# 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, 2010Draft 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

Wate r 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

.......................................................................................................................... 29Draft 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 m 2 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.

............................................................................................................. 24Draft iv August 2010 Figure 14. Geometric mean of chlorophyll a concentrations for all bay sites, 2001

– 09, and long

term geometric mean of chlorophyll a.

.................................................................................... 25Draft 1 August 2010 

### Executive Summary
This report was prepared by t he 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 pro tect 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 northeas t Gulf of Mexico having virtually no major freshwater inflows. The bay is characterized by low

- energ y 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 i s approxima tely 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 v ery 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 indicate s 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 Are as (CAMA) P rogram 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 biolog ical 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 evide nce 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 vari a bility

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

- = Empty cell/no data N/A = Not applicable Response V ariable Observed
H istorically ? Observed C urrently ? Explanation Source

Low dissolved oxygen ( DO ) (hypoxia/anoxia) No No St. Joseph Bay system is shallow, well

mixed, and open to the Gulf of Mexico FDEP (CAMA) 2009

Reduced clarity No No Secchi depths over the long

- term average 7 to 8 f ee t. FDEP(CAMA) 2009

Increased chlorophyll a concentrations No No Chl orophyll 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 off shore 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 h as 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 )
200 6 ; 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, ab undant juvenile fish and invertebrate community assoc iated 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 bloom s 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 historic al levels No Few historic al 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 biologica l 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



### Geographic al and Physical Description
St. Joseph Bay is a coastal lagoon in Gulf County, Florida (29.8° N latitude, 85.3° W longitude)

, semi

enclosed by the St. J oseph Peninsula. It is the only embayment in the northeast Gulf of Mexico that has no significant s ource of freshwater input (Heck et al. 2000)

. Although the Gulf County Canal connects the Gulf Intracoastal Waterway (GIWW) to the bay, and several small c reeks and bayous drain into the bay , freshwater input is minimal

. Estimates of t he 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 p rincipal 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

- ener gy 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.

P rotected lands in the St. Jo seph Bay Basin include T.H. Stone Memorial St. Joseph State Park, St. J oseph 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 (app roved for shellfish harvesting), is designated as an Outs tanding 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 temp eratures 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 avera ge 98%. The bay is well mixed, and hypoxia h as not been observed

. T urbidity 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 shoreline s (Figure 1)

. The deep area (9 to 18 m) in the northwest portion of the bay is extensive (Figure 1)

. Table 2 summarize s the bay’s p hysical characteristics.Draft 4 August 2010 Figure 1. Bathymetric map of St. Joseph Bay.Draft 5 August 2010 Table 2 . Physical c haracteristics of St. Joseph Bay

. Physical Charact eristic Values Source Estuarine surface area ( square kilometers [ km 2 ]) 178 km2 Hemming 2002

Watershed area (km 2 ) 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) F DEP ( CAMA )

Tidal range (m) Mean = 0.5 m Heck et al. 2000 Tidal freshwater inflow (1
, 000 cubic meters per day [m 3 d -1 ]) N egligible F DEP ( CAMA )

Salinity and salinity zones 23

- 40 ppt, with a mean of 33 ppt ; 30

- 36 practical salinity units ( psu ) F DEP ( CAMA ); Heck et al. 2000

Figure 2. St. Joseph Bay area Florida Land Use, Cover and Form Classification S ystem ( FLUCC S) 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 doe s 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 Co unty 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 FLUCC S.

Table 3. L and use in the St. Joseph Bay Basin , based on F LUCCS.
Land Use Type Area (km 2 ) (% area)
Water 164.96 km 2 (48.87% )
Wetlands 101.75 km 2 (30.14%) Upland Forests 30.64 km 2 (9.08%) Rangeland 16.35 km 2 (4.84%) Urban 13.30 km 2 ( 3.94%)
Barren Land 6.37 km 2 (1.89%) Utilities, etc. 3.37 km 2 (1.00%) Agriculture 0.83 km 2 (0.25%) Total 337.57 km 2



### Sources and Fates of N utrients
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 p oint 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 anthr opogenic 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 r educes 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 a tmospheric deposition of N was estimated based on data from the National Atmospheric Deposition Pr ogram’s Nat ional Trends Network (NADP

- NTN) station in Sumatra, Florida. Based on the NADP

- NTN loading data for the most recently reported year (2008), estimates fo r the atmospheric loading of nitrogen ammonia ( NH 4 ) and nitrate ( NO 3 ) 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 Var iable 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 andDraft 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, dred ging and development. M onitoring 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 propos ed 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 lig ht 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 cau sing decreased seagrass productivity and ultimately the large -s cale 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 epip hytes. 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 biolog ical com munity 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 ). Additio nal habitat in the bay consists of unvegetated sand areas and small, unquantified areas of other bottom communities (see T able 5 ). Seagrass coverage in St. Joseph Bay has been estimated to be 8,185

acres (33 km2) based on 1992

– 93 aerial photography (Sarge nt et al. 1995) and 6,671 acres (27 km2) based on hyperspectral imagery from 2006 ( FERI 200 6 ). 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 hyper s pectral sensor is significantly better than that of the aerial photography. Another source of error could be introduce d 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 C over

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 0.00Draft 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 usi ng protocols from the Southwest Florida Water Management Dis trict (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 th e 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, S ecchi dept h, epiphyte coverage (identified as clean, light, medium

, or heavy), and 3 shoots of each species to quantify the epiphyte load. DO , salinity, temperature, t urbidity, pH

, and photosynthetic active radiation (PAR) measurements were also taken at each location.

The p reserve 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 col lection 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 general ly summarize baseline conditions. Figure 4 shows the frequency of occurre nce of seagrass species and bare sand, from quadrats sampled between 2003 and 2009. It should be noted that this figure do es not indicate coverage, only the presence or absence of species, or bare sand. Seagrass coverage estimates are variable over the e ntire sampling period, likely due to the change in sampling technique. The methodology was consistent during the three most recen t years of sampling (2007 to 2009) and the results may be viewed as a current snapshot of seagrass coverage patterns.
T. te s tudinum was the dominant seagrass species by frequency and by coverage. Based on the Braun

B lanquet estimates (Ta ble 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. Th is 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 seagra ss 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. J oseph 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 Are as Inventory [FNAI] classification) and estimated areal coverage (from FDEP 2008)

. FNAI Natural Community Type Number of
Acres Description

Algal b ed Unknown Large populations of nondrift macro - or microalgae. Composite

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

Mollusk r eef Unknown Extensive concentrations of sessile mollusks occurring in intertidal and subtidal zones to a depth of 40 feet. Octocoral b ed Unknown Nonsessile benthic and pelagic inverteb rates and vertebrates ( e.g., sponges, mollusks, tube worms, burrowing shrimp, crabs, isopods, amphipods, sand dollars, and fishes) make up this hardbottom community. Seagrass b ed 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 ; hy perspectral 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 m arsh 762.58 Expanses of grasses, rushes, and sedges and associated flora and fauna along coastlines of low wave energy and river mouths. Unconsolidated

s ubstrate *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 BAREDraft 11 August 2010 Scallops
Seagras s 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 active ly 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 southeast ern, southern, and southwestern shores of the bay.

The FWRI’s Molluscan Fisheries Program surveys adult populations of the bay scallop on t he 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 b egun in Florida in 1994 (Arnol d et al. 200 9 ). 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- by

300

- 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 Wa ller

- Duncan K

- ratio t- test ( Statistical Analysis System [ SAS ] 1985). Where significant differences were found among years within a site, t hese differences are noted in the table of population abundance f or 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 Sca llop 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 m 2 transect. Results of the Waller

Duncan (W.D.) comparison of means (letters) are presented with the population means; the same letters den ote 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 set tling 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 13 2 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 dr aft 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 num ber 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 or iginal
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 durin g 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 maxim um number found on a single collector was 494. The strongest recruitment peak occurred in collectors retrieved in January, and recruitment was observed o n 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 nutrien t 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,
nutr ient 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 nu trients 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 bi valves 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 associate d 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 wa s used to collect species. Fis h standard length measurements we re taken for up to 20 individuals per specie s, and the rest we r e 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. Wate r quality parameters, including salin ity, temperature, DO , and pH

, we re collectedDraft 14 August 2010 at each site with a hand

- held YSI meter. A turbidity sample , as well as data on wind speed and directi on, tide

, and weather, we re also collected. The goal s of the project we re to describe the major trends in the
sp atial 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 abundance s and monitor ed the size class distribution of fish species in seagrass areas.

To date, th e project has provided baseline data on species u s ing 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 indicat es that high numbers of fish and invertebrate species, and high numbers of individuals, are u s ing 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 d ocumented

as a very important developmental habitat for green turtles in the northea stern Gulf of Mexico (McMichael 2004). Population models have suggested that protection of the juvenile life stage is crucial to sea turtle population recovery, and juveni les rely heavily on the nearshore environment (Crouse, Crowder

, and Caswell 1987). Juveniles u s e nearshore habitats as development grounds, while larger juveniles or subadults use them as foraging areas (McMichael 2004).

In January 2001, when water temp eratures 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 Un ited States until 2010 (Blackwelder 2001). In 2003, 42 juvenile turtles stranded due to cold in St. Joseph Bay : 39 green turtles, 2 Kemp’s r idleys, and 1 loggerhead. Most recently, in January 2010, extreme cold temperatures, with water temperatures in t he 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 th e area’s green sea turtle population is using the bay year

- round and is not migrating seasonally. Fur ther research is needed to fully understand how sea turtles are u s ing 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 200 1 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 seagrass es upon which these turtles forage has suffered damage from boat propellers (Foley et al

. 2007).Draft 15 August 2010 Table 7

. Species u s ing shallow seagrass habitat in St. Joseph Bay, 2006

– 08.

Sea T urtle M onitoring for P opulation I nformation and H abitat U se 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 P anhandle.

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 abundanc e, size classes, growth, habitat use, seasonal movements, and overwintering behaviors. Data collected during th e project are being used to address the theory ofDraft 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 turt le populations.

It is possible for a nthropogenic nutrient enrichment to impact sea turtles indirectly through bottom

- up food web change s (nutrient enrichment → excess phytopl ankton 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 (a nd therefore a lack of riverine

- based nutrient loading) and low ambient nutrient levels

. The fact that large numbers of sea turtles, and in particular juveni le green sea turtles, are using St. Joseph Bay, and depen d 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 M ortality E vent and the R ole of R ed 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 10 0 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 yearl y 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 b revetoxins, the naturally occurring neurotoxins produced by the red tide dinoflagellate K. brevi s, 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 intox ication 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. 20 07; Flewellin g 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 t he 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 bl oom 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 s tate . Harvesting areas are categorized based on their fecal coliform l evels 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 a s 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 r eopened 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) Li st

There are no i mpaired 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 G ulf of Mexico coast, and the imp airment will be addressed by a G ulf 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 o f nutrient enrichment. Seven sites are sampled monthly for TN, TP, chlorophyll a , and water clarity (Secchi depth), and 2 sites have da ta 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 scrutin y 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 F DEP anticipates that any
propose d water quality criteri on for chlorophyll a will be for corrected samples. T he uncorrected chlorophyll a data are expected to yield higher numbers than wh at F DEP will consider appropriate for the criteri on

. 2. The method for determining TN in water samples is not EPA approved, nor is it an approved method in the F DEP 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 F DEP SOPs. However, Bachmann and Canfield (1996) and Canfield et al. (2002) demonstrate d 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) sho wed that this preservation method did not significantly affect the analytical results.

Due to these inconsistencies between Project COAST lab analyses and F DEP 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 analyse s suggest that it is appropriate to u se the long

- term Project COAST datasets, in conjunction with other data sources, where available, to inform numeric nutrient criteria proposals.

Figure 6 shows l ong

- term average (2001

– 09) TN concentrations for individual St. Joseph Bay stations. Figure 7 presents b aywide 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 b aywide annual average TP conc entrations from 2001 to 2009. TP values are also low and stable across the bay, and over the monitoring period. Figure 10 shows l ong

- term average chlorophyll a and Secchi depth values for individual stations , and Figure 11 provides baywideDraft 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 w ater q uality m onitoring sites.Draft 20 August 2010 Figure 6. TN concentrations for St. Joseph Bay stations, 2001

– 09.

Figure 7

. Baywide m ean annual TN, 2001

– 09

. 0 50 100 150 200 250 300 350

2001 2002 2003 2004 2005 2006 2007 2008Total 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 2008Total 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 2008Cholorphyll (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 Pr eserve and LakeWatch / Project COAST for 2001 through 2009, f rom 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 an d physically fairly homogeneous with no salinity gradients

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

. Figures 1 2 through 1 4 show t he distributions of the geometric means for each parameter

. For all sites combined, the long

- term mean of the annual geometric mean s was calculated, and a log normal distribution function was fit to estimate the long

- term 75 th and 90 th percentile of the data (Table 8 ). TP concentrations were relatively low and s ta ble from 2001 to 2009, with fluctua tions of only a few micrograms per liter (μg/L). TN concentrations were also relatively low and st able over the 9- year period , ranging from 192 to 278 μg/ L

. Chlorophyll a concentrations were also lo w, with annual geomet ric means ranging from 1.1 to 3. 2 μ g/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 90 th percentile of annual geometric means are highlighted. Data TP (μ g/L) Log Normal Distibution TP (μ g/L) Empirical Percentile TN (μ g/L) Log Normal Distibution TN (μ g/L) Empirical Percentile Chlorophyll a (μ g/L) Log Normal Distibution Chlorophyll a (μ g/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 13.04 a 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 - 75 th percentile 14.99 14.29 254.47 253.35 2.44 2.29
90 th percentile 16.99 a 15.20 a 276.27 a 275.77 a 2.91 a 2.66 aDraft 24 August 2010 Figure 1 2 . Geometric mean of TP concentrations for all bay sites, 2001

– 09, and long

- term geometric mean of TP.

F

igure 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 2010TP (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 2010TN (μg/L) 

# Geometric Mean TN Concentration for SJB

Geometric mean TN
long term gm tnDraft 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 b etween Anthropogenic Nutrient Inputs and Adverse Biological Effects

The minimal a nthropogenic 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 p oint and nonpoint sources, contributes to low nutrient and chlorophyll concentrations in the bay (see T able 1 and F igure s 12 through 14 ). The most sensitive biological endpoint in St. Joseph Bay is seagrass, and the seagrass habitat is healthy based on hy perspectral 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

- trophic

level organisms.

St. Joseph Bay is fully meeting its Class II designated uses of shellfish p ropagation or harvesting

, with respect to nutrients, and the Class III uses deemed included within Class II, which are r ecreation, propagation
, and maintenance of a healthy

, well

- balanced population of fish and wildlife:

**•** The bay scallop populations are som e 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 2010chl a (μg/L) 

# Geometric Mean Chl A Concentration for SJB

Geometric Mean chl a
long term gm chl aDraft 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 ca use

- 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 crite rion 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 an d 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 surrou nding 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 statisti cal 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 exceed ed; 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 anDraft 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 long

term 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 compon ents 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 th at a eutrophic response occurs over such timeframes. If however, such a short

term response cannot be demonstrated, or there is no indicati on 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 deriv ed 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 a ssessment period, FDEP de rived criteria expressed as an annual geometric mean by using the 75 th 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 an nual 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

a veraged 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. I f 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

ne twork 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 t o be exceeded more
than twice in a five

- year period; and c) a n 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 geome tric mean shall not exceed the long term limit nor shall the average of all stations exceed the network average mo re 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 3.1Draft 29 August 2010 

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