Site-Specific Information 

in Support of 

Establishing Numeric Nutrient 

Criteria in Apalachicola 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 .............................................................................................. 4

Summary of Nutrient Studies by Dr. Robert J. Livingston (FSU).........................................................6

Biological Summary............................................................................................................. 10

SAV..............................................................................................................................................10

Phytoplankton..............................................................................................................................12

Oysters (Crassostrea virginica) (from Livingston 2010)...................................................................13

Infaunal Macroinvertebrates (from Livingston 2010).....................................................................13

Penaeid Shrimp (from Livingston 2010).........................................................................................13

Callinectes Sapidus (from Livingston 2010)....................................................................................14

Fishes (from Livingston 2010)........................................................................................................14

Presence and Frequency of Harmful Algal Blooms (HABs) ..............................................................15

Shellfish Production and Frequency/Duration of Bed Closures........................................................15

Quantification of Landings from Commercial/Recreational Fisheries..............................................16

Fish Kills.......................................................................................................................................16

Water Quality Studies ......................................................................................................... 17

ANERR Monitoring .......................................................................................................................17

Water Quality Studies by Paula Viveros (UF) and ANERR ...............................................................20

Water Quality Studies by Dr. Robert J. Livingston (FSU), 1972–2008...............................................30

Nutrient Loading Models..................................................................................................... 31

Waters on the 303(d) List..................................................................................................... 41

Impairment for Bacteria Not Necessarily Indicative of Anthropogenic Impact ................................44

Numeric Nutrient Criteria Recommendations ...................................................................... 45

References .......................................................................................................................... 50

Appendix A: Nutrients in Apalachicola River-Bay System ..................................................... 56

Appendix B: Fish Landings by County and Year for all Florida Counties except Walton......... 57

Appendix C: Apalachicola River Nutrient Loadings ............................................................... 58

Appendix D: Fish Kills Associated with K. brevis in Franklin County, 2001–June 21, 2010 ...... 59
Draft iii August 2010

List of Tables

Table 1. Checklist of nutrient enrichment symptoms for Apalachicola Bay................................................. 2

Table 2. Summary of the physical characteristics of Apalachicola Bay. ...................................................... 4

Table 3. Nutrient concentrations in the Apalachicola River, Mile 11 (from Frick et al. 1996). ..................10

Table 4. East Bay SAV species list (from Fahrny et al. 2006)......................................................................12

Table 5. Apalachicola Bay red tide tracking (FDACS).................................................................................15

Table 6. Mean nutrient measurements in Apalachicola Bay as determined by various researchers 

over time (Wanat 2010)............................................................................................................20

Table 7. Mean DIN concentration for different areas of Apalachicola Bay, in summer and winter, 

from Paula Viveros, UF (Wanat 2010)......................................................................................21

Table 8. Mean TDN concentration for different areas of Apalachicola Bay, in summer and winter, 

from Paula Viveros, UF (Wanat 2010)......................................................................................21

Table 9. Mean SRP concentration for different areas of Apalachicola Bay, in summer and winter, 

from Paula Viveros, UF (Wanat 2010)......................................................................................22

Table 10. Mean total dissolved phosphorus (TDP) concentration for different areas of 

Apalachicola Bay, in summer and winter, from Paula Viveros, UF (Wanat 2010). ..................22

Table 11. Mean salinity for different areas of Apalachicola Bay, in summer and winter, from 

Paula Viveros, UF (Wanat 2010)...............................................................................................23

Table 12. Mean chlorophyll a concentration for different areas of Apalachicola Bay, in summer 

and winter, from Paula Viveros, UF (Wanat 2010)...................................................................24

Table 13. Concentration flow regression equations for the Lake Seminole and Sumatra stations 

(Hydroqual)...............................................................................................................................32

Table 14. Upper distribution of Apalachicola River statistical nutrient loads (after Hydroqual 

2010).........................................................................................................................................32

Table 15. Impaired waters in the Apalachicola Bay Basin .........................................................................41

Table 16. Proposed numeric nutrient criteria for all segments of Apalachicola Bay, including TP, 

TN, and Chlorophyll a................................................................................................................49

 
Draft iv August 2010

List of Figures

Figure 1. Satellite photo of Apalachicola Bay, with labeled sections (from Wanat 2010)........................... 3

Figure 2. Map of the Apalachicola–Chattahoochee–Flint River Basin. Each separate basin is 

depicted by a different shade of green (from Wanat 2010)....................................................... 5

Figure 3. Nitrite-nitrate and orthophosphate loading in the Apalachicola, Choctawhatchee, 

Perdido, and Escambia Rivers (Livingston 2010). ....................................................................... 8

Figure 4. Livingston’s model of the Apalachicola Bay system, showing key features that result in 

extremely high primary and secondary productivity. ................................................................. 9

Figure 5. Percent SAV coverage in East Bay and ANERR monitoring sites, June 2005 (Edmiston 

2008).........................................................................................................................................11

Figure 6. ANERR long-term monitoring locations throughout Apalachicola Bay (Wanat 2010). ..............17

Figure 7. Cat Point (Gray) and Dry Bar (Blue) daily average salinity, 1993–2008 (solid lines are 

90-day moving average data; dashed lines are linear trend lines) (Wanat 2010). ..................18

Figure 8. Areal extent of salinity zones in Apalachicola Bay under various flow regimes. Map at 

left shows salinity contours in the bay when river flow is between 15,000 and 35,000 

cfs. Map at right shows salinity contours in the bay when river flow is below 15,000 

cfs (Wanat 2010). .....................................................................................................................18

Figure 9. DO (mg/L) at the three data logger locations, from 2008 ANERR data (Wanat 2010). .............19

Figure 10. Turbidity at the three data logger locations, from 2008 ANERR data (Wanat 2010)...............19

Figure 11. pH at the three data logger locations, from 2008 ANERR data (Wanat 2010).........................20

Figure 12. Chlorophyll a compared with river flow for four stations in the bay, 2002–09, from 

Paula Viveros, UF (Wanat 2010)...............................................................................................23

Figure 13. Phytoplankton composition, June 2008, by biovolume (μm3 mL-1); stars show station 

locations on map below; data from Paula Viveros, UF (Wanat 2010). ....................................24

Figure 14. Phytoplankton composition, July 2008, by biovolume (μm3 mL-1); stars show station 

locations on map below; data from Paula Viveros, UF (Wanat 2010). ....................................25

Figure 15. Phytoplankton composition, August 2008, by biovolume (μm3 mL-1); stars show 

station locations on map below; data from Paula Viveros, UF (Wanat 2010). ........................25

Figure 16. Map of Apalachicola Bay, showing station locations; stars show certain stations from 

figures above; data from Paula Viveros, UF (Wanat 2010)......................................................26

Figure 17. Phytoplankton composition, September 2008, by biovolume (μm3 mL-1); stars show 

station locations on map below; data from Paula Viveros, UF (Wanat 2010). ........................26

Figure 18. Phytoplankton composition, October 2008, by biovolume (μm3 mL-1); stars show 

station locations on map below; data from Paula Viveros, UF (Wanat 2010). ........................27

Figure 19. Phytoplankton composition, November 2008, by biovolume (μm3 mL-1); stars show 

station locations on map below; data from Paula Viveros, UF (Wanat 2010). ........................27

Figure 20. Map of Apalachicola Bay; stars show station locations from figures above; data from 

Paula Viveros, UF (Wanat 2010)...............................................................................................28

Figure 21. Phytoplankton species composition, December 2008, by biovolume (μm3 mL-1); stars 

show station locations on map below; data from Paula Viveros, UF (Wanat 2010)................28

Figure 22. Phytoplankton composition by biovolume (μm3 mL-1), January 2008; stars show 

station locations on map below; data from Paula Viveros, UF (Wanat 2010). ........................29
Draft v August 2010

Figure 23. Phytoplankton composition by biovolume (μm3 mL-1), February 2008; stars show 

station locations on map below; data from Paula Viveros, UF (Wanat 2010). ........................29

Figure 24. Map of Apalachicola Bay, showing station locations; stars show certain stations from 

figures above; data from Paula Viveros, UF (Wanat 2010)......................................................30

Figure 25. Apalachicola Bay system, showing the locations of long-term sampling stations 

(1972–84).................................................................................................................................. 31

Figure 26. Station map of the Apalachicola River, from Lake Seminole to the Gulf coast 

(HydroQual). .............................................................................................................................33

Figure 27. Flow compared with TN and TP concentrations for the Apalachicola River at Lake 

Seminole; data from Florida STORET and USGS 0235800 (HydroQual)....................................34

Figure 28. Flow compared with TN and TP concentrations for the Apalachicola River near 

Sumatra, data from USGS-2359170 (HydroQual).....................................................................35

Figure 29. TN and TP concentrations versus flow for the Apalachicola River at Lake Seminole and 

near Sumatra (post-1990) (HydroQual)....................................................................................36

Figure 30. TN and TP compared with flow for the Apalachicola River at Lake Seminole; data from 

Florida STORET and USGS 02358000. Graphs show data points, load based on 

regression analysis, annual geometric mean (HydroQual).......................................................37

Figure 31. TN and TP compared with flow for the Apalachicola River near Sumatra; data from 

USGS-2359170. Graphs show data points, load based on regression analysis, annual 

geometric mean (HydroQual). ..................................................................................................38

Figure 32. Annual geometric mean for TN and TP concentrations for the Apalachicola River at 

Lake Seminole and near Sumatra (HydroQual). .......................................................................39

Figure 33. Probability of annual geometric mean estimated unfiltered nutrient loads for the 

Apalachicola River at Lake Seminole and near Sumatra (HydroQual)......................................40
1 

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Executive Summary

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

with local scientists, to support the development of numeric nutrient criteria for Apalachicola Bay.1

Except for water withdrawal issues occurring far upstream of the bay, the Apalachicola system remains 

relatively free of human impacts. The Apalachicola River and Bay system is located in one of the least 

populated areas along the Gulf coast. The Apalachicola Estuary, which is dominated by freshwater 

inputs from the river, is a shallow, lagoon-and-barrier-island complex oriented along an east-west axis. 

Important habitats include Spartina/Juncus marshes, unconsolidated soft-sediment areas, and 

significant oyster reefs. The Apalachicola Estuary has been described as one of the most productive 

estuarine systems in the northern hemisphere. This bay is known for its oyster bars and oyster 

production, producing 90% of Florida’s and 10% of the nation’s oyster harvest (Edmiston 2008). 

 The 

primary purpose of the proposed numeric nutrient criteria is to protect healthy, well-balanced natural 

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

The main source of nutrients in Apalachicola Bay is the Apalachicola River, which dominates water 

quality in the bay and represents the chief source of freshwater input. Unlike most estuaries around the 

state, the critical issue in the Apalachicola has been significant, long-term reductions of river flow and 

associated reductions of loading of nutrients and organic matter. Periods of high nutrient and organic 

matter loading have been associated with relatively high and beneficial secondary production in this 

system. Reductions in freshwater flow and nutrients have been associated with adverse effects on the 

fisheries of the Apalachicola system (Livingston 2010). 

Since it is characterized as an alluvial system, maintaining phytoplankton biomass and secondary 

production of fish and oysters is the main concern in Apalachicola Bay. Phytoplankton is the main 

source of carbon in the bay (Chanton and Lewis 2002), but Wilson et al. (2009) suggest that benthic 

production is also important. The bay’s food webs are driven by in situ productivity and, consequently, 

the bay depends on the input of “new “nutrients to the system. It is for this reason that reductions of 

river flow (and coincidentally, nutrients) have, on occasion, adversely affected this system in the past 

(although recovery has been observed when flow and nutrients return). The Apalachicola Estuary is 

characterized by abundant phytoplankton production, which serves as the basis of a robust food web, 

yielding a high abundance of oysters, blue crabs, and commercially important fishes. 

Maintaining the existing and historical healthy conditions is the recommended approach for developing 

nutrient criteria for Apalachicola Bay. The greatest concern for the bay is potential reductions in 

nutrient loads from the river due to reductions in river discharge that would result in significant impacts 

to the food web. The data provided here demonstrate that the nutrient and chlorophyll concentrations 

provide for the overall health of the bay (Table 1). In fact, maintaining phytoplankton production is 

critical for protecting the bay’s robust food web.

 

1 Contributors to this report included Dr. Robert J. Livingston (Florida State University [FSU]), Jennifer Wanat and Lauren Levi (FDEP’s Office of 

Coastal and Aquatic Managed Areas [CAMA]), Jennifer Cherrier (Florida Agricultural and Mechanical University), Paula Viveros (University of 

Florida [UF]), Dr. Edward Phlips (UF), Dan Tonsmeire (Apalachicola River Keepers), Graham Lewis (Northwest Florida Water Management 

District [NWFWMD]), Andrew Thuman and Thomas Gallagher (Hydroqual) and Randy Snipes (FDEP).
2 

Draft August 2010

Table 1. Checklist of nutrient enrichment symptoms for Apalachicola Bay - = Empty cell/no data

N/A =Not Available

Response Variable Observed 

Historically 

or 

Currently?

Explanation Source

Low dissolved 

oxygen (DO) 

(hypoxia/anoxia)

Yes Hypoxia in the bay is normally not evident; however, low DO 

levels (< 4 milligrams per liter [mg/L]) have been noted in 

some areas. In East Bay, most hypoxic events that occur last 

less than 4 hours. The low DO episodes are not linked to 

nutrients and are not associated with adverse biological 

responses. 

Sanger et al. 2002; 

Wanat 2010; 

Edmiston 2008

Reduced clarity No Color ranges from 0 to over 300 platinum cobalt units (PCUs)

at individual stations but is generally in the 20 to 160 range, 

with lower values near the Gulf. High color levels, which are a 

natural condition associated with swamp runoff, generally 

occur at the river mouth and in the upper areas of East Bay.

Edmiston 2008; 

Wanat 2010; 

Livingston 2010

Increased 

chlorophyll a

concentrations

No Unlike most estuaries around the state, Apalachicola Bay is an 

alluvial system and has high primary and secondary 

productivity, supporting a multimillion-dollar fishery. 

Research has shown that elevated chlorophyll a values near 

the mouth and in East Bay are beneficial and help the system 

maintain its healthy condition. 

Livingston 2010

Phytoplankton 

blooms (nuisance or 

toxic)

Yes Occasional red tide events, which originate offshore and are 

transported to the bay by currents, affect the system. These 

events are not related to nutrients from the Apalachicola Bay 

system. The bay was last closed for shellfish harvesting due to 

red tides in 2005 and 2006.

Livingston 2010; 

Florida Department of 

Agriculture and Consumer 

Services (FDACS) 

Problematic 

epiphyte growth 

No No evidence of epiphyte growth. Due to natural high color 

and turbidity, submerged aquatic vegetation (SAV) is naturally 

rare in the system, except for oligohaline and fringing areas. 

- 

Problematic 

macroalgal growth

No There is no evidence of adverse macroalgal growth. -

SAV community 

changes or loss

Yes During periods of low river discharge and unusually high 

salinities in upper East Bay, reductions of fresh/brackish SAV 

have occurred. A 2005 hurricane also affected the 

fresh/brackish SAV. Note that none of these changes are 

associated with nutrients.

Edmiston 2008; 

Fahrny et al. 2006

Emergent or 

shoreline vegetation 

community changes 

or loss 

No - - 

Coral/hardbottom 

community changes 

or loss 

N/A This habitat type does not typically occur. - 

Impacts to benthic 

community

No Variability in benthic communities is associated with 

freshwater flow.

- 

Fish kills Yes Episodic fish kills occur due to Karenia brevis blooms moving in 

from offshore, not related to nutrients in Apalachicola Bay. 

The last reported fish kill was on November 8, 2005, at East 

Florida Fish and Wildlife 

Conservation Commission 

(FWCC) Fish and Wildlife 
3 

Draft August 2010

Point. Research Institute (FWRI) 

Geographic and Physical Description

Apalachicola Bay is a dynamic, highly productive estuary located in the Florida Panhandle. The bay is a 

bar-built, subtropical estuary characterized by large quantities of freshwater inflows from the

Apalachicola River. The bay is divided into four major parts: St. George Sound, Apalachicola Bay, East 

Bay, and St. Vincent Sound (Figure 1). Apalachicola Bay is designated as an Outstanding Florida Water

(OFW), a Class II shellfish harvesting waterbody, a National Estuarine Research Reserve (NERR), a U.S. 

Environmental Protection Agency (EPA) Gulf of Mexico Ecological Management Site, and a United 

Nations Educational, Scientific and Cultural Organization (UNESCO) Biosphere Reserve. Portions of the 

bay are also designated as an Area of Critical State Concern. Table 2 lists the physical characteristics of 

the bay, such as size, volume, watershed area, and depth.

Figure 1. Satellite photo of Apalachicola Bay, with labeled sections (from Wanat 2010). 

Tate’s Hell 

East Bay 

St. Vincent 

Island 

St. George 

Island 

Sike’s Cut

Apalachicola River 

Indian Pass

Little St. 

George Island 

West Pass

Dog Island

East Pass
4 

Draft August 2010

Table 2. Summary of the physical characteristics of Apalachicola Bay.

Data Values Source

Estuarine surface area 

(square kilometers [km2])

593 km2 Smith 2003; NOAA

Watershed area (km2) 51,000 Murrell and Caffrey 2005

Land use Primarily forested, pine 

flatwoods, and bottomland 

hardwoods 

Murrell and Caffrey 2005

Mean depth (meters [m]) 2.3 m ANERR

Volume (cubic meters [m3]) 1,074,990,400 m3 Smith 2003; NOAA

Tidal range (m) 0.58m Smith 2003; NOAA

Tidal freshwater inflow (1,000 cubic 

meters per day [1,000 m3d-1])

64,000 m3d-1 Smith 2003; NOAA

Mean water residence time days) 6 days Murrell and Caffrey 2005

Salinity and salinity zones

(practical salinity units)

Average salinity: 19 psu Smith 2003; NOAA

Sources and Fates of Nutrients 

The main source of the nutrients in Apalachicola Bay is the Apalachicola River, the primary source of 

fresh water entering the bay and the largest river in the state. The Apalachicola River is one part of the 

Apalachicola–Chattahoochee– Flint River system, whose basin is located in mainly three states (Figure 

2). The Apalachicola River provides 83% of the total nitrogen (TN) and 78% of the total phosphorus (TP) 

found in the bay (Edmiston 2008). 

The Apalachicola River dominates water quality in the bay system. As such, the river and the nutrients it 

delivers represent a major source of coastal productivity in the region (Livingston 1983, 1984; Livingston 

et al. 1997, 1999, 2000, 2002, and 2005). Because of the protective measures taken in the Apalachicola 

River floodplain, nutrient loading from sources in Florida is not of concern. In fact, a significant problem

for the Apalachicola is long-term reductions of river flow and associated reductions of the loading of 

nutrients and organic matter. High loading of nutrients and organic matter is associated with relatively 

high secondary production in this system. Periods of reduced water delivery are associated with

reductions in the fisheries of the Apalachicola system. Nutrients, as the foundation for the estuary’s 

productivity, are transported to the estuary both in the form of detritus and as compounds dissolved in 

the water column (Livingston 1984b). Nitrogen (N) is limiting in summer and during periods of lower 

river flow, while phosphorus (P) is limiting in winter, when water levels are typically higher. 

Phytoplankton productivity is most frequently limited by N availability, less often by P availability

(Iverson et al. 1997). 
5 

Draft August 2010

Figure 2. Map of the Apalachicola–Chattahoochee–Flint River Basin. Each separate basin is depicted 

by a different shade of green (from Wanat 2010). 
6 

Draft August 2010

Point sources that contribute nutrients to the river and bay include municipal wastewater treatment 

facilities (WWTFs), industrial wastewater facilities, and combined sewer overflows (Frick et al. 1996). 

There are a total of 15 facilities in the Apalachicola River Planning Unit: 6 domestic and 8 industrial 

wastewater facilities, and 1 concrete batch plant. The major domestic facilities are the city of 

Blountstown (design flow Q = 1.5 million gallons per day [MGD]), the city of Chattahoochee (Q= 0.5 

MGD), Florida State Hospital (Q = 1.3 MGD), and the town of Sneads (Q = 0.495 MGD). The only major 

industrial facility is the Gulf Power Scholz Steam Plant (Q = 129.6 MGD) (FDEP 2002). The only major 

surface water discharge facility in the Apalachicola Bay Planning Unit is the city of Apalachicola sewage 

treatment plant (design flow [Q] = 1.0 MGD), which discharges to a wetland, Huckleberry Creek, the Gulf 

Intracoastal Waterway (GIWW), and then the Apalachicola River. 

There are 6 small domestic wastewater plants with nonsurface discharges, the largest being Eastpoint 

Water and Sewer District (Q = 0.1650 MGD). There is only 1 industrial plant: Couch Ready Mix—

Eastpoint (FDEP 2002). These provide de minimis loads to the bay. 

Nonpoint sources that contribute nutrients to the bay include animal manure, fertilizer, runoff from 

agricultural areas, runoff from urban and suburban areas, septic systems, atmospheric deposition, and 

the decomposition of organic matter (Frick et al. 1996). Apalachicola Bay nutrient concentrations are 

primarily influenced by river flow, local rainfall, tidal interactions, residence time, flux from benthic 

sediments, and the resuspension of sediments (Lewis 2003). 

Summary of Nutrient Studies by Dr. Robert J. Livingston (FSU)

Nutrients adhere to the particulate organic matter (detritus) that eventually falls into the sediments of 

the shallow Apalachicola system. This nutrient-rich organic matter is colonized by microbial 

components to form the basis of important detrital food webs (Federle et al. 1983; White 1983; White 

et al. 1977, 1979a, 1979b). Infaunal (living in or on sediments), detritus-feeding macroinvertebrate 

assemblages that live in the sediments of the bay are dominated by various species of worms and 

crustaceans, including Mediomastus ambiseta, Hobsonia florida, Grandidierella bonnieroides, and 

Streblospio benedicti (Livingston 1984b). The infauna form the food base for sciaenid fishes (Atlantic 

croaker [Micropogonias undulates], spot [Leiostomus xanthurus], and sea trout [Cynoscion spp.]) that 

dominate the estuarine fish populations. Shallow depths and extremely high bottom productivity 

explain why the Apalachicola Estuary is a primary nursery area along the Gulf coast for blue crabs 

(Callinectes sapidus) and white shrimp (Litopenaeus setiferus). These species form the basis of highly 

lucrative fisheries in the region. 

The outer bay, having higher salinities than the upper parts of the Apalachicola Estuary, is dominated by 

species such as silver perch (Bairdiella chrysoura), pigfish (Orthopristis chrysoptera), least squid 

(Lolliguncula brevis), pink shrimp (Farfantepenaeus duorarum), brown shrimp (Farfantepenaeus 

aztecus), and various important game fishes.

Litter fall in the Apalachicola floodplain (800 grams per square meter [gm-2]) is higher than that noted in 

many tropical systems and almost all warm temperate systems (Elder and Cairns 1982). These authors 

found that the annual deposition of litter fall in the bottomland hardwood forests of the Apalachicola 

River floodplain approximates 360,000 metric tons. Seasonal river flooding transfers detritus from the 

wetlands to associated aquatic areas (Cairns 1981; Elder and Cairns 1982. 

Livingston et al. (1974) indicated that, in addition to providing particulate organics that fuel the bay 

system, river input determines nutrient loading to the estuary. Nutrient loading in the Apalachicola 
7 

Draft August 2010

River as it enters the bay is relatively high compared with that in other alluvial rivers along the northeast 

Gulf coast of Florida (Figure 3) (Livingston 2010). Of the 214,000 metric tons (mt) of carbon, 21,400 mt 

of N, and 1,650 mt of P that is delivered to the estuary over a given year, over half is transferred during 

the winter-spring flood peaks (Mattraw and Elder 1984). Studies conducted in the bay (Livingston 1976, 

1981a, 1983, 1984, 2000, 2002) corroborate the timing of these flow events with the delivery of 

nutrients and dissolved and particulate organic matter as an important factor in the maintenance of the 

estuarine primary production (autochthonous and allochthonous). There are direct links between the 

estuarine food webs and freshwater discharges (Livingston 1981a, 1983, 1984). Particulate organic 

carbon delivered to the estuary follows seasonal and interannual fluctuations that are closely associated 

with river flow (R2 = 0.738) (Livingston 1991). During summer and fall months, there is no direct 

correlation of river flow and detritus movement into the bay. By winter, there is a significant 

relationship between microdetrital loading and river flow peaks.

Phytoplankton productivity is a major determinant of secondary production in many coastal systems. 

Boynton et al. (1982) reported that the Apalachicola system has high phytoplankton productivity 

compared with other river-dominated estuaries, embayments, lagoons, and fjords around the world. 

Nixon (1988) showed that the Apalachicola Bay system ranks high in overall primary production 

compared with other such systems. Up to 50% of the phytoplankton productivity of the Apalachicola 

Estuary is explained by Apalachicola River flow (Myers 1977; Myers and Iverson 1977, 1981). 

In the Apalachicola system, orthophosphate availability limits phytoplankton during both low- and highsalinity winter periods and during the summer at stations with low salinity (Iverson et al. 1997). 

Conversely, N is limiting during summer periods of moderate to high salinity in the Apalachicola Estuary. 

Flow rates affect the development of nutrient limitation in the estuary. Nutrient limitation is highest 

during low-flow summer periods. 

The physiography of the Apalachicola Estuary is an important factor in the high primary productivity of 

the system. The bay is relatively shallow, and wind action frequently resuspends inorganic nutrients

(regenerated in the sediments) and mixes them into the euphotic zone, producing periodic peaks of 

phytoplankton production (Livingston et al. 1974; Iverson et al. 1997). In deeper estuaries, nutrients can 

be sequestered in the sediments, and thus can be unavailable for phytoplankton production. Shallow 

water depth is thus an important factor in the natural productivity of the Apalachicola Estuary. 

Recent studies have further documented the influence of the Apalachicola River on nutrient and organic 

carbon loading to the bay. Chanton and Lewis (1999) found that, despite inputs of large quantities of 

terrestrial organic matter, net heterotrophy in the Apalachicola Bay system was not dominant relative to 

net autotrophy, during a 3-year period. Chanton and Lewis (2002), using carbon (δ13C) and sulfur 

(δ34S) isotope data, noted clear distinctions between benthic and water column feeding types. They 

found that the estuary depends on river flows to provide floodplain detritus during high-flow periods, 

and dissolved nutrients for estuarine primary productivity (plants) during lower flows. Floodplain 

detritus is significant in the important East Bay nursery area, thus showing that peak flows are important 

in washing such detritus into the estuary. Winter/spring periods of high river flow and macrodetritus 

delivery to the bay (Livingston 1981a) are coincident with increased infaunal abundance (McLane 1980). 

Four out of the five dominant infaunal species at river-dominated stations are detritus feeders. The 

transformation of nutrient-rich particulate organic matter from periodic river-based influxes of dissolved 

and particulate organic matter coincides with abundance peaks of the detritus-based (infaunal) food 
8 

Draft August 2010

Figure 3. Nitrite-nitrate and orthophosphate loading in the Apalachicola, Choctawhatchee, Perdido, 

and Escambia Rivers (Livingston 2010).
9 

Draft August 2010

webs of the Apalachicola system (Livingston and Loucks 1978; White et al. 1979a, 1979b; Livingston 

1984b). A mechanism for the direct connection of increased infaunal abundance was described by 

Livingston (1983, 1984b), in which microbial activity at the surface of the detritus (Federle et al. 1983) 

leads to microbial successions (Morrison et al. 1977) that then provide food for a variety of detritivorous 

organisms (White et al. 1979a, 1979b; Livingston 1984b). Mortazavi et al. (2000a) found that 

phytoplankton productivity in river-dominated parts of the Apalachicola Estuary is limited by P in the 

winter (during periods of low salinity) and N during summer periods of high salinity. The dissolved 

organic nitrogen (DON) input is balanced by export from the estuary. Mortazavi et al. (2000b) 

determined temporal couplings of nutrient loading with primary production in the estuary. Around 75% 

of such productivity occurs from May through November, with primary control due to grazing. 

Mortazavi et al. (2000c) provided detailed accounts of the N budgets of the bay. These studies indicated 

that phytoplankton productivity is an important component of estuarine food webs along the Gulf coast, 

and that a combination of river-derived organic matter and autochthonous organic carbon provides the 

resources for consumers in river-dominated estuaries of the Gulf coast. Figure 4 presents a conceptual 

model of Apalachicola Bay’s trophodynamics.

Figure 4. Livingston’s model of the Apalachicola Bay system, showing key features that result in 

extremely high primary and secondary productivity. 
10

Draft August 2010

It should be noted that nutrient concentrations in the river fluctuate little over time, but riverine water

flow determines the loading of nutrient delivery to the bay (Table 3). The Apalachicola River illustrates 

the relationship between concentration and river flow (Table 3). Minimum and maximum values are 

actually 10th and 90th percentile values based on the number of samples for each parameter. An analysis 

of seasonal data shows a wide range of values in both dissolved nitrate and total phosphorus (TP) 

concentrations throughout the year, probably related to river flow differences. Further trend analysis 

shows little change in most nutrients over time in the lower river, except an increase in dissolved nitrate 

and a decrease in TP.

Table 3. Nutrient concentrations in the Apalachicola River, Mile 11 (from Frick et al. 1996). 

Parameter Number of 

Samples

Minimum Maximum Median

River flow (cubic feet per second [cfs]) 101 11,000 50,000 24,000 

TN (mg/L) 63 0.47 0.98 0.71 

Total inorganic N (TIN) (mg/L) 83 0.22 0.47 0.32 

Total organic N (TON) (mg/L) 55 0.17 0.68 0.35 

Dissolved ammonia (mg/L) 84 0.02 0.09 0.03 

Dissolved nitrate (mg/L) 98 0.17 0.42 0.27 

TP (mg/L) 101 0.02 0.09 0.05 

Other nutrient sampling done in the Apalachicola River around the same time includes nutrient 

concentrations in the lower Apalachicola River (Fulmer 1997; Mortazavi et al. 2000a, 2000b,); the results 

for 1994 to 1997 are as follows: 

Nitrate = 0.180 to 0.480 mg/L;

Mean dissolved inorganic nitrogen (DIN) = 0.350 mg/L;

Mean dissolved organic nitrogen (DON) = 0.183 mg/L;

Phosphate (soluble reactive phosphate [SRP]) = 0.001 to 0.016 mg/L; and 

Monthly average SRP = 0.0057 +/- 4.1 mg/L. 

Biological Summary 

 SAV 

SAV is generally a minor component of the habitats in Apalachicola Bay. The surveys of submerged 

vegetation listed by Livingston (1980) and CSA (1985) show significant differences in acreages. These 

differences are probably caused by mapping methods, calculation techniques, change in species 

(Myriophyllum), or the absence of data from eastern St. George Sound (CSA 1985). Apalachicola 

National Estuarine Research Reserve (ANERR) surveys show that the central eastern side of East Bay 

contains more submerged vegetation than previously reported, primarily the low-salinity taxa, Ruppia 

and Vallisneria (Fahrny et al. 2006). 

The Apalachicola River and Bay Basin went through an extended drought from 1999 to 2002 that 

resulted in record low flows for much of that period, including the absence of normal winter floods for 

several years. During this period, unusually high salinities were noted in upper East Bay from ANERR’s

System-Wide Monitoring Program (SWMP) data loggers (Figure 6). At the same time, staff began to 
11

Draft August 2010

detect, qualitatively, the disappearance of the fresh/brackish SAV normally seen in East Bay and the 

lower river. New studies (Fahrny et al. 2006) have documented a wider distribution of SAV in East Bay 

than was previously reported (Figure 5). In addition, more species have been documented than were

found in the past (Table 4), either due to a more detailed survey or a change in the SAV community over 

time. Unfortunately, after the most detailed SAV map for East Bay was created in 2005, Hurricane 

Dennis, with a storm surge of 2.5 m, significantly impacted the area. All the SAV in East Bay was 

eliminated and did not reappear that summer. The ANERR is documenting its recovery since the storm. 

The fresh and brackish water submerged species also provide habitat and nursery areas for numerous 

organisms. Dominant organisms associated with these vegetation beds include polychaetes, 

amphipods, chironomid larvae, snails, amphipods, mysids, crabs and shrimp, rainwater killifish, pipefish, 

silversides, and gobies (Livingston 1984c). Because of its position located between upland and 

unvegetated bay bottom habitats, submerged vegetation links dissimilar ecosystems. It acts much like

salt marshes in this respect and is important to the productivity of estuarine systems because it

functions as a nursery area, providing food and reducing predation pressure through habitat complexity.

Figure 5. Percent SAV coverage in East Bay and ANERR monitoring sites, June 2005 (Edmiston 2008). 
12

Draft August 2010

Table 4. East Bay SAV species list (from Fahrny et al. 2006).

Species Name Common Name Native/Invasive

Ceratophyllum demersum Coontail Native

Chara spp Muskgrass Native

Hydrilla verticillata Hydrilla Invasive

Myriophyllum aquaticum Parrot feather Invasive

Myriophyllum spicatum Eurasian watermilfoil Invasive

Najas guadalupensis Southern naiad Native

Najas minor Spiny naiad Native

Potamogeton pusillus Slender pondweed Native

Ruppia maritima Widgeon grass Native

Stuckenia pectinata Sago pondweed Native

Vallisneria americana Tapegrass Native

Zannichellia palustris Horned pondweed Native

Phytoplankton

Phytoplankton is the main source of carbon in the bay, fueling the productive food web (Chanton and 

Lewis 2002). Wilson et al. (2009) suggest that benthic production is also important. In either case, food 

webs are driven by in situ productivity and therefore depend on the input of “new” nutrients to the 

system. Compared with other estuaries in the Gulf of Mexico, phytoplankton productivity is high in 

Apalachicola Bay (Putland 2005). 

In 2008, a phytoplankton species composition study was performed throughout the bay by Paula Viveros 

and Dr. Ed Phlips from UF, along with ANERR staff. This study showed that diatoms dominated the 

community, with some dinoflagellate peaks and moderate cyanobacteria biomass during the summer of 

2008. A shift occurred in the fall of 2008, and while diatoms still dominated, cyanobacteria and 

dinoflagellates became less important. In the winter of 2008, diatoms still dominated, with some 

dinoflagellate peaks but few cyanobacteria. The most common diatom was Thalassiosira sp., the main 

dinoflagellate found was Protoperidinium sp., and the main cyanobacterium observed was 

Pseudosolenia calcaravis. Salinity, defined by freshwater inflow from the Apalachicola River, is 

considered to be the single most important determination of the distribution of organisms in the estuary

(Livingston 1983). 

Phytoplankton Species Composition

Phytoplankton species composition in Apalachicola Bay was dominated by diatoms during the summer 

of 2008, with some dinoflagellate peaks and moderate cyanobacteria biomass. In the fall of 2008, the 

bay was mostly diatom dominated, with reduced cyanobacteria and dinoflagellate densities. In the 

winter of 2009, the bay was mostly diatom dominated, with some dinoflagellate peaks and few 

cyanobacteria (see Figures 13 through 24).

The Apalachicola Estuary is characterized predominately by euryhaline species (those adapted to varying 

salinities) that can thrive in the extreme salinity variations of the bay. The actual distribution of the key 

estuarine species is based on microhabitat organizations that are ultimately based on various conditions 

related to river flow processes. The river continuum extends into the estuary as the freshwater and 

estuarine habitats overlap in their usage by juvenile forms of various types. 
13

Draft August 2010

Oysters (Crassostrea virginica) (from Livingston 2010) 

Oyster bars represent an important habitat in the Apalachicola Estuary, providing cover and food for 

diverse assemblages (Livingston 1984b). These include bryozoans, flatworms, annelids, gastropod and 

pelecypod mollusks, arthropod crustaceans, and fishes. Research on the extensive Apalachicola oyster 

(Crassostrea virginica) reefs goes back to the work of Swift (1896) and Danglade (1917). The 

Apalachicola Estuary has accounted for about 90% of Florida's commercial oyster fishery (Whitfield and 

Beaumariage 1977) and about 10% of the oyster production in the United States. 

Conditions in the Apalachicola Bay system are highly advantageous for oyster propagation and growth 

(Menzel 1981; Menzel and Nichy 1958; Menzel et al. 1966; Livingston 1984b), with reefs covering about 

7% (4,350 hectares [ha]) of bay bottom (Livingston 1984b). The growth rates of oysters in this region are 

among the most rapid of those recorded (Ingle and Dawson 1952, 1953), with harvestable oysters taken 

in 18 months. The abundant phytoplankton food source, which is a consequence of riverine nutrient 

inputs, accounts for this high growth rate. 

Appendix A contains more oyster information, including the distribution of oyster larvae, spat fall, new 

growth, percent mortality, location of study sites, and effects due to salinity.

Infaunal Macroinvertebrates (from Livingston 2010)

In terms of frequency of occurrence, the infaunal macroinvertebrate assemblages in East Bay are 

dominated by species such as Mediomastus ambiseta (below-surface deposit feeder and detritivorous 

omnivore), Hobsonia florida (above-surface deposit feeder and detritivorous omnivore), Grandidierella 

bonnieroides (grazer/scavenger and general omnivore), Streblospio benedicti (above-surface deposit 

feeder and detritivorous omnivore), and Parandalia americana (primary carnivore). Larger species of 

infaunal macroinvertebrates include the plankton-feeding herbivores Mactra fragilis and Rangia 

cuneata. Dominant epibenthic (living above sediments) macroinvertebrates in East Bay over the period 

of study include the palaemonetid shrimp (Palaemonetes spp., detritivorous omnivores), xanthid crabs 

(Rhithropanopeus harrisi, a sensitive primary carnivore), blue crabs (Callinectes sapidus, primary 

carnivores at less than 30 millimeters [mm]; secondary carnivores at more than 30 mm), and penaeid 

shrimp (L. setiferus, F. duorarum and F. aztecus, which are primary carnivores at less than 25 mm and

secondary carnivores at more than 25 mm). Most of these invertebrate species are browsers, grazers, 

or seize-and-bite predators. 

Penaeid Shrimp (from Livingston 2010)

The numerically dominant invertebrates of the Apalachicola system include white shrimp and blue crabs 

that, when combined, represented about 70% of the total numbers taken over a 14-year study period. 

The white shrimp, Litopenaeus setiferus, is the numerically dominant penaeid species in the 

Apalachicola system. White shrimp enter the bay during spring months, and are caught in otter trawls 

during the summer and fall months. Young-of-the-year white shrimp (less than 25mm) are first noted in 

East Bay during the early summer months, and they remain in the East Bay area throughout the 

summer. The second trophic unit of this species is concentrated in East Bay during the summer and fall 

months. The largest white shrimp trophic unit is located mainly just west of the river mouth and in parts 

of East Bay. White shrimp are largely absent in the bay by mid- to late November through December. 

White shrimp represent the most commercially valuable population in the Apalachicola Estuary, and are 

distributed in areas most affected by river flows. This distribution is compatible with the importance of 

freshwater inflows and the resulting productivity that accompanies such flows. The low numbers 
14

Draft August 2010

associated with drought conditions are compatible with the known aspects of white shrimp life history 

patterns.

Pink shrimp (Farfantepenaeus duorarum) and brown shrimp (Farfantepenaeus aztecus) occur in lower 

numbers than the white shrimp. Pink shrimp are usually associated with higher salinities than white 

shrimp, and young of the year also are most abundant during early fall in East Bay. This appears to be 

related to food availability in areas receiving freshwater flow. Young brown shrimp are most abundant 

during late spring, with the primary pattern of distribution just west of the river mouth and in East Bay 

areas. Once again, both species favor areas receiving direct freshwater runoff from the river. 

Callinectes Sapidus (from Livingston 2010) 

The blue crab (Callinectes sapidus) is another commercially important species in the Apalachicola 

system. Young-of-the-year blue crabs appear in the bay during the winter months and are largely 

concentrated in East Bay and along the main river channel of the bay. Secondary increases of this 

trophic unit occur during late summer to fall months in the upper bay. The next trophic stage appears in 

the bay during February, with secondary peaks during the summer months. This trophic stage is 

centered in East Bay. The largest blue crab trophic unit is found in the highest numbers during the

summer months in East Bay. In all three blue crab trophic stages, the East Bay nursery area appears to 

be the favorite habitat. Spatial-temporal blue crab distribution appears to be associated with the 

relationship of the individual trophic units to freshwater inputs from the river. 

The long-term trends of invertebrate distribution indicate that invertebrate numbers are associated with 

river flow, even though such manifestations of habitat preference vary by species and by trophic unit 

within each species. High invertebrate numbers during the drought of 1980 to 1981 were due in large 

part to blue crab predominance. Each species has a very different set of habitat needs throughout its 

ontological development, with major differences in the spatial/temporal patterns of habitat use. 

The one unifying feature that affects such distributions appears to be increased concentrations of 

invertebrate populations in areas associated with the entry of fresh water into the upper bay. These 

areas are notable for relatively high organic carbon and nutrient loading and associated productivity. 

Trophic unit distribution displays a broad spectrum of diverse phase interactions with river input to the 

bay over seasonal and interannual periods. Feeding habit changes are related to habitat-oriented 

differences in available food.

Fishes (from Livingston 2010)

Dominant fishes in East Bay include the plankton-feeding primary carnivore Anchoa mitchilli (bay 

anchovy) and benthic-feeding primary carnivores such as spot (Leiostomus xanthurus), hogchokers 

(Trinectes maculatus), young Atlantic croakers (Micropogonias undulates less than 70 mm) and silver 

perch (Bairdiella chrysoura 21 to 60 mm). Secondary carnivores among the dominant fishes include 

larger croakers (more than 70 mm), Gulf flounder (Paralichthys albigutta), and sand seatrout (Cynoscion 

arenarius). Tertiary carnivores in East Bay include the larger spotted seatrout (C. nebulosus), southern 

flounder (P. lethostigma), largemouth bass (Micropterus salmoides) and gar (Lepisosteus spp). Escept 

for the bay anchovies, all of the above species live near the sediment-water interface, with most of the 

trophic organization of the bay dependent on interactions among bottom-living infaunal and epibenthic 

(living above sediments) macroinvertebrates and fishes. The primary fish dominants, representing 

about 80% of total fish numbers taken over the sampling period, include bay anchovies, seatrout, spot, 

and Atlantic croaker. Appendix A provides complete information on each fish species. 
15

Draft August 2010

Presence and Frequency of Harmful Algal Blooms (HABs)

Occasional red tide events, which originate offshore and are transported to the bay by currents, affect 

the system. These events are not related to nutrients from the Apalachicola Bay system. The last 

closure of parts of the bay due to red tide was in 2005 and 2006. Area 1611 East was closed from 

September 2, 2005, to January 26, 2006, for a total of 145 days (FDACS) (Table 5). Most recently, 

K. brevis was found at 2 locations, at Pickalene Bar and Green Point in Wakulla County on April 27, 2010. 

Fewer than 1,000 cells were present at each site, and since the cells were found in such small quantities, 

no adverse effects were observed. These data are routinely collected by FDACS.

Table 5. Apalachicola Bay red tide tracking (FDACS). 

Shellfish Production and Frequency/Duration of Bed Closures

During the period of low river flows from 1999 to 2002, there was a collapse of oystering in the Eastern 

reefs from Cat Point to East Hole. In 2002, a field assessment by FDEP demonstrated that the reduced 

oyster productivity in eastern bay reefs was accompanied by large numbers of predators that included 

oyster drills, crown conchs, and sea urchins (G. S. Gunter, pers. comm.). With the return of higher river 
16

Draft August 2010

flows during 2003, there was a marked increase in oyster abundance observed at Cat Point and East 

Hole, accompanied by a reduction in oyster predators (G. S. Gunter, pers. comm.). 

During the 2002 collapse of the eastern oyster reefs, commercial oystering continued in northern 

sections of western bars, such as Dry Bar and upper St. Vincent Bar (G. S. Gunter, pers. comm.). The 

above observations during the 1999 to 2002 period of low river flows represented the field verification 

of model predictions made by Livingston et al. (2000). The model predicted that ongoing reductions of 

Apalachicola River flow, which are related, in part, to reservoir and other water management practices 

in Alabama and Georgia, would accentuate the adverse effects of natural droughts. Over prolonged 

periods, the resilience of the bay to such events would be systematically reduced, which would then 

lead to more permanent reductions in secondary production biomass (organisms such as oysters, 

shrimp, blue crabs, and sciaenid fishes) that depends on the interannual cycling of natural river flows 

into the bay.

The most recent period of low river flow (2007 to 2009) followed a similar pattern to that described for 

the 1999 to 2002 drought. Salinities in East Bay reached unprecedented high levels (greater than 30 

parts per thousand [ppt]), adversely affecting the highly productive eastern oyster bars through a 

combination of predation and disease (L. Edmiston, J. Wanat, and G. Lewis, pers. comm.). Cat Point, the 

leading oyster-producing reef in the bay, was particularly affected by excess predators during the recent 

drought. During the period of increased salinity, oyster catches were largely restricted to less 

productive bars in the western parts of the bay. These observations further verified the Livingston et al.

(2000) oyster model. For additional information on oysters, see Appendix A.

Quantification of Landings from Commercial/Recreational Fisheries

Stratified Random Sampling

The Florida Fish and Wildlife Conservation Commission (FWCC) collected a total of 249,676 fishes (174 

taxa) and selected invertebrates (17 taxa) from 840 Apalachicola Bay simple random samples (SRS) in 

2008 (FWCC 2008). Anchoa mitchilli (n=99,209) was the most numerous taxon collected, representing 

39.7% of the total catch. Lagodon rhomboides (n=19,916), Micropogonias undulatus (n=16,958), and 

Litopenaeus setiferus (n=11,410) were the next most abundant taxa collected, accounting for an 

additional 19.3% of the total catch. Thirty-three selected taxa (n=56,220) composed 22.5% of the total 

catch. Micropogonias undulatus (n=16,958), L. setiferus (n=11,410), and Leiostomus xanthurus 

(n=9,142) were the most abundant selected taxa, representing 15.0% of the annual catch. Collections in 

2008 included 5 species new to the Apalachicola Bay Fisheries Independent Monitoring (FIM) Program

collection, including Albula vulpes (bonefish), Ctenopharyngodon idella (grass carp), Microgobius carri 

(Seminole goby), Parablennius marmoreus (seaweed blenny), and Sicyonia parri (a rock shrimp) (FWCC 

2008).

The FIM Program’s 2008 Annual Data Summary Report contains additional information on landings. 

Fish Kills 

Appendix D lists reported fish kills in relation to the K. brevis bloom in Franklin County, from 2001 to 

June 21, 2010, from the FWRI fish kill database. Most of the sampling is done by members of the public, 

who call the FWRI hotline to report seeing dead fish. 
17

Draft August 2010

Water Quality Studies 

ANERR Monitoring

ANERR has a System-Wide Monitoring Program to monitor nutrients and has been collecting data since 

2002. The program includes spatial sampling at 11 sites around the bay, including a river site and an 

offshore site outside Sike’s Cut, and temporal sampling at East Bay over a diel cycle (approximately 25 

hours) (Figure 6). ANERR measures nitrate, nitrite, ammonium, SRP, and chlorophyll a. Nutrient 

concentrations in the river do not fluctuate greatly, and nutrient loading to the bay is controlled by the 

river flow. Other factors influencing nutrient concentrations are rainfall, tidal interactions, flux from 

sediments, and sediment resuspension. Nitrate concentrations in the system range from 0.003 to 0.400 

mg/L and average 0.193 mg/L. Phosphate concentrations range from 0.001 to 0.016 mg/L and average 

0.007 mg/L. Chlorophyll a values in the system range .2 to 32.2 mg/L and average 5.9 mg/L.

Figures 7 through 11 show ANERR data for salinity, turbidity, pH, and DO. The salinity data were

collected over a longer period, from 1993 to 2008 (Figures 7 and 8). DO (Figure 9), turbidity (Figure 10), 

and pH (Figure 11) are from 2008 data. Table 6 lists mean nutrient measurements in Apalachicola Bay as 

determined by various researchers over time. 

Figure 6. ANERR long-term monitoring locations throughout Apalachicola Bay (Wanat 2010). 
18

Draft August 2010

Figure 7. Cat Point (Gray) and Dry Bar (Blue) daily average salinity, 1993–2008 (solid lines are 90-day 

moving average data; dashed lines are linear trend lines) (Wanat 2010). 

Figure 8. Areal extent of salinity zones in Apalachicola Bay under various flow regimes. Map at left

shows salinity contours in the bay when river flow is between 15,000 and 35,000 cfs. Map at right 

shows salinity contours in the bay when river flow is below 15,000 cfs (Wanat 2010). 
19

Draft August 2010

Figure 9. DO (mg/L) at the three data logger locations, from 2008 ANERR data (Wanat 2010). 

Figure 10. Turbidity at the three data logger locations, from 2008 ANERR data (Wanat 2010). 
20

Draft August 2010

Figure 11. pH at the three data logger locations, from 2008 ANERR data (Wanat 2010). 

Table 6. Mean nutrient measurements in Apalachicola Bay as determined by various researchers over 

time (Wanat 2010). 

Summarized by Lewis 2003. 

Studies Nitrate (NO3) 

(mg/L)

Nitrogen 

Ammonia (NH4) 

(mg/L)

Phosphate 

(PO4) 

(mg/L)

Chlorophyll a

(mg/L)

Estabrook (1972–73) 0.091 0.017 0.006 6.5

Mortazavi (1993–96) 0.119 0.020 0.003 4.8

NWFWMD (2000–02) 0.059 0.016 0.008 4.6

Water Quality Studies by Paula Viveros (UF) and ANERR

UF and ANERR are studying the relationship between Apalachicola River discharge and a number of 

variables in the bay (correlative sampling), including salinity, chlorophyll, and nutrient concentrations

(Tables 7 through 12; Figures 12 through 24). They found an inverse relationship between salinity and 

discharge, and an inverse relationship between river discharge and chlorophyll a (i.e., as discharge 

increases, chlorophyll a decreases). Chlorophyll a values were higher in summer. They found that as 

river discharge increases, N increases, but P remains approximately the same. The phytoplankton 

community in the bay is dominated by diatoms, with higher biovolume in summer. In winter, there are 

much lower diatom volumes and some increases in dinoflagellates. Preliminary information on nutrient 

limitation analyses indicates that P is the limiting nutrient for algae in the river, while the bay and 

coastal area are colimited by N and P. 
21

Draft August 2010

Table 7. Mean DIN concentration for different areas of Apalachicola Bay, in summer and winter, from 

Paula Viveros, UF (Wanat 2010). 

Table 8. Mean TDN concentration for different areas of Apalachicola Bay, in summer and winter, from 

Paula Viveros, UF (Wanat 2010).

Mean DIN Concentration - μg L-1

Summer Winter

River (231) 388 472

North Bay E. Bay Bridge (171) 223 342

E. Bay Bottom (191) 88 123

East Bay Cat Point (221) 125 160

West Bay West Pass (131) 64 146

Dry Bar (141) 82 171

Central Bay Mid Bay (161) 121 238

Nick's Hole (211) 73 149

South Bay Pilot's Cove (151) 55 120

Offshore (201) 46 41

Mean Total Dissolved Nitrogen Concentration - μg L-1

Summer Winter

River (231) 460 625

North Bay E. Bay Bridge (171) 316 471

E. Bay Bottom (191) 314 357

East Bay Cat Point (221) 300 283

West Bay West Pass (131) 196 260

Dry Bar (141) 217 292

Central Bay Mid Bay (161) 233 401

Nick's Hole (211) 206 265

South Bay Pilot's Cove (151) 174 220

Offshore (201) 146 144
22

Draft August 2010

Table 9. Mean SRP concentration for different areas of Apalachicola Bay, in summer and winter, from 

Paula Viveros, UF (Wanat 2010).

Table 10. Mean total dissolved phosphorus (TDP) concentration for different areas of Apalachicola 

Bay, in summer and winter, from Paula Viveros, UF (Wanat 2010).

Mean Soluble Reactive Phosphorus Concentration - μg L-1

Summer Winter

River (231) 8 12

North Bay E. Bay Bridge (171) 5 9

E. Bay Bottom (191) 5 8

East Bay Cat Point (221) 5 5

West Bay West Pass (131) 3 3

Dry Bar (141) 4 4

Central Bay Mid Bay (161) 4 4

Nick's Hole (211) 4 4

South Bay Pilot's Cove (151) 4 3

Offshore (201) 3 2

Mean Total Dissolved Phosphorus Concentration - μg L-1

Summer Winter

River (231) 13 18

North Bay E. Bay Bridge (171) 12 12

E. Bay Bottom (191) 15 15

East Bay Cat Point (221) 16 13

West Bay West Pass (131) 15 13

Dry Bar (141) 13 11

Central Bay Mid Bay (161) 15 11

Nick's Hole (211) 12 12

South Bay Pilot's Cove (151) 16 13

Offshore (201) 21 14
23

Draft August 2010

Table 11. Mean salinity for different areas of Apalachicola Bay, in summer and winter, from Paula

Viveros, UF (Wanat 2010). 

Figure 12. Chlorophyll a compared with river flow for four stations in the bay, 2002–09, from Paula 

Viveros, UF (Wanat 2010).

Mean Salinity - psu

Summer Winter

River (231) 0 0

North Bay E. Bay Bridge (171) 14 8

E. Bay Bottom (191) 13 10

East Bay Cat Point (221) 27 19

West Bay West Pass (131) 30 20

Dry Bar (141) 25 17

Central Bay Mid Bay (161) 24 15

Nick's Hole (211) 27 18

South Bay Pilot's Cove (151) 30 22

Offshore (201) 34 33
24

Draft August 2010

Table 12. Mean chlorophyll a concentration for different areas of Apalachicola Bay, in summer and 

winter, from Paula Viveros, UF (Wanat 2010).

Figure 13. Phytoplankton composition, June 2008, by biovolume (μm3 mL-1); stars show station 

locations on map below; data from Paula Viveros, UF (Wanat 2010). 

Mean Chlorophyll a Concentration - μg L-1

Summer Winter

River (231) 5 2

North Bay E. Bay Bridge (171) 8 4

E. Bay Bottom (191) 13 11

East Bay Cat Point (221) 7 4

West Bay West Pass (131) 6 4

Dry Bar (141) 9 4

Central Bay Mid Bay (161) 7 5

Nick's Hole (211) 6 4

South Bay Pilot's Cove (151) 5 4

Offshore (201) 4 3

JUNE
25

Draft August 2010

Figure 14. Phytoplankton composition, July 2008, by biovolume (μm3

 mL-1); stars show station 

locations on map below; data from Paula Viveros, UF (Wanat 2010). 

Figure 15. Phytoplankton composition, August 2008, by biovolume (μm3

 mL-1); stars show station 

locations on map below; data from Paula Viveros, UF (Wanat 2010). 

JULY

AUGUST
26

Draft August 2010

Figure 16. Map of Apalachicola Bay, showing station locations; stars show certain stations from

figures above; data from Paula Viveros, UF (Wanat 2010). 

Phytoplankton Composition Fall 2008 by biovolume, μm3 ml-1 

Figure 17. Phytoplankton composition, September 2008, by biovolume (μm3

 mL-1); stars show station 

locations on map below; data from Paula Viveros, UF (Wanat 2010). 

September
27

Draft August 2010

Figure 18. Phytoplankton composition, October 2008, by biovolume (μm3

 mL-1); stars show station 

locations on map below; data from Paula Viveros, UF (Wanat 2010). 

Figure 19. Phytoplankton composition, November 2008, by biovolume (μm3

 mL-1); stars show station 

locations on map below; data from Paula Viveros, UF (Wanat 2010). 

October

November
28

Draft August 2010

Figure 20. Map of Apalachicola Bay; stars show station locations from figures above; data from Paula 

Viveros, UF (Wanat 2010). 

Figure 21. Phytoplankton species composition, December 2008, by biovolume (μm3

 mL-1); stars show 

station locations on map below; data from Paula Viveros, UF (Wanat 2010). 

December
29

Draft August 2010

Figure 22. Phytoplankton composition by biovolume (μm3

 mL-1), January 2008; stars show station 

locations on map below; data from Paula Viveros, UF (Wanat 2010).

 

Figure 23. Phytoplankton composition by biovolume (μm3

 mL-1), February 2008; stars show station 

locations on map below; data from Paula Viveros, UF (Wanat 2010). 

January

February
30

Draft August 2010

Figure 24. Map of Apalachicola Bay, showing station locations; stars show certain stations from 

figures above; data from Paula Viveros, UF (Wanat 2010). 

Water Quality Studies by Dr. Robert J. Livingston (FSU), 1972–2008

Dr. Livingston conducted research on the bay from 1972 to 2008 (see Figure 25 for station locations). 

During this time, he collected data on river flow, rainfall, salinity, temperature, DO, oxygen anomaly, pH, 

Secchi depth, and nutrients (ammonia [NH3], nitrite nitrogen [NO2], NO3, TIN, TN, PO4, and TP). Other 

water quality factors measured included National Council for Air and Stream Improvement (NCASI) 

color, turbidity, chlorophyll a, water/sediment/organism pollutants (metals, pesticides), SAV (quadrats 

and mapping), infaunal macroinvertebrates (cores), epibenthic invertebrates (seines, trawls), fishes 

(seines and trawls), and food web transformations (based on the stomach contents of fishes and 

invertebrates). The Livingston team also carried out physical modeling, oyster modeling, and nutrient 

loading calculations.

The aquatic habitats of the Apalachicola River floodplain depend on river flows in terms of frequency 

and duration of inundation and saturation. Floodplain vegetation is closely associated with the extent 

and timing of river flows and flooding. Seasonal flow changes are important to the life cycles of many 

terrestrial and aquatic species along the river. Since 80% to 85% of the fishes use the floodplain as a 

food source, wetlands inundation is a critical part of the life history of these species. The river 

dominates the Apalachicola Bay system as a source of fresh water, nutrients, and organic matter. 

Together with local rainfall and wind events, the river is closely associated with the estuarine salinity 

regime and coastal productivity (Livingston 1983, 1984, 2000, 2005; Livingston et al. 1997, 1999, 2000). 

Nutrient-induced phytoplankton productivity is an important component of estuarine food webs along 

the Gulf coast, and especially in the Apalachicola River. The alluvial river also provides river-derived 

nutrients and organic matter that fuel planktonic and detrital food webs. The combination of these 

sources of autochthonous and allochthonous organic carbon provides the resources for consumers in 

the Apalachicola Estuary. Reduced river flows and flooding will diminish this loading, leading to a 

collapse of useful productivity in receiving coastal areas. There is evidence that recent extended periods 

of low river flow have already adversely affected organic carbon loading to the bay (Livingston 2010).
31

Draft August 2010

 

Figure 25. Apalachicola Bay system, showing the locations of long-term sampling stations (1972–84). 

Nutrient Loading Models

Existing TN, TP, and flow data were analyzed and, considering flow to be an explanatory variable, longterm nutrient loads were estimated by Hydroqual (2010). Analyses were performed to assist in the 

development of TN and TP loads for the Apalachicola River to support nutrient criteria development in 

Apalachicola Bay.

Available water quality and flow data were obtained from the following sources: U.S. Geological Survey 

(USGS) for flow and water quality; and Florida STORET for water quality. Figure 26 shows the locations 

where river data were available, with the stations at the Lake Seminole outlet (Florida STORET at U.S. 

Highway 90 and USGS Gauge #02358000) and Sumatra (USGS Gauge #02359170) containing the most 

data. These two stations (Lake Seminole and Sumatra) were used to complete the river loading 

analyses. The data were used to develop concentration relationships to flow, so that the daily flow 

record could be used to develop long-term estimates of river concentrations and loads for TN and TP. 

Ultimately, annual geometric mean loads were developed to be used in developing protective loads to 

Apalachicola Bay. 

Figures 27 and 28 present the data obtained for flow, TN, and TP at Lake Seminole and Sumatra from 

1975 to 2009, along with the 2010 proposed EPA in-stream protective values (IPV) for TN (0.824 mg/L) 

and TP (0.043 mg/L) as horizontal dashed lines. The flow values range from about 5,000 to 200,000 cfs,
32

Draft August 2010

the TN values range from about 0.3 to 1.5 mg/L, and the TP values range from about 0.01 to 0.1 mg/L. 

These data were used to develop concentration relationships to flow using the data from 1990 to 2009 

(Figure 29). This period was chosen since pre-1990 TN data at Lake Seminole appeared less reliable and 

more variable than the post-1990 data. Although strong correlations between concentration and flow 

were not observed, generally increasing trends in concentration were observed with increasing flow. 

Log-log regressions were completed on the data, and Table 13 and Figure 31 present the resulting

equations. 

Table 13. Concentration flow regression equations for the Lake Seminole and Sumatra stations 

(Hydroqual). 

Location/Source TN Equation TP Equation

Lake Seminole 0.244Q0.116 0.0038Q0.223

Sumatra 0.675Q0.005 0.0008Q0.379

Figures 30 and 31 present the calculated daily loads based on the concentration-flow regression

equations and the daily flows at Lake Seminole and Sumatra from 1975 to 2009. The solid blue

horizontal lines in each panel represent annual geometric means of flow, TN load, and TP load. In

general, the calculated TN and TP loads compare well with the observed loads. 

Since the concentration-flow relationships are not very strong (little variation with flow), much of the 

load variation to Apalachicola Bay is due to the hydrology of the river. In order to incorporate the 

hydrology (flow) variation into developing nutrient criteria or protective nutrient loads, probability 

distributions of TN and TP loads were developed. Figures 32 and 33 present log probability distributions 

of calculated annual geometric means for TN and TP loads for the period from 1975 to 2009 at Lake 

Seminole, and from 1978 to 2009 at Sumatra. Table 14 shows the upper distribution of the nutrient 

loads at two stations in the Apalachicola River. Nutrient criteria structured to maintain this distribution 

of loads over time would assure that the necessary water flow and beneficial nutrient inputs needed to 

sustain the system would be delivered. For more information on the modeling, see Appendix C.

Table 14. Upper distribution of Apalachicola River statistical nutrient loads (after Hydroqual 2010). - = Empty cell/no data

- Lake Seminole Sumatra

TN load (lbs/day) 67%-81,633

95%-116,509

99%-130,085

Maximum-130,112

67%-93,582

95%-116,971

99%-118,274

Maximum-118,301

TP load (lbs/day) 67%-3,639

95%-5,375

99%-6,064

Maximum-6,065

67%-4,755

95%-6,459

99%-6,558

Maximum-6,560

 
33

Draft August 2010

Figure 26. Station map of the Apalachicola River, from Lake Seminole to the Gulf coast (HydroQual). 
34

Draft August 2010

Figure 27. Flow compared with TN and TP concentrations for the Apalachicola River at Lake Seminole; 

data from Florida STORET and USGS 0235800 (HydroQual).
35

Draft August 2010

Figure 28. Flow compared with TN and TP concentrations for the Apalachicola River near Sumatra, 

data from USGS-2359170 (HydroQual). 
36

Draft August 2010

Figure 29. TN and TP concentrations versus flow for the Apalachicola River at Lake Seminole and near 

Sumatra (post-1990) (HydroQual). 
37

Draft August 2010

Figure 30. TN and TP compared with flow for the Apalachicola River at Lake Seminole; data from 

Florida STORET and USGS 02358000. Graphs show data points, load based on regression analysis,

annual geometric mean (HydroQual). 
38

Draft August 2010

Figure 31. TN and TP compared with flow for the Apalachicola River near Sumatra; data from USGS2359170. Graphs show data points, load based on regression analysis, annual geometric mean 

(HydroQual).
39

Draft August 2010

Figure 32. Annual geometric mean for TN and TP concentrations for the Apalachicola River at Lake 

Seminole and near Sumatra (HydroQual). 
40

Draft August 2010

Figure 33. Probability of annual geometric mean estimated unfiltered nutrient loads for the 

Apalachicola River at Lake Seminole and near Sumatra (HydroQual). 
41

Draft August 2010

Waters on the 303(d) List 

Table 15 contains the Group 2 Verified 303(d) List for the Apalachicola Bay Basin, including several 

coastal waterbodies within the Apalachicola Bay region. 

Table 15. Impaired waters in the Apalachicola Bay Basin - = Empty cell/no data

N/A = Not Available 1 II = Class II; IIIM = Class III Marine

Planning Unit WBID Waterbody 

Segment 

Waterbody 

Type

Waterbody 

Class1

Parameters 

Assessed 

Using the 

Impaired 

Surface 

Waters Rule 

(IWR)

Concentration 

of Criteria or 

Threshold Not 

Met

Priority for 

TMDL 

Development

Projected 

Year for 

TMDL 

Development

Apalachicola 

Bay

1266 St. George 

Sound

Estuary 2 Mercury 

(based on fish 

consumption 

advisory)

Exceeds Florida 

Department of 

Health (FDOH) 

threshold 

(>0.3 milligrams 

per kilogram 

[mg/kg])

High N/A

Apalachicola 

Bay 

1266 St. George 

Sound

Estuary 2 Bacteria 

(in shellfish)

Exceeds 

Shellfish 

Evaluation and 

Assessment 

Section (SEAS) 

threshold

Medium 2008

Apalachicola 

Bay 

1274 Apalachicola 

Bay 

Estuary 2 Bacteria 

(in shellfish)

Exceeds SEAS 

threshold

Medium 2008 

Apalachicola 

Bay 

1274 Apalachicola 

Bay 

Estuary 2 Fecal 

Coliforms

≤14 Most 

probable 

number per 100 

milliliters 

(MPN/100mL)

Low 2003

Apalachicola 

Bay 

1274 Apalachicola 

Bay 

Estuary 2 Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A

Apalachicola 

Bay 

1288 Money 

Bayou

Estuary 3M Bacteria 

(in shellfish) 

Exceeds SEAS 

threshold

Medium 2008

Apalachicola 

Bay 

1288 Money 

Bayou

Estuary 3M Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A

Apalachicola 

Bay 

1289 Direct 

Runoff to 

Bay 

Estuary 3M Bacteria 

(in shellfish)

Exceeds SEAS 

threshold

Low N/A

Apalachicola 

Bay 

1289 Direct 

Runoff to 

Bay 

Estuary 3M Mercury 

(based on fish 

consumption 

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A
42

Draft August 2010

Planning Unit WBID Waterbody 

Segment 

Waterbody 

Type

Waterbody 

Class1

Parameters 

Assessed 

Using the 

Impaired 

Surface 

Waters Rule 

(IWR)

Concentration 

of Criteria or 

Threshold Not 

Met

Priority for 

TMDL 

Development

Projected 

Year for 

TMDL 

Development

advisory)

Apalachicola 

Bay 

1291 Indian 

Lagoon 

Estuary 3M Bacteria 

(in shellfish)

Exceeds SEAS 

threshold

Low N/A

Apalachicola 

Bay 

1291 Indian 

Lagoon 

Estuary 3M Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A

Apalachicola 

Bay 

1292 Direct 

Runoff to 

Bay 

Estuary 2 Bacteria 

(in shellfish)

Exceeds SEAS 

threshold

Low N/A

Apalachicola 

Bay 

1292 Direct 

Runoff to 

Bay 

Estuary 2 Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A

Apalachicola 

Bay 

8018 Gulf of 

Mexico 

(Franklin 

County, Gulf 

County)

Coastal 3M Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A

Apalachicola 

Bay 

8020 Gulf of 

Mexico 

(Franklin 

County, St. 

George 

Island)

Coastal 3M Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A

Apalachicola 

Bay 

8021 Gulf of 

Mexico 

(Franklin 

County, St. 

George 

Island)

Coastal 3M Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A

Apalachicola 

Bay 

8022 Gulf of 

Mexico 

(Franklin 

County, Dog 

Island)

Coastal 3M Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A

Apalachicola 

Bay 

8023 Gulf of 

Mexico 

(Franklin 

County, Dog 

Island)

Coastal 3M Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A

Apalachicola 

Bay 

1266A Carrabelle 

Beach 

Beach 3M Bacteria 

(Beach 

Advisories) 

≥21 days of 

beach 

advisories 

High N/A
43

Draft August 2010

Planning Unit WBID Waterbody 

Segment 

Waterbody 

Type

Waterbody 

Class1

Parameters 

Assessed 

Using the 

Impaired 

Surface 

Waters Rule 

(IWR)

Concentration 

of Criteria or 

Threshold Not 

Met

Priority for 

TMDL 

Development

Projected 

Year for 

TMDL 

Development

Apalachicola 

Bay 

1274A East Bay Estuary 2 Fecal 

Coliforms

≤14MPN/100 

mL

Low 2008 

Apalachicola 

Bay 

1274A East Bay Estuary 2 Bacteria 

(in shellfish)

Exceeds SEAS 

threshold

Medium 2008

Apalachicola 

Bay 

1274A East Bay Estuary 2 Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A

Apalachicola 

Bay 

1274B Apalachicola 

Bay 

Estuary 2 Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A

Apalachicola 

Bay 

1274B Apalachicola 

Bay 

Estuary 2 Bacteria 

(in shellfish)

Exceeds SEAS 

threshold

Medium 2008

Apalachicola 

Bay 

1274C Direct 

Runoff to 

Bay 

Coastal 2 Bacteria 

(in shellfish)

Exceeds SEAS 

threshold

Low N/A

Apalachicola 

Bay 

1274C Direct 

Runoff to 

Bay 

Coastal 2 Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A

Apalachicola 

Bay 

8020A St. George 

Island 11th

St. W

Beach 3M Bacteria 

(beach 

advisories) 

≥21 days of 

beach 

advisories 

High N/A

Apalachicola 

Bay 

8021A St. George 

Island 

Franklin 

Blvd. 

Beach 3M Bacteria 

(beach 

advisories) 

≥21 days of 

beach 

advisories 

High N/A

Apalachicola 

Bay 

8021B St. George 

Island 11th

St. E

Beach 3M Bacteria 

(beach 

advisories) 

≥21 days of 

beach 

advisories 

High N/A

Apalachicola 

Bay 

8022A St. George 

Island State 

Park 

Beach 3M Bacteria 

(beach 

advisories) 

≥21 days of 

beach 

advisories 

High N/A

Apalachicola 

Bay 

8019 Gulf of 

Mexico 

(Franklin 

County)

Coastal 3M Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A

New River 1256 Alligator 

Harbor

Estuary 3M Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

High N/A

New River 1278 East Bayou Estuary 3M Mercury 

(based on fish 

Exceeds FDOH 

threshold 

Low N/A
44

Draft August 2010

Planning Unit WBID Waterbody 

Segment 

Waterbody 

Type

Waterbody 

Class1

Parameters 

Assessed 

Using the 

Impaired 

Surface 

Waters Rule 

(IWR)

Concentration 

of Criteria or 

Threshold Not 

Met

Priority for 

TMDL 

Development

Projected 

Year for 

TMDL 

Development

consumption 

advisory)

(>0.3 mg/kg)

New River 1279 West Bayou Estuary 3M Mercury 

(based on fish 

consumption 

advisory)

Exceeds FDOH 

threshold 

(>0.3 mg/kg)

- N/A

New River 1279 West Bayou Estuary 3M Bacteria 

(in shellfish)

Exceeds SEAS 

threshold

- N/A

New River 1283 Blounts Bay Estuary 3M Bacteria 

(in shellfish)

Exceeds SEAS 

threshold

- N/A

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 

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 a microbial source tracking project she is conducting for FDEP: 

The main groups of indicator bacteria for recreational water quality assessment in use 

today include fecal coliforms, or a specific member of that group, Escherichia coli, in 

fresh water and the genus Enterococcus in both fresh and estuarine/marine waters. 

However, in order for the indicator concept to work optimally there are many 

assumptions that must hold true. One of the most important assumptions is that 

indicator bacteria must co-occur with human pathogens when pathogens are present 

and pose a human health risk. Unfortunately, recent research has indicated that this 
45

Draft August 2010

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.

Numeric Nutrient Criteria Recommendations 

The well-developed scientific database for the Apalachicola River and Bay system indicates that 

nutrients delivered to the bay from the Apalachicola River are integral to the welfare of this highly 

productive system. Reductions of nutrient inputs due to decreased river flow are accompanied by 

adverse changes in the overall secondary production of the estuary. There is currently no need for any 

reduction of nutrient loading to the bay from the river. Any attempt to restrict nutrients would be 

counterproductive to the key fisheries of the bay and would only add to the stress caused by recent 

increases in drought effects. 

For Apalachicola Bay, maintaining the upper distribution of the nutrient loads associated with healthy 

conditions is the numeric nutrient goal. Table 14 provides a quantitative basis for selecting nutrient 

loads from the Apalachicola River that would protect the trophic functioning of the bay. Nutrient 

criteria structured to maintain this distribution of loads over time would ensure that the necessary 

water flow and beneficial nutrient inputs needed to sustain the system would be delivered.

Proposed Numeric Nutrient Criteria 

Methodology 
46

Draft August 2010

For consistent application and for providing an appropriate level of protection, water quality criteria 

need to include magnitude, frequency, and duration components. The magnitude is a measure of how 

much of a pollutant may be present in the water without an unacceptable adverse effect. Duration is a 

measure of how long the pollutant may be above the magnitude, and frequency relates to how often 

the magnitude may be exceeded without adverse effects. It is preferred to derive the magnitude 

component of a criterion through a cause-effect relationship (such as those measured through toxicity 

testing). The magnitude would then be set at a level that would protect a majority of the sensitive 

aquatic organisms inhabiting the system. Absent a demonstrated cause-effect relationship, the 

magnitude may be set at a level designed to maintain the current data distribution, accounting for 

natural temporal variability, when the current conditions are protective of the designated uses of the 

waterbody. Since a criterion derived based on the existing data distribution has no direct link to any 

observed cause and effect relationship, it is assumed that maintaining the current data distribution will 

preserve the uses associated with that distribution. 

The frequency and duration components of the criteria are best established as additional descriptors of 

the reference condition data distribution. Specifically, these components should be part of a statistical 

test designed to determine whether the long-term distribution of data has shifted upward ( or in some 

cases, downward) from the reference distribution. This test would then be used to determine whether 

future monitoring data are consistent with the magnitude (long-term average) defined by the reference 

dataset. It is critical to account for the natural variability surrounding the magnitude expression and to 

control for statistical errors. 

The derivation of the magnitude, frequency and duration components of the numeric nutrient criteria 

for Apalachicola Bay 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.
47

Draft August 2010

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. 

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, 
48

Draft August 2010

then there is a potential that isolated areas of enrichment may be masked in the network spatial 

average. Therefore, the single station annual geometric mean has the benefit of assessing localized 

enrichment patterns. DEP has not decided whether both expressions of magnitude are needed in all 

cases, and we are seeking additional feedback from local experts and stakeholders.

Summary of the Proposed Criteria 

FDEP proposes three sets of potential criteria: a) a long-term geometric mean concentration; b) an 

annual geometric mean of values from a network of stations over a given area, not to be exceeded more 

than twice in a five-year period; and c) an annual geometric mean of values from a single location, not to 

be exceeded more than twice in a five-year period.

The proposed long-term criteria for the protection of a healthy, well-balanced aquatic community in 

Apalachicola Bay, as well the annual limits for each segment, are provided in Table 16. Due to the 

importance of providing a minimum nutrient load (and flow) to maintain the health of the bay, FDEP is 

evaluating the need to establish a minimum nutrient load for Apalachicola Bay, and is seeking input on 

this concept.
49

Draft August 2010

Table 16. Proposed numeric nutrient criteria for all segments of Apalachicola Bay, including TP, TN, 

and Chlorophyll a. For compliance purposes, the long term geometric mean shall not exceed the long 

term limit nor shall the average of all stations in a segment exceed the network average more than 

twice in a 5 year period. The last column shows the value which single station shall not exceed, by 

segment, more than twice in a 5 year period.

TP (ug/L)

Segment

Existing 

Long Term 

Geometric 

Mean 

Maximum 

Allowed 

Long Term 

Geometric 

Mean 

Annual Geometric 

Mean for a 

Network of 

Stations (2 of 5 

year exceedance 

rate)

Annual Geometric Mean for a 

Single Site (2 of 5 year 

exceedance rate)

Apalachicola Bay 0.042 0.046 0.073 0.077

East Bay 0.041 0.045 0.064 0.071

St George Sound 0.023 0.025 0.051 0.054

St. Vincent Sound 0.043 0.047 0.074 0.074

Bay Wide 0.041 0.046 0.070 0.077

TN (ug/L)

Segment

Existing 

Long Term 

Geometric 

Mean 

Maximum 

Allowed 

Long Term 

Geometric 

Mean 

Annual Geometric 

Mean for a 

Network of 

Stations (2 of 5 

year exceedance 

rate)

Annual Geometric Mean for a 

Single Site (2 of 5 year 

exceedance rate)

Apalachicola Bay 0.69 0.76 1.00 1.03

East Bay 0.68 0.74 0.85 0.89

St George Sound 0.45 0.50 0.57 0.59

St. Vincent Sound 0.64 0.70 0.75 0.75

Bay Wide 0.68 0.75 0.95 1.00

Chlorophyll a (ug/L)

Segment

Existing 

Long Term 

Geometric 

Mean 

Maximum 

Allowed 

Long Term 

Geometric 

Mean 

Annual Geometric 

Mean for a 

Network of 

Stations (2 of 5 

year exceedance 

rate)

Annual Geometric Mean for a 

Single Site (2 of 5 year 

exceedance rate)

Apalachicola Bay 5.14 5.65 11.08 12.75

East Bay 4.14 4.55 7.36 8.80

St George Sound 1.78 1.96 3.70 4.10

St. Vincent Sound 8.20 9.02 25.33 25.33

Bay Wide 5.42 5.97 10.45 12.91
50

Draft August 2010

References

Anderson, K. L., J. E. Whitlock, V. J. Harwood, and K. 2005. Persistence and differential survival of fecal 

indicator bacteria in subtropical waters and sediments. Appl. Environ. Microb. 71:3041–3048.

Boehm, A.B., N.J. Ashbold, J.M. Colford, Jr., L.E. Dunbar, L.E. Fleming, M.A. Gold, J.A. Hansel, P.R. Hunter, 

A.M. Ichida, C.D. McGee, J.A. Soller, and S.B. Weisberg. 2009. A sea change ahead for 

recreational water quality criteria. Journal of Water and Health 07.1: 9–20.

Bonadonna, L., R. Briancesco, M. Ottaviani, and E. Veschetti. 2002. Occurrence of Cryptosporidium 

oocysts in sewage effluents and correlation with microbial, chemical and physical water 

variables. Environ. Monit. Assess. 75:241–252.
51

Draft August 2010

Boynton, W. R., W. M. Kemp, and C. W. Keefe. 1982. Comparative analysis of nutrients and other 

factors influencing estuarine phytoplankton production. In: V. S. Kennedy (Ed.), Estuarine 

comparisons (New York: Academic Press, pp. 69-90). 

Byappanahalli, M. N., and R. S. Fujioka. 1998. Evidence that tropical soil environment can support the 

growth of Escherichia coli. Water Sci. Technol. 38:171–174.

Byappanahalli, M. N., D. A. Shively, M. B. Nevers, M. J. Sadowsky, and R. L. Whitman. 2003. Growth and 

survival of Escherichia coli and enterococci populations in the macro-alga Cladophora 

(Chlorophyta). Fems Microbiol. Ecol. 46:203–211.

Cairns, D. J. 1981. Detrital production and nutrient release in a southeastern flood-plain forest. M. S. 

Thesis, Florida State University, Tallahassee, FL. 

Chanton, J., and F. G. Lewis. 1999. Plankton and dissolved inorganic carbon isotopic composition in a 

river-dominated estuary: Apalachicola Bay, Florida. Estuaries 22: 575-583.

———. 2002. Examination of coupling between primary and secondary production in a riverdominated estuary: Apalachicola Bay, Florida, U. S. A. Limnol. Oceanogr. 47: 683-697.

Continental Shelf Associates, Inc(CSA). 1985. Apalachicola Bay Study: Submerged vegetation assessment 

of the Apalachicola Bay System. Prepared for the U.S. Army Corps of Engineers. Mobile District, 

Sea Grant Publication No. MASGP 84 020. 

Danglade, E. 1917. Conditions and extent of the water level oyster beds and barren bottoms in the 

vicinity of Apalachicola, Florida. Appendix V, Reports of the U.S. Commissioner of Fishes for 

1916, Bureau of fishes Document No. 841. 75 pp.

Edmiston, H. L. 2008. A river meets the bay: A characterization of the Apalachicola River and Bay 

system. Apalachicola National Estuarine Research Reserve (ANERR). 

Elder, J. F., and D. J. Cairns. 1982. Production and decomposition of forest litter fall on the Apalachicola 

River floodplain, Florida. U.S. Geological Survey Water-Supply Paper 2196.

Elder and Cairns. 1982. Production and decomposition of forest litter fall on the Apalachicola River 

floodplain, Florida. U. S. Geological Survey Water-Supply Paper 2196

Fahrny et al. 2006. Submerged Aquatic Vegetation Monitoring in Apalachicola Bay, Florida. Unpublished 

report to NOAA. Apalachicola National Estuarine Research Reserve. 24 pp. 

Federle et al. 1983. Modification of estuarine sedimentary microbiota by exclusion of epibenthic 

predators. Journal of Experimental Marine Biological Ecology 73: 81-94.

Florida Department of Environmental Protection. 2002. Basin status report: Apalachicola–Chipola. 

Tallahassee, FL: Division of Water Resource Management. 

Florida Fish and Wildlife Conservation Commission. 2008. Fisheries-Independent Monitoring Program 

2008 annual data summary report. 

Frick, E.A., G.R. Buell, and E.E. Hopkins. 1996. Nutrient sources and analysis of nutrient water-quality 

data, Apalachicola-Chattahoochee-Flint River basin, Georgia, Alabama, and Florida, 1972–90. 

U.S. Geological Survey Water-Resource Investigations Report 96-4101. Atlanta, GA. 

Federle, T. W. , R. J. Livingston, D. A. Meeter, and D. C. White. 1983. Modification of estuarine 

sedimentary microbiota by exclusion of epibenthic predators. J. Exp. Mar. Biol. Ecol. 73: 81-94.
52

Draft August 2010

Frick et al. 1996. Nutrient sources and analysis of nutrient water-quality data, ApalachicolaChattahoochee-Flint River basin, Georgia, Alabama, and Florida, 1972-90. USGS WaterResource Investigations Report, 96-4101, Atlanta, GA. 

Fulmer, J.M. 1997. Nutrient enrichment and nutrient input to Apalachicola Bay, Florida. MS Thesis, 

Florida state University. Tallahassee, FL. 58 pages. 

Gulf of Mexico Alliance (GOMA). 2009. Comments regarding pending EPA Clean Water Act, recreational 

water quality criteria. Prepared for the EPA stakeholders workshop, October 6–7, 2009, 

Chicago, IL. 

Harwood, V. J., A. D. Levine, T. M. Scott, V. Chivukula, J. Lukasik, S. R. Farrah, and J. B. Rose. 2005. 

Validity of the indicator organism paradigm for pathogen reduction in reclaimed water and 

public health protection. Appl. Environ. Microb. 71:3163–3170.

HydroQual Inc. June 23, 2010. Apalachicola River nutrient loadings. Technical memorandum prepared 

for the Florida Department of Environmental Protection, Tallahassee, FL. 

Ingle and Dawson. 1952. Growth of the American Oyster Crassostrea virginica (Gmelin) in Florida 

Waters. Bull. Mar. Sci. Gulf and Caribbean 2:393-404.

———. 1953. A survey of Apalachicola Bay, Technical Series No. 10. State of Florida Board of 

Conservation 38 pp.

Ishii, S., W. B. Ksoll, R. E. Hicks, and M. J. Sadowsky. 2006. Presence and growth of naturalized 

Escherichia coli in temperate soils from Lake Superior watersheds. Appl. Environ. Microb. 

72:612–621.

Iverson, R. L., W. Landing, B. Mortazavi, and J. Fulmer. 1997. Nutrient transport and primary 

productivity in the Apalachicola River and Bay. In: F. G. Lewis (Ed.), Apalachicola River and Bay 

freshwater needs assessment. Report to the ACF/ACT Comprehensive Study. Havana, FL: 

Northwest Florida Water Management District. Unpublished report. 

Jeng, H. W. C., A. J. England, and H. B. Bradford. 2005. Indicator organisms associated with stormwater 

suspended particles and estuarine sediment. J. Environ. Sci. Heal. A 40:779–791.

Ksoll, W. B., S. Ishii, M. J. Sadowsky, and R. E. Hicks. 2007. Presence and sources of fecal coliform 

bacteria in epilithic periphyton communities of Lake Superior. Appl. Environ. Microb. 73:3771–

3778.

Lemarchand, K., and P. Lebaron. 2003. Occurrence of Salmonella spp. and Cryptosporidium spp. in a 

French coastal watershed: Relationship with fecal indicators. Fems Microbiol. Lett. 218:203–

209.

Lewis, F.G., 2003. Presentation from Seminar for Apalachicola National Estuarine Research Reserve, 

March 2003. 

Livingston, R. J. 1976. Dynamics of organochlorine pesticides in estuarine systems and their effects on 

estuarine biota. Invited paper. Proceedings of the Third International Estuarine Research 

Federation Conference, Galveston Texas, October, 1975. Estuarine Processes I., 507-522.

Livingston, R.J. 1980. Critical Habitat Assessment of the Apalachicola Estuary and Associated Coastal 

Areas. Final Report, Coastal Plains Regional Commission, Tallahassee, Florida.
53

Draft August 2010

———. 1981a. River-derived input of detritus into the Apalachicola Estuary. In: R. D. Cross and D. L. 

Williams (Eds.), Proceedings of the national symposium on freshwater inflow to estuaries

(Washington, DC: U.S. Fish and Wildlife Service, pp. 320-332).

———. 1983. Resource Atlas for the Apalachicola Estuary. Report Number 55. Florida Sea Grant. 

———. 1984a. Long-term effects of dredging and open-water disposal on the Apalachicola Bay system. 

Final report. Washington, DC: National Oceanic and Atmospheric Administration. 

———. 1984b. The ecology of the Apalachicola Bay system: An estuarine profile. U.S. Fish and Wildlife 

Service FWS/PBS 82/05. 

———. 1984c. Field characterization study of a Gulf coastal seagrass system. Unpublished report for 

the U. S. Environmental Protection Agency.

———. 1991a. The rivers of Florida. New York: Springer-Verlag.

———. 2000. Eutrophication processes in coastal systems: Origin and succession of plankton blooms 

and effects on secondary production. Boca Raton, FL: CRC Press.

———. 2002. Trophic organization in coastal systems. Boca Raton, FL: CRC Press.

———. 2008a. Importance of river flow to the Apalachicola River-Bay system. Florida Department of 

Environmental Protection. 

———. 2008b. Water quality and seagrass survey in the Carrabelle River and St. George Sound. 

Unpublished report for the Apalachicola River Keepers and city of Carrabelle.

———. 2010. Nutrients in Apalachicola River-Bay system. Unpublished report for the Florida 

Department of Environmental Protection, Tallahassee, FL. 

Livingston, R. J., and O. L Loucks. 1978. Productivity, trophic interactions, and food-web relationships in 

wetlands and associated systems. In: P. E. Greeson, J. R. Clark, and J. E. Clark (Eds.), Wetland 

functions and values: The state of our understanding (Lake Buena Vista, FL: American Water 

Resources Association, pp. 101-119). 

Livingston, R. J., R. L. Iverson, R. H. Estabrook, V. E. Keys, and J. Taylor, Jr. 1974. Major features of the 

Apalachicola Bay system: Physiography, biota, and resource management. Florida Scientist 4: 

245-271. 

Livingston, R. J., X. Niu, F. G. Lewis, and G. C. Woodsum. 1997. Freshwater input to a Gulf estuary: 

Long-term control of trophic organization. Ecol. Appl. 7: 277-299.

Livingston, R. J., Howell, R. L., Niu, X., Lewis, F. G. and Woodsum, G. C. 1999. Recovery of oyster reefs 

(Crassostrea virginica) in a Gulf estuary following disturbance by two hurricanes. B. Mar. Sci., 

Gulf and Caribbean 64, 75-94. 

Livingston, R. J., F. G. Lewis, III, G.C. Woodsum, X. Niu, R. L. Howell, IV, and G. L. Ray et al. 2000. 

Coupling of physical and biological models: response of oyster population dynamics to 

freshwater input in a shallow Gulf estuary. Est. Coast. Shelf Sci.50: 655-672.

Livingston et al. 2005. Restoration of Aquatic Systems. CRC Press, Inc. Boca Raton, Florida, 424 pp.

Lund, V. 1996. Evaluation of E-coli as an indicator for the presence of Campylobacter jejuni and Yersinia 

enterocolitica in chlorinated and untreated oligotrophic lake water. Water Res. 30:1528–1534.

Mattraw, H. C., and J. F. Elder. 1984. Nutrient and detritus transport in the Apalachicola River, Florida. 

U. S. Geological Survey Water-Supply Paper 2196-C. 
54

Draft August 2010

McLane, B. G. 1980. An investigation of the infauna of East Bay-Apalachicola Bay. M. S. thesis, Florida 

State University, Tallahassee, FL. 

Menzel and Nichy. 1958. Studies of the distribution and feeding habits of some oyster predators in 

Alligator Harbor, Florida. Bulletin of Marine Science Gulf and Caribbean 8: 125-145.

Menzel et al. 1966. Oyster abundance in Apalachicola Bay, Florida in relation to biotic associations 

influenced by salinity and other factors. Gulf Research Reports 2: 73-96. 

Menzel R.W. 1983. Genetics and the potential for oyster production in Apalachicola Bay. Apalachicola 

Oyster Industry: Conference Proceedings. S. Andree, editor. Florida Sea Grant Program 57:22-26. 

Morrison et al. 1977. Evidence of microfloral succession of allochthonous plant litter in Apalachicola Bay, 

Florida, U. S. A. Marine Biology 41:229-240.

Mortazavi, B., R. L. Iverson, W. M. Landing, and W. Huang. 2000a. Phosphorus budget of Apalachicola 

Bay: A river-dominated estuary in the northeastern Gulf of Mexico. Mar. Ecol.-Prog. Ser. 198: 

33-42. 

Mortazavi, B., R. L. Iverson, W. M. Landing, F. G. Lewis, and W. Huang. 2000b. Control of phytoplankton 

production and biomass in a river-dominated estuary: Apalachicola Bay, Florida USA. Mar. 

Ecol.-Prog. Ser. 198: 19-31.

Mortazavi, B., R. L. Iverson, and W. Huang. 2000c. Dissolved organic nitrogen and nitrate in 

Apalachicola Bay, Florida: Spatial distributions and monthly budgets. Mar. Ecol.-Prog. Ser. 214: 

79-91.

Mortazavi et al. 2001. Dissolved organic nitrogen and nitrate in Apalachicola Bay, Florida, USA: spatial 

distributions and monthly budgets. Marine Ecology Progress Series 214:79-91. 

Murrell M. C., and Caffrey, J. M. 2005. High cyanobacterial abundance in three northeastern Gulf of 

Mexico estuaries. Gulf and Caribbean Research Vol. 17, 95-106, 97. 

Myers, V. B. 1977. Nutrient limitation of phytoplankton productivity in north Florida coastal systems: 

Technical considerations; spatial patterns; and wind mixing effects. Ph. D. dissertation, Florida 

State University, Tallahassee, FL. 

Myers, V. B., and R. J. Iverson. 1977. Aspects of nutrient limitation of phytoplankton productivity in the 

Apalachicola Bay system. In: R. J. Livingston (Ed.), Proceedings of the conference on the 

Apalachicola drainage system (St. Petersburg, FL: Florida Department of Natural Resources, 

Marine Resources Publication 26, pp. 67-74). 

———. 1981. Phosphorus and nitrogen limited phytoplankton productivity in Northeastern Gulf of 

Mexico coastal estuaries. In: B J. Nielson and L. E. Cronin (Eds.), Estuaries and nutrients (Clifton, 

NJ: Humana Press, pp. 569-582).

Nixon, S. W. 1988. Physical energy inputs and the comparative ecology of lake and marine ecosystems. 

Limnol. Oceanogr. 33: 1005-1025.

Putland, J. 2005. Ecology of Phytoplankton, Acartia Tonsa, and Micro Zooplankton in Apalachicola Bay, 

FL. Florida State University-Department of Oceanography. 

Rees, G., K. Pond, K. Johal, S. Pedley, and A. Rickards. 1998. Microbiological analysis of selected coastal 

bathing waters in the UK, Greece, Italy and Spain. Water Res. 32:2335–2340.

Smith, S.V. 2003. Preliminary NOAA estuarine typology database. 
55

Draft August 2010

Solo-Gabriele, H. M., M. A. Wolfert, T. R. Desmarais, and C. J. Palmer. 2000. Sources of Escherichia coli

in a coastal subtropical environment. Appl. Environ. Microb. 66:230–237.

Swift, F. 1896. Report of a survey of the oyster region of St. Vincent Sound, Apalachicola Bay, and St. 

George Sound, Florida. U.S. Commission of Fish and Fisheries. Report of the U.S. Commission for 

1896. Appendix 4, pp. 187-221.

Topp, E., M. Welsh, Y. C. Tien, A. Dang, G. Lazarovits, K. Conn, and H. Zhu. 2003. Strain-dependent 

variability in growth and survival of Escherichia coli in agricultural soil. Fems Microbiol. Ecol. 

44:303–308.

Wanat, J. 2010. Estuarine nutrient criteria: Apalachicola Bay background Information. Presentation for 

February 11, 2010, public meeting on numeric nutrient criteria development, Apalachicola. 

White, D. C. 1983. Analysis of microorganisms in terms of quantity and activity in natural environments: 

Microbes in their natural environments. Society for General Microbiology Symposium 34: 37-66.

White, D. C., R. J. Bobbie, S. J. Morrison, D.K. Oesterhof, C. W. Taylor, and D. A. Meeter. 1977. 

Determination of microbial activity of lipid biosynthesis. Limnol. Oceanogr. 22: 1089-1099.

White, D. C., R. J. Livingston, R. J. Bobbie, and J. S. Nickels. 1979a. Effects of surface composition, water 

column chemistry, and time of exposure on the composition of the detrital microflora and 

associated macrofauna in Apalachicola Bay, Florida. In: R. J. Livingston (Ed.), Ecological 

processes in coastal and marine systems (New York: Plenum Press, pp. 83-116).

White, D. C., W. M. Davis, J. S. Nickels, J. D. King, and R. J. Bobbie. 1979b. Determination of the 

sedimentary microbial biomass by extractable lipid phosphate. Oecologia 40: 51-62.

Whitfield, W.K., Jr., and Beaumariage, D.S. 1977. Shellfish management in Apalachicola Bay: Past, 

present, and future. Proceedings of the Conference on the Apalachicola Drainage System. Eds. 

R. J. Livingston and E. A. Joyce, Jr. Florida Department of Natural Resources Mar. Res. Publ. 26: 

130-140.

Whitman, R. L., D. A. Shively, H. Pawlik, M. B. Nevers, and M. N. Byappanahalli. 2003. Occurrence of 

Escherichia coli and enterococci in Cladophora (Chlorophyta) in nearshore water and beach sand 

of Lake Michigan. Appl. Environ. Microb. 69:4714–4719.
56

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Appendix A: Nutrients in Apalachicola River-Bay System 

Report written by Dr. Robert J. Livingston, retired FSU professor, for FDEP. The report is found under 

the name Appendix A for Apalachicola Bay Report.doc

Livingston, R.J. 2010. Nutrients in Apalachicola River-Bay system. Unpublished report for the Florida 

Department of Environmental Protection. 

. This report outlines the various research done by 

Dr. Livingston from 1970 to 2008; it includes a physical description of the Apalachicola Bay and River 

system, nutrients in the Apalachicola system, dominant species found in the Apalachicola system, the 

trophic organization of the bay, recent drought trends and bay productivity, and conclusions. 
57

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Appendix B: Fish Landings by County and Year for all Florida Counties except Walton

An Excel spreadsheet that shows pounds caught and trips made per Florida county for each year from 

1998 to 2008, except for Walton County. The only county that was used in preparing this report was 

Franklin County because it encompasses all of Apalachicola Bay. This spreadsheet covers finfish, 

invertebrates, and shrimp, and also provides a grand total for landings. The Excel file is found under the 

name Appendix B for Apalachicola Bay Report.xlsx. 
58

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Appendix C: Apalachicola River Nutrient Loadings

This memorandum summarizes the analyses performed by HydroQual Inc. to assist in the development 

of TN and TP loads for the Apalachicola River, in order to support nutrient criteria development in 

Apalachicola Bay. While these analyses may not result in specific nutrient criteria values, the objective is 

to present an approach and corresponding results that can be used for the development of final values. 

Existing TN, TP, and flow data were analyzed and, considering flow to be an explanatory variable, longterm nutrient loads were estimated. In addition, Apalachicola Bay water quality data from ANERR’s

System Wide Monitoring Program were analyzed.

HydroQual Inc. June 23, 2010. Apalachicola River nutrient loadings. Technical memorandum prepared 

for the Florida Department of Environmental Protection, Tallahassee, FL. 
59

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Appendix D: Fish Kills Associated with K. brevis in Franklin County, 2001–June 21, 2010

Source: FWRI fish kill database

Note: Specimen count is the number of specimens found dead. Most of the sampling is carried out by members of the public, who call the 

FWRI fish kill hotline to report the dead fish. 

Report

Number

*Date

Reported

City *Count

y

Call 

Categor

y 

*Probabl

e

Cause

Waterbody 

Name

Specime

n Count

Comment

100901 10/9/2001 St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island

40 Pompano, 

Trout

112401 11/24/200

1 

St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island

99 Species 

Unknown– 

Also 

reporting 

respiratory 

irritation.

112501 11/25/200

1 

St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island

200 Mullet–

Beach at 10th

St. West on 

St. George 

Island

112501 11/25/200

1 

St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island

100 Mullet

112601 11/26/200

1 

St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island

200 Mullet

112601 11/26/200

1 

Panama 

City

Frankli

n 

Fish Kill Red Tide St. 

Andrews 

State Park

200 Mullet

112601 11/26/200

1 

St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island

50 Whiting–Also 

reporting 

respiratory 

irritation.

112701 11/27/200

1 

St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island

50 Mullet, 

Catfish–Also 

reporting 

respiratory 

irritation.

112801 11/28/200

1 

St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island

80 Catfish, 

Mullet

091602 9/16/2002 Apalachicol

a 

Frankli

n 

Fish Kill Red Tide Gulf City 

Canal

100 Mullet– 

Near 

chemical 

plant, all 

along canal. 

Gulf City 

Canal

091902 9/19/2002 Apalachicol

a 

Frankli

n 

Fish Kill Red Tide St. Joseph 

Bay

200 Lizardfish, 

Pigfish, 

Pinfish, 

Gafftopsail, 

Catfish–Most 

decomposed
60

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, mouth 

gaping, no 

lesions, 

gasping. 

091903 9/19/2003 Apalachicol

a 

Frankli

n 

Fish Kill Red Tide St George 

Island

100s Bonnethead 

Shark, 

Needlefish, 

Hardhead 

Catfish– 1⁄2 

mile west of 

Lighthouse. 

092003 9/20/2003 Apalachicol

a 

Frankli

n 

Fish Kill Red Tide St George 

Island

100s Flounder, 

Croaker, 

Whiting, 

Baitfish–

Odor of red 

tide, 

respiratory 

irritation.

092003 9/20/2003 Apalachicol

a 

Frankli

n 

Fish Kill Red Tide St George 

Island

20 Flounder, 

Ladyfish–

Was on St. 

George 

Island State 

Park 

09/20/03. 

Saw several 

dozen small 

flounder and 

ladyfish 

washed 

ashore. 

Were dead 

but intact 

(not 

decomposed

). Family and 

I started 

coughing.

092103 9/21/2003 Apalachicol

a 

Frankli

n 

Fish Kill Red Tide St George 

Island

5 Remora–I 

previously 

submitted a 

report and 

gave "pilot 

fish" as one 

of the dead 

fish species 

seen. That 

was 

incorrect, it 

was 

Remoras. 
61

Draft August 2010

There were 5 

of them and 

they were all 

approximatel

y 12 inches 

long.

092103 9/21/2003 Apalachicol

a 

Frankli

n 

Fish Kill Red Tide St Josephs 

Island

100 Flounder, 

Species 

Unknown–I 

was at St. 

George 

Island today 

and stunned 

at the dead 

fish and eels 

on the 

beach. I have 

gone there 

for years and 

never seen 

anything like 

this. They 

were 

continuing to 

wash in. 

There were 

even Pilot 

Fish.

092303 9/23/2003 St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island 

Beach

Unknow

n Count

Croaker, 

Pinfish, 

Unidentified 

Species–Has 

someone 

reported the 

fish kill yet?–

Yes

041204 4/12/2004 East Point Frankli

n 

Fish Kill Red Tide St Joe Bay 12 Spot, Catfish, 

Spider Crab–

FDEP is 

heading over 

there to do 

some counts 

and collect a 

few 

specimens.

041604 4/16/2004 East Point Frankli

n 

Fish Kill Red Tide St Joseph 

Bay

9 Red Drum, 

Shad–This 

kill already 

reported by 

FDEP.

082505 8/25/2005 Carrabelle Frankli

n 

Fish Kill Red Tide Dog Island 100s Snapper, Red 

Drum, Black 
62

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Grouper, 

Pinfish, 

Grunt–Due 

south of Dog 

Island 4 

miles to 11 

miles out.

082905 8/29/2005 Carrabelle Frankli

n 

Fish Kill Red Tide Carrabelle 

to B Tower

200 Hog Snapper, 

Grunt, 

Grouper–

Also east of 

Dog Island.

083005 8/30/2005 Alligator 

Point

Frankli

n 

Fish Kill Red Tide Bald Point 

State Park

100s Grouper, 

Horned Fish, 

Baitfish–Has 

72 dead fish–

sending 

water 

sample. 

Ocklocknee 

River–at 

mouth.

083005 8/30/2005 East Point Frankli

n 

Fish Kill Red Tide St Joseph 

Bay

Unknow

n Count

Shark, 

Grouper, 

Species 

Unknown–

Reporting 

respiratory 

irritation.

083005 8/30/2005 St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island

Unknow

n Count

Trout, 

Whiting, 

Puffer, 

Catfish, Eel, 

Redfish– 

Casa Del Mar 

to St George 

Island 

Plantation.

083005 8/30/2005 St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island

1000s Grouper, 

Redfish, 

Trout, 

Snapper, 

Grunt, Eel, 

Catfish–East 

Side Gorrie 

Drive.

0909010

5 

9/1/2005 St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island

20-100 Puffer, 

Grouper, 

Catfish, 

Species 

Unknown–

Bad smell.
63

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090405 9/4/2005 St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island

1000s Eel, 

Flounder, 

Catfish–Do 

not call–

tourist–gone. 

Reporting 

eye and 

respiratory 

irritation.

090405 9/4/2005 St George 

Island

Frankli

n 

Fish Kill Red Tide 1 1⁄2 Mi. 

State Park 

Entrance

1000s Shark, Eel, 

Dolphin

090505 9/5/2005 East Point Frankli

n 

Fish Kill Red Tide St George 

Island 

Plantation

100 Species 

Unknown–

The dead fish 

were seen 

on the bay 

side of St. 

George 

Island 

Plantation 

(west end).

090505 9/5/2005 St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island

Unknow

n Count

Species 

Unknown–

There are 

many large 

fish.

090605 9/6/2005 East Point Frankli

n 

Fish Kill Red Tide Little St 

George 

Island

3 Tiger Shark–

We found 

the sharks 

washed up 

on the beach 

of Little St. 

George 

Island. The 3 

were 

approximatel

y 6 to 8 feet 

in length and 

partially 

decomposed

. There has 

been an 

ongoing red 

tide event on 

the island, 

but the 

sharks were 

more 

decomposed 

than 

anything 
64

Draft August 2010

else.

090705 9/7/2005 East Point Frankli

n 

Fish Kill Red Tide St George 

Island Bay

20-100 Eel, Snapper, 

Grouper–

Reporting 

respiratory 

irritation 

also.

091705 9/17/2005 Apalachicol

a 

Frankli

n 

Fish Kill Red Tide Crooked 

Island 

Sound

5547 Mullet, Red 

Drum, 

Sheepshead, 

Stingray, 

Trout, Jack 

Crevalle–

Unbelievable 

number of 

dead and 

dying fish, 

many, many 

thousands. 

Other 

species 

included 

menhaden, 

scaled 

sardine, 

southern 

stargazer, 

sharksucker, 

flounder, 

spanish 

mackerel, 

king 

mackerel.

091805 9/18/2005 St George 

Island

Frankli

n 

Fish Kill Red Tide Nick's Hole 1000s Species 

Unknown–

Fish are from 

small to 

medium size.

092605 9/26/2005 Carrabelle Frankli

n 

Fish Kill Red Tide Carrabelle 

Beach

1000s Redfish, 

Hammerhea

d Shark, 

Croaker, 

Puffer–3 

miles south 

of 

Carrabelle. 

Ho Hum 

Travel Park.

092605 9/26/2005 Carrabelle Frankli

n 

Fish Kill Red Tide Carrabelle 

Beach

1000s Redfish, 

Sheepshead, 

Toadfish, 

Hammerhea
65

Draft August 2010

d Shark, 

Baitfish, 

Stingray, 

Baitfish

092605 9/26/2005 St George 

Island

Frankli

n 

Fish Kill Red Tide St George 

Island

86 Mullet, 

Catfish, 

Batfish–

Many dead 

fish there 

were on the 

beach. The 

smell was 

awful. Rough 

surf from 

Hurricane 

Rita helped 

wash much 

off the beach 

and the red 

tide was so 

strong.

092605 9/26/2005 St Teresa 

Beach

Frankli

n 

Fish Kill Red Tide Alligator 

Point & 

FSU Marine 

Lab

Unknow

n Count

Bonnethead 

Shark, 

Stingray, 

Flounder, 

Pigfish

092805 9/28/2005 St George 

Island

Frankli

n 

Fish Kill Red Tide Park 

Entrance

1000s Flounder, 

Catfish, Red 

Grouper–

Flounder are 

small.

092805 9/28/2005 Carrabelle Frankli

n 

Fish Kill Red Tide St George 

Sound

2002 Stingray, 

Grunt–The 

fish were 

washed up 

along the 

bank. 

Probably 

between 4 to 

6 per foot of 

the 

shoreline. 

This 

Saturday, 

this was 

along the 

shore at my 

home.

092905 9/29/2005 Carrabelle Frankli

n 

Fish Kill Red Tide Carrabelle 

Beach

100s Red Drum, 

Mullet, 

Shark, 

Stingray, 
66

Draft August 2010

Species 

Unknown–

Reporting 

respiratory 

irritation.

092905 9/29/2005 Carrabelle Frankli

n 

Fish Kill Red Tide Carrabelle 

Beach

306 Mullet, Red 

Drum, 

Shark–Went 

to beach 

myself and 

observed the 

dead fish. 

Can see dead 

fish all the 

way down 

the beach as 

far as you 

can see.

100105 10/1/2005 Carrabelle Frankli

n 

Fish Kill Red Tide St George 

Sound

20-100 Pinfish, 

Hammerhea

d Shark–

Willing to 

take water 

samples.

100205 10/2/2005 Carrabelle Frankli

n 

Fish Kill Red Tide St George 

Sound

100s Shark, 

Stingray, 

Pinfish, Red 

Drum, 

Mullet–A lot 

of sharks, 

but few rays.

100505 10/5/2005 Lanark Frankli

n 

Fish Kill Red Tide Dog Island 1000s Stingray, 

Shark, 

Species 

Unknown–

Would like 

us to collect 

samples.

100505 10/5/2005 Carrabelle Frankli

n 

Fish Kill Red Tide St George 

Sound

Unknow

n Count

Pinfish, 

Anchovy, 

Shark, 

Toadfish, 

Croaker, Gulf 

Flounder

100705 10/7/2005 St George 

Island

Frankli

n 

Fish Kill Red Tide Plantation 

Airstrip

1015 Mullet, 

Trout–Small 

inlet from 

the bay near 

our house 

full of dead 

mullet and a 

few other 
67

Draft August 2010

species.

100705 10/7/2005 St George 

Island

Frankli

n 

Fish Kill Red Tide Resort 

Vacation 

Properties

Unknow

n Count

Species 

unknown–I 

am not sure 

of how many 

or what kind.

101005 10/10/200

5 

St George 

Island

Frankli

n 

Fish Kill Red Tide Randolf 

Tray Canal

100s Mullet, 

Pinfish–Dead 

fish are 

mostly 

Pinfish. West 

of bridge.

101005 10/10/200

5 

Apalachicol

a 

Frankli

n 

Fish Kill Red Tide Alligator 

Bay

1000 Alewives–

Noticed a 

red tide 

smell to the 

air.

110805 11/8/2005 East Point Frankli

n 

Fish Kill Red Tide West Pass–

Apalachicol

a 

25 Gar