Site-Specific Information 

in Support of 

Establishing Numeric Nutrient 

Criteria for St. Joseph Bay

Division of Environmental Assessment and Restoration

Standards and Assessment Section

Florida Department of Environmental Protection

Tallahassee, FL 32399

August 13, 2010 
Draft ii August 2010

Table of Contents 

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

Geographical and Physical Description................................................................................... 3

Sources and Fates of Nutrients .............................................................................................. 6

Biological Summary............................................................................................................... 7

Seagrasses as the Key Biological Response Variable in St. Joseph Bay ..............................................7

Scallops........................................................................................................................................11

Juvenile Fishes and Selected Invertebrates....................................................................................13

Sea Turtles...................................................................................................................................14

2004 Bottlenose Dolphin Mortality Event and the Role of Red Tide (K. brevis) ................................16

Shellfish Harvesting......................................................................................................................17

Waters on the 303(d) List..................................................................................................... 17

Water Quality Studies ......................................................................................................... 18

St. Joseph Bay Aquatic Preserve and Florida LakeWatch/Project COAST Program 

Monitoring...................................................................................................................................18

Water Quality Analyses by FDEP ...................................................................................................23

Numeric Nutrient Criteria Recommendations ...................................................................... 25

Relationship between Anthropogenic Nutrient Inputs and Adverse Biological Effects.....................25

Proposed Nutrient and Chlorophyll Criteria ...................................................................................26

References .......................................................................................................................... 29
Draft iii August 2010

List of Tables

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

Table 1b. Checklist of additional environmental factors for St. Joseph Bay ................................................ 3

Table 2. Physical characteristics of St. Joseph Bay....................................................................................... 5

Table 3. Land use in the St. Joseph Bay Basin, based on FLUCCS................................................................. 6

Table 4. Percentage of sampled quadrats (1 m2) in Braun-Blanquet cover abundance classes.................. 8

Table 5. St. Joseph Bay natural communities (based on Florida Natural Areas Inventory [FNAI] 

classification) and estimated areal coverage (from FDEP 2008)..............................................10

Table 6. Adult bay scallop density at each of 20 stations sampled at the St. Joseph Bay study site, 

1994–2008. Scallop density at each station is reported per 600 m2 transect. Results 

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

population means; the same letters denote averages that were not different at a 

significance level of 0.05...........................................................................................................12

Table 7. Species using shallow seagrass habitat in St. Joseph Bay, 2006–08............................................15

Table 8. Summary of data analysis for St. Joseph Bay, all stations combined (8 stations), 2001–

09. .............................................................................................................................................23

Table 9. Proposed numeric nutrient criteria for St. Joseph 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 exceed the network average more than 

twice in a 5 year period, nor shall an individual station exceed the single station 

average more than twice in a 5 year period.............................................................................28

List of Figures

Figure 1. Bathymetric map of St. Joseph Bay............................................................................................... 4

Figure 2. St. Joseph Bay area Florida Land Use, Cover and Form Classification System (FLUCCS) 

land use map............................................................................................................................... 5

Figure 3. Location of St. Joseph Bay in relation to the larger Apalachicola and St. Andrews Basins............ 7

Figure 4. Frequency of occurrence of seagrass species and bare sand, in sampled quadrats, 

spring 2003–09. ........................................................................................................................10

Figure 5. Location of St. Joseph Bay Aquatic Preserve water quality monitoring sites..............................19

Figure 6. TN concentrations for St. Joseph Bay stations, 2001–09. ...........................................................20

Figure 7. Baywide mean annual TN, 2001–09. ..........................................................................................20

Figure 8. TP concentrations for St. Joseph Bay stations, 2001–09.............................................................21

Figure 9. Baywide mean annual TP, 2001–09............................................................................................21

Figure 10. Chlorophyll a and Secchi depth values for St. Joseph Bay stations, 2001–09...........................22

Figure 11. Baywide mean annual chlorophyll a, 2001–09 .........................................................................22

Figure 12. Geometric mean of TP concentrations for all bay sites, 2001–09, and long-term 

geometric mean of TP...............................................................................................................24

Figure 13. Geometric mean of TN concentrations for all bay sites, 2001–09, and long-term 

geometric mean of TN. .............................................................................................................24
Draft iv August 2010

Figure 14. Geometric mean of chlorophyll a concentrations for all bay sites, 2001–09, and longterm geometric mean of chlorophyll a. ....................................................................................25
Draft 1 August 2010

 

Executive Summary

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

with local scientists, to support the development of site-specific numeric nutrient criteria for St. Joseph 

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. Joseph Bay is a coastal lagoon in Gulf County, Florida, enclosed by the St. Joseph Peninsula. It is the 

only embayment in the northeast Gulf of Mexico having virtually no major freshwater inflows. The bay

is characterized by low-energy current regimes (Heck et al. 2000) and is adjacent to the larger basins of 

St. Andrew Bay to the west and Apalachicola to the east. The bay is approximately 15 miles long, and 6 

miles wide at its widest point. Salinities are high, essentially the same as the Gulf of Mexico. A lack of 

riverine input and sandy sediments contribute to very clear waters, and St. Joseph Bay supports one of 

the densest stocks of seagrass beds in northwest Florida, as well as a high diversity of associated plants 

and animals. Seagrass beds are the most nutrient-sensitive biological community in St. Joseph Bay, and 

seagrass mapping conducted in 1993 and 2006 indicates that seagrass coverages are robust and stable. 

Table 1a provides a checklist of potential nutrient enrichment symptoms in St. Joseph Bay, and Table 1b 

lists additional environmental factors.

Comprehensive studies by FDEP’s Coastal and Aquatic Managed Areas (CAMA) Program concluded that

biological communities in St. Joseph Bay are healthy based on estimated percent coverage of seagrass, 

epiphyte load, canopy height, and associated organisms. The measurements of all of these attributes 

indicate good biological condition.

Nutrient limitation studies (Fourqurean and Cai 2001) have shown that St. Joseph Bay exhibits 

phosphorus (P) limitation, potentially due to the minimal delivery of phosphorus from freshwater 

sources (Johnson et al.2006). 

Because the evidence demonstrates that biological communities in this coastal area are healthy and well 

balanced, the appropriate approach for developing numeric nutrient criteria is to maintain the nutrient

levels within the range of natural variability. 

FDEP proposes criteria for total phosphorus (TP), total nitrogen (TN), and chlorophyll a. The technical 

approach for criteria development and the numeric criteria, are given in the Numeric Nutrient Criteria 

Recommendations section. 
Draft 2 August 2010

 

Table 1a. Checklist of potential nutrient enrichment symptoms in St. Joseph Bay - = Empty cell/no data

N/A = Not applicable 

Response Variable Observed 

Historically?

Observed 

Currently? 

Explanation Source

Low dissolved 

oxygen (DO) 

(hypoxia/anoxia)

No No St. Joseph Bay system is shallow, wellmixed, and open to the Gulf of Mexico FDEP (CAMA) 2009 

Reduced clarity No No Secchi depths over the long-term 

average 7 to 8 feet. 

FDEP(CAMA) 2009

Increased 

chlorophyll a

concentrations

No No Chlorophyll a concentrations are low 

throughout the bay. 

FDEP CAMA/LakeWatch–

Project COAST data (2000–

09)

Phytoplankton 

blooms (nuisance 

or toxic)

Yes Sporadic Episodic Karenia brevis blooms that 

begin in offshore waters and are 

transported inshore by currents

(1999–2000; 2004; 2007).

Florida Fish and Wildlife 

Conservation Commission 

(FWCC) Fish and Wildlife 

Research Institute (FWRI) 

http://research.myfwc.co

m/features/category_main

.asp?id=2309; FDEP 

(CAMA) 2009

Problematic 

epiphyte growth 

No No Qualitative epiphyte assessments, but 

no conclusive results. 

FDEP (CAMA) 2009 

Problematic 

macroalgal growth

No No No problematic macroalgal growth 

has been reported for the system.

-

Submerged 

aquatic vegetation 

(SAV) community 

changes or loss

No No Estimates of SAV coverage vary, but 

areas with SAV are stable. 

Communities dependent on 

seagrasses are characterized as

healthy.

Sargent et al. 1995; 

Florida Environmental 

Research Institute (FERI) 

2006; 

FDEP (CAMA) 2009

Emergent 

vegetation 

community 

changes or loss 

No Yes Unquantified amount of marsh loss 

due to physical disturbance. 

-

Coral/hardbottom 

community 

changes or loss 

N/A N/A - -

Impacts to benthic 

community

No No A 3-year study by CAMA shows a 

diverse, abundant juvenile fish and 

invertebrate community associated

with seagrass. Scallop population is 

healthy. 

FDEP (CAMA) 2009

Fish kills Yes Sporadic Related to K. brevis blooms or 

brevetoxins present in the water 

column when blooms not observed. 

The blooms originate offshore.

FWRI 

http://research.myfwc.co

m/fishkill/
Draft 3 August 2010

 

Table 1b. Checklist of additional environmental factors for St. Joseph Bay - = Empty cell/no data

Factors Observed? Explanation Source

Increased nutrient loading or 

concentrations from historical

levels

No Few historical data to compare with 

current regime. 

-

Mitigating factors that could 

prevent nutrient expression

Yes Grazers were shown to mitigate the 

effects of nutrient enrichment in 

controlled, in situ studies in St. Joseph Bay.

Heck et al. 2000

Other significant stressors to 

biological communities

Yes Physical disturbance to seagrass 

community from boat propellers.

Sargent et al. 1995; 

FDEP (CAMA) 2009

Natural episodic events 

contributing to nutrient regime 

(e.g., seasonal or hydrologically 

driven)

Yes No major freshwater inflows to drive 

nutrient regime, but hurricanes and other 

storms have impacts. 

FDEP (CAMA) 2009

Geographical and Physical Description

St. Joseph Bay is a coastal lagoon in Gulf County, Florida (29.8° N latitude, 85.3° W longitude), semienclosed by the St. Joseph Peninsula. It is the only embayment in the northeast Gulf of Mexico that has

no significant source of freshwater input (Heck et al. 2000). Although the Gulf County Canal connects 

the Gulf Intracoastal Waterway (GIWW) to the bay, and several small creeks and bayous drain into the 

bay, freshwater input is minimal. Estimates of the inflow from the Gulf County Canal amount to less 

than 1% of the bay’s total volume (Northwest Florida Water Management District [NWFWMD] 2000). 

The principal sources of fresh water to the bay include rainfall, ground water from the underlying 

confined upper Floridan aquifer, and overland flow (Wren and Blitch 2010). 

The bay is characterized by low-energy current regimes (Heck et al. 2000). St. Joseph Bay is adjacent to

the larger basins of St. Andrew Bay to the west and Apalachicola to the east. St. Joseph Bay is 

approximately 15 miles long, and 6 miles wide at its widest point. 

Protected lands in the St. Joseph Bay Basin include T.H. Stone Memorial St. Joseph State Park, St. Joseph 

Bay Aquatic Preserve, St. Joseph Bay State Buffer Preserve, St. Vincent National Wildlife Refuge, and 

Eglin Air Force Base managed areas. St. Joseph Bay is a Class II waterbody (approved for shellfish 

harvesting), is designated as an Outstanding Florida Water (OFW), and is a U.S. Environmental 

Protection Agency (EPA) Gulf of Mexico Ecological Management Site (GEM). 

Water temperatures in the bay range from 7° to 33°C, with peak temperatures generally occurring in 

July and August, and the lowest temperatures occurring in December and January. The pH in the bay 

averages 8.0. Salinities approximate those in the Gulf of Mexico, ranging from 23 to 40 parts per 

thousand (ppt), with a mean of 33 ppt (Wren and Blitch 2010). DO saturations average 98%. The bay is 

well mixed, and hypoxia has not been observed. Turbidity values range from 0 to 49 nephelometric 

turbidity units (NTUs), with the higher values typically associated with storm events. The mean turbidity 

under conditions not associated with storm events is 0.94 NTUs. The average depth is 6.4 meters (m), 

with a range from 10.7 m in the northwest region of the bay, near the opening to the Gulf, to 0.9 m in 

the southern portion of the bay, and along the shorelines (Figure 1). The deep area (9 to 18 m) in the 

northwest portion of the bay is extensive (Figure 1). Table 2 summarizes the bay’s physical 

characteristics.
Draft 4 August 2010

 

Figure 1. Bathymetric map of St. Joseph Bay.
Draft 5 August 2010

 

Table 2. Physical characteristics of St. Joseph Bay. 

Physical Characteristic Values Source 

Estuarine surface area 

(square kilometers [km2]) 

178 km2 Hemming 2002

Watershed area (km2) 337.57 km2 Conmy 2010 

Land use See Figure 2 below Schaeffer, EPA 

Mean depth (m) 6.4 m (10.7m at northern tip; 0.9m 

in southern portion)

FDEP (CAMA) 

Tidal range (m) Mean =0.5 m Heck et al. 2000

Tidal freshwater inflow 

(1,000 cubic meters per day 

[m3

d-1]) 

Negligible FDEP (CAMA) 

Salinity and salinity zones 23-40 ppt, with a mean of 33 ppt; 

30-36 practical salinity units (psu )

FDEP (CAMA); 

Heck et al. 2000 

Figure 2. St. Joseph Bay area Florida Land Use, Cover and Form Classification System (FLUCCS) land 

use map. 
Draft 6 August 2010

 

The very small St. Joseph Bay watershed (337 km2) is a narrow area of land directly adjacent to St. 

Joseph Bay, between the larger St. Andrew Bay and Apalachicola Bay Basins (Figure 3). It is not

considered a watershed in the typical sense, in that it does not have significant freshwater inflows. It 

represents local land uses affecting the bay through direct, sheet flow runoff and minor drainages. The 

bay is hydrologically connected to East Bay in the St. Andrew Bay Basin through the GIWW and the Gulf 

County Canal, which drains directly into St. Joseph Bay. A large percentage (approximately 79%) of the 

land use of this small area is water and wetlands. Table 3 shows the land use in the basin, based on 

FLUCCS. 

Table 3. Land use in the St. Joseph Bay Basin, based on FLUCCS.

Land Use Type Area (km2) (% area) 

Water 164.96 km2(48.87%)

Wetlands 101.75 km2 (30.14%)

Upland Forests 30.64 km2 (9.08%)

Rangeland 16.35 km2 (4.84%)

Urban 13.30 km2 (3.94%)

Barren Land 6.37 km2 (1.89%)

Utilities, etc. 3.37 km2 (1.00%)

Agriculture 0.83 km2 (0.25%)

Total 337.57 km2 

Sources and Fates of Nutrients 

Sources of nutrients to St. Joseph Bay include point source discharges, nonpoint source inputs (septic 

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

atmospheric deposition. 

There are 2 permitted facilities with point source discharges to surface waters in the vicinity of Port St. 

Joe: The city of Port St. Joe (34.75 million gallons per day [MGD]) and Premier Chemicals LLC (13.50 

MGD). An additional facility, the Barrier Dunes/Sea Cliff wastewater treatment plant, has implemented 

a reuse system and does not discharge to surface waters. 

Nonpoint source inputs of nutrients include septic tanks and stormwater runoff. There are 1,271 septic 

tanks in the vicinity of St. Joseph Bay. Although septic systems are a potential source of anthropogenic 

nitrogen (N) and P to St. Joseph Bay, water quality monitoring in the bay over the past 9 years indicates 

no elevated concentrations of nutrients or chlorophyll (see the section on Water Quality Studies). 

Although stormwater runoff is another potential nutrient source, the area of urban land uses is very 

small, and there is no evidence that current inputs from stormwater are resulting in elevated nutrient 

concentrations or chlorophyll in the bay. Recent stormwater management improvements in the area 

include the 2007 installation of Buck Griffin Lake, a 7-acre wet detention facility that reduces 

stormwater inputs to the bay for approximately 70% of Gulf County, and the 2008 installation of Baltzell 

Pond, a half-acre wet detention facility that reduces inputs from downtown Port St. Joe. Estimates of 

natural sources of nutrient inputs such as leaf litter have not been quantified. 
Draft 7 August 2010

 

Figure 3. Location of St. Joseph Bay in relation to the larger Apalachicola and St. Andrews Basins.

Loading from the atmospheric deposition of N was estimated based on data from the National 

Atmospheric Deposition Program’s National Trends Network (NADP-NTN) station in Sumatra, Florida. 

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

atmospheric loading of nitrogen ammonia (NH4) and nitrate (NO3) for St. Joseph Bay are 0.96 and 7.11 

kilograms per hectare per year (kg/ha/yr), respectively. 

Biological Summary 

Seagrasses as the Key Biological Response Variable in St. Joseph 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 
Draft 8 August 2010

 

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 

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 N and P lead 

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

and causing decreased seagrass productivity and ultimately the large-scale loss of seagrasses (Duarte

1995). This explanation, while valid, does not give a complete picture of synergistic factors controlling 

seagrass production. “Top-down” 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, 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 coastal lagoons such as St. Joseph Bay. 

Seagrass beds are the most sensitive biological community in St. Joseph Bay for the development of 

nutrient criteria. Seagrass meadows in St. Joseph Bay are dominated by turtle grass (Thalassia 

testudinum) but also contain shoal grass (Halodule wrightii) and manatee grass (Syringodium filiforme). 

Additional habitat in the bay consists of unvegetated sand areas and small, unquantified areas of other 

bottom communities (see Table 5). Seagrass coverage in St. Joseph Bay has been estimated to be 8,185 

acres (33 km2) based on 1992–93 aerial photography (Sargent et al.1995) and 6,671 acres (27 km2)

based on hyperspectral imagery from 2006 (FERI 2006). The discrepancy between the two estimates 

has not been fully explained, but it is likely due to measurement differences between the imaging 

techniques. On the older aerial photographs, darker areas of sand may have been mistakenly identified 

as seagrass. The spatial resolution of the hyperspectral sensor is significantly better than that of the 

aerial photography. Another source of error could be introduced through geographic information 

system (GIS) techniques, which involve calculating the area based on drawing polygons around areas of 

identified seagrass. A Coastal Zone Management (CZM) grant for 2010 will provide for additional 

hyperspectral imagery in order to track trends since 2006. 

Table 4. Percentage of sampled quadrats (1 m2) in Braun-Blanquet cover abundance classes. 

St. Joseph Bay 

Seagrass Coverage 

75%–100% 

Cover

50%–75% 

Cover

25%–50% 

Cover

5%–25% 

Cover

<5% Cover No Cover

2007 (N=84) 52.38 20.20 15.47 9.52 2.38 0.00

2008 (N=83) 44.57 26.50 13.25 9.63 6.02 0.00

2009 (N=95) 77.80 12.60 4.21 5.26 0.00 0.00
Draft 9 August 2010

 

Seagrass Monitoring 

The St. Joseph Bay Aquatic Preserve began a seagrass monitoring program in 2002. The overall 

objectives of this ongoing program were to gather baseline data on seagrass health and to better 

understand potential environmental and human effects on the seagrass community. The project was 

established using protocols from the Southwest Florida Water Management District (SWFWMD) and the 

Charlotte Harbor Aquatic Preserve. Five fixed transects were established to represent seagrass 

conditions in specific locations around the bay. Each transect was monitored biannually, both early and 

late in the growing season (May–June and September–October). At 50 m intervals, a 1-square-meter 

(m2) quadrat was deployed, and the following data were collected: identification of seagrass species

present, percent cover using Braun-Blanquet coverage estimates, water depth, Secchi depth, epiphyte 

coverage (identified as clean, light, medium, or heavy), and 3 shoots of each species to quantify the 

epiphyte load. DO, salinity, temperature, turbidity, pH, and photosynthetic active radiation (PAR) 

measurements were also taken at each location. 

The preserve shifted to using fixed point sampling in 2005, due to time and staff constraints. This 

sampling method allowed staff to assess a larger spatial area and to better represent the entire bay 

system. Due to inconsistencies in data collection methods and reporting, it is difficult to characterize 

temporal trends in seagrass coverage or seagrass epiphyte load from these studies. It is possible, 

however, to generally summarize baseline conditions. Figure 4 shows the frequency of occurrence of 

seagrass species and bare sand, from quadrats sampled between 2003 and 2009. It should be noted 

that this figure does not indicate coverage, only the presence or absence of species, or bare sand. 

Seagrass coverage estimates are variable over the entire sampling period, likely due to the change in 

sampling technique. The methodology was consistent during the three most recent years of sampling 

(2007 to 2009) and the results may be viewed as a current snapshot of seagrass coverage patterns. 

T. testudinum was the dominant seagrass species by frequency and by coverage. Based on the BraunBlanquet estimates (Table 4), St. Joseph Bay is characterized by dense to moderately dense seagrass 

coverage. 

Boats operating in shallow waters, especially waters less than 6 feet deep, can scar seagrass beds. This 

is happening in many coastal areas throughout the state, including St. Joseph Bay. A 1995 statewide 

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

beds. Impacted acreage in St. Joseph Bay was approximately 59.3% of the total, with 51.4% lightly 

scarred, 6.6% moderately scarred, and 1.3% severely scarred (Sargent et al.1995). 

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

resources to address the issue. Management recommendations include education, channel marking, 

increased enforcement, and limited motoring zones (Sargent et al. 1995). Additionally, scarred areas 

may be restored 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. 

Supporting Biological Information

Seagrass is the key biological response variable in St. Joseph Bay with respect to nutrients, and an 

evaluation of the health of seagrasses as keystone habitat species should ideally include an assessment 

of the health of key groups of organisms that depend on seagrasses for all or part of their life cycle. To 

describe this biological support function of seagrasses, this report focuses on the condition of 

populations of scallops, juvenile fishes, selected invertebrates, and sea turtles (especially juvenile green 

sea turtles). 
Draft 10 August 2010

 

Figure 4. Frequency of occurrence of seagrass species and bare sand, in sampled quadrats, spring 

2003–09. 

TTES=T. testudinum, SFIL=S. filiforme, HWRI=H. wrightii, and BARE=sand bottom. 

Table 5. St. Joseph Bay natural communities (based on Florida Natural Areas Inventory [FNAI] 

classification) and estimated areal coverage (from FDEP 2008). 

FNAI Natural 

Community Type

Number of

Acres

Description

Algal bed Unknown Large populations of nondrift macro- or microalgae.

Composite 

substrate

Unknown A combination of natural communities such as "beds" of algae and seagrasses.

Mollusk reef Unknown Extensive concentrations of sessile mollusks occurring in intertidal and subtidal 

zones to a depth of 40 feet.

Octocoral bed Unknown Nonsessile benthic and pelagic invertebrates and vertebrates (e.g., sponges, 

mollusks, tube worms, burrowing shrimp, crabs, isopods, amphipods, sand 

dollars, and fishes) make up this hardbottom community.

Seagrass bed 8,185 

6,671 

Extensive stands of vascular plants in subtidal (rarely intertidal) zones, in clear, 

coastal waters where wave energy is moderate. (Differing estimates result 

from the use of different imagery and spatial scales; hyperspectral imagery 

data will be collected again in 2010–11, to compare with 2006 data.)

Sponge bed Unknown Dense populations of sessile invertebrates of the phylum Porifera, Class 

Demospongiae. 

Tidal marsh 762.58 Expanses of grasses, rushes, and sedges and associated flora and fauna along 

coastlines of low wave energy and river mouths.

Unconsolidated 

substrate

*Mudflats 

Unknown

*52.51

Expansive, open areas of subtidal, intertidal, and supratidal zones that lack 

dense populations of sessile plant and animal species. 

Mudflats are a type of unconsolidated substrate formed by sediment 

deposited by the changing tides. 

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

2003 2004 2005 2006 2007 2008 2009

% of Occurrence

YEAR

Frequency of Occurrence of Seagrass Species and No Cover in St. Joseph Bay 

Aquatic Preserve Spring 2003-2009

TTES SFIL HWRI BARE
Draft 11 August 2010

 

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. Adults use both the interior and edges of the 

Thalassia beds in St. Joseph Bay (Bologna and Heck 1999). 

Because bay scallops are an annual species, local populations exhibit extreme variability and periodically 

collapse due to natural events such as salinity fluctuations. As in all estuaries and coastal waters that 

support scallops in Florida, populations fluctuate greatly from year to year in St. Joseph Bay. Despite 

this variability, St. Joseph Bay has one of the healthiest populations of bay scallops in Florida (FDEP 

CAMA 2009). Bay scallops are distributed within the shallow waters along the southeastern, southern, 

and southwestern shores of the bay.

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

of Florida from Pine Island Sound to St. Andrew Bay. 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. 2009). The program also monitors recruitment and 

reports on restoration activities. The St. Joseph Bay Aquatic Preserve partnered with the FWRI to assist 

with these surveys in 1995. 

The sampling protocol consists of diver transect surveys at replicate and randomly located stations at 

each study site during the spring. At each station, 1 diver is deployed on each side of a 300 m transect 

line, and the diver counts scallops within 1 m of the line along its length. All scallops within that 2-by300-m area (600 m2) are counted. Twenty transects were sampled in St. Joseph Bay, for a total of 

12,000 m2 sampled in the bay. Within each site, differences in mean scallop abundance among years 

were statistically compared using a Waller-Duncan K-ratio t-test (Statistical Analysis System [SAS] 1985). 

Where significant differences were found among years within a site, these differences are noted in the 

table of population abundance for 1994 to 2009 (Table 6).

The scallop abundance data presented in Table 6 indicates that from 1994 to 2008, there was great 

interannual variability and intersite variability in St. Joseph Bay. This pattern is typical of a healthy 

scallop population in west Florida estuaries and coastal waters. A current snapshot of the adult scallop 

populations and spat recruitment in St. Joseph Bay in the past two seasons is summarized below. This 

summary illustrates the year-to-year fluctuations that characterize scallop populations. 

2008 Scallop Survey Results

The scallop population in St. Joseph Bay decreased from a healthy population (>25 scallops per 600 m2) 

in 2007, to a transitional one (5 to 25 scallops per 600 m2) in 2008 (Table 6). Scallops were not recorded 

at six of the 20 stations, particularly in the areas lining the western shore of the bay south of the state 

park. In 2008, the average per transect was roughly one fifth of the mean of the previous 14 years. A 

red tide event, which originated offshore, was observed in November 2007 and likely reduced the 

available spawning stock and the number of recruits settling onto grass blades and collectors, translating 

into low adult abundances during spring 2008 (Arnold et al. 2009).
Draft 12 August 2010

 

Table 6. Adult bay scallop density at each of 20 stations sampled at the St. Joseph Bay study site, 

1994–2008. Scallop density at each station is reported per 600 m2 transect. Results of the WallerDuncan (W.D.) comparison of means (letters) are presented with the population means; the same

letters denote averages that were not different at a significance level of 0.05.

Recruitment monitoring occurred at 4 St. Joe Bay stations in 2008 and was limited at all 4 sites, likely 

due to the red tide event in November 2007. There was a small recruitment peak in February, with the 

majority of new individuals located at Station 1 near the mouth of the bay, and then minimal 

recruitment until November. A strong recruitment peak (the highest in the state in 2008) was observed 

in December, with 3,258 scallops settling on the 12 deployed collectors. While the December spatfall 

occurred at all stations, 86.8% was recorded at the 2 stations near the mouth of the bay, possibly 

suggesting that the larvae were transported into the bay from an outside source. Of the 132 collectors 

deployed in 2008, 16 (12.1%) were not retrieved, 69 (52.3%) retrieved had 0 scallops, and 47 (35.6%) 

had bay scallops.

2009 Scallop Survey Results

Note that data for the 2009 survey are considered to be preliminary and that the report is in draft form. 

Twenty stations were surveyed in St. Joseph Bay in 2009. The scallop population in St. Joseph Bay 

shifted from a transitional population in 2008 to a healthy one in 2009. Scallops were found at all 20 

stations, with almost half of the total number found observed at 1 station located in slightly deeper 

water and patchy seagrass coverage. Of the 369 scallops measured in 2009, shell heights during the 

June sampling effort ranged from 24 to 75 millimeters (mm), the average was 48.0 mm, and the most

frequent shell height recorded was 45 mm (Arnold 2009). 
Draft 13 August 2010

 

Recruitment monitoring in St. Joseph Bay occurred at 4 stations, each with 3 replicates, from January 

through April 2009. Beginning in March, sampling was conducted at 12 stations (including the original 

4), each with a single replicate, positioning the collectors around the bay. All collectors retrieved during 

May through December were part of the new study design. Of the 120 collectors deployed in 2009, 102 

were recovered, and 12 were lost during shipment to FWRI. Of those 90 collectors processed, spat were 

present on 64 (71.1%), and no scallops were observed on the remaining 26 collectors. The total spat 

observed at this site in 2009 was 1,855, the average was 20.6 per collector, and the maximum number 

found on a single collector was 494. The strongest recruitment peak occurred in collectors retrieved in 

January, and recruitment was observed on all 10 retrieval dates, except for the lost collectors that were 

retrieved in late July. 

Although St. Joseph Bay did not have a large number of adults in 2008, recruitment was very high 

towards the end of the year, and this was reflected in 2009 in the shift of the adult population from 

“transitional” to “healthy.” 

The relationship between scallop populations and nutrient inputs is a complex one, and very limited 

data exist to address the issue. Because they are filter-feeders of phytoplankton, and phytoplankton 

production is driven by N and P, some level of nutrient inputs is necessary to maintain healthy 

populations of all bivalves, including scallops (S. Geiger, FWRI, pers. comm., 2010). The optimal level has 

not been quantified, and is likely variable among areas due to differences in hydrologic conditions, 

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

scallops, because of associated low DO and seagrass loss (S. Geiger, FWRI, pers. comm., 2010). 

One plausible, yet untested hypothesis, is that increases in nutrients can be responsible for 

phytoplankton community shifts from diatom dominated to dinoflagellate dominated (as in Perdido Bay; 

Livingston 2006), resulting in a condition where there is insufficient phytoplankton of the correct form 

and size for the bivalves to filter (S. Geiger, FWRI, pers. comm., 2010).

Despite the limited information on the effects of nutrients on scallops, it has been established that the 

relatively low nutrient concentrations and chlorophyll a values in St. Joseph Bay are associated with 

healthy scallop populations and healthy seagrass beds on which the scallops are dependent.

Juvenile Fishes and Selected Invertebrates

The productivity of invertebrates (e.g., amphipods, mussels, crabs, and worms) within St. Joseph Bay is 

the highest ever recorded in seagrass beds (Valentine and Heck 1993). A number of animals appear to 

occur at greater densities in St. Joseph Bay than in most other places in the northern Gulf of Mexico, 

including stone crabs, scallops, horse conchs (the largest gastropod in North America), lightning whelks, 

and pen shells (Beck et al. 2000). Heck et al. (2003) found evidence for a strong link between seagrass 

abundance and abundances of juvenile finfish and shellfish. 

In 2006, the St. Joseph Bay Aquatic Preserve established a program to monitor juvenile fishes and 

selected invertebrates. Data on species abundances, size structure, and habitat associations were 

collected monthly at 7 fixed monitoring stations to identify community and species characteristics and 

essential habitat that species use during various critical life stages. A 70-foot (21.3 m) seine net was 

used to collect species. Fish standard length measurements were taken for up to 20 individuals per 

species, and the rest were counted. This project was modeled after the juvenile fish sampling project 

that FWRI’s Fisheries Independent Monitoring Program has conducted for 15 years in several systems 

around the state. Water quality parameters, including salinity, temperature, DO, and pH, were collected 
Draft 14 August 2010

 

at each site with a hand-held YSI meter. A turbidity sample, as well as data on wind speed and direction, 

tide, and weather, were also collected. The goals of the project were to describe the major trends in the 

spatial and temporal distribution of major fish and invertebrate species among various habitats within 

the St. Joseph Bay system, and to relate the occurrence, abundance, and seasonality of fish and 

invertebrate species to natural environmental variations such as temperature and salinity regimes, and 

periodic events such as storms. This project estimated the relative abundances and monitored the size 

class distribution of fish species in seagrass areas. 

To date, the project has provided baseline data on species using shallow seagrass habitat within the 

preserve (see Table 7). Although it is premature to report on temporal trends in the fish and 

invertebrate communities in St. Joseph Bay, this study indicates that high numbers of fish and 

invertebrate species, and high numbers of individuals, are using the seagrass habitats of St. Joseph Bay. 

Sea Turtles

The extensive seagrass beds of St. Joseph Bay provide significant foraging habitat for juvenile green sea 

turtles (Chelonia mydas) and for the Kemp’s ridley sea turtle (Lepidochelys kempii), both federally 

endangered species. Juvenile green turtles employ specific foraging habitats and are capable of 

navigating to specific habitats if displaced due to cold weather. St. Joseph Bay was recently documented 

as a very important developmental habitat for green turtles in the northeastern Gulf of Mexico 

(McMichael 2004). Population models have suggested that protection of the juvenile life stage is crucial 

to sea turtle population recovery, and juveniles rely heavily on the nearshore environment (Crouse, 

Crowder, and Caswell 1987). Juveniles use nearshore habitats as development grounds, while larger 

juveniles or subadults use them as foraging areas (McMichael 2004). 

In January 2001, when water temperatures dropped below 6° C in St. Joseph Bay, 403 marine turtles 

were found stranded and cold-stunned within the bay. Ten Kemp’s ridley, 5 loggerhead, and 388 green 

turtles were collected, making this the largest stranding event ever documented in the United States 

until 2010 (Blackwelder 2001). In 2003, 42 juvenile turtles stranded due to cold in St. Joseph Bay: 39 

green turtles, 2 Kemp’s ridleys, and 1 loggerhead. Most recently, in January 2010, extreme cold 

temperatures, with water temperatures in the southern portion of the bay between 4° and 10°C for 

almost a week, led to the stranding of 1,750 sea turtles. The presence of juvenile turtles in 

northwestern Florida waters at this time of year suggests that these turtles overwintered in this area 

and entered a torpid state once water temperatures decreased below an unspecified threshold 

temperature (McMichael 2004). This information indicates that the area’s green sea turtle population is

using the bay year-round and is not migrating seasonally. Further research is needed to fully understand 

how sea turtles are using nearshore habitats throughout their life cycle, so that adequate protection can 

be given to these threatened and endangered species. 

Another important discovery associated with the 2001 cold stranding and mortality event was related to 

juvenile green turtle diet. The majority of the material found in the gastrointestinal tracts of the green 

turtles that died was turtle grass (T. testudinum). This was the first time turtle grass has been identified 

as the primary diet of juvenile green turtles in the United States. Green turtles in St. Joseph Bay appear 

to have few direct threats, but the seagrasses upon which these turtles forage has suffered damage 

from boat propellers (Foley et al. 2007). 
Draft 15 August 2010

 

Table 7. Species using shallow seagrass habitat in St. Joseph Bay, 2006–08. 

Sea Turtle Monitoring for Population Information and Habitat Use 

The beaches adjacent to St. Joseph Bay on the St. Joseph peninsula serve as valuable nesting habitat for 

the threatened loggerhead sea turtle (Caretta caretta) and the green sea turtle. These turtles nest along 

the entire 17-mile stretch of the peninsula. This nesting activity represents approximately one-third of 

all sea turtle nesting in the Panhandle. 

The University of Florida has been using netting techniques (set-netting and strike-netting) to capture 

turtles in St. Joseph Bay since 2001. The purpose of this effort is to gather information regarding species 

assemblage, population abundance, size classes, growth, habitat use, seasonal movements, and 

overwintering behaviors. Data collected during the project are being used to address the theory of 
Draft 16 August 2010

 

developmental migration in turtles using the Gulf of Mexico. Research is expected to continue through 

2011 in St. Joseph Bay. 

This work should contribute new information to support management and stewardship in this area, 

where increasing development and recreation are expected to result in increased human/sea turtle 

interactions. Past studies in St. Joseph Bay yielded approximately 70 turtles caught per year using both 

netting methods, and future increased efforts may allow the capture of up to 150 turtles per year (750 

over the 5-year period). Continued netting will further delineate important foraging areas, provide 

information on residence times and seasonality of use, elucidate sea turtle population parameters and 

the use of these habitats at multiple scales, and identify potential threats, while expanding the

knowledge of in-water sea turtle populations.

It is possible for anthropogenic nutrient enrichment to impact sea turtles indirectly through bottom-up 

food web changes (nutrient enrichment → excess phytoplankton and epiphyte growth → seagrass loss 

and loss of dependent organisms), but this is an unlikely scenario in St. Joseph Bay due to the lack of 

significant freshwater inputs (and therefore a lack of riverine-based nutrient loading) and low ambient 

nutrient levels. The fact that large numbers of sea turtles, and in particular juvenile green sea turtles,

are using St. Joseph Bay, and depend on the bay’s Thalassia beds as a food source, is evidence that 

nutrients are not having a “bottom-up” effect on food webs in this system. 

2004 Bottlenose Dolphin Mortality Event and the Role of Red Tide (K. brevis)

A mortality event for bottlenose dolphins (Tursiops truncatus) occurred in the Florida Panhandle 

between March 10 and April 13, 2004, beginning in St. Joseph Bay. Over 100 dolphins stranded dead 

between Escambia and Franklin Counties, 70% of which were in St. Joseph Bay and surrounding areas of 

Gulf County (Flewelling et al. 2005; National Oceanic and Atmospheric Administration [NOAA] 2004). 

Naar et al. (2007) reported a “coincident mortality of large redfish” but no other animal mortalities, 

while Gaydos (2006) cites reports of “hundreds of dead marine fish and invertebrates” and “large 

numbers of dead fish, jellyfish, and birds” in the area. 

The yearly average number of dolphin strandings for all Panhandle counties is 21.4 (Gaydos 2006), and 

so this unusually high number of deaths prompted the National Oceanic and Atmospheric 

Administration to declare the event an official “Unusual Mortality Event” (UME) and initiate an 

investigation (NOAA 2004). NOAA found brevetoxins, the naturally occurring neurotoxins produced by 

the red tide dinoflagellate K. brevis, at high concentrations in the stomach contents of all dolphins 

examined and at variable levels in their tissues. The brevetoxin concentrations were at levels greater 

than or equal to those observed in previous marine mammal mortality events associated with Florida 

red tides (Gaydos 2006). The investigation of the mortality event suggested acute intoxication through 

the ingestion of menhaden that had ingested K. brevis cells (Flewelling et al. 2005; Gaydos 2006). 

Results indicate that brevetoxins are not always lethal to fish, and the live fish serve as vectors to higher 

trophic levels (Naar et al. 2007; Flewelling 2005). 

The bloom responsible for the event was never detected. No signs of red tide were observed in St. 

Joseph Bay, including discolored water or aerosol effects (Gaydos 2006). It is possible that the bloom 

occurred offshore, but the levels of brevetoxin in fish and in seagrass epiphytes indicate the bloom was 

in the St. Joseph Bay region but occurred before the onset of the dolphin mortality and went 

undetected. 
Draft 17 August 2010

 

Confounding the understanding of this mortality event is the fact that the southwest Florida coast has 

significant blooms of K. brevis nearly annually, without elevated numbers of dolphin deaths. Blooms in 

the Panhandle are less frequent than those in southwest Florida. In addition, little is known about the 

ecology of dolphin populations in the Panhandle, or about their patterns of use of St. Joseph Bay and 

surrounding areas. 

Because St. Joseph Bay is an oligotrophic system, with virtually no freshwater inflows and low ambient 

nutrient levels (see the section on Water Quality Studies) that have been very stable over the past 10 

years, there is no reason to suspect that any local or regional anthropogenic nutrient sources 

contributed to the maintenance of the K. brevis bloom that caused the 2004 dolphin mortality event. 

For a further discussion of K. brevis bloom dynamics, nutrient sources, and temporal and spatial trends, 

see the document, Overview of FDEP Approaches for Nutrient Criteria Development in Marine Waters. 

Shellfish Harvesting

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

Consumer Services (FDACs) regulates shellfish harvesting in the state. Harvesting areas are categorized 

based on their fecal coliform levels and any pollution sources that may be in the vicinity. St. Joseph Bay 

is consistently classified as “approved.” The “approved” classification of the national Shellfish Sanitation 

Program indicates that “waters are removed from actual and potential pollution sources so that fecal 

material, pathogenic microorganisms, and poisonous or deleterious substances are not present in 

dangerous concentrations” (FDACS 2009). Approved areas are generally not affected by rainfall or river 

discharge, and they are typically closed only during emergency situations such as hurricanes or sewage 

spills. 

FDACS and the FWRI also monitor shellfish harvesting areas for harmful algal blooms (HABs), for the 

protection of public health from shellfish toxicity. This monitoring program follows the guidelines of the 

Interstate Shellfish Sanitation Conference. 

Blooms of K. brevis are associated with fish kills, neurotoxic shellfish poisoning, and an airborne irritant 

in seaspray that can cause respiratory discomfort in humans and other animals. This phenomenon 

occurs when K. brevis concentrations increase above normal background levels. Red tide concentrations 

above 250,000 cells/liter can cause fish kills; however, concentrations as low as 5,000 cells/liter may 

cause shellfish to become toxic if the animals are exposed long enough. Shellfish become toxic by 

feeding on dinoflagellates and absorbing toxin into their digestive tissues. Toxic shellfish may cause 

illness in humans and other animals when ingested. Shellfish areas are closed to harvesting when 

concentrations in the vicinity exceed 5,000 cells/liter. Field studies indicate that shellfish may retain 

toxicity for 2 to 4 weeks; therefore, after concentrations return to normal in the water, shellfish meats 

must be tested for toxicity before the area may be reopened to shellfish harvesting. St. Joseph Bay has 

been closed for shellfish harvesting in association with periodic elevated red tide concentrations. 

Waters on the 303(d) List 

There are no impaired waters for St. Joseph Bay on the Cycle 2 Verified List (2010) listed for nutrients or 

DO (FDEP 2010a). The only verified impairment for St. Joseph Bay is a listing for mercury. However, this 

listing, which is based on tissue levels in king fish and sharks, is for the entire Gulf of Mexico coast, and 

the impairment will be addressed by a Gulf of Mexico Total Maximum Daily Load (TMDL) in 2012.
Draft 18 August 2010

 

Water Quality Studies 

St. Joseph Bay Aquatic Preserve and Florida LakeWatch/Project COAST Program Monitoring

The St. Joseph Bay Aquatic Preserve formed a partnership with the University of Florida 

LakeWatch/Project COAST Program in 2001 to begin monitoring water quality in St. Joseph Bay. This 

effort was begun to document short-term variability and long-term changes in the bay’s health. Two 

important objectives of this project are to detect levels of nutrients and any effects of nutrient 

enrichment. Seven sites are sampled monthly for TN, TP, chlorophyll a, and water clarity (Secchi depth), 

and 2 sites have data loggers recording continuous measurements (every 30 minutes) for temperature, 

DO, pH, salinity, turbidity, and depth. The sondes collecting continuous data are retrieved and deployed 

on a 2-week rotation. Figure 5 slows the locations of the water quality monitoring sites.

FDEP notes that the following details about sample analysis methods 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. The Impaired Surface 

Waters Rule (IWR) (Chapter 62-303, Florida Administrative Code [F.A.C.]) requires 

that chlorophyll a data be corrected for phaeophytin, and FDEP anticipates that any

proposed water quality criterion for chlorophyll a will be for corrected samples. The 

uncorrected chlorophyll a data are expected to yield higher numbers than what FDEP 

will consider appropriate for the criterion. 

2. The method for determining TN in water samples is not EPA approved, nor is it an 

approved method in the FDEP Standard Operating Procedures (SOPs). Bachmann 

and Canfield (1996) describe this method and provide data showing that it produces 

results comparable to EPA-approved methods for TN in fresh water. Water samples 

are frozen before analysis, which also does not conform to FDEP SOPs. However, 

Bachmann and Canfield (1996) and Canfield et al. (2002) demonstrated that TN 

results are not significantly affected by freezing. Project COAST samples are held 

frozen for a maximum of three 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 these inconsistencies between Project COAST lab analyses and FDEP SOPs and EPA guidance, 

FDEP conducted several analyses comparing the water chemistry results from Project COAST 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. 

Figure 6 shows long-term average (2001–09) TN concentrations for individual St. Joseph Bay stations. 

Figure 7 presents baywide annual average TN concentrations, from 2001 to 2009. These values are 

relatively low and stable over time. Figure 8 shows long-term average TP concentrations for individual 

stations, and Figure 9 provides baywide annual average TP concentrations from 2001 to 2009. TP values 

are also low and stable across the bay, and over the monitoring period. Figure 10 shows long-term 

average chlorophyll a and Secchi depth values for individual stations, and Figure 11 provides baywide 
Draft 19 August 2010

 

annual average chlorophyll a concentrations. Nutrient and chlorophyll a concentrations indicate an 

oligotrophic system. 

Figure 5. Location of St. Joseph Bay Aquatic Preserve water quality monitoring sites. 
Draft 20 August 2010

 

Figure 6. TN concentrations for St. Joseph Bay stations, 2001–09. 

Figure 7. Baywide mean annual TN, 2001–09. 

0

50

100

150

200

250

300

350

2001 2002 2003 2004 2005 2006 2007 2008

Total nitrogen (ugL)

Year

Mean Annual Total Nitrogen (TN) Concentrations for St. Joseph Bay Aquatic Preserve 

2001-2008

TN Linear (TN)
Draft 21 August 2010

 

Figure 8. TP concentrations for St. Joseph Bay stations, 2001–09. 

Figure 9. Baywide mean annual TP, 2001–09. 

0

2

4

6

8

10

12

14

16

18

2001 2002 2003 2004 2005 2006 2007 2008

Total phosphorus (ugL)

Year

Mean Annual Total Phosphorus (TP) Concentrations in St. Joseph Bay Aquatic Preserve 

2001-2008

TP Linear (TP)
Draft 22 August 2010

 

Figure 10. Chlorophyll a and Secchi depth values for St. Joseph Bay stations, 2001–09 

Figure 11. Baywide mean annual chlorophyll a, 2001–09

0

1

2

3

4

5

6

2001 2002 2003 2004 2005 2006 2007 2008

Cholorphyll (ugL)

Year

Mean Annual Chlorophyll (CHLA) Concentrations in St. Joseph Bay Aquatic Preserve 

2001-2008

CHLA Linear (CHLA)
Draft 23 August 2010

 

Water Quality Analyses by FDEP

FDEP analyzed the data from the joint sampling program of CAMA’s St. Joseph Bay Aquatic Preserve and 

LakeWatch/Project COAST for 2001 through 2009, from 8 stations throughout the bay. Not every 

station had sufficient data for each year, and so stations were pooled. Grouping the stations was 

appropriate because the system is small and physically fairly homogeneous with no salinity gradients. 

For all stations combined, annual geometric means were calculated for TP, TN, and chlorophyll a. 

Figures 12 through 14 show the distributions of the geometric means for each parameter. For all sites 

combined, the long-term mean of the annual geometric means was calculated, and a log normal 

distribution function was fit to estimate the long-term 75th and 90th percentile of the data (Table 8). TP 

concentrations were relatively low and stable from 2001 to 2009, with fluctuations of only a few 

micrograms per liter (μg/L). TN concentrations were also relatively low and stable over the 9-year 

period, ranging from 192 to 278 μg/L. Chlorophyll a concentrations were also low, with annual 

geometric means ranging from 1.1 to 3.2 μg/L, and a long-term geometric mean of 2.0 ug/L.

Table 8. Summary of data analysis for St. Joseph Bay, all stations combined (8 stations), 2001–09. - = Empty cell/no data

LN = natural logarithm

GM = geometric mean

C.I. = confidence interval. 

a

Long-term geometric means and the 90th percentile of annual geometric means are highlighted. 

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 2.568 - 5.448 - 0.693 - 

Standard deviation LN 

TP

0.206 - 0.135 - 0.294 - 

N 147 - 146 - 142 - 

95% C.I. 0.03 - 0.02 - 0.05 - 

Long-term GM 13.04a 13.19 a 232.25 a 234.15 a 2.00 a 2.07 a

Lower 95% C.I. 12.61 - 227.17 - 1.90 - 

Upper 95% C.I. 13.49 - 237.46 - 2.10 - 

75th percentile 14.99 14.29 254.47 253.35 2.44 2.29

90th percentile 16.99 a 15.20 a 276.27 a 275.77 a 2.91 a 2.66 a
Draft 24 August 2010

 

Figure 12. Geometric mean of TP concentrations for all bay sites, 2001–09, and long-term geometric 

mean of TP. 

Figure 13. Geometric mean of TN concentrations for all bay sites, 2001–09, and long-term geometric 

mean of TN. 

0

2

4

6

8

10

12

14

16

18

20

2000 2002 2004 2006 2008 2010

TP (μg/L)

Geometric Mean TP Concentration for SJB

Geometric Mean TP 

long term gm tp 

0

50

100

150

200

250

300

2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010

TN (μg/L)

Geometric Mean TN Concentration for SJB

Geometric mean TN

long term gm tn
Draft 25 August 2010

 

Figure 14. Geometric mean of chlorophyll a concentrations for all bay sites, 2001–09, and long-term 

geometric mean of chlorophyll a. 

Numeric Nutrient Criteria Recommendations 

Relationship between Anthropogenic Nutrient Inputs and Adverse Biological Effects

The minimal anthropogenic nutrient inputs currently are not causing adverse biological effects in St. 

Joseph Bay. The lack of a major freshwater inflow carrying a terrestrial-based nutrient load, and the 

relatively low level of inputs from local point and nonpoint sources, contributes to low nutrient and 

chlorophyll concentrations in the bay (see Table 1 and Figures 12 through 14). The most sensitive 

biological endpoint in St. Joseph Bay is seagrass, and the seagrass habitat is healthy based on 

hyperspectral imaging surveys, transect surveys, and epiphyte coverage, and is supporting healthy 

groups of organisms—in particular, fish and invertebrates, scallops, and juvenile green sea turtles. 

Adverse impacts to the bay that require further management action or research include physical 

damage to seagrasses (prop scarring) and K. brevis bloom dynamics and its effects on higher-trophiclevel organisms.

St. Joseph Bay is fully meeting its Class II designated uses of shellfish propagation or harvesting, with 

respect to nutrients, and the Class III uses deemed included within Class II, which are recreation, 

propagation, and maintenance of a healthy, well-balanced population of fish and wildlife:

• The bay scallop populations are some of the healthiest in the state. 

• Shellfish harvesting is consistently classified as “approved,” indicating that waters 

are not adversely affected by actual or potential pollution sources. 

• Fish and invertebrate data show high abundances in seagrass beds. 

0

0.5

1

1.5

2

2.5

3

3.5

2000 2002 2004 2006 2008 2010

chl a (μg/L)

Geometric Mean Chl A Concentration for SJB

Geometric Mean chl a 

long term gm chl a 
Draft 26 August 2010

 

• Juvenile sea turtles are using seagrass habitat in high numbers throughout the year. 

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

providing for full aquatic life use support. FDEP therefore proposes nutrient concentration targets that 

reflect the current conditions as reported from 2001 to 2009 water quality monitoring data. 

Proposed 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 St. Joseph 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 
Draft 27 August 2010

 

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

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

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

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

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

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

long-term dataset for each segment of the waterbody.

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

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

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

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

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

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

periods should be used. 

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

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

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

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

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

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

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

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

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

Previous proposals by EPA have utilized three-year assessment periods to express the duration nutrient 

criteria components. Although it is possible to construct a test that achieves the 10 percent Type I error 

rate target over a 3-year period, a slightly longer period (5 years) will provide better control for Type II 

error and will more fully capture climatic cycles (e.g., el nino, la nina), which tend to be longer than 

three years in Florida (and may actually be on a multi-decadal scale). Furthermore, a five year period is 

more consistent with both the State’s five year 303(d) assessment and NPDES permit renewal cycles.

Given a five year assessment period, FDEP derived criteria expressed as an annual geometric mean by 

using the 75th percentile of the annual geometric means from the long-term dataset. FDEP 

demonstrated that setting the criteria at this percentile results in a magnitude that, when expressed as 

an annual geometric mean not to be exceeded more than twice during a five-year period, will achieve 

the targeted 10 percent error rate. The magnitude component of the criteria (not to be exceeded more 

than twice in a 5 year period) was established to allow for two separate assessments:
Draft 28 August 2010

 

• 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. 

Because it is small, well-mixed, and fairly uniform in its physical characteristics, St. Joseph Bay is treated 

as a single 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.

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

Joseph Bay, as well the annual limits for single stations, are provided in Table 9.

Table 9. Proposed numeric nutrient criteria for St. Joseph 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 exceed the network average more than twice in a 5 year period, nor shall an 

individual station exceed the single station average more than twice in a 5 year period. 

Parameter (μg/L) Existing Long Term 

Geometric Mean

Maximum allowed 

Long Term 

Geometric Mean

Annual Geometric 

Mean for a 

Network of 

Stations (2 out of 5 

year exceedance 

rate)

Annual Geometric 

Mean for a Single 

Station (2 out of 5 

year exceedance 

rate)

Total Phosphorus 

(TP)

13.1 14.5 16.6 17.2

Total Nitrogen 

(TN)

225 248 279 308

Chlorophyll a 2.0 2.2 2.8 3.1
Draft 29 August 2010

 

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