Site-Specific Information 

in Support of 

Establishing Numeric Nutrient 

Criteria for Choctawhatchee Bay

Florida Department of Environmental Protection

Tallahassee, FL 32399

August 13, 2010 
Draft ii July 2010

Table of Contents

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

Geographic and Physical Description ..................................................................................... 4

Sources and Fates of Nutrients .............................................................................................. 7

Biological Summary............................................................................................................... 8

Seagrasses in Choctawhatchee Bay.................................................................................................8

Tidal Marshes in Choctawhatchee Bay ..........................................................................................15

Phytoplankton..............................................................................................................................17

Invertebrates ...............................................................................................................................18

Fisheries in Choctawhatchee Bay ..................................................................................................22

Shellfish Harvesting......................................................................................................................25

Red Tide and Associated Animal Mortality Events.........................................................................26

Water Quality Studies ......................................................................................................... 27

CBA Partnership with University of Florida LakeWatch/Project COAST Program.............................27

CBA/Okaloosa-Walton College Long-Term Sampling and Data Coordination..................................28

FDEP Water Quality Analyses........................................................................................................32

Waters on the 303(d) List..................................................................................................... 36

Numeric Nutrient Criteria Recommendation........................................................................ 37

Relationship between Anthropogenic Nutrient Inputs and Adverse Biological Effects.....................37

Proposed Numeric Nutrient and Chlorophyll Criteria......................................................................38
Draft iii July 2010

List of Tables

Table 1a. Checklist of nutrient enrichment symptoms in Choctawhatchee Bay .......................................... 2

Table 1b. Checklist of additional environmental factors in Choctawhatchee Bay....................................... 3

Table 2. Choctawhatchee Bay physical characteristics................................................................................ 6

Table 3. Choctawhatchee Bay seagrass status, 1992 (from Ruth and Handley 2002). .............................11

Table 4. Vascular plants from Hogtown Bayou tidal marshes (from Keppner and Keppner 2003). ..........15

Table 5. Benthic macroinvertebrates reported from Choctawhatchee Bay (after Foster 2000 and 

Fox et al. 2001). ........................................................................................................................19

Table 6. In 1993, a total of 513,517 organisms, representing 108 taxa, were collected...........................23

Table 7. 1994 Fixed-station sampling yielded 459,835 organisms representing 117 taxa........................24

Table 8. 1995 fixed-station sampling yielded 470,763 organisms representing 105 taxa.........................24

Table 9. 1996 stratified random sampling by seine and trawl yielded 462,945 organisms 

representing 711 taxa...............................................................................................................25

Table 10. Summary of the spatial water chemistry analyses from six sections along the 

horizontal length of the Choctawhatchee Bay. Section 1 is located along the east side 

of the bay near the Choctawhatchee River. Section 6 is located along the west side of 

the bay near East Pass. Small letters next to each mean represent statistically 

significant differences (Terrell 2010). .......................................................................................30

Table 11. Temporal water chemistry analyses over a 40-year period of record, 1968–2007 

(Terrell2010). ............................................................................................................................31

Table 12. Summary of the spatial water chemistry analyses for three sections (based on surface 

salinity) along the horizontal length of Choctawhatchee Bay, 2000–09. Small letters 

next to each mean represents statistically significant differences (Lazzarino and 

Terrell 2010)..............................................................................................................................31

Table 13. Summary of data analysis for Choctawhatchee Bay, all stations combined, 1996–2009..........32

Table 14. Mean surface and bottom turbidity for Choctawhatchee Bay salinity-based regions, 

2000–09 (from Lazzarino and Terrell 2010)..............................................................................36

Table 15. Waterbodies in the Choctawhatchee Bay Planning Unit proposed for DELISTING from 

the 1998 303(d) list for either nutrients or DO (FDEP 2010b)...................................................36

Table 16. Proposed numeric nutrient criteria for all segments of Choctawhatchee 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..........................................................................................................................40
Draft iv July 2010

List of Figures

Figure 1. Map of Choctawhatchee Bay and adjacent urban areas and land management areas. ............. 5

Figure 2. Location of Choctawhatchee Bay watershed and estuary (Schaeffer 2010). ............................... 6

Figure 3. Land uses in the Choctawhatchee Bay watershed, with areal coverages and 

percentages of total area (from Schaeffer 2010). ...................................................................... 7

Figure 4. Choctawhatchee Bay segments for seagrass mapping study.....................................................11

Figure 5. Seagrass coverage in Choctawhatchee Bay, 1992......................................................................13

Figure 6. Choctawhatchee Bay seagrass coverage comparison, 1992 and 2003 (Alexander 2010)..........14

Figure 7. Western Choctawhatchee Bay seagrass coverage comparison, 1992 and 2003 

(Alexander 2010).......................................................................................................................14

Figure 8. Location of Hogtown Bayou study area for vascular plant inventory and invertebrate 

sampling (Keppner and Keppner 2003). ...................................................................................17

Figure 9. Location of Choctawhatchee Bay biological sampling stations, 1985–98 (Livingston 

2010).........................................................................................................................................19

Figure 10. Phytoplankton cell numbers and species richness at mid-bay stations in 

Choctawhatchee Bay and East Pass Lagoon (Station 36e), averaged from monthly 

data, September 1985–August 1995 (Livingston 2010). ..........................................................20

Figure 11. Phytoplankton bloom numbers at mid-bay stations in Choctawhatchee Bay and East 

Pass Lagoon (Station 36e), averaged from monthly data, September 1985–August 

1995 (Livingston 2010). ............................................................................................................21

Figure 12. Total numbers of infauna and fish, averaged from monthly data from September 

1985–August 1995 (Livingston 2010). ......................................................................................22

Figure 13. Choctawhatchee Bay is located in the Panhandle region of Florida, within Okaloosa 

and Walton Counties (top). Currently, the CBA samples almost 90 stations sampled 

monthly throughout Choctawhatchee Bay (bottom). Each red dot is a sampling 

station.......................................................................................................................................28

Figure 14. Trend of annual geometric means for TP in Choctawhatchee Bay, 1996–2009, and 

long-term geometric mean.......................................................................................................33

Figure 15. Trend of annual geometric means for TN in Choctawhatchee Bay, from IWR dataset, 

1996–2009, and long-term geometric mean............................................................................33

Figure 16. Trend of annual geometric means for chlorophyll a in Choctawhatchee Bay, from IWR 

dataset, 1996–2009, and long-term geometric mean..............................................................34

Figure 17. Comparison of annual geometric means for TP for Choctawhatchee Bay regions based 

on salinity, from IWR dataset, 1996–2009. ..............................................................................34

Figure 18. Comparison of annual geometric means for TN for Choctawhatchee Bay regions 

based on salinity, from IWR dataset, 1996–2009.....................................................................35

Figure 19. Comparison of annual geometric means for chlorophyll a for Choctawhatchee Bay 

regions based on salinity, from IWR dataset, 1996–2009........................................................35
Draft 1 July 2010

Executive Summary

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

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

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

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

Choctawhatchee Bay is a large estuary aligned along an east-west axis with a major alluvial river basin

(the Choctawhatchee River) at the east end and a gulf pass (East Pass) in the western region. 

Freshwater input is largely from the Choctawhatchee River, with secondary inflows from a series of 

bayous located primarily in the northern sections of the bay. The estuary was originally oligohaline, and 

seawater entered the system only through periodic breaks in the barrier islands (Hemming and Brown 

2004; Morang 1992). In response to dredging the pass in 1929, a strong halocline and subsequent

hypoxia developed, and a layer of “liquid mud” formed in the benthic zone (Livingston 1987; Ruth and 

Handley 2002).

The primary sources of nutrient loading to the estuary are the Choctawhatchee River and secondary 

inflows. Other sources of nutrients include 5 point sources to surface waters (in the Choctawhatchee 

Bay Planning Unit), nonpoint sources (stormwater runoff and septic tanks), natural inputs (leaf litter), 

atmospheric deposition, and ground water. 

Seagrass beds and tidal marshes are the primary productive habitats in Choctawhatchee Bay, and both 

have experienced significant historical losses in the system, particularly in the western portion of the 

bay. The causes of the seagrass and marsh loss are largely unknown, but suspected factors are the 

physical changes to the system that followed increased salinity in the system. Water quality studies 

indicate nutrient and chlorophyll concentrations throughout the bay are relatively low and do not 

appear to be limiting seagrass or tidal marsh growth and recovery. Although the biological resources of 

the bay have changed due to physical and salinity modifications, the data indicate that nutrients are not 

currently problematic, and therefore the control of nutrient inputs would not improve biological 

condition. FDEP therefore recommends setting numeric nutrient criteria at current (1996–2009) levels. 
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Table 1a. Checklist of nutrient enrichment symptoms in Choctawhatchee Bay

- - Empty cell/no data

N/A = Not applicable 

Response Variable Observed 

Historically?

Observed 

Currently? 

Explanation Source

Low dissolved oxygen (DO) 

(hypoxia/anoxia)

Yes Yes Yes, associated with strong halocline that developed following opening 

of East Pass and continues currently. Seasonal hypoxia in certain 

bayous and lagoons. 

Livingston 1986, 2010; 

Ruth and Handley 2002

Reduced clarity Yes Yes High turbidity and color are associated with high flow in the 

Choctawhatchee River. The layer of highly organic fine sediments 

(“liquid mud”) reduces clarity and contributes to low DO.

Livingston 2010; 

U.S. Air Force (USAF) 1996

Increased chlorophyll a

concentrations

Yes No Chlorophyll a concentrations are generally low in all regions of the bay. 

Historic increases (1967-2007) in eastern sections of bay. 

STORET (Impaired Surface Waters 

Rule [IWR]) data; CBA data

Phytoplankton blooms 

(nuisance or toxic)

Yes Episodic Episodic Karenia brevis blooms; diatom blooms in Destin Harbor (1986–

88); diatom bloom in Chula Vista Bayou (2006); episodic presence of 

harmful species but not in bloom numbers. 

Florida Fish and Wildlife Conservation 

Commission (FWCC) Fish and Wildlife 

Research Institute (FWRI) 

http://research.myfwc.com/features

/category_main.asp?id=2309; 

Livingston 2010 

Problematic epiphyte 

growth 

No No No problematic epiphytic growth has been reported; however, detailed 

studies of epiphytes on seagrasses in Choctawhatchee Bay have not 

been conducted. 

- 

Problematic macroalgal 

growth

No No No problematic macroalgal growth has been reported for the system; 

records of macroalgae in the system were not found. 

- 

Submerged aquatic 

vegetation (SAV) 

community changes or loss

Yes Yes Anecdotal evidence for decline of fresh and brackish macrophytes

following opening of East Pass, due to subsequent salinity changes. 

Loss of saltwater SAV has continued, although estimates vary. 

Decreased transparency (due to turbidity) is a likely cause. Halodule

beds in Hogtown Bayou are healthy. 

Burch 1983; USAF 1996; 

Ruth and Handley 2002; 

Livingston 2010

Emergent vegetation 

community changes or loss 

Yes No Anecdotal evidence for decline of tidal marshes following opening of 

East Pass and subsequent salinity changes. Compared with other Gulf 

estuaries, there is little emergent vegetation, but reasons are unclear. 

USAF 1996; 

Livingston 2010

Coral/hardbottom 

community changes or loss 

N/A N/A - - 

Impacts to benthic 

community

Yes Yes Low productivity in infaunal and epibenthic communities compared 

with other regional Gulf estuaries; salinity stratification and high 

organic silts (resulting in low DO), are contributing factors. 

Livingston 2010; USAF 1996

Fish kills Yes Episodic Primarily related to Karenia brevis blooms FWRI 

http://research.myfwc.com/fishkill/
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Other - - - - 

Table 1b. Checklist of additional environmental factors in Choctawhatchee Bay

Factors Observed? Explanation Source

Increased nutrient loading or concentrations from 

historical levels

No CBA analyzed a combined dataset (1968–2007), to study temporal trends. 

No significant increases in concentrations, except for TN in NWFWMD 

Segment 4 (corresponds to portion of “Middle CB” segment used by CBA 

and FDEP).

Terrell 2010

Mitigating factors that could prevent nutrient 

expression

Yes Turbidity, color Terrell 2010 

Other significant stressors to biological 

communities

Yes Salinity stratification and associated hypoxia; layer of organic fine 

sediments referred to as “liquid mud”; turbidity from Choctawhatchee 

River; poor flushing. 

Livingston 2010

Natural episodic events contributing to nutrient 

regime (e.g., seasonal or hydrologically driven)

Yes Choctawhatchee River flow a major controlling factor of nutrient and 

sediment loads. 

Schaeffer 2010; 

Livingston 2010
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Geographic and Physical Description

Choctawhatchee Bay is a large estuary in Okaloosa and Walton Counties, Florida, with a length of 43 

kilometers (km), and a width varying between 2 and 10 km. The surface area of the bay is 

approximately 348 square kilometers (km2). The bay is aligned along an east-west axis, with a major 

alluvial river basin, the Choctawhatchee River, at the eastern end. A small but influential pass to the 

Gulf of Mexico (East Pass) is in the western region, immediately west of Destin (Livingston 2010). The 

bay has shallow shelf areas and relatively steep slopes that eventually level out to average depths of 3 

meters in eastern sections and 8 meters in western sections (Livingston 2010).

The Choctawhatchee River provides approximately 90% of the freshwater input to the bay system, with 

secondary inflows from a series of bayous located mainly in the northern sections of the bay. The river 

has a broad floodplain and floods seasonally. It is the fourth longest river in Florida and the third largest 

in terms of discharge (Fernald and Purdum1998; Schaeffer 2010), with an annual average discharge rate 

of 243 cubic meters per second (m3

 s-1) (8,580 ft3 s-1) (Northwest Florida Water Management District

[NWFWMD] 1996). Major tributaries of the Choctawhatchee River include the Pea and Little 

Choctawhatchee Rivers, and Holmes, Wrights, Bruce, and Pine Log creeks (NWFWMD 2002). Other 

sources of fresh water to the bay include many small creeks and bayous that drain directly to the bay, 

the most significant being Turkey, Rocky, Swift, and Alaqua Creeks. There are 13 Floridan aquifer springs 

in the Choctawhatchee River Basin that contribute clear, alkaline water. Rainfall, surficial ground water, 

and overland flow also contribute significant amounts of fresh water to the estuary (USAF 1996). 

Average net precipitation in the system is estimated at 50 inches per year (Blaylock 1983). 

Historically, marine waters entered the bay only through periodic breaks in the barrier islands (Hemming

and Brown 2004). However, an artificial channel, East Pass, was opened in 1929 to provide a permanent 

pass through the previously intermittent opening. The opening of East Pass resulted in increased 

salinity and the subsequent loss of marshes, swamps, and seagrass beds throughout the bay (Livingston 

2010; Ruth and Handley 2002). The bay opens to the Gulf Intracoastal Waterway (GIWW) in the east, 

connecting Choctawhatchee Bay to West Bay (of the St. Andrews system). In the west, the bay opens to

Santa Rosa Sound and the GIWW, connecting Choctawhatchee Bay to the Pensacola Bay system 

(Blaylock 1983). The GIWW is regularly maintained by the U.S. Army Corps of Engineers. Pensacola Pass 

is separated from the west side of the bay by an 84-km (52-mile) portion of the GIWW that was initially 

dredged in the 1940s (NWFWMD 1996).

Choctawhatchee Bay is a highly stratified system with minimal tidal exchange (tidal range is 0.15 m). 

Water exchange with the Gulf of Mexico is limited to the narrow, shallow East Pass (Blaylock 1983; 

Livingston 1986; USAF 1996). The strong halocline (a noticeable change in salt concentrations between 

surface waters and deeper waters) is due to reduced tidal mixing (Blaylock 1983; Collard 1976), and 

hypoxia is a common and persistent phenomenon due to the vertical stratification. The significant 

freshwater influence from the Choctawhatchee River, accompanied by the influx of salt water from the 

Gulf of Mexico, causes salinity fluctuation and stratification. Salinities range from 0 to 34 parts per 

thousand (ppt) on an east-to-west gradient, from the river delta to the East Pass opening to the Gulf. 

Water temperatures range from 13.7 ̊ to 19.8°C, with peak temperatures generally occurring in July and 

August, and the lowest temperatures in December and January. The pH in the bay ranges from 7.0 to 
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8.1 standard units (SU). Depths range from 3 to 13 m, with a mean depth of 3.8 m (Schaeffer 2010). 

The bay has shallow shelf areas and relatively steep slopes that eventually level out to average depths of 

3 m in eastern sections and 8m in western sections (Livingston 2010). Table 2 summarizes the bay’s 

physical characteristics.

Much of the watershed in the vicinity of Choctawhatchee Bay is publicly owned, including Rocky Bayou 

State Park and managed areas within Eglin Air Force Base. Large portions of the bay are Class II waters 

(approved for shellfish harvesting). The easternmost part of the bay and the river delta, as well as Rocky 

Bayou State Park Aquatic Preserve, are designated as Outstanding Florida Waters (OFWs) (Rule 62-

302.700, Florida Administrative Code [F.A.C.]), worthy of special protection because of their natural 

attributes. Figure 1 contains a map of Choctawhatchee Bay showing major urban centers and publicly 

owned land management areas.

The bay has four basic natural habitats: shallow slope areas (vegetated, unvegetated, and oyster beds), 

deep central basin regions (unvegetated), bayous, and a river delta area. 

Figure 1. Map of Choctawhatchee Bay and adjacent urban areas and land management areas. 
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Table 2. Choctawhatchee Bay physical characteristics. 

Physical Characteristic Values Source 

Estuarine surface area (km2) 348 km2 Florida Marine Research 

Institute (FMRI) 1993

Watershed area (km2) 13x103 km2 Schaeffer 2010

Land use See Figure 3 Schaeffer 2010

Mean depth (m) 3.8 m Schaeffer 2010

Tidal range (m) 0.15 m Ruth and Handley 2002 

Salinity and salinity zones 0-34% 

Strong halocline

FMRI 1993

Choctawhatchee Bay Basin 

The Choctawhatchee Bay Basin encompasses nearly 13,856 km2 (5,350 square miles [mi2]) and spans 

portions of northwest Florida and south Alabama (Figure 2). Approximately 42% of the basin is in north 

Florida, with the rest in rural portions of south Alabama. Much of the watershed is composed of forest, 

agricultural, and rural land uses, with a large portion of the basin in Florida part of Eglin Air Force Base

(Figure 3). Figure 3 also shows the areal extent of each land use type and percentage of the total 

watershed area. In addition, the watershed contains a portion of the sandhill lakes area of Washington

County. 

Figure 2. Location of Choctawhatchee Bay watershed and estuary (Schaeffer 2010). 
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Figure 3. Land uses in the Choctawhatchee Bay watershed, with areal coverages and percentages of total area

(from Schaeffer 2010). 

Sources and Fates of Nutrients 

Sources of nutrients to Choctawhatchee Bay include the Choctawhatchee River, numerous small creeks 

and bayous that drain directly to the bay, point source discharges, nonpoint source inputs (septic tanks 

and stormwater from urban and agricultural areas), natural inputs (plant leaf litter), and atmospheric 

deposition. 

For FDEP water quality assessment purposes, the Choctawhatchee Bay watershed is divided into the Pea 

River, Choctawhatchee River, and Choctawhatchee Bay Planning Units. There are no permitted 

domestic or industrial wastewater facilities in the Pea River Planning Unit, and only 1 closed landfill. 
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There are 20 permitted domestic wastewater facilities and 4 industrial facilities in the Choctawhatchee 

River Planning Unit. Four of the permitted domestic wastewater facilities (Chipley, Bonifay, Graceville, 

and Noma) discharge directly into surface waters, and a fifth (Vernon) discharges into percolation ponds 

that overflow into surface waters. These facilities are concentrated in the Holmes Creek watershed

(FDEP 2006). There are also 12 permitted wastewater discharges that do not discharge directly to 

surface waters. The Choctawhatchee River Planning Unit contains 11 landfills, 5 of which are active. 

There is also 1 delisted Superfund site. The Pea River and Choctawhatchee River watersheds largely 

depend on onsite sewage treatment and disposal systems (OSTDS, or septic tanks) for the treatment 

and disposal of wastewater (NWFWMD 2002). 

There are 5 permitted wastewater facilities in the Choctawhatchee Bay Planning Unit with direct 

discharge to surface water. Three of these are concrete batch plants, while the remaining 2 are 

industrial waste facilities. An additional 25 permitted facilities (21 domestic waste and 4 industrial 

waste) have no direct surface water discharge but instead handle plant effluent in reuse systems. There 

are 18 landfills in the planning unit, 6 of which are active. Several areas in the vicinity of 

Choctawhatchee Bay rely substantially on OSTDS for the treatment and disposal of wastewater (Knight 

and Wallman 2007), although initiatives to extend sewer service into areas near the bay are ongoing. 

Approximately 78% of the land area in the Choctawhatchee Bay Planning Unit is composed of upland 

forest and wetlands. Approximately 12.5% of the land area is urban and built-up, primarily in the coastal 

area of the watershed. These human land uses can be associated with nonpoint discharges of pollutants 

and eroded sediments. This stormwater runoff enters Choctawhatchee Bay through the 

Choctawhatchee River; through numerous bayous, creeks, and ditches; and as overland sheet flow. 

Stormwater runoff is a potential threat to water quality in the bay, delivering suspended sediments,

nutrients, and, potentially, pesticides to the estuary. Estimates of natural sources of nutrient inputs 

such as leaf litter remain unquantified. 

Atmospheric deposition data for the watershed are available from the National Atmospheric Deposition 

Program’s National Trends Network (NADP-NTN), which has a collection site in Sumatra, Florida (FL 23). 

Based on its loading data for the most recently reported year (2008), the NTN estimates for atmospheric 

loading of NH4 and NO3 for Choctawhatchee Bay are 0.96 and 7.11 kilograms per hectare per year (kg

ha-1 yr-1), respectively. 

Biological Summary 

Seagrasses in Choctawhatchee Bay 

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

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

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

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

Heck 2001). Seagrasses enhance sediment stability, decrease wave energy, and increase water clarity 

(see reviews by Phillips and McRoy 1980; McRoy and Helfferich 1977). 

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

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

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

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

communities have been proposed as “coastal canaries”—biological indicators of changing coastal 
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conditions (Orth et al. 2006). Seagrasses have been shown to be adversely impacted by anthropogenic

nutrient enrichment (Orth and Moore 1983; Tomasko et al. 1996). 

Reduced underwater light penetration appears to be a primary driver of seagrass decline. The accepted 

thinking on this process is that increased inputs of nitrogen and phosphorus lead to theexcess growth of 

phytoplankton and epiphytic algae reducing available light to the seagrasses and causing decreased 

seagrass productivity and ultimately large-scale seagrass losses (Duarte 1995). This explanation, while 

valid, does not give a complete picture of the synergistic factors controlling seagrass production. “Topdown” food web effects must also be considered. In controlled, in situ experimental studies in St. 

Joseph Bay, Heck et al. (2000), found that mesograzers (amphipods, caridean shrimp, gastropods, and 

hermit crabs) controlled the effects of nutrient enrichment on the abundance of epiphytes. It is 

therefore critical to consider the role of “top-down” effects from overfishing or other food web 

disruptions in assessments of nutrient enrichment in estuaries such as Choctawhatchee Bay. 

The seagrass beds in Choctawhatchee Bay are considered extremely important because they support 

diverse populations of fish and invertebrates, including many recreational and commercial species 

(NWFWMD 1996). Seagrass beds in Choctawhatchee Bay contain primarily shoal grass (Halodule 

wrightii) and wigeon grass (Ruppia maritima). Shoal grass has flat, narrow leaves and a shallow root 

system. It has been characterized as rather tolerant of environmental stressors, withstanding heat, 

desiccation, and turbidity more readily than Thalassia testudinum (turtle grass) or Syringodium filiforme

(manatee grass) (USAF 1996; Dawes et al. 2004). Shoal grass can grow in deeper, lower-light conditions

than other seagrass species and can colonize disturbed areas, preparing sediments for the recruitment 

of other species (Wolfe 1988). Populations of shoal grass occur mainly in the western portion of the 

bay. Wigeon grass is found primarily in Hogtown Bayou (Figure 3); it is most common in brackish waters 

but can tolerate higher salinities (USAF, 1996). 

Trends in Seagrass Distribution 

Although the seagrass beds in Choctawhatchee Bay are considered crucial habitat, only limited studies 

have been conducted in the bay to determine the status and trends of those seagrass resources. As part 

of a larger study that covered the entire Gulf of Mexico, McNulty et al. (1972) reported 3,057 acres of 

seagrasses in Choctawhatchee Bay. This mapping was done with limited field verification, and seagrass 

species were not identified. The interpretation of aerial photographs by Burch (1983) indicated 

significant loss of seagrass beds for most areas in the bay between 1949 and 1985. Burch also noted

that early aerial photography (1949–1980) was at various, potentially incompatible scales and did not 

cover the entire bay at any one time. Ruth and Handley (2002) found that these differences make direct 

comparisons to current data difficult. 

Further standardized mapping of seagrass beds in Choctawhatchee Bay, at the appropriate spatial and 

temporal scales, is needed to determine historical and current trends in various zones of the bay. Indepth monitoring of seagrass health, including acquiring data on species present, coverage, epiphyte

loads, associated organisms, N:P ratios, and other parameters, is also needed in the Choctawhatchee 

Bay system.
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1992 U.S. Geological Survey National Wetlands Research Center Seagrass Mapping Study (Ruth and 

Handley, 2002)

The most extensive mapping study of seagrass coverage for the Choctawhatchee Bay area was 

conducted in 1992 by the U.S. Geological Survey (USGS) National Wetlands Research Center (NWRC) by 

using natural-color aerial photography taken in 1992 at a 1:24,000 scale, as part of the northeastern Gulf 

of Mexico seagrass mapping project. This study differentiated between continuous and patchy seagrass 

areas and reported on historical change. For the study, the bay was divided into three segments, as 

follows (Figure 4): 

• Western Choctawhatchee Bay includes all areas west of the U.S. Highway 293 MidBay Bridge to Brooks Bridge, where Santa Rosa Sound begins. This is the most saline 

segment of the bay and includes the deepest sections, up to 13 m. It is also 

historically the area with the most shoreline development, including the cities of Fort 

Walton Beach, Destin, Niceville, and Valparaiso, as well as Eglin Air Force Base. This 

section contains East Pass, the connection to the Gulf of Mexico. 

• Middle Choctawhatchee Bay, the largest bay segment, covers the area east of the 

Mid-Bay Bridge to the State Road 331 Bridge. Most of the northern shore consists of 

the Eglin Air Force Base Wildlife Management Area and contains several creeks and 

bayous. The southern shoreline contains Horseshoe and Hogtown Bayous and the 

Sandestin resort. Most of this section of the bay is classified as Class II waters 

(shellfish propagation and harvesting) and contains the majority of the bay’s oyster 

resources. 

• Eastern Choctawhatchee Bay includes all areas east of the State Road 331 Bridge

and contains the Choctawhatchee River delta. The Choctawhatchee River is 

designated as an OFW, and the eastern portion of the bay is classified as Class II 

waters (shellfish propagation and harvesting). Water depths average 3 m in this 

portion of the bay. 

The data show that seagrass beds occurred primarily in the western and middle sections of the bay, 

which are the higher-salinity areas of the bay (Table 3 and Figure 5). The total seagrass coverage for 

Choctawhatchee Bay was 4,261 acres (Table 3). Data indicate that most seagrass areas were patchy 

beds (3,477 acres), with only 783 acres of continuous beds. Most patchy seagrass coverage, and nearly 

all continuous coverage, was located in the western, higher-salinity segment of the bay. 

Because the segments of the bay have very different physical characteristics, it is possible to make only 

general observations about changes over time. Figures 6 and 7 show the results of a seagrass coverage 

comparison for Choctawhatchee Bay and Western Choctawhatchee Bay, respectively, in 1992 and 2003.
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Table 3. Choctawhatchee Bay seagrass status, 1992 (from Ruth and Handley 2002).

- = Empty cell/no data

Data source: USGS photointerpretation of 1:24,000-scale natural color aerial photography flown by Stennis Space Center (NASA), fall 1992

Bay Segment Classification Ha Acres

Western Continuous 317 783

- Patchy 1,109 2,739

Middle Continuous 0.4 1 

- Patchy 297 733

Eastern Continuous - - 

- Patchy 2 5 

Total Continuous 314 784

- Patchy 1,408 3,477

Grand Total - 1,722 4,261

Figure 4. Choctawhatchee Bay segments for seagrass mapping study.
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Other Factors Affecting Seagrasses

Significant riverine input and poor flushing heavily influence the hydrodynamics of the bay and may be 

in part responsible for fluctuations of seagrass coverage. Ruth and Handley (2002) suggest that 

historical eutrophication and propeller scarring by boats are in part responsible for seagrass loss. 

Boats operating in shallow waters, especially waters less than 2 m, can scar seagrass beds. This is 

occurring in many coastal areas throughout the state, including Choctawhatchee Bay. A 1995 statewide 

study by the FWRI used aerial photography to investigate the severity of propeller scarring in seagrass 

beds. The impacted acreage in Choctawhatchee Bay was approximately 390 acres (approximately 11.3% 

of the total estimated SAV coverage of 3,450 acres). Approximately 9% was lightly scarred, 2.3% was 

moderately scarred, and there were no severely scarred areas (Sargent et al. 1995). 

FDEP has recognized the need to reduce the scarring of seagrasses by boats and committed resources to 

address the issue. Management recommendations include education, channel marking, increased 

enforcement, and limited motoring zones (Sargent et al. 1995). Additionally, the restoration of scarred 

beds may be enhanced by attracting shorebirds to an affected area through the deployment of perching 

areas. The nutrient input from the resulting bird guano encourages SAV to grow in the scarred zone 

(Kenworthy et al. 2000). 

FWRI geographic information system (GIS) data layers (2003) indicate that SAV was reduced to an 

estimated 2,604 acres in Choctawhatchee Bay. Preliminary 2009 data from Lazzarino and Terrell (2010), 

however, indicate 3,555.8 total acres of seagrass beds in Choctawhatchee Bay (Table 4). They are 

currently conducting a study to quantify seagrass coverage in Choctawhatchee Bay using Landsat 5 TM 

imagery and extensive ground-truthing. Lazzarino and Terrell (2010) suggest that the 2003 mapping 

work underestimated the total coverage for the bay because all of the seagrass coverage in the 

Hogtown Bayou area was missed. This omission was possibly due to a poor visual signature for this 

area. 

Livingston (2010) suggests that the spatial and temporal pattern of seagrass loss may be related to

changes in the optical characteristics of the water column (i.e., changes in color, turbidity, etc.). Most of 

the losses have been in deeper regions, while SAV coverage has actually increased in shallower areas. 

Livingston (2010) asserts that these patterns of change indicate that reduced light transmission is 

responsible for the observed response. 

Table 4. Choctawhatchee Bay total seagrass coverage estimates, in acres.

*Estimate missed all seagrass coverage in Hogtown Bayou area. 

**Data are preliminary but include extensive groundtruthing.

1992 

(USGS) 

(Ruth and Handley 2002)

2003 

(FWRI)*

2009 

(Lazzarino and Terrell)**

4,261 2,064 3,556
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Figure 5. Seagrass coverage in Choctawhatchee Bay, 1992.
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Figure 6. Choctawhatchee Bay seagrass coverage comparison, 1992 and 2003 (Alexander 2010). 

Figure 7. Western Choctawhatchee Bay seagrass coverage comparison, 1992 and 2003 (Alexander 2010). 
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Tidal Marshes in Choctawhatchee Bay 

The fringing (emergent) vegetation zones in the Choctawhatchee Bay system are not well developed, 

and the area of marsh habitat is lower than that found in other estuaries in the region. Emergent 

vegetation is limited to a few peripheral areas bordering bayous, Live Oak Point, and the marshes 

around the river delta (Livingston 2010). In 1972, emergent marsh coverage was estimated to be 2,816 

acres (NOAA 1991). Livingston (1986) calculated that 1,855 acres of marsh were present in 1976, based 

on USGS topographic maps, and NOAA (1991) calculated that 2,700 acres of marsh were present in 

1985, based on aerial photographs. A 1988 NOAA survey of the areal extent of coastal wetlands in Gulf 

of Mexico estuaries found that Choctawhatchee Bay had 2,700 acres of salt marsh, and 3,700 acres of 

freshwater marsh (Reyer et al. 1988). An FDEP estimate of emergent marsh based on FWRI GIS data 

layers (1994–2006) was 2,411 acres. 

The discrepancies among estimates illustrate the difficulty of comparing the results from different 

imagery and methods of calculating area. Livingston (1986) found the dominant species to be the salttolerant perennial Juncus roemerianus, with significant coverage by Spartina alterniflora. A complete 

vegetation survey of marshes in Choctawhatchee Bay has not been conducted, but Keppner and 

Keppner (2003), surveyed the Hogtown Bayou area (including the smaller bayous Mussett Bayou, 

Hewett Bayou, and Mack Bayou) (Figure 8). Keppner and Keppner (2003) found a total of 61 species of 

vascular plants in fresh, brackish, and salt marshes (Table 4). The fresh marshes contained 42 plant 

species, while the brackish and salt marshes contained 5 and 14 species, respectively. Livingston (1986) 

and others note that there is historical anecdotal evidence for the loss of marshes in Choctawhatchee 

Bay following the opening of East Pass and the shift from a primarily fresh system to a more saline, 

stratified system. 

Table 4. Vascular plants from Hogtown Bayou tidal marshes (from Keppner and Keppner 2003). 

- = Empty cell/no data

Family Genus and Species 

Salt marsh -

Aquifoliaceae Ilex vomitoria 

Asteraceae Baccharis halimifolia 

Asteraceae Iva frutescens 

Convolvulaceae Ipomea sagittata 

Cyperaceae Eleocharis robinsii 

Cyperaceae Scirpus robustus 

Gentianaceae Sabatia stellaris 

Juncaceae Juncus roemerianus 

Malvaceae Kosteletzkya virginica 

Plumbaginaceae Limonium carlinianum 

Poaceae Distichlis spicata 

Poaceae Paspalum vaginatum 

Poaceae Spartina patens 

Asclepiadaceae Cyananchum angustifolium

Brackish marsh -

Asteraceae Baccharis angustifolia 

Cyperaceae Cladium jamaicense 

Cyperaceae Fuirena breviseta 

Cyperaceae Scirpus etuberculatus 

Fabaceae Sesbania punicea 
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Family Genus and Species 

Freshwater marsh - 

Apiaceae Hydrocotyle bonariensis 

Asteraceae Aster chapmanii 

Asteraceae Bigelowia nudata

Asteraceae Coreopsis linifolia 

Asteraceae Helianthus angustifolium 

Asteraceae Eupatorium mohrii

Clusiaceae Hypericum hypericoides 

Clusiaceae Hypericum mutilum 

Cyperaceae Carex festucacea 

Cyperaceae Cyperus polystachyos 

Cyperaceae Dichromena colorata 

Cyperaceae Dichromena latifolia 

Cyperaceae Fimbrystylis autumnalis 

Cyperaceae Psilocarya nitens 

Cyperaceae Rhynchospora cephalantha

Cyperaceae Rhynchospora ciliaris 

Cyperaceae Rhynchospora fascicularis

Cyperaceae Rhynchospora wrightiana 

Cyperaceae Scleria reticularis 

Droseraceae Drosera capillaris 

Eriocaulaceae Eriocaulon decangulare 

Haemodoraceae Lophiola americana 

Juncaceae Juncus abortivus 

Juncaceae Juncus acuminatus 

Juncaceae Juncus marginatus 

Lentibulariaceae Utricularia biflora 

Lentibulariaceae Utricularia cornuta 

Liliaceae Aletris lutea 

Onagraceae Ludwigia decurrens 

Onagraceae Ludwigia linearis 

Onagraceae Ludwigia linifolia 

Onagraceae Ludwigia pilosa 

Poaceae Dicanthelium scabriusculum

Poaceae Echinochloa colona 

Poaceae Erianthus strictus 

Poaceae Manisuris rugosa

Poaceae Panicum verrucosum 

Scrophulariaceae Agalinis linifolia 

Scrophulariaceae Bacopa monnieri 

Xyridaceae Xyris baldwinii

Xyridaceae Xyris fimbriata 

Xyridaceae Xyris jupicai 

Total number of species 61
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Figure 8. Location of Hogtown Bayou study area for vascular plant inventory and invertebrate sampling 

(Keppner and Keppner 2003). 

Phytoplankton

In Choctawhatchee Bay, Blaylock (1983) observed peaks in phytoplankton production correlated with 

freshwater inflow, which in turn was associated with increases in nutrient concentrations. Chlorophyll 

peaks occurred during a period of high rainfall in April and following a hurricane in September 1975. 

Livingston conducted monthly biological sampling of Choctawhatchee Bay from 1985 to 1998 (Livingston

2010), including phytoplankton sampling and taxonomic analysis. Figure 9 shows the locations of the 

fixed sampling stations. In addition, a 2006 study examined phytoplankton assemblages in several 

bayous in the Choctawhatchee Bay system (Livingston 2010). 

Phytoplankton cell numbers (Figure 10) were lowest at the river mouth and highest at Stations C38 and 

C36e. Species richness was lowest in the eastern parts of the bay, and increased in the western 

sections, with peaks at Stations C38 and C36e. From 1985 to 1986, the dominant species collected were 

Chaetoceros spp., Coscinodiscus spp., Skeletonema costatum, Pyrocystis sp., Chaetoceros coarctatus, 

Cyclotella sp., and Ceratium tripos. Blooms (Skeletonema costatum, Falcula hyalina) were found mainly 

in Old Pass Lagoon (C36e) (Figure 11). The highest annual average phytoplankton numbers were noted 

in Old Pass Lagoon and extreme western sections of the bay, with annual averages greater than other 
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stations in the bay. In contrast to Blaylock (1983), Livingston (1986) reported peak phytoplankton 

numbers during December; low numbers occurred in spring and summer months, which are periods of 

high predation by herbivorous organisms (i.e., zooplankton, meroplankton) (Livingston 2010). 

In April 2006, water samples were taken at stations throughout Choctawhatchee Bay, including several 

bayous, and preserved and analyzed by Dr. A.K.S.K. Prasad, at Florida State University (FSU). 

Phytoplankton species identifications and cell counts were conducted. No blooms were present, except 

for the Chula Vista Bayou surface sample, where bloom concentrations (> 106 cells L-1) of Chaetoceros 

affinis were observed. A potentially harmful diatom, Pseudonitzschia (possibly pseudodelicatissima) sp.,

was present in almost all of the stations examined but not in bloom densities. According to the Manual 

of Harmful Marine Microalgae (Hallegraeff et al. 2003), Pseudonitzschia may produce domoic acid, a 

toxin that causes amnesic shellfish poisoning (ASP). It is important to note, however, that domoic acid

was not present in these samples. Cyclotella choctawhatcheeana and Chaetoceros laevis were also 

present. The overall assemblages in all of the stations were similar. The dinoflagellates Prorocentrum 

triestinum. P. micans, and P. cordatum (syn. P. minimum) were present in very low numbers. All three 

species are known to form red tide blooms. Karenia brevis was not observed. No harmful 

raphidophytes were encountered. For a detailed description of phytoplankton analytical methods and 

the results for each station, see Livingston (2010). 

Invertebrates 

Livingston sampled infauna and benthic macroinvertebrates as part of a biological sampling program in

Choctawhatchee Bay (Livingston 2010). Infaunal samples were taken monthly with coring devices at the

fixed stations in Choctawhatchee Bay from 1985 to 1998 (Figure 9). Epibenthic invertebrates and fishes

were collected monthly for the same period and stations, with 5 m otter trawls. Species were identified, 

biomass was calculated, and all biological data were transformed to trophic units. Infaunal numbers 

were generally lower at 2 stations in the upper parts of the western bay and at the mid-bay (deeper) 

stations. Peak numbers were in western sections of the bay near East Pass. 

The overall numbers of trophic units were lowest at the mouth of the Choctawhatchee River and at the 

mid-bay stations. The distribution of FII (infauna, epibenthic invertebrates, and fish) biomass followed 

this pattern, while the FII species richness was lower at the mid-bay stations, with increases in the 

western parts of the bay. The bay infauna were particularly reduced in deeper parts of the bay. Figure 

12 presents an analysis of fish and infaunal numbers in bayou areas. The highest numbers of infauna

were found in eastern bayous, areas that were not adversely affected by urban development. Infaunal 

numbers were lowest in lower Rocky Bayou and Boggy Bayou (Stations 28 and 29). Fish numbers were 

highest in the eastern bayous, with marked reductions in Hogtown Bayou (Station 17), Garnier Bayou, 

and Old Pass Lagoon. Overall, the numbers of infauna and fishes were lowest in areas receiving 

stormwater runoff from urban areas. 

Foster (2000) provided an extensive systematic list of invertebrates for Choctawhatchee Bay that 

contains 209 species in 175 genera in 7 phyla. For the complete taxa list, see Keppner and Keppner

(2003). Heard et al. (2000, 2002) reported on the benthic invertebrate community of Choctawhatchee 

Bay in relation to Gulf sturgeon foraging. Fox et al. (2001) provided a list of macroinvertebrate species 

related to sturgeon locations. Table 5 contains a summary list of the taxa reported by Foster (2000) and 

Fox et al. (2001) for Choctawhatchee Bay. These studies do not compare invertebrate taxa richness or 

abundance in Choctawhatchee Bay to other regional estuaries. 
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Table 5. Benthic macroinvertebrates reported from Choctawhatchee Bay (after Foster 2000 

and Fox et al. 2001). 

Phylum Number of 

Genera

Number of 

Species

Cnidaria 3 3 

Platyhelminthes 1 1 

Nemertea Not stated 3 

Annelida 71 83

Mollusca 36 47

Arthropoda 60 68

Echinodermata 4 4 

Total 175 209

Figure 9. Location of Choctawhatchee Bay biological sampling stations, 1985–98 (Livingston 2010). 
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Figure 10. Phytoplankton cell numbers and species richness at mid-bay stations in Choctawhatchee Bay and East 

Pass Lagoon (Station 36e), averaged from monthly data, September 1985–August 1995 (Livingston 2010). 

Phytoplankton

0

5000000

10000000

15000000

20000000

25000000

30000000

003D007D

011D

015D019D022D025D031D034D038D

36ED

station

0

5

10

15

20

25

30

35

40

# taxa

TOTALN NBRTAXA
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Figure 11. Phytoplankton bloom numbers at mid-bay stations in Choctawhatchee Bay and East Pass Lagoon 

(Station 36e), averaged from monthly data, September 1985–August 1995 (Livingston 2010). 

Phytoplankon blooms

1

1000

1000000

1000000000

003D007D

011D

015D019D022D025D031D034D038D

36ED

station

Skeletonema costatum Chaetoceros socialis Falcula hyalina
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Figure 12. Total numbers of infauna and fish, averaged from monthly data from September 1985–August 1995

(Livingston 2010).

Fisheries in Choctawhatchee Bay 

Commercial and sport fisheries are important in the area, as is oyster harvesting (Ruth and Handley

2002). Commercially and recreationally important fish and shellfish include shrimp (Penaeus spp.), 

eastern oysters (Crassostrea virginica), spotted seatrout (Cynoscion nebulosus), gulf menhaden 

(Brevoortia patronus), red drum or redfish (Sciaenops ocellatus), blue crab (Callinectes sapidus), Gulf 

flounder (Paralichthys albigutta), striped mullet (Mugil cephalus), and white mullet (Mugil curema). 

The Choctawhatchee Bay system supports the gulf sturgeon (Acipenser oxyrinchus), a federally 

threatened species, which migrates through the bay into the Choctawhatchee River to spawn. In the 

Choctawhatchee River and Bay system, juvenile (age 1 to 6 years) Gulf sturgeon migrate and use habitat 

differently than they do in other regional systems. Instead of remaining near the river mouth for the 

entire year, they use Choctawhatchee Bay in the winter, returning upriver to resting areas in the spring 

(USFWS 2003). A study of sub-adult (age 4 to 7 years) Gulf sturgeon in Choctawhatchee Bay found that 

78% of tagged fish remained in the bay the entire winter, with the rest in connected waters and the Gulf 

of Mexico (USFWS 2003). These findings illustrate the importance of Choctawhatchee Bay as a 

wintering area to this protected species. 

The Choctawhatchee Basin is home to the Okaloosa darter (Etheostoma okaloosae), another federally 

endangered species. This small fish is known only from the main channels and small tributaries of 6 

clear stream systems that drain into Rocky and Boggy Bayous of Choctawhatchee Bay. Over 98% of the

range of the Okaloosa darter is within the Eglin Air Force Base Wildlife Management Area, affording the 

species considerable protection from development and habitat disturbance. Populations have been 

Bayou infaunal and fish numbers

0

20

40

60

80

100

120

140

005D009D013D017D027D028D029D040D041D

36ED

station

0

200

400

600

800

1000

1200

1400

fish numbers

TOTATinfN TOTALfishN
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stable or increasing in the past 15 years, and significant habitat restoration has taken place. These 

developments have led to a recent proposal to change the status of the Okaloosa darter from

endangered to threatened (USFWS 2010). 

Marine Fisheries Independent Monitoring 

The FMRI (currently FWRI) Marine Fisheries Independent Monitoring Program conducted fixed station 

sampling of fishes and invertebrates in Choctawhatchee Bay from 1993 to 1995. This sampling was part 

of a larger sampling effort that also included stratified random sampling in the Choctawhatchee 

Bay/Santa Rosa Sound system (1993–96). The 8 fixed station locations were based on representative 

bay habitat types. Collections were made monthly with three gear types: beach seine, offshore seine, 

and trawl. In 1996, only stratified random sampling was conducted, also with three gear types: beach 

seine, offshore seine, and trawl. These data provide valuable information on the life history, growth, 

and recruitment for each species collected. These data also provide general information on the 

ecological condition of the bay. Data from the program have been used to develop stock assessments 

for blue crab, red drum, mullet, and spotted sea trout. Preliminary recruitment indices have been 

developed for many of these species and can be tested against adult landings when the fish are large 

enough to enter the fishery(FMRI, 1993–96). Tables 6 through 9 show catch statistics for numerically 

dominant taxa from fixed station sampling in Choctawhatchee Bay from 1993 to 1996 (FMRI, 1993–96). 

Table 6. In 1993, a total of 513,517 organisms, representing 108 taxa, were collected. 

Species Number % 

Lagodon rhomboides 318,090 61.9

Brevoortia spp. 73,082 14.2

Leiostomus xanthurus 72,103 14.0

Menidia spp. 16,863 3.3

Penaeus spp. 5,285 1.0

Orthopristis chrysoptera 4,745 .92

Eucinostomus spp. 2,659 .52

Membras martinica 2,664 .52

Mugil spp. 2,475 .48

Anchoa spp. 2,332 .45

Micropogonias undulatus 2,191 .42

Callinectes sapidus 1,897 .37

Gobiosoma robustum 1,841 .36

Bairdiella chrysoura 1,310 .26

Syngnathus scovelli 534 .1

Sciaenops ocellatus 511 .09

Subtotal 508,582 99.03

Total 513,517 100 
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Table 7. 1994 Fixed-station sampling yielded 459,835 organisms representing 117 taxa. 

Species Number % 

Anchoa spp. 249,024 54.2

Leiostomus xanthurus 123,471 26.9

Lagodon rhomboides 37,309 8.1

Menidia spp. 11,390 2.5

Mugil spp. 10,963 2.4

Eucinostomus spp. 9,623 2.1

Brevoortia spp. 6,056 1.3

Penaeus spp. 1,751 .4

Callinectes sapidus 1,675 .4

Orthopristis chrysoptera 1,141 .25

Bairdiella chrysoura 768 .17

Prionotus scitulus 680 .15

Cynoscion arenarius 618 .13

Gobiosoma robustum 542 .12

Subtotal 455,011 98.95

Total 459,835 100 

Table 8. 1995 fixed-station sampling yielded 470,763 organisms representing 105 taxa. 

Species Number % 

Leiostomus xanthurus 324,330 68.9

Lagodon rhomboides 74,101 15.7

Mugil spp. 24,274 5.2

Menidia spp. 13,787 2.9

Brevoortia spp. 8,647 1.8

Anchoa spp. 4,333 .9

Micropogonias undulatus 3,606 .8

Penaeus spp. 3,361 .7

Eucinostomus spp. 3,169 .7

Orthopristis chrysoptera 1,254 .3

Callinectes sapidus 1,166 .2

Bairdiella chrysoura 771 .2

Gobionellus boleosoma 650 .1

Clupeidae spp. 530 .1

Subtotal 463,979 98.5

Total 470,763 100 
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Table 9. 1996 stratified random sampling by seine and trawl yielded 462,945 organisms representing 711 taxa. 

Beach and offshore seine sampling results 

Species Number % 

Leiostomus xanthurus 68,674 34.4

Menidia spp. 53,703 26.9

Lagodon rhomboides 18,696 9.4

Mugil cephalus 12,483 6.2

Harengula jaguana 11,726 5.9

Anchoa mitchilli 8,911 4.5

Eucinostomus spp. 5,580 2.8

Brevoortia spp. 4,912 2.5

Anchoa lyolepis 2,584 1.3

Anchoa hepsetus 1,695 0.8

Subtotal 188,964 94.7

Total 199,900 100

Trawl sampling results

Species Number % 

Leiostomus xanthurus 231,233 87.9

Micropogonias undulatus 7,185 2.7

Anchoa mitchilli 6,208 2.4

Brevoortia spp. 5,943 2.3

Lagodon rhomboides 6,050 2.3

Penaeus duorarum 730 0.3

Callinectes sapidus 664 0.3

Penaeus spp. (<15 mm pohl) 459 0.2

Bairdiella chrysoura 378 0.1

Anchoa lyolepis 375 0.1

Subtotal 259,225 98.6

Total 263,045 100

Shellfish Harvesting 

The Shellfish Environmental Assessment Section (SEAS) of the Florida Department of Agriculture and 

Consumer Services (FDACs) regulates shellfish harvesting in the state. SEAS conducts comprehensive

surveys of shellfish harvesting areas to ensure that shellfish are grown and harvested in a safe and 

sanitary manner. For the purposes of regulating shellfish harvesting in Florida, “shellfish” are defined as 

edible taxa of oysters, clams, and mussels. These filter-feeding mollusks filter up to 400 gallons of water 

per day, retaining much of the dissolved and suspended material, including microorganisms and 

chemical contaminants. 

The primary species of shellfish harvested in Choctawhatchee Bay is the eastern oyster (Crassostrea 

virginica). The northern hard-shell clam or quahog (Mercenaria spp.) and the brackish water or marsh 

clam (Rangia cuneata) are also found in Choctawhatchee Bay but not in commercial quantities. 

Choctawhatchee Bay represents less than one-tenth of 1% of commercial shellfish landings and value in 

Florida. Harvesting areas are categorized based on their fecal coliform levels, and any pollution sources 
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that may be in the vicinity. Choctawhatchee Bay shellfish harvesting areas (contained in the “Middle”

and “Eastern” areas of the bay) are classified as “conditionally approved” and “prohibited” (Knight and 

Wallman 2007).

Oyster harvesting seasons in Choctawhatchee Bay are currently January 1 to June 30, and October 1 to 

December 31. 

Red Tide and Associated Animal Mortality Events 

A red tide event and associated bottlenose dolphin mortalities were reported for Choctawhatchee Bay 

and nearshore Gulf waters from August 1999 to January 2000 (Livingston 2002). Over 100 dolphins 

died, and researchers found brevetoxins (the Karenia brevis toxin) in the animals’ systems. 

A red tide event was present in the Florida Panhandle from August to December 2005, following the 

northwest transport of a red tide event initiated in the eastern Gulf of Mexico. The FWRI investigated 

aquatic animal mortalities in Choctawhatchee Bay during and following this red tide event. Garnier 

Bayou was the most adversely affected area of the bay. Dead species reported included Gulf sturgeon 

(Acipenser oxyrinchus desotoi), bay anchovies (Anchoa mitchilli), skipjack shad (Alosa chrysochloris), and 

juvenile spot (Leiostomus xanthurus). NOAA, with assistance from FWRI, investigated associated 

bottlenose dolphin mortalities. High concentrations of brevetoxins were found in the internal organs of 

fish (sturgeon, gar, and multiple juvenile fishes), and indications were that the toxin exposure was 

postbloom (FWRI website). High levels of brevetoxin were detected in several food web components, 

and brevetoxin is considered the primary cause of the fish kills and marine mammal mortalities. The 

findings also suggest that brevetoxin may persist in estuarine and coastal waters, and circulate through 

the food web after a Karenia brevis bloom has ended. Animals can be exposed to lethal doses of 

brevetoxin weeks to months after a bloom has dissipated (FWRI website). 

No other harmful algal bloom (HAB) species or toxins have been identified in connection with the 

Choctawhatchee Bay aquatic animal mortalities. Although background levels of a potentially toxic 

diatom (Pseudonitzschia sp.) were detected in some samples, no domoic acid (the toxin produced by the 

diatom) was present in any biological or water samples tested. As part of the Choctawhatchee Bay 

mortality investigation, FDEP provided data on contaminant sampling from Garnier Bayou. The results 

indicate that no other contaminants were involved in the ongoing fish kill (FWRI website). FWRI staff 

have indicated that red tide (Karenia brevis) outbreaks are an offshore phenomenon, but may migrate 

toward shore. K. brevis, however, is a marine species and does not survive in lower salinity (<20 ppt) 

environments, such as nearshore or estuarine waters. Based on these factors, FWRI staff maintain that 

the effects of added nutrient loads coming from man’s activities on the land and delivered to estuaries 

and coastal waters are not responsible for initiating the offshore blooms or exacerbating blooms in 

Florida’s waters. Preliminary studies by FWRI scientists indicate that the major nutrient source for K. 

brevis is from species mortality, linked with a red tide event. Therefore, based on current information, 

waters will not be placed on Florida’s list of impaired waters based on the outbreak of red tide. In 

summary, when it is determined that a specific, reoccurring HAB adversely affects the designated use of 

a particular waterbody and is caused by pollutant, that waterbody will be added to FDEP’s verified list of 

impaired waters.
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Water Quality Studies 

CBA Partnership with University of Florida LakeWatch/Project COAST Program

The CBA formed a partnership with the University of Florida (UF) LakeWatch/Project COAST Program in 

1996 to begin the coordination of water quality monitoring in Choctawhatchee Bay. This effort was 

initiated to document spatial variability and long-term changes in the bay’s water quality. As part of the 

program, 90 stations are sampled monthly for TN, TP, chlorophyll a, and water clarity (Secchi depth), 

and the samples are sent to the UF LakeWatch program for analysis. For each station, DO, pH, turbidity, 

temperature, and salinity are measured at the surface and bottom. The CBA also collects quarterly color 

readings. 

FDEP notes the following details about sample analysis methods that may require additional scrutiny 

before using the results of the data to inform water quality standards development: 

1. Chlorophyll a is reported without correction for phaeophytin. FDEP has determined 

that phaeophyton-corrected chlorophyll a are more appropriate for water quality 

criteria, and therefore the uncorrected (less accurate) chlorophyll a data may be 

considered as estimated values. 

2. The method for the determination of TN in water samples is not an EPA-approved 

method, nor is it an approved method in the FDEP Standard Operating Procedures 

(SOPs). Bachmann and Canfield (1996) describe this method and provide data that

show the method produces results comparable to EPA-approved methods for TN in 

fresh water. Water samples are frozen before analysis, another method that also 

does not conform to FDEP SOPs. However, Bachmann and Canfield (1996) and 

Canfield et al. (2002) demonstrate that TN results are not significantly affected by 

freezing. Project COAST samples are held frozen for a maximum of 3 months before 

analysis. 

3. TP samples are also frozen, rather than acidified, before analysis. Canfield et al. 

(2002) showed that this preservation method did not significantly affect the 

analytical results. 

Due to the inconsistencies between Project COAST lab analyses and FDEP SOPs and EPA requirements, 

FDEP conducted several analyses in which the water chemistry results from Project COAST were 

compared with results from concurrent sampling by other entities that used National Environmental 

Laboratory Accreditation Conference (NELAC)-certified labs and approved methods. The results of these 

analyses suggest that it is appropriate to use the long-term Project COAST datasets, in conjunction with 

other data sources, where available, to inform numeric nutrient criteria proposals. 
Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 28 July 2010

CBA/Okaloosa-Walton College Long-Term Sampling and Data Coordination 

Study Area

Choctawhatchee Bay is located in the Panhandle region of northwest Florida (Figure 13). The main 

tributary to the bay is the Choctawhatchee River at the eastern end of the bay, while East Pass, located 

near the west end of the bay, is the only direct outlet to the Gulf of Mexico. The bay is approximately 

29.2 miles from east to west and about 3 miles wide at its widest point. Choctawhatchee Bay has a 

surface area of 86,295 acres and is the third largest estuarine system on the Gulf coast of Florida 

(McNulty et al. 1972). The bay has a maximum depth of 43 feet just north of the East Pass. Two 

channels, Santa Rosa Sound to the west and the Intracoastal Waterway to the east, connect 

Choctawhatchee Bay to Pensacola Bay, and to West Bay in Panama City, respectively (Blaylock 1983).

Figure 13. Choctawhatchee Bay is located in the Panhandle region of Florida, within Okaloosa and Walton 

Counties (top). Currently, the CBA samples almost 90 stations sampled monthly throughout Choctawhatchee 

Bay (bottom). Each red dot is a sampling station.
Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 29 July 2010

Project Scope 

Walton and Okaloosa Counties are like any other coastal Floridian county, in that they are experiencing 

record high population growth rates, and the expected population growth rates for each county are 

staggering. A comprehensive evaluation of the current and historical water quality is needed. The 

water quality of the estuary system is evaluated first spatially along the horizontal stretch of the bay and 

then temporally over the 40 years of data record.

Data Summary 

The CBA of Okaloosa-Walton College in Niceville, Florida, has been coordinating monthly water sampling 

within the Choctawhatchee Basin for over 10 years. All available water chemistry data (EPA data 

collected in 1968, University of West Florida [UWF] data collected in 1975, CAMA data collected in 

1985–87, and CBA/LakeWatch data collected from 1991 to 2007) have been joined into one dataset and 

assigned to 1 of 6 sections based on their location (Section 1 is located near the river, and Section 6 is 

located near East Pass). Different researchers have collected data over a time span of 40 years. 

Different field sampling techniques, laboratory methods, and station locations were used throughout all 

studies. 

Spatial differences in water quality were evaluated by calculating averages for each of the six sections. 

T-tests were performed on the means to determine if the means were statistically different from each 

other. Temporal differences in water quality were determined by following the methods described by 

Terrell et al. (2000).

Table 10 summarizes water chemistry data over the 40 years of data collection. Average TP, TN, 

chlorophyll, color, and turbidity were highest in Section 1 (nearest the Choctawhatchee River) and 

gradually decreased moving west to Section 6. Secchi depth was typically lowest in Section 1 and 

increased traveling west to Section 6.

Table 11 temporally summarizes water quality parameters over the 40 years of record within each 

section. Seasonal differences exist in the sections of the bay closest to the river but not in sections of 

the bay closer to East Pass. Table 12 summarizes water quality data for 2000 to 2009, collected by the 

CBA, for 3 regions delineated by surface salinity. 

Conclusions

The importance of long-term, routine sampling is critical for the preservation of overall good water 

quality in Choctawhatchee Bay. Groups such as the CBA are providing a valuable, cost-efficient service 

to water resource managers throughout the state by coordinating a long-term, routine sampling 

program, providing outreach and education to the local community and municipal staffs on how to be 

good environmental stewards with the water resources, and executing localized restoration projects to 

help correct specific problems identified through monitoring. 
Nutrient Criteria Technical Support Document Choctawhatchee Bay

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Table 10. Summary of the spatial water chemistry analyses from six sections along the horizontal length of the 

Choctawhatchee Bay. Section 1 is located along the east side of the bay near the Choctawhatchee River. Section 

6 is located along the west side of the bay near East Pass. Small letters next to each mean represent statistically 

significant differences (Terrell 2010). 

- = Empty cell/no data

Section (sig) - 1(a) 2(b) 3(c) 4(d) 5(e) 6(f)

Period of 

Record

- 1968–2007 1968–007 1968–2007 1968–2007 1968–2007 1968–2007

TP (mg/L) N 208 139 208 155 142 179

- Mean 0.027(a) 0.018(bcdf) 0.016(bcdf) 0.016(bcdf) 0.012(e) 0.016(bcdf)

- Range 0.000- 

0.170

0.001-

0,085

0.000-

0.120

0.000-

0.160

0.001-

0.052

0.000-0.063

TN (mg/L) N 210 138 210 157 144 181

- Mean 0.456(a) 0.302(b) 0.239(cdef) 0.226(cdef) 0.223(cdef) 0.233(cdef)

- Range 0.000-

3.070

0.105-

0.600

0.000-

0.503

0.000-

1.000

0.105-

0.800

0.000-1.513

Chlorophyll 

(μg/L)

N 169 118 186 135 124 158

- Mean 6(ab) 6(ab) 3(cdef) 3(cdef) 4(cdef) 3(cdef)

- Range 0-66 1-19 0-23 0-19 1-70 0-17

Secchi depth 

(m)

N 195 136 205 114 100 129

- Mean 1.07(a) 1.53(b) 2.14(c) 2.44d(f) 3.37(e) 2.63(df)

- Range 0.10-2.7 0.36-4.27 0.65-5.79 0.00-6.17 1.07-7.92 0.83-7.00

Color (PCU) N 148 79 158 116 55 128

- Mean 46(a) 30(b) 19(cdef) 17(cdef) 12(cdef) 15(cdef)

- Range 5-250 3-115 3-95 0-71 3-50 0-61

Turbidity 

(NTU)

N 266 545 571 351 318 361

- Mean 8(abe) 6(abce) 4(bcef) 5(abcef) 3(bcef) 3(cef)

- Range 0-301 0-250 0-214 0-828 0-158 0-105
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Table 11. Temporal water chemistry analyses over a 40-year period of record, 1968–2007 (Terrell2010).

Parameter Section Seasonality Prob>F Temporal Significance

TP 1 3° 0.9878 No significant change

TN 1 None 0.0148 Significant decrease

Chlorophyll 1 6° 0.0405 Significant increase

Secchi depth 1 3° 0.5333 No significant change

TP 2 2° 0.239 No significant change

TN 2 2° 0.0576 No significant change

Chlorophyll 2 6° 0.0421 Significant increase

Secchi depth 2 4° 0.3213 No significant change

TP 3 None 0.9608 No significant change

TN 3 2° 0.1045 No significant change

Chlorophyll 3 None 0.899 No significant change

Secchi depth 3 None <.0001 Significant increase

TP 4 None 0.9403 No significant change

TN 4 None 0.0208 Significant increase

Chlorophyll 4 None 0.7825 No significant change

Secchi depth 4 None <.001 Significant increase

TP 5 None 0.0012 Significant decrease

TN 5 None 0.7782 No significant change

Chlorophyll 5 None 0.1095 No significant change

Secchi depth 5 None 0.038 Significant increase

TP 6 None 0.0426 Significant decrease

TN 6 None 0.4069 No significant change

Chlorophyll 6 None 0.8094 No significant change

Secchi depth 6 None 0.6415 No significant change

Table 12. Summary of the spatial water chemistry analyses for three sections (based on surface salinity) along 

the horizontal length of Choctawhatchee Bay, 2000–09. Small letters next to each mean represents statistically 

significant differences (Lazzarino and Terrell 2010). 

NTU = Nephelometric Turbidity Unit

Mean (STD) (statistical significance) Western (a) Middle (b) Eastern (c) 

Number of samples 1,074 2,586 995 

TP (μg/L) 12 (6) (a) 16 (8) (b) 25 (12) (c) 

TN (μg/L) 246 (89) (a) 269 (100) (b) 413 (126) (c) 

Chlorophyll a (μg/L) 4 (4) (a) 5 (4) (b) 9 (13) (c) 

Secchi depth (m) 3 (1) (a) 2 (1) (b) 1 (0) (c) 

Color (PCU) 9 (6) (a) 16 (17) (b) 22 (19) (c) 

Bottom depth (m) 0.5 - 11.3 0.34 - 11.0 0.30 - 4.88 

Surface salinity (ppt) 22 (6) (a) 18 (8) (b) 11 (9) (c) 

Bottom salinity (ppt) 27 (6) (a) 25 (8) (b) 17 (8) (c) 

Surface turbidity (NTU) 4 (18) (a) 11 (64) (b) 13 (37) (c) 

Bottom turbidity (NTU) 6 (21) (a) 16 (69) (b) 18 (41) (c) 
Nutrient Criteria Technical Support Document Choctawhatchee Bay

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FDEP Water Quality Analyses 

FDEP analyzed all of the data available for Choctawhatchee Bay from the IWR database. The period of 

record was February 1996 to December 2009, and the spatial scale covered the entire bay system (all 

segments with waterbody identification numbers [WBIDs] characterized as “estuary”). For the IWR 

data, annual geometric means for the entire bay were calculated for TP, TN, and chlorophyll a. 

Table 12 shows the results of these calculations. Figures 14 through 16 show trends over the 14-year 

period and the long-term geometric means for each parameter. TP, after an initial increase from 1996

to 1998, decreased from 1998 to 2002, and was relatively steady from 2002 to 2009. TN concentrations 

were relatively steady over the 14-year period, until a spike in 2008. This spike appears attributable to 

localized increases at Chula Vista Bayou over a 3-month period, and the event is still being investigated. 

Chlorophyll a concentrations were relatively low and steady, with annual geometric means ranging from 

2.7 to 3.4 ug/L and a long-term geometric mean of 2.95 ug/L. It is important to note that a large 

percentage (approximately 75%) of the chlorophyll a data were reported as below the minimum detect 

limit (mdl) of 5 μg/L. Values reported as “below detect” were assigned a value equal to one-half of the 

mdl (2.5 μg/L).

Figures 14 through 16 show the distributions of the baywide geometric means. For all stations pooled, 

the long-term mean annual geometric mean was calculated, and a log normal distribution function was 

fitted to estimate the long-term 75th and 90th percentile of the data (Table 13). 

FDEP also grouped stations into the three regions used by the CBA. These regions are based on salinity, 

with mean annual surface salinities of 22 ppt (West), 18 ppt (Middle), and 11 ppt (East). They roughly 

correspond to USGS regions based on physical landmarks: west of the Mid-Bay Bridge, between the 

Mid-Bay Bridge and U.S. Highway 331 Bridge, and east of the U.S. Highway 331 Bridge (Terrell 2010). 

Figures 17 through 19 compare the distributions of the geometric means for TP, TN, and chlorophyll a

for each region. 

Table 13. Summary of data analysis for Choctawhatchee Bay, all stations combined, 1996–2009. 

- = Empty cell/no data

LN = Natural logarithm

GM = Geometric mean

C.I. = Confidence interval. 

* Long-term GMs and the 90th percentile of annual GMs are highlighted. 

Choctawhatchee 

Bay Data

TP (μg/L) 

Log Normal 

Distibution

TP (μg/L)

Empirical 

Percentile

TN (μg/L) 

Log Normal 

Distibution

TN (μg/L)

Empirical 

Percentile

Chlorophyll a 

(μg/L) 

Log Normal 

Distibution

Chlorophyll a

(μg/L)

Empirical 

Percentile

Mean LN TP 3.029 - 6.013 - 1.083 - 

Standard deviation

LN TP

0.438 - 0.207 - 0.090 - 

N 2,027 - 1,120 - 1,820 - 

95% C.I. 0.02 - 0.01 - 0.00 - 

Long-term GM 20.67* 22.70 * 408.58* 416.92* 2.95* 2.96*

Lower 95% C.I. 20.28 - 403.64 - 2.95 - 

Upper 95% C.I. 21.07 - 413.58 - 2.95 - 

75th percentile 27.78 26.26 469.94 450.79 3.14 3.18

90th percentile 36.25 * 39.27* 533.02* 525.99* 3.31* 3.21*
Nutrient Criteria Technical Support Document Choctawhatchee Bay

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Figure 14. Trend of annual geometric means for TP in Choctawhatchee Bay, 1996–2009, and long-term 

geometric mean. 

Figure 15. Trend of annual geometric means for TN in Choctawhatchee Bay, from IWR dataset, 1996–2009, and 

long-term geometric mean. 

0

5

10

15

20

25

30

35

40

45

50

1995 2000 2005 2010

Annual Geometric Means TP

Choctawhatchee Bay

annual geometric 

mean TP 

long term geometric 

mean TP 

0

100

200

300

400

500

600

700

1995 2000 2005 2010

Annual Geometric Means TN 

Choctawhatchee Bay

annual geometric 

mean TN 

long term geometric 

mean TN 
Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 34 July 2010

Figure 16. Trend of annual geometric means for chlorophyll a in Choctawhatchee Bay, from IWR dataset, 1996–

2009, and long-term geometric mean. 

Figure 17. Comparison of annual geometric means for TP for Choctawhatchee Bay regions based on salinity,

from IWR dataset, 1996–2009. 

0

20

40

60

80

100

120

140

1994 1996 1998 2000 2002 2004 2006 2008 2010

Comparison of TP Geometric Means 

Choctawhatchee Bay Regions 

East CB TP

River Mouth TP

Middle CB TP

West CB TP

0

0.5

1

1.5

2

2.5

3

3.5

4

1995 2000 2005 2010

Annual Geometric Means Chl a

Choctawhatchee Bay

annual geometric 

mean chl a 

long term geo mean 
Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 35 July 2010

Figure 18. Comparison of annual geometric means for TN for Choctawhatchee Bay regions based on salinity, 

from IWR dataset, 1996–2009. 

Figure 19. Comparison of annual geometric means for chlorophyll a for Choctawhatchee Bay regions based on 

salinity, from IWR dataset, 1996–2009. 

0

100

200

300

400

500

600

700

800

900

1995 2000 2005 2010

Comparison of TN Geometric Means 

Choctawhatchee Bay Regions

East CB TN

River Mouth CB TN

Middle CB TN

West CB TN

0

1

2

3

4

5

6

1996 1998 2000 2002 2004 2006 2008 2010

Comparison of Chl a Geometric Means 

Choctawhatchee Bay Regions 

East CB CHL A

River Mouth CB CHL A

Middle CB CHL A

West CB CHL A
Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 36 July 2010

A significant factor in Choctawhatchee Bay’s water quality is high turbidity resulting from the large 

sediment load of the Choctawhatchee River. Table 14 summarizes mean surface and bottom turbidity 

for a 10-year sampling period (2000–09) (Lazzarino and Terrell 2010). 

Table 14. Mean surface and bottom turbidity for Choctawhatchee Bay salinity-based regions, 2000–09 (from

Lazzarino and Terrell 2010). 

Mean (STD) Western Middle Eastern 

Surface Turbidity (NTU) 4(18) 11(64) 13(37)

Bottom Turbidity (NTU) 6(21) 16(69) 18(41)

Waters on the 303(d) List 

No impaired waters within the Choctawhatchee Bay Planning Unit on the Cycle 2 Verified List (2010) are 

listed for nutrients or DO (FDEP 2010a). Table 15 lists the waterbodies proposed for delisting. In the 

Choctawhatchee Bay Planning Unit, waters are listed as impaired for the following parameters: mercury 

(in fish tissue), bacteria, and fecal coliform bacteria. 

Table 15. Waterbodies in the Choctawhatchee Bay Planning Unit proposed for DELISTING from the 1998 303(d) 

list for either nutrients or DO (FDEP 2010b).

Waterbody Name Type WBID Impairment(s)

Joe’s Bayou Estuary 906 Nutrients (historic chlorophyll a) 

Choctawhatchee Bay 

(Middle Segment 2)

Estuary 778C DO , nutrients (chlorophyll a, historic 

chlorophyll a) 

Choctawhatchee Bay 

(Upper Segment) 

Estuary 778D Nutrients (historic chlorophyll a) 

Mercury impairments are not related to anthropogenic nutrient inputs. The relationship between 

bacteria and anthropogenic nutrients is more complex, because although potential sources of bacteria 

may also be sources of nutrients, the presence of fecal coliform or enterococci bacteria does not 

necessarily indicate the presence of anthropogenic nutrients. 

The use of fecal coliforms as indicators of the presence of human pathogens has been under scrutiny in 

Florida for the past decade. One of the priorities of the Gulf of Mexico Alliance (GOMA) is 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). The workgroup expressed concern 

that the EPA recreational criteria were derived in places that do not represent Gulf of Mexico conditions, 

and that the use of fecal indicators was not appropriate for waters primarily influenced by animal 

sources. Areas in the Gulf of Mexico for which 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). Choctawhatchee Bay falls into several of these categories: heavy 

rainfall, subtropical latitude, and large amounts of organic detritus/CDOM. 

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. FDEP recognizes that fecal coliform and 
Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 37 July 2010

enterococci bacteria may indicate a human source, or may co-occur with anthropogenic nutrient inputs, 

but 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 excerpted from a review conducted by Dr. V.J. Harwood of the University of South 

Florida (USF) as part of an MST project she is conducting for FDEP: 

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

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

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

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

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

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

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

assumption is often false by showing that the presence of indicator bacteria do not 

always correlate well with the presence of pathogens such as Salmonella, 

Campylobacter, Cryptosporidium, Giardia, or enteric viruses (Anderson et al. 2005; 

Bonadonna et al. 2002; Harwood et al. 2005; Lemarchand and Lebaron 2003; Lund 1996; 

Rees et al. 1998).

One important reason for the lack of correlation between traditional fecal indicator 

bacteria and pathogens is that the indicator bacteria are not specific to humans, nor to 

other hosts known to shed human pathogens in their feces, but are present in the 

intestines of all warm-blooded animals and some cold-blooded animals (Souza et al.

1999). Because not all animals are equally likely to carry human pathogens, 

contamination from all sources does not represent an equal health risk. Thus, some 

sources of fecal contamination in water are of greater concern than others. 

Furthermore, there is increasing evidence of naturalized or environmentally adapted 

strains indicator bacteria (both coliforms and enterococci) that are capable of persisting 

in a culturable form for extended periods, or even growing, in a wide variety of 

environmental matrices, including terrestrial soils, aquatic sediments, and attached to 

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, which may 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 Recommendation 

Relationship between Anthropogenic Nutrient Inputs and Adverse Biological Effects

There is considerable evidence to demonstrate that the nutrient regime in Choctawhatchee Bay is not 

adversely affecting biological condition. A reduction in nutrients would not lead to recovery of seagrass 
Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 38 July 2010

beds or tidal marshes, or improve the condition of biological resources in the bay. FDEP therefore 

proposes nutrient concentration targets that reflect the current conditions as reported from 1974 to 

2009 water quality monitoring data. 

Proposed Numeric Nutrient and Chlorophyll Criteria 

Methodology 

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

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

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

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

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

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

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

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

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

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

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

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

preserve the uses associated with that distribution. 

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

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

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

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

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

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 Choctawhatchee 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 
Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 39 July 2010

that a ten percent change in a water quality parameter represents an insignificant departure from the 

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

geometric mean, which was calculated as the geometric mean of the annual geometric means of the 

long-term dataset for each segment of the waterbody.

Because it is not always practical to assess compliance with the criteria on the same long-term basis, 

FDEP also developed criteria expressed as an annual geometric mean so that estuaries could be assessed 

on an annual basis. It should be noted that the duration and frequency components of the criteria must 

be linked to the response timeframe of the sensitive endpoint. Short-term averaging periods (e.g., 1 to 

30 days) might be appropriate for nutrient criteria where a sufficiently robust cause-effect relationship 

has demonstrated that a eutrophic response occurs over such timeframes. If however, such a shortterm response cannot be demonstrated, or there is no indication of use impairment, longer averaging 

periods should be used. 

Since the duration and frequency components of the criteria must be consistent with the derivation of 

the magnitude component, the long-term geometric mean target cannot simply be applied as an annual 

mean. Doing so would result in an unacceptability high Type I failure rate (identifying a healthy system 

as being impaired) since approximately 50 percent of the individual yearly means are expected to be 

above the long-term mean. Therefore, the long-term target must be adjusted to allow for the 

application to a shorter duration with an acceptable Type I error rate of no more than a 10 percent.

An annual criterion with an approximate 10 percent Type I error rate for a given frequency was derived 

by appropriately accounting for the annual variability above the mean. This annual target concentration 

was derived as an upper percentile of the distribution of the annual geometric mean concentrations. 

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 Niño, La Niña), 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. 
Nutrient Criteria Technical Support Document Choctawhatchee Bay

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The two expressions of magnitude differ in the handling of within-segment spatial variability. The 

network average magnitude was calculated based on the distribution of spatially averaged annual 

geometric means, while the single site magnitude was calculated using the distribution of station annual 

geometric means. Use of the network average magnitude is appropriate for assessing overall segment 

status. However, a network average is only representative of overall segment status if it is relatively 

homogeneous. If the segment is not well mixed, is very large, or contains localized nutrient sources, 

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

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

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

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

Summary of the Proposed Criteria

FDEP 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 targets for the protection of a healthy, well-balanced aquatic community in 

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

Table 16. Proposed numeric nutrient criteria for all segments of Choctawhatchee 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. N/A=Not applicable, because data were not sufficient for this analysis; criteria not yet proposed for 

segment 

Total Phosphorus (μg/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)

West 17 19 28 30

Central 16 18 25 26

East 23 25 26 27

Baywide 18 19 26 29

Total Nitrogen (μg/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)

Central 373 410 516 523
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Draft 41 July 2010

Middle 342 376 452 460

East 399 439 447 453

Baywide 370 407 502 514

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)

West 3.59 3.95 5.18 5.31

Central 2.84 3.12 3.64 3.71

East N/A N/A N/A N/A

Baywide 2.93 3.22 4.26 4.79
Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 42 July 2010

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