution and high discharge volumes, these wells are 

of particular interest. Specifically, the data represent the best available insight into the spatial 

distribution of NO2+NO3-N in the Floridan aquifer beneath the semiconfined portion of the study area. 

Data from the 29 city of Tallahassee wells were then aggregated into several subsets based on location. 

The semiconfined well dataset (716 values from 27 wells, excluding the 2 Woodville wells) showed no 

significant trend in NO2+NO3-N concentration over time. The median concentration from this set of 

wells is 0.33 mg-N/L (n=716, mean=0.35, stdev=0.17). 

For the 20 city of Tallahassee wells south of Interstate 10, the median concentration was 0.36 mg-N/L 

(n=556, mean=0.38, stdev=0.16). Lastly, the 6 southernmost wells (south of Tram Road/Orange Avenue 

and adjacent to the Cody Scarp) had a median concentration of 0.48 mg-N/L (n=208, mean=0.48, 

stdev=0.16). These results show an increasing trend in NO2+NO3-N from north to south in Leon County 

under the semiconfining unit.

Wastewater Treatment Facilities

According to FDEP records, there are 69 WWTFs in Leon and Wakulla Counties (Appendix A, Table A-6, 

Figure A-46). Of the 59 WWTFs within the semiconfined and unconfined areas, 21 are domestic and 38 

are industrial. The total design capacity of the WWTFs, both domestic and industrial, is 38.05 MGD. The 

majority of this capacity (32.06 MGD) is for domestic plants operated by the city of Tallahassee. The 

remaining facilities have a combined capacity of slightly less than 6 MGD.

Commercial Fertilizer Application

The city of Tallahassee records indicate a 1999 application of 44,000 kg-N to 691 ha at its facility. Since 

the SESF is the only area designated as pasture and cropland in the unconfined portion of Leon County, 

the N application to the SESF is assumed to represent all the commercial fertilizer applied to this area.

Fenholloway/Econfina Studies

Dr. R. J. Livingston Long-Term Study, 1970–2004 (FSU) 

Dr. R. J. Livingston carried out a long-term study of the Fenholloway and Econfina areas from 1970 to 

2004. Figure 29 shows the study area, with a full complement of sampling stations. A Use Attainability 

Analysis (UAA), led by FDEP, was performed from 1991 through 1994 in support of evaluating the 

feasibility of changing the designated use classification of the Fenholloway River from Class V

(navigation, utility, and industrial) to Class III (recreation and a well-balanced population of fish and 

wildlife) (FDEP 1994). 

Extensive biological studies were preformed during the UAA, and it was determined that approximately 

24 km2 (9 square miles [mi2

]) of seagrasses offshore of the Fenholloway River had been adversely 

affected by the Buckeye Florida pulp mill effluent discharge, compared with the relatively natural Aucilla 

and Econfina nearshore areas (Livingston et al. 1998a). The study showed that light limitation due to 

the higher color from the Fenholloway River (caused by the discharge of treated wastewater from the 

mill) was the primary factor affecting seagrass growth. The study recommended that color reduction be 
Draft 45 August 2010

based on annual averages found in what was considered to be a potential seagrass habitat about 1.5 

miles offshore of the Fenholloway River (Station F10). 

To restore seagrasses in this area of the Fenholloway system, water quality models developed by 

HydroQual, Inc. projected that a 50% reduction in the historical treated wastewater color from the 

Buckeye Florida plant would be required to achieve a median color level of 36 PCUs at Station F10. This 

color level would be comparable to conditions in the Econfina system. 

Figure 29. Map showing positions of sampling stations in the Econfina and Fenholloway River

estuarine systems over the total sampling period. Additional charts indicate the sampling regimes 

associated with various field activities carried out during the 1970–2004 sampling period (Livingston). 
Draft 46 August 2010

BVA Water Quality Monitoring for Buckeye Florida, 2004–09 

BVA initiated a water quality monitoring program in 2004 for Buckeye Florida to (1) monitor the

relationship between nutrient loading due to Buckeye’s discharge and the occurrence of phytoplankton 

blooms (both HABs and non-noxious blooms) in Apalachee Bay, (2) monitor chlorophyll a in the system 

as a measure of water quality impairment, (3) monitor seagrass assemblages in the system in relation to 

regional climate, hydrology, and water quality, and (4) annually assess seagrass communities in 

Apalachee Bay from the Aucilla River to Spring Warrior Creek. 

BVA sampled 5 stations in both the Fenholloway River (F06, F10, F11, F14, and F16) and Econfina River 

(E06, E08, E10, E11, and E09) drainages on a monthly basis (growing season, May through October) from

2005 to 2009 (Figure 30; Table 12). Stations E06-F06, E08-F10, E10-F11, E11-F14, and E09-F16 have 

been considered physically equivalent and were defined as “cognates” by Livingston (2004a, b) and BVA

(2005, 2006, 2007, 2008, 2009) for comparison purposes, with the Econfina River stations being the 

defined “reference” condition (a site-specific alternative criteria [SSAC] was established for the 

Fenholloway River and Estuary for iron, DO, and transparency). In the SSAC, FDEP identified the 

Econfina River and Estuary as a minimally disturbed reference system and was used in the SSAC because 

it is similar to the Fenholloway River, except for the Buckeye point source discharge. The Econfina River 

has been demonstrated to have benign human land uses in the basin, healthy biological communities in 

freshwater portions, and diverse communities of algae, invertebrates, vegetation, and fish inhabiting the 

river and associated estuary (Livingston 2006). Additionally, a comprehensive seagrass survey was

conducted in both the Econfina and Fenholloway Estuaries and Apalachee Bay (Figure 31). Table B-2 in

Appendix B lists the data types collected by BVA from 2004 to 2009. 

Figure 32 summarizes the DO data collected at the 10 stations from 2004 to 2009. DO concentrations

were typically greater than 5 mg/L at each station; however, concentrations of less than 5 mg/L were 

measured at the mouth of the Econfina and Fenholloway Rivers. Figure 33 summarizes particulate 

carbon, N, and P data collected from 2006 to 2009. Figure 34 shows total dissolved nitrogen (TDN) and 

total dissolved phosphorus (TDP). The highest nutrient levels were encountered in the mouth of the 

Fenholloway River (Station F06) and the monitoring station to the east of the mouth of the Fenholloway 

River in the typical path of the river plume (Station F14). 

Figure 35 summarizes water column color data for 2004 to 2009. Yearly average color at the mouth of

each river has generally been higher at Fenholloway Station F06 compared with its Econfina cognate; 

however, in 2004, 2005, 2008, and 2009, the intra-annual variation in color within a station was greater 

than the between-station variation. Since 2004, the estuarine cognates E10-F11, E08-F10, and E11-F14 

have shown considerable variations within and between years such that, in general, pronounced color 

differences between cognate stations are no longer apparent. There has been no difference in water 

color at cognate Stations E09 and F16 in Apalachee Bay; the low color seen at Stations E09 and F16 

indicates probable background levels in the bay proper and a region beyond the influence of riverine 

discharge.

Figures 36 and 37 summarize water column chlorophyll a data for 2004 to 2009. While there was

variability in the range of chlorophyll a measured at the 10 stations, annual averages were typically less 

than 5 μg/L, which is low compared with many other estuaries in the Gulf of Mexico. Chlorophyll a

values measured at offshore Stations E09 and F16 were extremely low, indicating little phytoplankton 

biomass in the bay proper.
Draft 47 August 2010

Phytoplankton data for the Fenholloway and Econfina stations were collected monthly (May–October) 

from 2005 to 2009 (data were also collected in 2004 at several stations). Table 5 provides bloom data 

for specific phytoplankton taxa at the routine monitoring stations. It should be noted that blooms in the 

two systems are transitory—high phytoplankton densities detected in any one month are typically gone 

by the succeeding sampling period. The frequencies and magnitudes of specific taxa blooms were 

similar in both systems, with considerable intra- and inter annual variation. Phytoplankton taxa diversity 

(H’) data between cognate stations has exhibited considerable interannual variation (Figure 16).

One of the first objectives established for the Fenholloway River monitoring program was to determine 

if there was a relationship between Buckeye’s pulp mill discharge and the occurrence of phytoplankton 

blooms (both HABs and non-noxious blooms) in Apalachee Bay. The potentially harmful algal taxa, 

Pseudo-nitzschia pseudodelicatissima and Pseudo-nitzschia cf. brasiliana, were commonly collected in 

both the Fenholloway and Econfina systems. Pseudo-nitzschia species are considered harmful because 

of their potential to produce the toxin, domoic acid, which causes amnesic shellfish poisoning (ASP); 

however, Pseudo-nitzschia is common and widespread in all Florida coastal waters. Based on data 

collected from 2004 to 2009, it was concluded that there is no difference in the occurrence of blooms 

and HABs between the Fenholloway and Econfina River Estuaries. The red tide–causing organism, 

K. brevis, was not collected from any of the 10 monitoring stations between 2005 and 2009, consistent 

with periodic red tide reports provided by FWRI. 

Figures 38 and 39 shows the measured TP, TN, and chlorophyll a concentrations for the Econfina River 

and Fenholloway River areas, respectively. For more figures and tables from BVA, see Appendix B. 

Figure 30. Locations of BVA discrete water quality monitoring stations for the Econfina and 

Fenholloway Rivers. 
Draft 48 August 2010

Table 12. Latitudes and longitudes for discrete water quality stations for the Fenholloway and 

Econfina Estuaries (from BVA). 

Fenholloway 

River Station

Fenholloway 

River 

Latitude

Fenholloway 

River

Longitude

Econfina 

River Station

Econfina 

River

Latitude 

Econfina 

River

Longitude

F06 29.98380 83.78330 E06 30.03711 83.92605

F10 29.95117 83.78517 E08 30.01283 83.93150

F11 29.96067 83.80750 E10 30.02400 83.95317

F14 29.95810 83.76280 E11 30.02398 83.90960

F16 29.90800 83.78516 E09 29.96966 83.93160

Figure 31. Seagrass sample locations for the Econfina and Fenholloway Rivers, August 2009 (from 

BVA). 
Draft 49 August 2010

Figure 32. DO (mg/L) recorded at the Econfina and Fenholloway stations during the growing season 

from May through October (2004–09) (from BVA). 
Draft 50 August 2010

Figure 33. Top left graph shows particulate carbon at each station, top right graph shows particulate 

N at each station, and bottom graph shows particulate P for each station, 2006–09 (from BVA). 
Draft 51 August 2010

Figure 34. Graphs of TDN and TDP (mg/L) for each station during the growing season from May

through October, 2006–09 (from BVA). 
Draft 52 August 2010

Figure 35. Water color data summarized by cognate stations for the Buckeye Florida project, 2004–09

(from BVA). 

Figure 36. Chlorophyll a (mg/L) for each station during the growing season from May through 

October, 2004–09 (from BVA). 
Draft 53 August 2010

Figure 37. Chlorophyll a data summarized by cognate stations, 2004–09, Buckeye Florida project (from BVA). 
Draft 54 August 2010

Figure 38. Measured TP, TN, and chlorophyll a for the Econfina River area, Stations E06, E08, E09, E10, and E11 (annual calculations include 

May through October data only) (data from BVA; calculations by HydroQual). 
Draft 55 August 2010

Figure 39. Measured TP, TN, and chlorophyll a for the Fenholloway River area, Stations F06, F10, F11, and F16 (annual calculations include 

May–October data only) (data from BVA; calculations by HydroQual). 
Draft 56 August 2010

EPA 1999 Nutrient Study

The EPA’s Ecological Assessment Branch in Athens, Georgia, completed a nutrient study of the Econfina 

and Fenholloway systems in 1999 (EPA 2000). The objectives of the study included assessing 

phytoplankton blooms in the Fenholloway near shore areas, determining relationships between color 

and phytoplankton biomass in the two study areas, analyzing nutrient loading and color contributions 

from point sources, determining light profiles, and analyzing DO concentrations in the study areas. 

Sampling periods were as follows: December 1998 (full sampling), March 1999 (reduced sampling), June 

1999 (reduced sampling), and August through September 1999 (reduced sampling). No phytoplankton 

blooms were noted during the four sampling periods, an observation backed up by pH and DO results. 

The results of the EPA study indicated that chlorophyll a concentrations were low in both estuaries, with 

maximum concentrations noted at 10 μg/L in the Fenholloway Estuary. Results from Marine Algal 

Growth Potential Tests (AGPT) were higher in the Fenholloway system but were greater than 10 mg/L (a 

potential eutrophication threshold) only in June 1999. Nutrient addition experiments indicated that 

most of the samples in both estuaries were N limited. Bioavailable P was 5 times greater in the 

Fenholloway Estuary compared with the Econfina, while bioavailable N was similar in both systems, 

except for the June study period, when the average for the Fenholloway system was 5 times that of the 

reference area. The Buckeye TN and TP discharge constituted 97% of the point source load to the 

Fenholloway River, and nutrient concentrations in the Fenholloway River were about 10 times those in 

the Econfina River. The EPA study indicated that there were net releases of nutrients from the 

Fenholloway estuarine sediments, while there were net fluxes to sediments in the Econfina system. 

Color values for the Fenholloway River averaged 880 PCUs, while the reference Econfina River averaged 

160 PCUs. Light was found to be limiting to plant growth in the Fenholloway Estuary (less than 1% of 

surface illumination at 2-foot depths compared with greater than 10% in the Econfina Estuary). DO was 

collected at 2 different sites and was very low in the Fenholloway River, where it averaged 4.4 and 5.6 

mg/L, compared with the Econfina, where DO was 5.5 and 6.1 mg/L. DO averaged 3.4 mg/L in the 

Fenholloway Estuary compared with 4.0 mg/L in the Econfina. DO concentrations were occasionally 

lower than the 4.0 mg/L Class III marine water quality standard in both systems, and the EPA is currently 

evaluating a “natural background” SSAC for DO, based on the conditions in the Econfina, that was 

adopted by the state’s Environmental Regulation Commission (ERC) in May 2010. 

Steinhatchee Estuary Sampling, Project COAST, 1997–present 

Ten sites in the Steinhatchee Estuary have been sampled monthly since 1997 as part of Project COAST

(Figure 40), with Dr. Tom Frazer of UF as the principal investigator (PI). This project measures TN, TP, 

chlorophyll a, light extinction coefficient, Secchi depth, color, salinity, DO, and temperature. Water 

quality analyses are conducted at UF by the LakeWatch Program. FDEP Aquatic Preserve staff provided 

a dataset through 2008. This is the most extensive and comprehensive dataset available for the region. 

Dr. Frazer presented these results at the public meeting on February 23, 2010, for numeric nutrient 

criteria planning in Crystal River (Figure 41; Frazer and Jacoby 2010). Means for the whole area have 

remained stable over time, with a seasonal cycle of higher nutrients and chlorophyll a in the summer 

(Figure 40). Chlorophyll a and TP concentrations were higher than usual during 2004 and 2005, when 

the region experienced numerous hurricanes and abnormally high rainfall.

FDEP conducted additional analyses of Project COAST data for the Steinhatchee Estuary. Annual 

geometric means of TN, TP, and chlorophyll a (uncorrected) were calculated for each station each year 

and plotted against annual mean salinity (Figure 42). There is a clear negative relationship between 
Draft 57 August 2010

salinity and TN, and between salinity and TP. Geometric mean TN ranged from 400 to 800 μg/L at 0 to

10 ppt salinity, and from 250 to 500 μg/L at 20 to 35 ppt salinity. Geometric mean TP ranged from 25 to 

55 μg/L at 0 to 10 ppt salinity, and from 10 to 25 μg/L at 25 to 35 ppt salinity. Chlorophyll a

concentrations peaked at 20 ppt salinity 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 phenomenon is consistent with results found in the Suwannee, 

Waccasassa, and Withlacoochee Estuaries, and this “chlorophyll hump” is an important component of 

estuarine primary, and subsequent secondary, productivity.

Figure 40. Locations of Project COAST sampling sites in the Steinhatchee Estuary. Sites 1 and 2 are in 

the river channel but mean salinities at those sites are greater than 5 ppt (Charbonneau 2010). 
Draft 58 August 2010

Figure 41. Monthly average TN, TP, and uncorrected chlorophyll a for 10 estuarine stations in the 

Steinhatchee Estuary, collected by Project COAST, 1997–2008 (Frazer and Jacoby 2010).

0

100

200

300

400

500

600

700

800

Mar-96 Aug-97 Dec-98 May-00 Sep-01 Jan-03 Jun-04 Oct-05 Mar-07 Jul-08

TN (ug/L)

Steinhatchee Monthly Average Total Nitrogen (TN) 

1997 through 2008 Estuarine Stations

0

5

10

15

20

25

30

35

40

45

Mar-96 Aug-97 Dec-98 May-00 Sep-01 Jan-03 Jun-04 Oct-05 Mar-07 Jul-08

TP (ug/L)

Steinhatchee Monthly Average Total Phosphorus (TP) 

1997 through 2008 Estuarine Stations

0

2

4

6

8

10

12

14

Mar-96 Aug-97 Dec-98 May-00 Sep-01 Jan-03 Jun-04 Oct-05 Mar-07 Jul-08

CHL-a (ug/L)

Steinhatchee Average Chlorophyll-a (CHL-a)

1997 through 2008 Estuarine Stations 
Draft 59 August 2010

Figure 42. Annual average salinity plotted as a predictor of (1) annual geometric mean TN, (2) annual 

geometric mean TP, and (3) annual geometric mean uncorrected chlorophyll a at 10 sites in the 

Steinhatchee Estuary, 1997–2007. Linear trend lines fitted for TN and TP, and a 2nd-order polynomial 

fitted for chlorophyll a, for demonstration purposes.

y = -11.507x + 714.96

R2 = 0.681

0

200

400

600

800

1000

0 10 20 30 40

Total nitrogen (μg/L)

Annual Average Salinity

y = -1.1287x + 49.997

R2 = 0.8031

0

10

20

30

40

50

60

0 10 20 30 40

Total Phosphorus (μg/L)

Annual Average Salinity

y = -0.0178x2 + 0.6373x - 0.5314

R2 = 0.6585

0

1

2

3

4

5

6

7

8

0 10 20 30 40

Chlorophyll a (uncorrected; μg/L)

Annual Average Salinity
Draft 60 August 2010

The Project COAST Program analyzed for chlorophyll a without phaeophytin correction from 1997 to 

2006, but began correcting for phaeophytin in 2007. FDEP policy dictates that phaeophytin-corrected 

data are preferable for assessment purposes, and thus a comparison between corrected and 

uncorrected values is helpful. Data were available to correlate chlorophyll a corrected for phaeophytin 

vs. uncorrected values for 2007 (11 to 12 samples per site) and 2008 only (3 samples per site). The 2 

measurements are very highly correlated (Figure 43), and the geometric means were typically within 1

μg/L of each other (Table 13). The highest geometric mean corrected chlorophyll a for 2007 was 5.79 

μg/L at Station 2, which is located where the river channel opens out into the Gulf. 

Figure 43. Relationship between individual sample analyses of uncorrected chlorophyll a and 

phaeophytin-corrected chlorophyll a for 10 sites sampled monthly in the Steinhatchee Estuary in 2007 

and the first part of 2008.

y = 0.8839x - 0.1264

R2 = 0.988

0

5

10

15

20

25

30

0 5 10 15 20 25 30

Corrected Chlorophyll 

a (μg/L)

Uncorrected Chlorophyll a (μg/L)

Uncorrected vs. Corrected Chlorophyll a for Steinhatchee Estuary Sites, 

2007-2008 

(n=15 months at 10 sites)
Draft 61 August 2010

Table 13. Comparison between station geometric means for 2007 (n = 11, or 12 monthly samples) and 

uncorrected and phaeophytin-corrected chlorophyll a (μg/L) measurements.

Site Uncorrected Corrected % Difference

1 2.18 1.65 24%

2 7.05 5.79 18%

3 2.54 2.01 21%

4 1.03 0.83 19%

5 1.00 0.84 15%

6 1.15 1.01 12%

7 1.76 1.44 18%

8 1.25 1.10 12%

9 1.46 1.36 7%

10 0.83 0.67 20%

SRWMD Monitoring in the Steinhatchee Estuary

The SRWMD has monitored one site in the Steinhatchee Estuary since 2002 (with some sampling in 

1995) (Figure 44). Robbie McKinney from the SRWMD conducted LOWESS regression analysis for this 

site and presented the results at the February 23, 2010, public meeting in Crystal River. He did not 

detect any trend over time for NO2+3, ammonia, TP, or orthophosphate but noted a decreasing trend in 

TKN over time (Figure 45). Experts present at the meeting opined that the trend was probably related to 

changes in the amount of fresh water due to rain patterns, rather than to any real decline in TKN.

FDEP conducted additional analyses of these data, which were retrieved from STORET. All available TN 

and TP data are plotted in Figure 46, and Table 14 shows geometric means for years with greater than 4 

data points. TN and TP at this site range from near detect to as high as 1.5 mg/L of TN and 80 μg/L of TP 

(Figure 46).
Draft 62 August 2010

Figure 44. Location of the Steinhatchee Sound Station (STN060C1) sampled by the SRWMD. 

Figure 45. TKN for the Steinhatchee station (2002–09) (from McKinney 2010). 
Draft 63 August 2010

Figure 46. All available TN and TP data for Steinhatchee Estuary Site STN060C1, sampled by the 

SRWMD. 

Table 14. Annual geometric mean concentrations of chlorophyll a (uncorrected), TN, and TP for 

Station STN060C1 in the Steinhatchee Estuary, sampled by SRWMD. - = Empty cell/no data

X = Fewer than four data points were available, and so the annual geometric mean was not calculated.

- 2002 2003 2004 2005 2006 2007 2008 2009

Chlorophyll a (μg/L) 1.09 X 1.63 3.39 5.06 1.43 1.44 1.65

TN (mg/L) 0.674 X X 0.998 0.606 X 0.493 X 

TP (mg/L) 0.013 0.023 0.018 X X X 0.022 0.040

Existing Regional Nutrient Loading Models, HydroQual Inc. 

Tom Gallagher and Christhian Mancilla of Hydroqual prepared a document for FDEP that summarizes 

the analysis performed to support and assist the development of TN and TP criteria for several streams 

located in the Apalachee Bay area. The objective of this analysis was to present an approach for 

nutrient criteria development. Existing TN, TP, and flow data were analyzed, and long-term nutrient 

concentrations were estimated with flow as an explanatory variable. 

For the analysis, nutrient data were obtained for the Econfina, Aucilla, St. Marks, and Steinhatchee

Rivers. TN and TP data were retrieved from the SRWMD website, the Florida STORET online database, 

and the EPA STORET online database. Daily flow records were obtained from the U.S. Geological Survey 

(USGS) online data retrieval interface for several flow stations located along these rivers. The most 

downstream flow stations were selected for the analysis and, if long-term flow measurements were not 

available or tidal influence was noticed, the next upstream flow station that met both criteria was then 

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0

0.5

1

1.5

2

2.5

3

1/31/1993

10/28/1995

7/24/19984/19/20011/14/2004

10/10/2006

7/6/20094/1/2012

Total Phosphorus (mg/L)

Total Nitrogen (mg/L)

Steinhatchee Estuary SRWMD Site STN060C1 Nutrients 

TN

TP
Draft 64 August 2010

selected. Several water quality stations were identified in the vicinity of the selected USGS flow 

stations. Table C-2 (in Appendix C) lists the selected water quality stations. 

Figures C-2 through C-9 (in Appendix C) present temporal plots of TN and TP data for the selected 

stations. These figures also include daily flow records for times when the nutrient data were collected. 

Assuming flow to be an explanatory variable for the TN and TP concentrations, relationships between 

measured daily flows and nutrient concentrations were developed. Figures C-10 to C-13 in Appendix C 

depict the developed flow–concentration relationships for TN and, similarly, Figures C-14 to C-17 in 

Appendix C depict the equivalent relationships for TP. 

These relationships allowed the calculation of long-term daily nutrient concentrations (1950 to 2009) as 

defined by long-term daily flows. Figures C-18 to C-21, and Figures C-22 to C-25 (upper two panels), in 

Appendix C present the long-term measured flows and computed long-term nutrient concentrations for

TN and TP, respectively. Because the EPA’s proposed numeric nutrient water quality criteria for flowing 

waters within the state—specifically, the proposed In-stream Protection Values (IPVs)—are based on 

annual geometric means, Figures C-18 to C-25 (bottom panel) in Appendix C summarize the annual 

geometric means corresponding to the computed long-term nutrient concentrations for TN and TP. The 

EPA has proposed TN and TP IPVs of 0.824 and 0.043 mg/L, respectively, for the Panhandle region of 

Florida. These IPVs are indicated by the red dotted lines on Figures C-18 to C-25 (bottom panel) in 

Appendix C. (for more information and the tables and figures from the HydroQual analysis, see Appendix 

C).

Waters on the 303(d) List 

Of the various waters in the Apalachee Bay Basin, only the Fenholloway River has been placed on the 

303(d) list for a parameter other than bacteria or mercury (see Table 15). The parameters listed for the 

Fenholloway (BOD, DO, and nutrients) are currently addressed by an EPA-approved TMDL and by the 

ongoing NPDES permitting process. 
Draft 65 August 2010

Table 15. Impaired waters in the greater Apalachee Bay planning units. - = Empty cell/no data

IIIM = Class III marine 

Planning 

Unit 

WBID Waterbody 

Segment 

Name 

Waterbody

Type 

Waterbody

Class

Parameters 

Included on 

the 1998 

303(d) List 

Parameters 

Assessed 

Using the 

IWR

Concentration 

Causing 

Impairment

Coastal 

Watershed and 

Apalachee Bay 

8026 Coastal 

Apalachee 

Gulf West 

Coastal 3M - Bacteria 

(in shellfish)

Conditionally 

approved for 

shellfish 

Coastal 

Watershed and 

Apalachee Bay 

8026B Shell Point Beach 3M - Bacteria 

(beach 

advisories) 

>21 days of 

beach closures

Ochlockonee/ 

St. Marks

8999 Gulf Coast Coastal/

Estuary

3M - Mercury 

(based on fish 

consumption 

advisory)

>0.3mg/kg

Fenholloway 3473A Fenholloway 

at Mouth 

Estuary 3M BOD 5 day BOD Median BOD= 

3.5 mg/L

Fenholloway 3473A Fenholloway 

at Mouth 

Estuary 3M DO DO <4.0 mg/L

Fenholloway 3473A Fenholloway 

at Mouth 

Estuary 3M Nutrients Nutrients 

(chlorophyll 

a) 

Median 

TN=2.39 mg/L; 

median 

TP=0.64 mg/L; 

median 

BOD=3.50 

mg/L 

Other Coastal 8032A Dekle Beach Beach 3M - Bacteria >21 days of 

advisories in 

year

Other Coastal 8032B Keaton Beach Beach 3M - Bacteria >21 days of 

advisories in 

year

Other Coastal 8032C Cedar Beach Beach 3M - Bacteria >21 days of 

advisories in 

year

Other Coastal 8032E Hagens Cove 

Beach

Beach 3M - Bacteria >21 days of 

advisories in 

year

Steinhatchee 3573C Steinhatchee 

River

Estuary 3M - Fecal 

Coliform 

>400 

counts/100mL

Impairment for Bacteria Not Necessarily Indicative of Anthropogenic Impact

The use of fecal coliforms as an indicator 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 (MST) and pathogen-detection 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). It expressed concern that the EPA 

recreational criteria were derived in places that do not represent Gulf of Mexico conditions, and that the 
Draft 66 August 2010

use of fecal indicators was not appropriate for waters primarily influenced by natural animal sources. 

Areas in the Gulf of Mexico for which the workgroup thought the EPA criteria might 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, but that there is ample evidence to caution against assuming 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 an MST 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, or 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 

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.
Draft 67 August 2010

Numeric Nutrient Criteria Recommendations 

Based upon data from 1971 to the present, Apalachee Bay is currently biologically healthy and fully 

supports its designated use, except for a small area near the Fenholloway River. A TMDL has been 

completed and approved by the EPA for the Fenholloway River, and it is expected to be implemented 

within the next 5 years, resulting in the full restoration of the Fenholloway system. Therefore, except 

for the Fenholloway, maintaining the current nutrient regime is the recommended approach for the bay. 

Note that riverine inputs provide the predominant source of nutrients to the bay, and these nutrient 

loads naturally vary as a function of rainfall. Since the bay has been demonstrated to be healthy, 

maintaining the existing nutrient loads from the rivers will result in fully protective criteria. 

Five major rivers flow into Apalachee Bay, and criteria have been established for each river system to 

maintain the overall health of the bay. Table 16 shows the TN and TP loads and concentrations for the 

main rivers in the greater Apalachee Bay area, excluding the Fenholloway (which is addressed via the 

EPA-approved TMDL). The loading numbers were calculated by HydroQual, using flow data from USGS 

stations in the rivers, as well as data from water quality stations in the vicinity of the selected USGS 

stations. The full approach is explained above, and Appendix C contains the tables and graphs 

supporting the approach.

The water quality station used for the St. Marks River is Station 3528, St. Marks at HWY 98 Newport. 

The sampling period for this station is 1998 to 2009, and data were obtained from FDEP STORET. The 

water quality station used for the Aucilla River is Station AUC0501C1, Aucilla River at US 27 near Lamont. 

The sampling period for the station is 2000 to 2009, and data were obtained from the SRWMD. Water 

quality data for the Econfina River, received from the SRWMD via Florida STORET, were taken from two 

stations: Station ECN010C1, Econfina River near Perry, had a sampling period of 1989 to 1992, and 1999

to 2009; and Station 6976, Econfina River at Cabbage Cove, had a sampling period of 1999 to 2009. 

Water quality data for the Steinhatchee River, received from the SRWMD via Florida STORET, also 

consisted of two stations: Station STN030C1, Steinhatchee River near Cross City, was sampled from 

1999 to 2009; and Station 6978, Steinhatchee River near Tennile had a sampling period of 1999 to 2009. 

The various water quality studies in the report for the St. Marks River show that nutrient concentrations 

were generally low throughout the St. Marks/Apalachee Bay system, except in the upper reaches of the 

Wakulla River. Nitrate+nitrite concentrations in the upper tidal reaches of the Wakulla River (U.S. 

Highway 98 Bridge) average three times greater than those observed on the St. Marks at Newport (U.S. 

Highway 98 Bridge). 

Once the water reaches the bay, TN and TP are lower in the bay than in the upper tidal reaches of the 

river. The Fenholloway River is the only river in the greater Apalachee Bay area that historically had

water quality problems and adverse effects to biological communities. Although the mill has affected

the water quality of the Fenholloway River since 1954, regulatory actions (a UAA and reclassification, 

TMDLs developed and approved for biochemical oxygen demand [BOD] and nutrients, and an SSAC 

developed for transparency) and subsequent improvements by the facility suggest that the system will 

be restored. FDEP is currently in the process of modifying the National Pollutant Discharge Elimination 

System (NPDES) permit for Buckeye that will include actions required of the facility to fully meet the 

designated use.
Draft 68 August 2010

Table 16. TN and TP loads and concentrations for the St. Marks, Aucilla, Econfina, and Steinhatchee 

Rivers. 1 St. Marks loads (1950–2009) were calculated by HydroQual from USGS Station: 02326900 near Newport, and thus do not include Wakulla 

River nutrients. Concentration data are from LakeWatch 2001 estuarine stations; the sites used were WAK1-3, sampled on January 10, March 

23, and May 17, 2001. 2 Aucilla loads (1950–2009) were calculated by HydroQual from USGS Station: 02326512 near Scanlon. Concentration data are from LakeWatch 

2001 estuarine stations; the sites used were TAY1-3, sampled on January 10, March 23, and May 17, 2001. 3 Econfina loads (1950–2009) were calculated by HydroQual from USGS Station: 02326000 near Perry. Concentrations are annual geometric 

means for the Econfina River area, Stations E06, E08, E09, E10, and E11 (annual calculations include May–October data only). Data are from 

BVA, and calculations performed by HydroQual. 4 Steinhatchee loads were calculated by HydroQual from USGS Station: 02324000 near Cross City. Concentration data are from Project COAST 

(1997–2008). Monthly average TN and TP were collected for 10 estuarine stations in the Steinhatchee Estuary.

System TN Loads

(ranges)

(lbs/day)

TN Loads

(long-term 

geometric 

means)

(lbs/day)

TP Loads

(ranges)

(lbs/day)

TP Loads

(long-term 

geometric 

means)

(lbs/day)

TN 

Concentration

(long-term 

geometric 

means)

(mg/L) 

TP 

Concentration

(long-term 

geometric 

means)

(mg/L) 

St. Marks1 400-4,000 1,337 70-340 155 0.36 0.04

Aucilla2 100-6,000 2,040 10-370 120 1.1 0.06

Econfina3 100-1,700 478 1-95 40 0.89 0.09

Steinhatchee4 <100-3,500 760 1-280 62 0.92 0.08

Numeric Nutrient Criteria 

Methodology 

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 
Draft 69 August 2010

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 the Greater Apalachee Bay Area 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 

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. 

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. 
Draft 70 August 2010

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 

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 intends to propose three sets of potential criteria for greater Apalachee Bay when sufficient data 

are available: 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. FDEP is in the process of collecting nutrients and chlorophyll a at 12 stations 

throughout Apalachee Bay. Until sufficient data are available to calculate concentration-based criteria as 

described above, interim criteria would consist of preventing increases in the loads from the St. Marks, 

Aucilla, Econfina, and Steinhatchee Rivers, as shown in Table 16. The Fenholloway River loads are 

addressed via an EPA approved TMDL.
Draft 71 August 2010

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Draft 76 August 2010

Appendix A: Long-Term (1971–2004) Response of the Econfina and Fenholloway Drainages 

(Apalachee Bay) to the Discharge of Pulp Mill Effluents: Nutrient Loading, Limitation and 

Distribution. 

This unpublished report was written by Dr. Robert J. Livingston, retired professor from FSU, for the 

Florida Department of Environmental Protection. It outlines a long-term study (1970–2004) by Dr. 

Livingston and his students on the Econfina and Fenholloway systems (Apalachee Bay). The report is 

available at Apalachee nutrient reprt1 livingstondoc.doc. The report includes results and discussion for 

rainfall and river flows, nutrient loading, and water quality in the Fenholloway and Econfina systems, 

light distribution, nutrient limitation, sediment quality, plankton, submerged aquatic vegetation, 

invertebrates, fishes, and restoration.

Livingston, R. J. 2010. Long-term (1971–2004) response of the Econfina and Fenholloway drainages 

(Apalachee Bay) to the discharge of pulp mill effluents: Nutrient loading, limitation and distribution. 

(Unpublished report) for The Florida Department of Environmental Protection. 
Draft 77 August 2010

Appendix B: Rainfall and Seagrass Coverage Figures of the Fenholloway and Econfina Systems 

(from BVA Research for Buckeye Florida L.P.) 

BVA initiated a water quality monitoring program in 2004 for Buckeye Florida (Buckeye) to monitor the

relationship between nutrient loading due to Buckeye’s discharge and the occurrence of phytoplankton 

blooms (both HABs and non-noxious blooms) in Apalachee Bay; monitor chlorophyll a in the system as a 

measure of water quality impairment; monitor seagrass assemblages in the system in relation to 

regional climate, hydrology, and water quality; and annually assess seagrass communities in Apalachee 

Bay from the Aucilla River to Spring Warrior River. The following figures show rainfall, discharge, and 

seagrass change in the Econfina and Fenholloway systems. 
Draft 78 August 2010

Figure A-1. Seasonal rainfall for Perry, Florida, 1998–2009. Top graph shows 1998–2002 data, and 

bottom graph shows 2003–09 data (from BVA). 
Draft 79 August 2010

Figure A-2. Discharge compared with 1977–2009 annual average for the Fenholloway and Econfina 

Rivers (from BVA). 

Table A-1. Latitudes and longitudes for discrete water quality stations for the Fenholloway and 

Econfina Estuaries (from BVA data). 

Fenholloway 

River Station

Fenholloway 

River Station 

Latitude

Fenholloway 

River Station 

Longitude

Econfina 

River Station

Econfina 

River Station 

Latitude

Econfina 

River Station 

Longitude

F06 29.98380 83.78330 E06 30.03711 83.92605

F10 29.95117 83.78517 E08 30.01283 83.93150

F11 29.96067 83.80750 E10 30.02400 83.95317

F14 29.95810 83.76280 E11 30.02398 83.90960

F16 29.90800 83.78516 E09 29.96966 83.93160
Draft 80 August 2010

Table A-2. Data collected from 10 BVA monitoring stations listed in Table A-1. - = Empty cell/no data

*Nutrient data are from Chesapeake Bay Laboratory, MD. 

*Phytoplankton data are from Dr. A.K.S.K Prasad, FSU. 

- Years Collected Frequency of 

Collection

Variables Measured Location in Water 

Column

Nutrients 2005-present Monthly from MayOctoberNitrogen ammonia (NH4); 

nitrate (NO3); 

nitrite nitrogen (NO2); 

phosphate (PO4); 

total dissolved phosphorus (TDP); 

Total dissolved nitrogen (TDN); 

 (PC); 

(PN); 

 (PP); 

silicate (Si) 

Subsurface

General water 

quality

2005-present Monthly from MayOctoberTemperature; 

salinity; 

specific conductance; 

DO; 

DO % saturation; 

pH; 

turbidity; 

color; 

Secchi depth

Subsurface

Light 2006-present Monthly from MayOctober% light on bottom with 4π PAR sensor Subsurface; 

Bottom

Light 2004–05 Monthly from MayOctober% light on bottom with 2π sensor Subsurface; 

Bottom

Phytoplankton 2005-2009 Monthly from MayOctoberChlorophyll a; 

taxa abundance; 

class abundance; 

taxa diversity; 

taxa biovolume

Water column

Seagrass 2006-present Monthly from MayOctoberTaxa-specific density; 

taxa-specific biomass; 

macroalgae composition; 

macroalgae biomass

– 

Seagrass survey 2005-present August Taxa-specific density; 

Secchi depth; 

light

Apalachee Bay from 

west of Econfina to 

Spring Warrior
Draft 81 August 2010

Figure A-3. Distribution and abundance of seagrasses in the Econfina and Fenholloway Estuaries and 

Apalachee Bay, 1992 (from BVA). 
Draft 82 August 2010

Figure A-3. Distribution and abundance of seagrasses in the Econfina and Fenholloway Estuaries and 

Apalachee Bay, 1992 (from BVA). 
Draft 83 August 2010

Figure A-5. Percent coverage for the Econfina and Fenholloway Estuaries and Apalachee Bay, 2005 

(from BVA). 
Draft 84 August 2010

Figure A-6. Percent coverage for the Econfina and Fenholloway Estuaries and Apalachee Bay, 2009 

(from BVA). 
Draft 85 August 2010

Appendix C: Apalachee Bay Nutrient Criteria Support Analysis from HydroQual

This document summarizes the analysis performed to support and assist the development of TN and TP 

criteria for several streams located in the Apalachee Bay area. Existing TN, TP and flow data have been 

analyzed and, considering flow to be an explanatory variable, long-term nutrient concentrations have 

been estimated. Nutrient data were obtained for the following rivers: Econfina, Aucilla, St. Marks, and 

Steinhatchee. TN and TP data was retrieved from the SRWMD website, the FDEP STORET online 

database, and the EPA STORET online database. Daily flow records were obtained from the USGS online 

data retrieval interface for several flow stations located along these rivers. This document includes 

numerous figures and tables to help illustrate the TN and TP for the Econfina, Aucilla, St. Marks, and 

Steinhatchee Rivers. 

HydroQual, Inc. June 9, 2010. Apalachee Bay nutrient criteria aupport analysis. Technical 

memorandum for the Florida Department of Environmental Protection.