Site-Specific Information 

in Support of 

Establishing Numeric Nutrient 

Criteria for St. Andrew 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 of Nutrients.............................................................................................................. 7

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

Seagrass as the Key Biological Endpoint for St. Andrew Bay...........................................................10

Scallops........................................................................................................................................14

Other Key Habitats and Biological Resources.................................................................................16

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

FDEP Water Quality Analyses........................................................................................................17

Water Quality Analysis and Development of a Nutrient Criteria Approach Based on a 

Light Extinction Coefficient (Ke) (Hydroqual) .................................................................................23

Water Quality Monitoring by SAB-RMA (in partnership with the University of Florida 

[UF] Baywatch Program) ..............................................................................................................27

Waters on the 303(d) List..................................................................................................... 28

Numeric Nutrient Criteria Recommendations ...................................................................... 30

References .......................................................................................................................... 35
Draft iii July 2010

List of Tables

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

Table 2. St. Andrew Bay physical characteristics. ........................................................................................ 7

Table 3. Seagrass coverage for the entire St. Andrew Bay study area (includes East Bay, North 

Bay, St. Andrew Sound, St. Andrew Bay, and West Bay), USGS–U.S. Department of 

Agriculture (USDA) National Wildlife Research Center (NWRC) mapping................................13

Table 4. Estimates of seagrass acreage in St. Andrew Bay, 1992–2003, from USGS-NWRC 

mapping of seagrass coverage in northern Gulf of Mexico (Fitzhugh 2010b).........................14

Table 5. Adult bay scallop density at each of 13 stations sampled at the St. Andrew Bay study 

site during each June from 1994 through 2006, and for those same 13 stations plus 

an additional 7 stations added for the 2007–08 survey. Scallop density at each 

station is reported per 600 square meter (m2

) transect. The results of the WallerDuncan (W.D.) comparison of means (letters) are presented with the population 

means only for the original 13 sample stations for which the experimental design was 

balanced; similar letters denote averages that were not different at a significance 

level of 0.05. ‘Z’ indicates that the station was not sampled during that year. Note 

that the mean and standard deviation for 2007 and 2008 presented in the table are 

calculated from the original 13 stations only. ..........................................................................15

Table 6. Rare/endangered species in the St. Andrew Bay system. ............................................................17

Table 7. Summary of St. Andrew Bay system dissolved oxygen (DO) data................................................18

Table 8. Summary of West Bay water quality data, 1991–2008 (Hydroqual 2010) ..................................23

Table 9. Summary of TN data for the St. Andrew Bay system from SAB-RMA/UF Baywatch water 

quality monitoring program, 1990–2006. ................................................................................27

Table 10. Summary of TP data for the St. Andrew Bay system from SAB-RMA/UF Baywatch water 

quality monitoring program, 1990-2006..................................................................................27

Table 11. Summary of (uncorrected) chlorophyll a data for the St. Andrew Bay system from SABRMA/UF Baywatch water quality monitoring program, 1990–2006. ......................................27

Table 12. Waterbodies in the St. Andrew Bay Planning Unit that are on the 2010 Integrated 

Assessment (Cycles 1 and 2) verified list for impairments for either nutrients or DO 

(FDEP 2010a). *Note that these waterbodies are tributaries to the bay, not segments 

of the bay.................................................................................................................................. 29

Table 13. Waterbodies in the St. Andrew Bay Planning Unit that are proposed for delisting from 

the 1998 303(d) list for either nutrients or DO (FDEP 2010b).*Note that these 

waterbodies are tributaries to the bay, not segments of the bay. ...........................................29

Table 14. Proposed numeric nutrient criteria for all segments of St. Andrew 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 a single station shall not exceed, by segment, more than twice 

in a 5 year period. .....................................................................................................................33
Draft iv July 2010

List of Figures

Figure 1. Location of St. Andrew Bay, and geographic features (NWFWMD, 2000). ................................... 5

Figure 2. Location and delineation of the hydrologically linked segments of St. Andrew Bay. .................... 6

Figure 3. Bathymetric map of St. Andrew Bay system (Conmy 2010).......................................................... 7

Figures 4 and 5. Location of point source discharges in western (top) and eastern(bottom) 

portions of the St. Andrew Bay Planning Unit. ........................................................................... 9

Figure 6. Land use and land cover map and area calculation in the St. Andrew Bay watershed 

(Conmy 2010)............................................................................................................................10

Figure 7. St. Andrew Bay seagrass coverage trends, 1953 and 2003 (FDEP 2010). Trends were 

analyzed using aerial photography (black and white, 1:20K scale: 1953, 1964) (color, 

1:24K scale: 1980, 1992, 2003).................................................................................................12

Figure 8. Trend of annual geometric means of TP in the St. Andrew Bay system and the longterm geometric mean for the sampling period.........................................................................19

Figure 9. Trend of annual geometric means of TN in the St. Andrew Bay system and the longterm geometric mean for the sampling period.........................................................................19

Figure 10. Trend of annual geometric means of chlorophyll a in the St. Andrew Bay system and 

the long-term geometric mean for the sampling period. .........................................................20

Figure 11. Comparison of geometric means of TP among bay segments..................................................20

Figure 12. Comparison of geometric means of TN among bay segments. ................................................21

Figure 13. Comparison of geometric means of chlorophyll a among bay segments.................................21

Figure 14. Comparison between West Bay segments of annual geometric means of TN. ........................22

Figure 15. Comparison between West Bay segments of annual geometric means of TP..........................22

Figure 16. Chlorophyll a relationships in West Bay (Hydroqual 2010).......................................................25

Figure 17. Light extinction coefficient (Ke) relationships in West Bay (Hydroqual 2010)..........................26
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 St. Andrew 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. 

St. Andrew Bay is a large estuary with a small volume of freshwater input. Econfina Creek, Deer Point 

Lake Reservoir, the Gulf Intracoastal Waterway (GIWW), and smaller creeks and bayous are the primary 

sources of freshwater inflow, with a combined total discharge of less than 28.3 cubic meters per second 

(m3/s) (Handley et al. 2007). The low sediment load results in very clear waters, which in turn support 

extensive seagrass beds. Salinities are high, and often exceed 30 parts per thousand (ppt) (Brim 1998). 

St. Andrew Bay is biologically diverse and supports a large number of rare, endemic, and protected 

plants and animals. Seagrass species are an important foundation species and provide a host of 

ecosystem services. Economically important fisheries depend on the seagrass beds. 

Sources of nutrient loading to the estuary come from the freshwater inflows listed above, as well as 

point sources (primarily wastewater treatment facilities [WWTFs]), nonpoint sources (stormwater runoff 

and septic tanks), natural inputs (leaf litter), atmospheric deposition, and ground water. 

Seagrasses are the most sensitive biological endpoint in the St. Andrew Bay system, and data indicate 

that overall coverage has increased baywide approximately 14% from 1992 to 2003, after a decrease of 

approximately 8% from 1953 to 1992 (Brim and Handley 2002; Fitzhugh 2010b). Water quality studies 

indicate nutrient and chlorophyll concentrations throughout the bay are relatively low, and support 

healthy seagrass communities. FDEP therefore recommends setting numeric nutrient criteria at current 

(2000–09) levels. 

Based on FDEP Impaired Surface Waters Rule (IWR) data, and supporting historical and current data, 

FDEP recommends numeric nutrient criteria for TN, TP, and chlorophyll a. An explanation of the 

technical approach, along with the numeric criteria, are given in the Numeric Nutrient Criteria 

Recommendations section of this report. 
Draft 2 July 2010

Table 1a. Checklist of nutrient enrichment symptoms in St. Andrew Bay -= Empty cell/no data; N/A = Not available 

Response Variable Observed 

Historically?

Observed 

Currently? 

Explanation Source

Low dissolved oxygen 

(DO) (hypoxia/anoxia)

No No No reports of low DO. - 

Reduced clarity No West Bay System is clear, salinities approach those of the Gulf, and there 

is little freshwater input or turbidity, except for West Bay.

Conmy 2010

Increased chlorophyll a

concentrations

No No Chlorophyll a concentrations are low throughout the bay. STORET (IWR) data 2000–09 

Phytoplankton blooms 

(nuisance or toxic)

No Episodic Episodic Karenia brevis blooms in 1999–2000, 2003, 2005, and 

2007, with origins outside the bay.

Florida Fish and Wildlife Conservation 

Commission (FWCC) Fish and Wildlife 

Research Institute (FWRI) 

http://research.myfwc.com/features/

Problematic epiphyte 

growth 

No West Bay Epiphyte growth in West Bay Bowl area higher than in West Bay 

Arm.

Fitzhugh 2010a 

Problematic macroalgal 

growth

No No No problematic macroalgal growth has been reported for the 

system. 

- 

Submerged aquatic 

vegetation (SAV) 

community changes or 

loss

Yes No, except for 

West Bay 

“Bowl” 

SAV coverage has been increasing (14% from 1992 to 2003) 

after an 8% decline from 1953 to 1992. Coverage has increased 

in West Bay, but not in the West Bay “Bowl,” potentially due to 

historical physical disturbance.

Brim and Handley 2002; 

Handley and Fitzhugh 2010b 

Emergent vegetation 

community changes or 

loss 

No No None reported. - 

Coral/hardbottom 

community changes or 

loss 

N/A N/A - - 

Impacts to benthic 

community

No No None reported. - 

Fish kills Yes Episodic Primarily related to Karenia brevis blooms. FWRI 

http://research.myfwc.com/fishkill/
Draft 3 July 2010

Table 1b. Checklist of additional environmental factors in St. Andrew Bay. 

Factors Observed? Explanation Source

Increased nutrient loading or 

concentrations from historical levels

No Historical levels are not well documented, but current concentrations from 

multiple datasets (1990s to 2009) are not at levels indicating impairment. 

STORET (IWR) data; 

Hydroqual, St. Andrew Bay 

Resource Management 

Association (SAB-RMA) 

data

Mitigating factors that could prevent 

nutrient expression

Yes Turbidity, color Hydroqual 2010

Other significant stressors to biological 

communities

Yes Physical factors such as scarring from boat propellers, historical aquaculture 

in West Bay, poor flushing, sedimentation and turbidity from anthropogenic 

activities. 

Sargent, et. al 1995; 

Brim and Handley 2002

Natural episodic events contributing to 

nutrient regime (e.g., seasonal or 

hydrologically driven)

Yes No major riverine inputs, but system is impacted by hurricanes, tropical 

storms, winter storms. 

Fitzhugh 2010b 
Draft 4 July 2010

Geographic and Physical Description

St. Andrew Bay is a high-salinity estuarine system located in the Panhandle of Florida in the Gulf Coastal 

Lowlands physiographic region. The estuary is situated almost entirely within Bay County in northwest 

Florida (Figure 1). The St. Andrew Bay watershed lies entirely within northwest Florida, encompassing 

approximately 750,000 acres in Bay, Gulf, Jackson, Calhoun, Washington, and Walton Counties 

(Northwest Florida Water Management District [NWFWMD] 2000). 

Panama City is the primary municipality surrounding the bay. Tourism and the military are the primary 

industries adjacent to the St. Andrew system, although much of Bay County is rural and supports 

silviculture. Other industries include Smurfit-Stone Container Co., Arizona Chemical, Port of Panama 

City, the Panama City-Bay County International Airport, and the Northwest Florida Beaches International 

Airport (which opened in 2010). Publicly owned, protected lands in the watershed include Camp Helen 

State Park, St. Andrews State Park, and St. Andrews Aquatic Preserve (FDEP, Coastal and Aquatic 

Managed Areas [CAMA] website, 2010). 

The St. Andrew Bay system is made up of four hydrologically linked bays—West Bay, North Bay, East 

Bay, and St. Andrew Bay proper—with a combined area of approximately 243 square kilometers 

(km2)(Figure 2). St. Andrew Sound is an adjacent coastal lagoon, although not directly connected to St. 

Andrew Bay. St. Andrew Bay is connected to the Gulf of Mexico through the man-made and maintained 

west pass and the intermittent east pass, and branches inland into the East, North, and West segments. 

The mean depth is 4 meters (m), with a maximum depth of 12 m (Conmy 2010) (Figure 3). Because of 

the depth and minimal tidal range, and the lack of major freshwater input, the bay is relatively poorly 

flushed. 

There are no major riverine inputs to St. Andrew Bay, but minor sources of freshwater inflow include 

Econfina Creek, Deer Point Lake Reservoir (the primary source of drinking water for Bay County), the 

GIWW, and smaller creeks and bayous. These sources have a combined total discharge of less than 28.3

m3/s (Handley et al. 2007). The small volume of freshwater input is responsible for minimal sediment 

loading (Brim 1998). The low sediment load results in low turbidity and very clear waters, which in turn 

support extensive seagrass beds. Other factors that contribute to the bay’s clarity are its spring-fed 

tributaries, low amounts of silty clay in local soils, and the filtering effect of the seagrasses and marshes. 

Salinities are high, and often exceed 30 ppt (Brim 1998). As a result of the low freshwater inflow, deep 

basin, and strong influence of Gulf of Mexico water, the St. Andrew Bay system is described as a deep, 

clear, high-salinity system (Keppner and Keppner 2001). Table 2 lists the physical characteristics of the 

St. Andrew Bay system. The St. Andrew bay system is biologically diverse and supports a large number of 

rare, endemic, and protected plants and animals. Seagrass species are important foundation species in 

the system and provide a host of ecosystem services. Economically important fisheries depend on the 

seagrass beds. 
Draft 5 July 2010

Figure 1. Location of St. Andrew Bay, and geographic features (NWFWMD, 2000). 
Draft 6 July 2010

Figure 2. Location and delineation of the hydrologically linked segments of St. Andrew Bay. 
Draft 7 July 2010

Table 2. St. Andrew Bay physical characteristics. 

Physical Characteristic Values Source

Estuarine surface area (km2) 243 km2 Conmy 2010

Watershed area (km2) 2,800 km2 Conmy 2010

Mean depth (m) 4m (up to 12 m) Conmy 2010 

Tidal range (m) 0.67m (spring) 

0.06m (neap)

Brim and Handley 2002

Mean water residence time 

(days)

Ranges 35 (SAB) to 98 

(West Bay) days (1%)

Hydroqual 2010

Salinity and salinity zones 31 (average) Conmy 2010 

Figure 3. Bathymetric map of St. Andrew Bay system (Conmy 2010). 

Sources of Nutrients 

Sources of nutrients to the St. Andrew Bay system include freshwater inflows (Econfina Creek, Deer 

Point Reservoir, and GIWW), point source discharges (primarily wastewater treatment facilities), 

nonpoint source inputs (septic tanks, stormwater from urban and agricultural areas), natural inputs 

(plant leaf litter), and atmospheric deposition. 

Twenty-one point source facilities discharge domestic and industrial wastewater directly into surface 

waters in the St. Andrew Bay watershed. An additional 23 facilities discharge to sprayfields, percolation 

ponds, and other nonsurface water areas. Figures 4 and 5 show the location of direct and indirect 

discharges in the St. Andrew Bay planning unit (of the Choctawhatchee-St. Andrew Basin). In 1999, Bay 

County built an advanced wastewater treatment plant that eliminated 5 small point source discharges. 

This facility uses reclaimed water for upland irrigation. The current Panama City Beach surface water 

discharge (discharge is to West Bay) is scheduled to be removed before December 31, 2010. The 

discharge will be redirected to an upland disposal site on the west side of State Road 79. Anthropogenic 
Draft 8 July 2010

nonpoint sources of nutrients include septic tanks and stormwater runoff. Septic systems in waterfront 

areas, even when functioning properly, may contribute nutrients to the bay through ground water 

(Knight and Wallman 2007). While septic systems are a source of anthropogenic nitrogen and 

phosphorus to St. Andrew Bay, routine water quality monitoring by FDEP and other data collectors 

indicates that concentrations of nutrients and chlorophyll a are not elevated , and are not causing 

adverse impacts to biological communities in the system (see the Water Quality Studies section). 

Stormwater enters the system through rainfall-driven runoff and has the potential to contribute 

anthropogenic and natural sources of nutrients to the St. Andrew Bay system. The land uses of the St. 

Andrew Bay watershed are largely upland forest (including silviculture) (53%) and water and wetlands 

(30%) (Figure 6). Approximately 8% of the land use is urban, most of which is the greater Panama City 

area adjacent to the bay. Five percent of the land use in the watershed is agriculture and rangeland. 

Stormwater runoff, particularly from the highly developed urban areas around the bay, is considered a 

potential threat to water quality in St. Andrew Bay, but there is no evidence that current inputs from 

stormwater result in elevated nutrient concentrations or chlorophyll in the bay. Estimates of natural 

sources of nutrient inputs such as leaf litter remain unquantified. 

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

Program’s National Trends Network (NADP-NTN), which has a collection site in the Panhandle (FL23, in 

Sumatra, Florida). Based on data for the most recently reported year (2008), estimates for atmospheric 

loading of nitrogen ammonia (NH4) and nitrate (NO3) for St. Andrew Bay are 0.96 and 7.11 kilograms per 

hectare per year (kg/ha/yr), respectively. 
Draft 9 July 2010

Figures 4 and 5. Location of point source discharges in western (top) and eastern(bottom) portions of 

the St. Andrew Bay Planning Unit. 
Draft 10 July 2010

Figure 6. Land use and land cover map and area calculation in the St. Andrew Bay watershed (Conmy 

2010). 

Biological Summary 

Seagrass as the Key Biological Endpoint for St. Andrew 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; FDEP 2009). Seagrasses enhance sediment stability, decrease wave energy, increase water 

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

and McRoy 1980; McRoy and Helfferich 1977; Zieman and Zieman 1989). 
Draft 11 July 2010

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

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

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

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

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

conditions (Orth et al. 2006). 

Seagrasses 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 the excess 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. “Top-down” food web effects must also be considered. In controlled, 

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

(amphipods, caridean shrimp, gastropods, 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 St. 

Andrew Bay. 

Nearly 20,000 acres of seagrasses extend through the St. Andrew Bay system, the largest stock in the 

Panhandle. The seagrass communities in the St. Andrew Bay system are essential for the commercially 

and recreationally important bay scallop, blue crab, penaeid shrimp, spotted seatrout, mullet, and 

redfish (NWFWMD 2000). Turtle grass (Thalassia testudinum) is the dominant seagrass species and 

provides the most habitat in St. Andrew Bay. This subtidal species grows to depths of 1.8 to 2.4 m in St. 

Andrew Bay proper and in St. Andrew Sound. Light attenuation appears to limit maximum growth 

depths to 1.2 to 1.8 m in the interior bay segments. There are also extensive beds of manatee grass 

(Syringodium filiforme) and shoal grass (Halodule wrightii). Manatee grass is found within turtle grass 

beds, or less often in pure stands near the influence of clear, highly saline water entering the bay from 

the Gulf (Brim and Handley 2002). 

Shoal grass is a pioneer species that dominates the shallow and intertidal bay areas. These beds can be 

exposed to the air in winter when north winds push large amounts of water from the bay, and in spring 

when north winds combine with low spring tides (Brim and Handley 2002). Wigeon grass (Ruppia 

maritima) occurs in some of the fresher parts of the bay, including some bayous. Star grass and paddle 

grass (Halophila spp.) have been noted on rare occasions within turtle grass beds in the south part of St. 

Andrew Bay (Brim and Handley 2002). 

Historical Trends and Current Status of Seagrass Coverage 

The U.S. Geological Survey (USGS) produced a series of historical seagrass maps, which the U.S. Fish and 

Wildlife Service (USFWS) used to analyze SAV coverage trends for St. Andrew Bay. These maps were 

created from black-and-white aerial photographs taken in 1953 and 1964, and from color aerial 

photography taken in 1980. Note that these photographs were taken at various scales and that no 

“groundtruthing” took place to verify the relationship between the images and actual seagrass 

coverage, leading to a degree of inherent error in this analysis. Table 3 shows the results of the 

historical trends analysis. The estimate of overall seagrass loss from 1953 to 1992 was 8% (Brim and 

Handley 2002). 
Draft 12 July 2010

To document the more recent and current status of seagrass coverage in St. Andrew Bay, the USGS used 

1992 and 2003 color aerial photography, and strict photointerpretation and digitization standards. 

Other important aspects of the protocol included groundtruthing, quality control, and peer review (Brim 

and Handley 2002). Because the most recent effort in 2003 repeated the same imaging, mapping, and 

groundtruthing techniques as the 1992 study, the results of these 2 years are more comparable and 

reliable than the historical trends data. Based on this analysis, there was an overall baywide increase in 

seagrass coverage of approximately 14 % from 1992 to 2003, and all regions of the bay experienced 

increases in coverage (Table 4). Although seagrass coverage increased in all regions of the bay, including

West Bay, seagrass recovery was not observed in the subregion of the West Bay “Bowl.” Total seagrass 

overage in 2003 was comparable to 1953 (11,232 acres versus 11,848, respectively, although continuous 

coverage was greater in 2003, and patchy coverage less, than in 1953) (Figure 7). 

Figure 7. St. Andrew Bay seagrass coverage trends, 1953 and 2003 (FDEP 2010). Trends were 

analyzed using aerial photography (black and white, 1:20K scale: 1953, 1964) (color, 1:24K scale: 1980, 

1992, 2003). 
Draft 13 July 2010

Table 3. Seagrass coverage for the entire St. Andrew Bay study area (includes East Bay, North Bay, St. 

Andrew Sound, St. Andrew Bay, and West Bay), USGS–U.S. Department of Agriculture (USDA) National 

Wildlife Research Center (NWRC) mapping. 

Coverage 1953 1964 1980 1992 2003

Continuous 3,773 5,394 5,688 4,225 6,429

Patchy 8,075 6,234 4,500 5,607 4,803

Total 11,848 11,629 10,190 9,832 11,232
Draft 14 July 2010

Table 4. Estimates of seagrass acreage in St. Andrew Bay, 1992–2003, from USGS-NWRC mapping of 

seagrass coverage in northern Gulf of Mexico (Fitzhugh 2010b). - = Empty cell/no data

- East Bay North 

Bay

St 

Andrew

Sound

St 

Andrew

Bay

West 

Bay

Total

2003 - - - - - -

Continuous 960 1,638 247 1,862 1722 6,429

Patchy seagrass 1,763 338 690 1,197 815 4,803

All seagrass 2,724 1,975 937 3,060 2,537 11,232

1992 - - - - - - 

Continuous 1,631 988 54 1,324 227 4,224

Patchy seagrass 890 877 857 1,258 1,725 5,607

All seagrass 2,520 1,866 912 2,582 1,952 9,832

% change 1992–2003 +8.1% +5.9% +2.7% +18.5% +30.0% +14.2%

Scallops 

Seagrass beds are essential habitat for the bay scallop (Argopecten irradians). Juveniles attach to grass 

blades as they make their transition from planktonic larvae to adults. They live elevated in the canopy 

for 1 to 2 months until they grow larger and actively “swim.” As in all estuaries and coastal waters that 

support scallops in Florida, populations fluctuate greatly in St. Andrew Bay. Because bay scallops are an 

annual species, local populations exhibit extreme variability and periodically collapse due to natural 

events such as salinity fluctuations. Bay scallops are distributed in the St. Andrew Bay system primarily 

in St. Andrew Bay proper. 

The FWRI Molluscan Fisheries Program surveys adult populations of the bay scallop on the west coast of 

Florida from Pine Island Sound to St. Andrew Bay (Table 5). The primary objective of these surveys is to 

assess changes in scallop population abundance that may occur in response to management and 

restoration efforts begun in Florida in 1994 (Arnold et al. 2008). The program also monitors recruitment 

and reports on restoration activities. 

A current snapshot of the adult scallop populations and spat recruitment in St. Andrew Bay in the past 2 

seasons is summarized below. This summary illustrates the fluctuations that characterize scallop 

populations. St. Andrew Bay adult scallop abundance decreased in 2008 and continued to be classified 

as “collapsed.” Scallops were recorded at 11 of 20 survey stations, but at no site were they abundant. 

New individuals to the scallop population were estimated using spat collectors. At the 10 St. Andrew 

Bay stations, scallop recruits were recorded during each retrieval event in 2008, with a peak in March 

and then again in November through December. Of the 90 collectors deployed in 2008, 9 (10.0%) were 

not retrieved, 11 (12.2%) retrieved had 0 scallops, 50 (55.6%) had bay scallops, and 5 (5.6%) had calico 

scallops. Other Pectinid species were observed on the collectors deployed at this site during 2008, 

including Ravenel’s (Pecten raveneli) and Rough (Aequipecten muscosus) scallops.
Draft 15 July 2010

Table 5. Adult bay scallop density at each of 13 stations sampled at the St. Andrew Bay study site

during each June from 1994 through 2006, and for those same 13 stations plus an additional 7 stations 

added for the 2007–08 survey. Scallop density at each station is reported per 600 square meter (m2

) 

transect. The results of the Waller-Duncan (W.D.) comparison of means (letters) are presented with 

the population means only for the original 13 sample stations for which the experimental design was 

balanced; similar letters denote averages that were not different at a significance level of 0.05. ‘Z’ 

indicates that the station was not sampled during that year. Note that the mean and standard 

deviation for 2007 and 2008 presented in the table are calculated from the original 13 stations only.

St. Andrew Bay scallop abundance increased in 2009, reaching a healthy status (>25 scallops/600m2) for 

the first time in 13 years. Scallops were recorded at 13 of the 20 survey stations, with no scallops found 

in the north end of the bay. Of the 261 scallops measured in 2009, shell heights during the June 

sampling effort ranged from 14 to 69 (millimeters [mm]), the average was 45.5 mm, and the most 

frequent shell heights recorded were 45 and 48 mm. Even though the population status reached a 

healthy level, it is not a resilient population, and restoration efforts will continue in this estuary. 

Recruitment monitoring occurred at 10 stations in the St. Andrew Bay area in 2009. Of the 110 

collectors deployed in 2009, 102 were recovered and processed. Of those 102 collectors, spat were 

present on 79 (77.5%, which was the highest rate of monitored sites statewide in 2009). The total spat 

observed at this site in 2009 was 2,639, the average was 25.9 per collector, and the maximum number 

found on a single collector was 235. 
Draft 16 July 2010

The relationship between scallop populations and nutrient inputs is complex, and very limited data exist 

to address the issue. Because they are filter-feeders of phytoplankton, and phytoplankton production is 

driven by nitrogen and phosphorus, some level of nutrient inputs is necessary to maintain healthy 

populations of all bivalves, including scallops (Geiger, pers. comm. 2010). The optimal level has not 

been quantified and is likely to be variable among areas due to differences in hydrologic conditions, 

nutrient cycling, and habitat. Nutrient loadings that lead to excessive eutrophication are harmful to 

scallops if they are associated with low DO and seagrass loss (Geiger, pers. comm. 2010). 

One plausible, yet untested, hypothesis about nutrient effects on scallops or other bivalves is that as 

nutrient levels rise, the phytoplankton community shifts from one dominated by diatoms to a 

dinoflagellate-dominated community. This shift would decrease the abundance of phytoplankton of the 

correct form and size for the bivalves to filter (Geiger, pers. comm. 2010). 

Despite the limited information on the effects of nutrients on scallops, it is clear that the relatively low 

nutrient concentrations and chlorophyll a values in St. Andrew Bay would not limit scallop populations. 

Other Key Habitats and Biological Resources 

The St. Andrew Bay system is one of the most diverse ecosystems in North America, rivaling Florida’s

Indian River Lagoon, which is characterized as the most biologically diverse estuary in the United States 

(Brim and Handley 2002). The estuary supports approximately 3,643 species of fish, birds, mammals, 

reptiles, and shellfish, including a significant number of rare, endemic, and protected species (Table 6). 

St. Andrew Bay also supports a number of commercially important fish and shellfish species, including 

Spanish mackerel, king mackerel, spotted sea trout, mullet, grouper, pompano, flounder, shrimp, blue 

crab, and scallops (FDEP CAMA website, 2010). 

Key recreational uses include fishing, swimming, snorkeling, diving, canoeing, kayaking, bird-watching, 

and other tourism-related activities. 
Draft 17 July 2010

Table 6. Rare/endangered species in the St. Andrew Bay system. - = Empty cell/no data

State listings are taken from the FWCC; federal listings are taken from the USFWS. 

E = Endangered; T = Threatened; T (s/a) = Threatened due to similarity in appearance; SSC = Species of Special Concern; N/A= information not 

available or no designation listed

Common Name Scientific Name State Federal

Fish - - - 

Gulf sturgeon Acipenser oxyrhynchus SSC N/A

Salt marsh topminnow Fundulus jenkinsi SSC N/A

Reptiles - - - 

American alligator Alligator mississipiensis SSC T (s/a)

Atlantic loggerhead turtle Caretta caretta caretta T T 

Atlantic green turtle Chelonia mydas mydas E E 

Kemp's ridley sea turtle Lepidochelys kempi E E 

Birds - - - 

Southeastern snowy plover Charadrius alexandrinus tenuirostris T N/A

Piping plover Charadrius melodus T T 

Arctic peregrine falcon Falco peregrinus tundrius E T 

American oystercatcher Haematopus palliatus SSC N/A

Bald eagle Haliaeetus leucocephalus T T 

Brown pelican Pelecanus occidentalis SSC N/A

Least tern Sterna antillarum T N/A

Mammals - - - 

Choctawhatchee beach mouse Peromystus polionotus allophrys E E 

Florida manatee Trichechus manatus E E 

Water Quality Studies 

FDEP Water Quality Analyses 

FDEP analyzed a dataset retrieved from STORET for the IWR for an assessment of St. Andrew Bay. Data 

were collected from January 2000 to December 2009, and the spatial scale covered the entire bay 

system (all segments with waterbody identification [WBID] numbers characterized as “estuary”). For 

the IWR data, all stations were combined, and annual geometric means were calculated for total 

phosphorus (TP), total nitrogen (TN), and chlorophyll a. Figures 8 through 10 show the distribution of

the baywide geometric means and the long-term geometric means for each parameter. Annual 

geometric means for TP were low, ranging from 12.1 to 24.8 μg/L, with a long term geometric mean of 

15.5 μg/L. Annual geometric means for TN fluctuated, but were overall relatively low, ranging from 

277.4 to 561.4 μg/L, with a long-term geometric mean of 403.64 μg/L. Chlorophyll a concentrations 

were low, with annual geometric means ranging from 1.9 to 4.5 micrograms per liter (μg/L) and 

displaying a decreasing trend after 2003. The long term geometric mean was 2.8 μg/L. It is important to 

note that approximately one-third 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).

In an additional analysis, FDEP grouped stations into the following segments: West Bay, North Bay, St. 

Andrew Bay, East Bay, and Grand Lagoon. These regions are commonly used geographic delineations in 
Draft 18 July 2010

water quality and biological studies of the system. Figures 11 through 13 show the results of a 

comparison of trends in the geometric means among the various bay segments from 2000 to 2009 for 

TP, TN, and chlorophyll a. Geometric means for TP, TN, and chlorophyll a track relatively closely for each 

of the bay segments over the 10 year period, with the exception of North Bay, which has spikes for TP 

and TN in 2003 and 2007, and a spike in 2003 for chlorophyll. Data for North Bay also were limited, and 

were not sufficient to calculate geometric means for 6 out of the 10 years of record. 

FDEP also analyzed a dissolved oxygen (DO) dataset from STORET, collected from 1967-2010. For 

analysis, these data were separated into an historic (1967-1999) and a recent (2000-2010) period. A 

summary of the DO data is shown in Table 7.

Table 7. Summary of St. Andrew Bay system dissolved oxygen (DO) data

Mg/L = Milligrams per liter

2000-2010 1967-1999

Segment N Percent 

less than 

5mg/L

Percent 

less than 

4 mg/L

Mean 

(mg/L)

N Percent 

less than 

5mg/L

Percent 

less than 

4 mg/L

Mean

(mg/L)

St. Andrew Bay 666 17% 9% 6.85 2053 17% 10% 6.75

East Bay 3769 22% 10% 6.72 6192 9% 5% 7.23

Grand Lagoon 188 13% 6% 7.01 262 15% 6% 6.74

Mouth 181 7% 3% 7.24 278 18% 11% 6.58

North Bay 2716 24% 12% 6.34 3872 8% 4% 7.18

West Bay 3094 18% 7% 6.72 2707 6% 3% 7.39

To determine if there were localized adverse water quality impacts in the West Bay “Bowl,” an area with 

extensive historical seagrass loss and little recovery, FDEP also divided West Bay into the West Bay 

“Bowl” and the West Bay “Arm,” and compared TN and TP over the same 10-year sampling period. 

Figures 14 and 15 show the results of this comparison. Annual geometric means of TN for the 2 areas 

tracked very closely over the entire sampling period. TP did not track as closely, but the overall trend 

was similar, and the differences in mean values were small (a maximum of 10 μg/L). Based on these 

results, FDEP concluded that it is appropriate to group the West Bay “Bowl” and “Arm” stations.
Draft 19 July 2010

Figure 8. Trend of annual geometric means of TP in the St. Andrew Bay system and the long-term 

geometric mean for the sampling period. 

Figure 9. Trend of annual geometric means of TN in the St. Andrew Bay system and the long-term 

geometric mean for the sampling period. 

0

5

10

15

20

25

30

1995 2000 2005 2010

TP μg/L

St. Andrew Bay Geometric Mean Total Phosphorus 

annual geo mean 

long term geo mean 

0

100

200

300

400

500

600

1998 2000 2002 2004 2006 2008 2010

TN μg/L

St. Andrew Bay Geometric Mean Total Nitrogen 

annual geo mean TN 

Baywide 

long term geo mean 

TN
Draft 20 July 2010

Figure 10. Trend of annual geometric means of chlorophyll a in the St. Andrew Bay system and the 

long-term geometric mean for the sampling period. 

Figure 11. Comparison of geometric means of TP among bay segments.

0

0.5

1

1.5

2

2.5

3

3.5

4

4.5

5

1998 2000 2002 2004 2006 2008 2010

Chlorophyll a μg/L

St. Andrew Bay 

Geometric Mean Chl a

St. Andrew Bay 

Geometric Mean Chl a

long term geo mean 

0

5

10

15

20

25

30

35

40

45

50

1998 2000 2002 2004 2006 2008 2010

TP μg/L

St. Andrew Bay System Total Phosphorus 

SAB

West Bay

North Bay 

East Bay

Baywide

Grand Lagoon TP 
Draft 21 July 2010

Figure 12. Comparison of geometric means of TN among bay segments.

Figure 13. Comparison of geometric means of chlorophyll a among bay segments. 

0

100

200

300

400

500

600

700

800

900

1998 2000 2002 2004 2006 2008 2010

TN μg/L

St. Andrew Bay System Total Nitrogen 

SAB TN

West Bay TN 

North Bay TN

East Bay TN

Baywide TN 

Grand Lagoon TN

0

2

4

6

8

10

12

1998 2000 2002 2004 2006 2008 2010

Chlorophyll a μg/L

St. Andrew Bay System Chlorophyll a 

SAB Chl a 

West Bay Chl a 

North Bay Chl a

East Bay Chl a 

Baywide Chl a 

Grand Lagoon Chl a
Draft 22 July 2010

Figure 14. Comparison between West Bay segments of annual geometric means of TN. 

Figure 15. Comparison between West Bay segments of annual geometric means of TP. 

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

2000 2002 2004 2006 2008 2010

TN μg/L

West Bay "Arm" vs. "Bowl" Total Nitrogen

ARM geo mean TN

BOWL geo mean TN 

0

0.005

0.01

0.015

0.02

0.025

2000 2002 2004 2006 2008 2010

TP μg/L 

West Bay "Arm" vs. "Bowl" Total Phosphorus

ARM geo mean TP

BOWL geo mean TP 
Draft 23 July 2010

Water Quality Analysis and Development of a Nutrient Criteria Approach Based on a Light Extinction 

Coefficient (Ke) (Hydroqual)

Hydroqual, Inc., used data available from the IWR database and STORET from 1990 to 2008 to 

investigate the relationships between TN, TP, chlorophyll a, color, and Secchi depth in West Bay (Table 

8). In addition, a light extinction coefficient, Ke, was calculated using Secchi depth and an empirically 

derived constant (1.7). Data were analyzed to determine what relationships exist between parameters 

and how the various parameters affect light extinction. In addition, Hydroqual assessed the existing 

seagrass coverage and the water depths associated with the seagrass beds to determinate the water 

depth where seagrasses can grow in the bay. Chlorophyll a and various nutrient parameters were 

strongly correlated, except for nitrate/nitrite (NO2+NO3) (Figure 16). 

Hydroqual noted that these relationships could be used to determine bay nutrient levels for a given 

target chlorophyll a level. For example, if the historic minimum level of 5.54 μg/L were used as a target 

(the Impaired Waters Rule uses the historic minimum value as one of the impairment thresholds for 

estuaries), the resulting TN and TP concentrations would be 355 and 21 μg/L, respectively. These 

nutrient concentrations are similar to the existing levels in West Bay. (The FDEP IWR long term 

geometric means were 407 μg/L TN and 15 μg/L TP, and Hydroqual arithmetic means were 378 μg/L and

19 μg/L.) Hydroqual found no correlation between chlorophyll a and salinity over a range of 5 to 35 

ppt, which may indicate that freshwater sources of nutrients do not contribute significantly to 

chlorophyll a levels in West Bay. Figure 17 presents the observed relationships between light extinction 

and chlorophyll a, color, turbidity, and salinity. All relationships show a positive trend, with the 

strongest for chlorophyll a and turbidity. 

Hydroqual also used multiple linear regression to determine the relationship between light extinction 

and chlorophyll a and color. Based on this relationship, existing algal productivity is not limiting seagrass 

productivity in the bay. For example, using this equation and light extinction coefficients for a 1.5 m 

water depth (the average maximum water depth to which seagrasses extend is 1.3 m), and an average 

color of 28.9 platinum-cobalt units (PCU), the resulting chlorophyll a values providing between 15% to 

25% bottom light range from 8 to 20 μg/L, which is much higher than existing levels. In addition, the 

contribution of chlorophyll a to the total light extinction coefficient is small. At 5.54 μg/L chlorophyll a, 

the contribution is approximately 17%. Existing water column transparency as a function of chlorophyll 

a, color, and background conditions at this water depth, is sufficient to provide 15% to 25% of surface 

PAR at the bottom light for seagrass survival and growth in West Bay. The percentage of surface light 

required for seagrass growth varies depending on individual species requirements, epiphyte coverage, 

and site specific conditions, but typically ranges between 15 and 25% (Dixon, 2000)(Steward, et. al, 

1995). 

Table 8. Summary of West Bay water quality data, 1991–2008 (Hydroqual 2010) - = Empty cell/no data

Mg/L = Milligrams per liter

PCU = Platinum Cobalt Unit

Year Chlorophyll a

(μg/L)

TN 

(mg/L)

TP 

(mg/L)

Color 

(PCU)

Secchi 

Depth 

(m)

Light 

Extinction

Ke (1/m)

1991 5.00 0.394 0.015 - 1.95 0.87

1992 3.85 0.269 0.015 - 1.95 0.87

1993 3.50 0.319 0.014 - 1.67 1.02

1994 3.71 0.268 0.021 - 1.62 1.05

1995 2.77 0.279 0.015 23.8 2.31 0.74
Draft 24 July 2010

1996 4.88 - 0.028 31.3 1.90 0.90

1997 4.07 0.292 0.017 20.0 2.90 0.59

1998 4.28 0.417 0.022 36.0 1.56 1.09

1999 3.54 0.300 0.017 - 2.25 0.76

2000 4.93 0.275 0.019 - 1.93 0.88

2001 6.55 0.366 0.028 30.0 1.51 1.13

2002 5.08 0.344 0.019 26.3 2.03 0.84

2003 5.89 0.409 0.02 42.9 2.22 0.77

2004 4.79 0.355 0.017 30.0 2.74 0.62

2005 4.88 0.425 0.013 38.3 2.91 0.58

2006 5.22 0.563 0.015 22.5 3.04 0.56

2007 5.75 0.557 0.019 21.1 1.08 1.58

2008 4.09 0.602 0.022 24.7 - - 

Average 4.60 0.378 0.019 28.9 2.09 0.87

 
Draft 25 July 2010

Figure 16. Chlorophyll a relationships in West Bay (Hydroqual 2010). 
Draft 26 July 2010

Figure 17. Light extinction coefficient (Ke) relationships in West Bay (Hydroqual 2010). 
Draft 27 July 2010

Water Quality Monitoring by SAB-RMA (in partnership with the University of Florida [UF] Baywatch 

Program) 

SAB-RMA, in partnership with the UF Baywatch Program, has routinely sampled water quality in the St. 

Andrew Bay system since 1990. Tables 9 through 11 summarize TN, TP, and chlorophyll a (uncorrected) 

data in the St. Andrew Bay system from 1990 to 2006. Total nitrogen (TN) concentrations are relatively 

low, with median values between 210 and 290 μg/L for each of the segments and a range of 50-1,000 

μg/L, except for Grand Lagoon, with a median concentration of 410 μg/L , and a range of 110-1,450 

μg/L. Total phosphorus (TP) concentrations are also low, with median values between 12 and 17 μg/L 

for all of the segments, and a range of 3-390 μg/L, except for Grand Lagoon, with a median 

concentration of 28 μg/L , and a range of 4-350 μg/L. Chlorophyll a concentrations are also low, with 

medians between 2 and 4 μg/L, and a range of 0-18 μg/L for all segments except Grand Lagoon, with a 

median of 5, and a range of 0-80 μg/L. 

Table 9. Summary of TN data for the St. Andrew Bay system from SAB-RMA/UF Baywatch water 

quality monitoring program, 1990–2006. 

TN Number of 

samples

Mean/Median

(μg/L)

Standard 

Deviation

(μg/L)

Range (μg/L)

West Bay “Bowl” 103 312/290 119 50-690

West Bay “Arm” 314 269/250 95 40-590

St. Andrew Bay 460 236/210 118 60-1,000

Grand Lagoon 436 458/410 215 110-1,450

Table 10. Summary of TP data for the St. Andrew Bay system from SAB-RMA/UF Baywatch water 

quality monitoring program, 1990-2006. 

TP Number of 

samples

Mean/Median

(μg/L)

Standard 

Deviation

(μg/L)

Range

(μg/L)

West Bay “Bowl” 103 21.5/17 14.5 8-138

West Bay “Arm” 315 14.6/13 5.3 3-45

St. Andrew Bay 464 16.3/12 27.5 3-390

Grand Lagoon 437 35.8/28 30 4-350

Table 11. Summary of (uncorrected) chlorophyll a data for the St. Andrew Bay system from SABRMA/UF Baywatch water quality monitoring program, 1990–2006. 

Chlorophyll a Number of 

samples

Mean/Median

(μg/L)

Standard 

Deviation

(μg/L)

Range

(μg/L)

West Bay “Bowl” 104 4.7/4 2.8 1-17

West Bay ”Arm” 316 3.7/3 2.5 1-17

St. Andrew Bay 488 2.6/2 2 0-18

Grand Lagoon 442 8.3/5 9.4 0-80
Draft 28 July 2010

Waters on the 303(d) List 

Waterbodies within the St. Andrew Bay Planning Unit that are listed for nutrient or DO impairments are 

shown in Table 12. These impairment listings are from an integrated assessment (Cycles 1 and 2)

verified list. Table 13 shows waters proposed for delisting. In the St. Andrew Bay Planning Unit, waters 

are also listed as impaired for the following parameters: mercury (in fish tissue), bacteria, and fecal 

coliform bacteria. 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 the U.S. Environmental Protection Agency’s (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). 

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 

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 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).
Draft 29 July 2010

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.” 

Table 12. Waterbodies in the St. Andrew Bay Planning Unit that are on the 2010 Integrated 

Assessment (Cycles 1 and 2) verified list for impairments for either nutrients or DO (FDEP 2010a). 

*Note that these waterbodies are tributaries to the bay, not segments of the bay. 

Waterbody Name Type WBID Impairment(s)

Direct Runoff to Bay Stream* 1060 DO (nutrients and biochemical oxygen 

demand [BOD])

(chlorophyll a) 

Little Sandy Creek Stream* 1155 DO (nutrients–nitrogen)

Direct Runoff to Bay Stream* 1184 DO (nutrients and BOD)

(chlorophyll a) 

Parker Creek Stream* 1141A DO (nutrients and BOD) 

Table 13. Waterbodies in the St. Andrew Bay Planning Unit that are proposed for delisting from the 

1998 303(d) list for either nutrients or DO (FDEP 2010b).*Note that these waterbodies are tributaries 

to the bay, not segments of the bay. 

Waterbody Name Type WBID Impairment(s)

Peach Creek Stream* 986 Nutrients (historical chlorophyll a) 

Western Lake Outlet Estuary 1009 Nutrients (historical chlorophyll a) 

Direct Runoff to Bay Estuary 1053 Nutrients (chlorophyll a and historical 

chlorophyll a) 

Parker Bay Estuary 1141 DO and nutrients (chlorophyll a and 

historical chlorophyll a) 

Pitts Bay Estuary 1172 Nutrients (chlorophyll a) 

West Bay Estuary 1061A Nutrients (historical chlorophyll a) 
Draft 30 July 2010

Numeric Nutrient Criteria Recommendations

St. Andrew Bay is fully meeting its Class II designated uses, “shellfish propagation or harvesting,” and 

“recreation, propagation and maintenance of a healthy, well-balanced population of fish and wildlife,” 

indicating that current nutrient levels are fully protective, as follows:

• Seagrasses (the most sensitive biological endpoint) are healthy, and coverage 

increased 14% baywide from 1992 to 2003. 

• Bay scallop populations increased in 2009, attaining “healthy” status. Recruitment 

in 2009 was the strongest of all sites monitored in the state. 

• The estuary supports approximately 3,643 species of fish, birds, mammals, reptiles, 

and shellfish, including a significant number of rare, endemic, and protected species. 

This diversity in St. Andrews Bay rivals that of the Indian River Lagoon (described as 

the most biologically diverse estuary in North America).

There is considerable evidence to demonstrate that existing nutrient levels in St. Andrew Bay are

providing for full aquatic life use support. It should be noted that the West Bay “Bowl” segment 

experienced significant loss of seagrass following predominantly physical disturbance from a 1970s 

aquaculture operation. Although seagrass coverage in West Bay as a whole is now increasing, 

seagrasses have not recovered in the West Bay “Bowl”. However, the current nutrient and chlorophyll a

concentrations in this area should provide for full recovery of seagrasses. FDEP therefore proposes 

nutrient concentration criteria that would maintain the current conditions, as reported from 2000 to 

2009 water quality monitoring data for each segment of the bay. 

Proposed Numeric Nutrient Criteria 

Methodology 

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

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

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

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

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

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

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

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

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

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

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

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

preserve the uses associated with that distribution. 
Draft 31 July 2010

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 St. Andrew Bay is described briefly below. More details concerning the statistical approaches used 

can be found in the document Overview of FDEP Approaches for Nutrient Criteria Development in 

Marine Waters (FDEP 2010).

Magnitude 

The magnitude component can be set at a variety of values based on the frequency and duration that 

will be used to determine compliance. For the “healthy existing conditions” approach, FDEP established 

the magnitude at: a) an adjusted long-term central tendency (geometric mean) of the distribution, 

expressed as a long-term geometric mean never to be exceeded; and b) an annual geometric mean, not 

to be exceeded more than two times over a five- year period. The long-term average condition was 

adjusted to a level that represents an insignificant increase from the baseline. Allowing for an 

insignificant increase accounts for uncertainty in the estimate of the mean and partially addresses the 

fact that the reference based approach fails to identify a threshold of imbalance, and thus is highly 

prone to excessive Type I error. For the purpose of antidegradation evaluations, EPA has established 

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

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

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

long-term dataset for each segment of the waterbody.

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 
Draft 32 July 2010

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. 

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.
Draft 33 July 2010

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

Andrew Bay as well the annual limits for each segment, are provided in Table 14. 

Table 14. Proposed numeric nutrient criteria for all segments of St. Andrew 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 a single station shall not exceed, by segment, 

more than twice in a 5 year period.

N/A=not available. Data did not meet sufficiency requirements for analysis, so criteria not yet proposed for segment

*Baywide analysis did not include Grand Lagoon or Mouth segments 

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)

Central Bay 16.5 18.2 25.6 29.9

East Bay 13.8 15.2 20.1 25.9

Grand Lagoon 14.2 15.6 26.5 36.6

Mouth 9.0 9.9 12.5 13.7

North Bay 11.5 12.7 14.8 16.4

West Bay 16.1 17.7 22.3 26.1

Baywide* 16.1 17.8 22.7 26.4

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 Bay 419 461 626 651

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

Grand Lagoon 407 448 552 569

Mouth 322 354 508 526

North Bay N/A N/A N/A N/A

West Bay 415 456 555 582

Baywide* 415 456 575 626

Chlorophyll a (ug/L)
Draft 34 July 2010

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 Bay 4.6 5.0 5.8 5.8

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

Grand Lagoon 2.5 2.7 3.2 3.4

Mouth 2.1 2.3 3.0 3.0

North Bay N/A N/A N/A N/A

West Bay 3.3 3.6 5.5 6.4

Baywide* 3.5 3.9 5.8 6.1
Draft 35 July 2010

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