# Site

- Specific Information in Support of Establishing Numeric Nutrient
Criteria for St. Andrew Bay

Florida Department of Environmental Protection Tallahassee, FL 32399

August 13

, 2010Draft ii July 2010 

### Table of Contents

Executive Summary

............................................................................................................... 1
Geographic and Physical Description

..................................................................................... 4

Sources of Nutrients

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

............................................................................................................. 10

Seagrass as the Key Biological Endpoint for St. Andrew Bay

........................................................... 10

Scallops

................................................................................................ ........................................ 14

Other Key Habitats and Biological Resources

................................................................................. 16



### Water Quality Studies

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

........................................................................................................ 17

Water Quality Analysis and Development of a Nutrient Criteria Approach Based on a Light Extinction Coefficient (Ke) (Hydroqual)

................................................................................. 23

Water Quality Monitoring by SAB

- RMA (in partnership with t he University of Florida [UF] Baywatch Program)

.............................................................................................................. 27



### Waters on the 303(d) List

..................................................................................................... 28

Numeric Nutrient Criteria Recommendations

...................................................................... 30

References

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

### List of Tables

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

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

........................................................................................ 7 Table 3. Seagrass coverage for the entire St. Andrew Bay study area (includes East Bay, North Bay, St. Andrew Sound, St. Andrew Bay, and West Bay), USGS

– U.S. Department of Agriculture (USDA) National Wildlife Research Center (NWRC) mapping.

............................... 13
Table 4. Estimates of seagrass acreage in St. Andrew Bay, 1992

– 2003, from USG S- NWRC mapping of seagrass coverage in northern Gulf of Mexico (Fitzhugh 2010b).

........................ 14

Table 5. Adult bay scallop density at each of 13 stations sampled at the St. Andrew Bay study site during each June from 1994 through 2006, and for those same 13 stations plus an additional 7 stations added for the 2007

– 08 survey. Scallop density at each station is reported per 600 square meter (m 2 ) transect. The results of the Waller

Duncan (W.D.) comparison of means (letters) are presented with the population means only for the original 13 sample stations for which the experimental design was balanced; similar letters denote averages that were not different at a significance level of 0.05. ‘Z’ indicates that the station was not sampled during that year. Note that the mean and standard deviation for 2007 and 2008 presented in the table are calculated from the original 13 stations only.

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

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

................................................ 18

Table 8. Summary of West Bay water quality data, 1991

– 2008 (Hydroqual 2010)

.................................. 23
Table 9. Summary of TN data for the St. Andrew Bay system from SAB

- RMA/UF Baywatch water quality monitoring program, 1990

– 2006.

................................................................................ 27
Table 10. Summary of TP data for the St. Andrew Bay system from SAB

- RMA/UF Baywatch water quality monitoring program, 1990

- 2006.

................................................................................. 27 Table 11. Summary of (uncorrected) chlorophyll a data for the St. Andrew Bay system from SAB

RMA/UF Baywatch water quality monitoring program, 1990

– 2006.

...................................... 27
Table 12. Waterbodies in the St. Andrew Bay Planning Unit that are on the 2010 Integrated Assessment (Cycles 1 and 2) verified list for impairments for either nutrients or DO (FDEP 2010a). *Note that these waterbodies are tributaries to the bay, not segments of the bay.

................................................................................................ ................................ . 29
Table 13. Waterbodies in the St. Andrew Bay Planning Unit that are proposed for delisting from the 1998 303(d) list for either nutrients or DO (FDEP 2010b).*Note that these waterbodies are tributaries to the bay, not segments of the bay.

........................................... 29
Table 14. Proposed numeric nutrient criteria for all segments of St. Andrew Bay, including TP, TN, and chlorophyll a. For compliance purposes, the long term geometric mean shall not exceed the long term limit nor shall the average of all stations in a segment exceed the network average more than twice in a 5 year period. The last column shows the value which a single station shall not exceed, by segment, more than twice in a 5 year period.

..................................................................................................................... 33Draft iv July 2010 

### List of Figures

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

................................... 5
Figure 2. Location and delineation of the hydrologically linked segments of St. Andrew Bay.

.................... 6
Figure 3. Bathymetric map of St. Andrew Bay system (Conmy 2010).

......................................................... 7 Figures 4 and 5. Location of point source discharges in western (top) and eastern(bottom) portions of the St. Andrew Bay Planning Unit.

........................................................................... 9
Figure 6. Land use and land cover map and area calculation in the St. Andrew Bay watershed (Conmy 2010).

........................................................................................................................... 10 Figure 7. St. Andrew Bay seagrass coverage trends, 1953 and 2003 (FDEP 2010). Tren ds were analyzed using aerial photography (black and white, 1:20K scale: 1953, 1964) (color, 1:24K scale: 1980, 1992, 2003).

................................................................................................ 12
Figu re 8. Trend of annual geometric means of TP in the St. Andrew Bay system and the long

term geometric mean for the sampling period.

........................................................................ 19
Figure 9. Trend of annual geometric means of TN in the St. Andrew Bay system and the long

term geometric mean for the sampling period.

........................................................................ 19
Figure 10. Trend of annual geometric means of chlorophyll a in the St. Andrew Bay system and the long

- term geometric mean for the sampling period.

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

................................................. 20
Figure 12. Comparison of geometric means of TN among bay segments.

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

................................ 21
Figure 14. Comparison between West Bay segments of annual geometric means of TN.

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

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

...................................................... 25 Figure 17. Light extinction coefficient (Ke) relationships in West Bay (Hydroqual 2010).

......................... 26Draft 1 July 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 numeric nutrient criteria for St. Andrew Bay. The primary purpose of the proposed numeric nutrient criteria is to protect healthy

, well

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

St. Andrew Bay is a large estuary with a small volume of freshwater input

. Econfina C reek, Deer Point Lake Reservoir, the Gulf Intracoastal W aterway (GIW W)

, and smaller creeks and bayous are the primary

sources of freshwater inflow, with a combined total discharge of less than 28.3 cubic meters per second ( m3/s ) ( Handley et al

. 2007 ). The low sediment load results in very clear waters, which in turn suppo rt extensive seagrass beds. Salinities are high, and often exceed 30 parts per thousand ( ppt ) (Brim 1998). St. Andrew Bay is biologically diverse and supports a large number of rare, endemic, and protected plants and animals. Seagrass species are an imp ortant foundation species and provide a host of ecosystem services. Economically important fisheries depend on the seagrass beds.

Sources of nutrient loading to the estuary come from the freshwater inflows listed above, as well as point sources (primarily wastewater treatment facilities [WWTFs] ) , nonpoint sources (stormwater runoff and septic tanks), natural inputs (leaf litter), atmospheric deposition, and ground water.

Seagrass es are the most sensitive biological endpoint in the St. Andrew Bay system, and data indicate that overall coverage has increas ed baywide approximately 14% from 1992 to 2003, after a decrease of approximately 8% from 1953 to 1992 (Brim and Handley 2002; Fitzhugh 2010 b ). Water quality studies indicate nutrient and chlorophyll concentrations throughout the bay are relatively low , and support healthy seagrass communities . FDEP therefore recommends setting numeric nutrient criteria at current ( 2000

– 09) levels.

Based on FDEP Impaired Surface Waters Rule (IWR) data, and s upport ing historical and current data,

FDEP recommend s numeric nutrient criteria for TN, TP, and chlorophyll a

. An explanation of the technical approach

, along with the numeric criteria, are given in the Numeric Nutrient Criteria
Recommendations section o f this report.Draft 2 July 2010 Table 1 a . Checklist of nutrient enrichment symptoms in St. Andrew Bay

- = Empty cell/no data; N/A = Not available Response Variable Observed Historically? Observed Currently? Explanation Source

Low dissolved oxygen ( DO ) (hypoxia/anoxia) No No No reports of low DO. -

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

is little freshwater input or turbidity, except for West Bay. Conmy 2010

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

– 09

Phytoplankton blooms

(nuisance or toxic) No Episodic Episodic Karenia brevis blooms in 1999

– 2000

, 2003

, 2005 , and

2007

, with origins outside the bay. Florida Fish and Wildlife Conservation Commission (FWCC) Fish and Wildlife Research Institute (FWRI) http://research.myfwc.com/features/ Problematic epiphyte
growt h No West Bay Epiphyte growth in West Bay Bowl area higher than in West Bay

Arm. Fitzhugh 2010 a

Problematic macroalgal growth No No No problematic macroalgal growth has been reported for the
system. -

S ubmerged aquatic

vegetation (S AV ) community changes or
loss Yes No, except for West Bay

“ Bowl ” SAV coverage has been increasing (14% from 1992 to 2003) after an 8% decline from 1953 to 1992. Coverage has increased in West Bay, but not in the West Bay “ Bowl ,” potentially due to
historic al physical disturbance. Brim and Handley 2002; Handley and Fitzhugh 2010 b

Emergent vegetation community changes or
loss No No None reported. -

Coral/hardbottom community changes or
loss N/A N/A - -

Impacts to benthic community No No None reported. -

Fish kills Yes Episodic Primarily related to Karenia brevis blooms. F WRI http://research.myfwc.com/fishkill/Draft 3 July 2010 Table 1b. Checklist of additional environmental factors in St. Andrew Bay

.

Factors Observed? Explanation Source Increased nutrient loading or
concentrations from historic al levels No Historic al levels are not well documented, but current concentrations from multiple datasets ( 19 90s to 2009) are not at levels indicating impairment

. STORET (IWR) data ; Hydroqual, St. Andrew Bay Resource Management
Association ( SAB

- RMA )
data Mitigating factors that could prevent nutrient expression Yes Turbidity, color Hydroqual 2010

Other significant stressors to biological
communities Yes Physical factors such as scarring from boat propellers

, historic al aquaculture in West Bay

, poor flushing

, sedimentation and turbidity from anthropogenic

activities

. Sargent, et. al 1995; Brim and Handley 2002

Natural episodic events contributing to
nutrient regime ( e.g., seasonal or hydrologically driven) Yes No major riverine inputs, but system is impacted by hurricanes, tropical storms, winter storms. Fitzhugh 2010 bDraft 4 July 2010 

### Geographic and Physical Description

St. Andrew Bay is a high

- salinity estuarine system located in the Panhandle of Florida in the Gulf Coastal Lowlands physiographic region. The estuary is situated almost entirely within Bay County in northwest
Florida (Figure 1). The St. Andrew Bay watershed lies entirely within northwest Florida, encompassing approximately 750,000 acres in Bay, Gulf, Jackson, Calhoun, Washington, and Walton Counties (N orthwest Florida Water Management District [N WFWMD ] 2000).

Panama City is the primary municipality surrounding the bay. Tourism and the military are the primary industries adjacent to the St. Andrew system, although much of Bay County is rural and supports
silviculture. Other industries include Smurfit

- Stone Container Co., Arizona Chemical, Port of Panama City, the Panama City

- Bay County International Airport , and the Northwest Florida Beaches International Airport (which open ed in 2010). Public ly owned , protected lands in the watershed include Camp Helen State Park, St. Andrews State Park, and St. Andrews Aquatic Preserve (FDEP, Coastal and Aquatic Managed Areas [CAMA] website, 2010 ).

The St. Andrew Bay system is made up of four hydrologic ally linked bays

— West Bay, North Bay, Eas t Bay

, and St. Andrew Bay proper

— with a combined area of approximately 243 square kilometers ( km2 ) (Figure 2)

. St. Andrew Sound is an adjacent coastal lagoon, although not directly connected to St. Andrew Bay. St. Andrew Bay is connected to the Gulf of Mexico through the man

- made and maintained
west pa ss and the intermittent east pass , and branches inland into the East, North, and West segments. The mean depth is 4 meters ( m) , with a maximum depth of 12 m (Conmy 2010) (Figure 3). Because of the depth and minimal tidal range, and the lack of major freshwater input, the bay is relatively poorly
flushed.

There are no major riverine input s to St. Andrew Bay , but minor sources of freshwater inflow include Econfina Creek, Deer Point Lake Reservoir (the primary source of drinking water for Bay County) , the

GIWW

, and smaller creeks and bayous. These sources have a combined total discharge of less than 28.3 m3/s ( Handley et al. 2007 ). The small volume of freshwater input is responsible for minimal s ediment loading (Brim 1998). The low sediment load results in low turbidity and very clear waters , which in turn support extensive seagrass beds. Other factors that contribute to the bay’s clarity are its spring

- fed

tr ibutaries, low amounts of silty clay in local soils

, and the filtering effect of the seagrasses and marshes

. Salinities are high, and often exceed 30 ppt (Brim 1998). As a result of the low freshwater inflow, deep basin, and strong influence of Gulf of Mexico water, the St. Andrew Bay system is described as a deep,
clear

, high

- salinity system (Keppner and Keppner 2001). Table 2 lists the physical characteristics of the St. Andrew Bay system. The St. Andrew bay system is biologically diverse and supports a large number of

rar e, endemic, and protected plants and animals. Seagrass species are important foundation species in the system and provide a host of ecosystem services. Economically important fisheries depend on the seagrass beds.Draft 5 July 2010 Figure 1. Location of St. Andrew Bay, and geographic features (NWFWMD, 2000)

.Draft 6 July 2010 Figure 2. Location and delineation of the hydrologically linked segments of St. Andrew Bay

.Draft 7 July 2010 Table 2

. St. Andrew Bay physical characteristics

. Physical C haracteristic Values Source
Estuarine surface area (km 2 ) 243 km2 Conmy 2010
Watershed area (km 2 ) 2, 800 km2 Conmy 2010 Mean depth (m) 4m (up to 12 m) Conmy 2010 Tidal range (m) 0.67m (spring) 0.06m (neap) Brim and Handley 2002

Mean water residence time (days) Ranges 35 (SAB) to 98 (West Bay) days (1%) Hydroqual 2010

Salinity and salinity zones 31 (av erage ) Conmy 2010

Figure 3

. Bathymetric map o f St. Andrew Bay system (Conmy 2010).



### Sources of Nutrients

Sources of nutrients to the St. Andrew Bay system include freshwater inflows (Econfina Creek, Deer Point Reservoir, and GIWW), p oint source discharges (primarily wastewater treatment facilities )

, nonpoint source inputs (septic tanks, stormwater from urban and agricultural areas), natural inputs ( plant leaf litter ), and atmospheric deposition.

Twenty

- one point source facilities discharge domestic and industrial wastewater directly into surface waters in the St. Andrew Bay watershed. An additional 23 facilities discharge to sprayfields, percolation ponds, and other nonsurface water areas. Figures 4 and 5 show the location of direct and indirect
di scharges in the St. Andrew Bay planning unit (of the Choctawhatchee

- St. Andrew Basin). In 1999, Bay County built an advanced wastewater treatment plant that eliminated 5 small point source discharges. This facility uses reclaimed water for upland irrigation. The current Panama City Beach surface water discharge (discharge is to West Bay) is scheduled to be removed before December 31, 2010. T h e discharge will be redirected to an upland disposal site on the west side of State Road 79

. AnthropogenicDraft 8 July 2010 n onpoint source s of nutrients include septic tanks and stormwater runoff. Septic systems in waterfront areas, even when functioning properly, may contribute nutrients to the bay through ground water (Knight and Wallman 2007). While septic systems are a source of anthropogenic nitrogen and phosphorus to St. Andrew Bay, routine water quality monitoring by FDEP and other data collectors
indicates that concentrations of nutrients and chlorophyll a are not elevated , and are not causing adverse impacts to biological communities in the system (s ee the Wa ter Quality Studies section ).

Stormwater enters the system through rainfall

- driven runoff and has the potential to contribute anthropogenic and natural sources of nutrients to the St. Andrew Bay system. The land uses of the St. Andrew Bay watershed are largely upland forest (including silviculture) ( 53% ) and water and wetlands ( 30%) (Figure 6 ). Approximately 8% of the land use is urban, most of which is the greater Panama City area adjacent to the bay. Five percent of the land use in the watershed is agriculture and rangeland. Stormwater runoff, particularly from the highly developed urban area s around the bay, is considered a potential threat to water quality in St. Andrew Bay, but the re is no evidence that current inputs from stormwater result in elevated nutrient concentrations or chlorophyll in the bay. Estimates of natural
sources of nutr ient inputs such as leaf litter remain unquantified.

A tmospheric deposition data for the area are available from the National Atmospheric Deposition Program’s National Trends Network (NADP

- NTN) , which has a collection site in the Panhandle ( FL23, in Sumatra, Florida ). Based on data for the most recently reported year (2008), estimates for atmospheric loading of nitrogen ammonia ( NH 4 ) and nitrate ( NO 3 ) for St. Andrew Bay are 0 .96 and 7.11 kilograms per hectare per year (kg/ha/yr) , respectively.Draft 9 July 2010 Figures 4 and 5. Location of point source discharges in western (top) and eastern(bottom) portions of
the St. Andrew Bay Planning Unit.Draft 10 July 2010 Figure 6. Land use and land cover map and area calculation in the St. Andrew Bay watershed (Conmy 2010).



### Biological Summary

Seagrass as the Key Biological Endpoint for St. Andrew Bay Seagrasses are important marine foundation species and are highly productive plants (Hughes et al. 2009). Their extensive root systems and dense, structured leaf canopies form habitat and provide food for a wide array of organisms, including commercially and recreationally important fish and invertebrates, wading birds, manatees, and sea turtles (Short and Wyl lie

- Echeverria 1996; Williams and Heck 2001; FDEP 2009). Seagrasses enhance sediment stability, decrease wave energy, increase water clarity, provide and stabilize habitats, and provide food and feeding pathways (see reviews by Phillips and McRoy 1980 ; Mc Roy and Helfferich 1977 ; Zieman and Zieman 1989).Draft 11 July 2010 Adverse impacts to seagrasses come from a variety of sources, including reduced water quality and clarity, overgrazing, and physical damage from boats, dredging and development . 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 proposed as “coastal canaries”

— biological indicators of changing coastal conditions (Orth et al. 2006).

Seagrasses have been shown to be adversely impacted by anthropogenic nutrient enrichment (Orth and Moore 1983; Tomasko et al. 1996). Reduced underwater light penetration appears to be a primary
driver of seagrass decline. The accepted thinking on this process is that increased inputs of nitrogen and phosphorus lead to the excess growth of phytoplankton and epiphytic algae, reducing available light to the seagrasses and causing decreased seagrass productivity and ultimately large

- scale seagrass loss es (Duarte 1995 ). This explanation, while valid, does not give a complete picture of the synergistic factors controlling seagrass production. “Top

- down” food web effects must also be considered. In control led,

in situ experimental studies in St. Joseph Bay, Florida, Heck et al. (2000) found that mesograzers (amphipods, caridean shrimp, gastropods, and hermit crabs) controlled the effects of nutrient enrichment on the abundance of epiphytes. It is therefore critical to consider the role of “top

- down” effects from overfishing or other food web disruptions in assessments of nutrient enrichment in St. Andrew Bay

.

Nearly 20,000 acres of seagrasses extend through the St. Andrew Bay system, the largest stock i n the
Panhandle. The s eagrass communities in the St. Andrew Bay system are essential for the commercially and recreationally important bay scallop, blue crab, penaeid shrimp, spotted seatrout, mullet, and redfish (NWFWMD 2000). Turtle grass ( Thalassia te studinum ) is the dominant seagrass species and provides the most habitat in St. Andrew Bay. This subtidal species grows to depths of 1.8 to 2.4 m in St. Andrew Bay proper and in St. Andrew Sound. Light attenuation appears to limit maximum growth depths t o 1.2 to 1.8 m in the interior bay segments. There are also extensive beds of manatee grass ( Syringodium filiforme ) and shoal grass ( Halodule wrightii ). Manatee grass is found within turtle grass beds, or less often in pure stands near the influence of clear, highly saline water entering the bay from
the G ulf (Brim and Handley 2002)

.

Shoal grass is a pioneer species that dominates the shallow and intertidal bay areas. These beds can be exposed to the air in winter when north winds push large amounts of water from the bay, and in spring
when north winds combine with low spring tide s ( Brim and Handley 2002 ). Wigeon grass ( Ruppia
maritima ) occurs in some of the fresher p arts of the bay, including some bayous. Star grass and paddle grass ( Halophila spp.) have been noted on rare occasions within turtle grass beds in the south part of St.
Andrew Bay (Brim and Handley 2002).

Historical Trends and Current Status of Seagrass Coverage

The U.S. Geological Survey ( USGS) produced a series of historical seagrass maps

, which the U.S. Fish and Wildlife Service ( USFWS ) used to analyze SAV coverage trends for St. Andrew Bay. These maps were
created from black

- and

- white aerial photo graphs taken in 1953 and 1964

, and from color aerial photography taken in 1980. Note that these photograph s were taken at various scales and that n o

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

coverage, leading to a degree of inherent error in this analysis. Table 3 shows t he results of the
historical trends analysis. The estimate of overall seagrass loss from 195 3 to 1992 was 8% (Brim and Handley 2002).Draft 12 July 2010 To document the more recent and current status of seagrass coverage in St. Andrew Bay, the USGS used 1992 and 2003 color aerial photography, and strict photointerpreta t ion and digitization standards. Other important aspects of the protocol included groundtruthing, quality control, and pe er review (Bri m and Handley 2002). Because the most r ecent effort in 2003 repeated the same imaging

, mapping , and groundtruthing techniques as the 1992 study, the results of these 2 years are more compar able and
reliable than the historic al trends data. Based on this analysis, there was an overall baywide increase in seagrass coverage of approx imately 14 % from 1992 to 2003, and a ll regions of the bay experienced

increase s in coverage (Table 4)

. Although seagrass coverage increased in all region s of the bay, including West Bay, seagrass recovery was not observed in the subregion of the West Bay “B owl .” Total seagrass overage in 2003 was comparable to 1953 (11,232 acres versus 11,848, respectively, although continuous coverage was greater in 2003, and patchy coverage less, than in 1953) (Figure 7)

.

Figure 7 . St. Andrew Bay seagrass coverage trends, 1953 and 2003 (FDEP 2010). Trends were analyzed using aerial photography (black and white, 1:20K scale: 1953, 1964) (color, 1:24K scale: 1980, 1992, 2003).Draft 13 July 2010 Tab le 3. Seagrass c overage for the entire St. Andrew Bay study area (includes East Bay, North Bay, St. Andrew Sound, St. Andrew Bay, and West Bay) , USGS

– U.S. Department of Agriculture (USDA) National Wildlife Research Center ( NWRC ) mapping

. C overage 1953 1964 1980 1992 2003

C ontinuous 3, 773 5, 394 5, 688 4, 225 6, 429

P atchy 8, 075 6, 234 4, 500 5, 607 4, 803
Total 11,848 11,629 10,190 9,832 11

, 232Draft 14 July 2010 Table 4. E stimates of seagrass acreage in St. Andrew Bay , 1992

– 2003, from USGS

- NWRC mapping of

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

- = Empty cell/no data

- East Bay North Bay St
Andrew
Sound St
Andrew

Bay West Bay Total

2003

- - - - - -
Continuous 960 1, 638 247 1, 862 1722 6, 429
Patchy seagrass 1, 763 338 690 1, 197 815 4, 803

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

, 232

1992 - - - - - -
Continuous 1, 631 988 54 1, 324 227 4, 224
Patchy seagrass 890 877 857 1, 258 1, 725 5, 607

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

% change 1992

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

Scallops Seagrass beds are essential habitat for the bay scallop ( Argopecten irradians ). Juveniles attach to grass blades as they make their transition from planktonic larvae to adults. They live elevated in the canopy
for 1 to 2 months until they grow larger and actively “ swim .” As in all estuaries and coastal waters that support scallops in Florida, populations fluctuate greatly in St. Andrew Bay. Because bay scallops are an annual species, local populations exhibit extreme variability and periodically collapse due to natural events such as salinity fluctuations

. Bay scallops are distributed in the St. Andrew Bay system primarily in St. Andrew Bay proper.

The FWRI Molluscan Fisheries P rogram surveys adult populations of th e bay scallop on the west coast of Florida from Pine Island Sound to St. Andrew Bay (Table 5) . The primary objective of these surveys is to assess changes in scallop population abundance that may occur in response to management and
restoration efforts b eg un in Florida in 1994 (Arnold et al. 2008). The program also monitors recruitment and reports on restoration activities.

A current snapshot of the adult scallop populations and spat recruitment in St. Andrew Bay in the past 2 seasons is summarized below. This summary illustrates the fluctuations that characterize scallop populations. St. Andrew Bay adult scallop abundance decreased in 2008 and continued to be classified as “collapsed.” Scallops were recorded at 11 of 20 survey stations, but at no site were they abundant.

New individuals to the scallop population were estimated using spat collectors. At the 10 St. Andrew Bay stations, scallop recruits were recorded during each retrieval event in 2008, with a peak in March and then again in November through December. Of the 90 collectors deployed in 2008, 9 (10.0%) were not retrieved, 11 (12.2%) retrieved had 0 scallops, 50 (55.6%) had bay scallops, and 5 (5.6%) had calico scallops. Other Pectinid species were observed on the collectors deployed at t his site during 2008, including Ravenel’s ( Pecten raveneli ) and Rough ( Aequipecten muscosus ) scallops.Draft 15 July 2010 Table 5. Adult bay scallop density at each of 13 stations sampled at the St. Andrew Bay study site during each June from 1994 through 2006, and for those same 13 stations plus an additional 7 stations added for the 2007

– 08 survey. Scallop density at each station is reported per 600 square meter ( m 2 )

transect. The results of the Waller

- Duncan (W.D.) co mparison of means (letters) are presented with the population means only for the original 13 sample stations for which the experimental design was balanced; similar letters denote averages that were not different at a significance level of 0.05. ‘Z’
indic ates that the station was not sampled during that year. Note that the mean and standard deviation for 2007 and 2008 presented in the table are calculated from the original 13 stations only.

St. Andrew Bay scallop abundance increased in 2009, reaching a healthy status (>25 scallops/600m 2 ) for the first time in 13 years. Scallops were recorded at 13 of the 20 survey stations, with no scallops found in the north end of the bay. Of the 261 scallops measured in 2009, shell heights during the June sampling effort ranged from 14 to 69 ( millimeters [ mm ]) , the average was 45.5 mm , and the most frequent shell heights recorded were 45 and 48 mm . Even though the population status reached a healthy level, it is not a resilient population, and restoration efforts w ill continue in this estuary.

Recruitment monitoring occurred at 10 stations in the St. Andrew Bay area in 2009. Of the 110 collectors deployed in 2009, 102 were recovered and processed. Of those 102 collectors, spat were present on 79 (77.5%, which was the highest rate of monitored sites statewide in 2009). The total spat observed at this site in 2009 was 2,639, the average was 25.9 per collector, and the maximum number found on a single collector was 235.Draft 16 July 2010 The relationship between scallop populations and nutrient inputs is complex, and very limited data exist to address the issue. Because they are filter

- feeders of phytoplankton, and phytoplankton production is driven by nitrogen and phosphorus, some level of nutrient inputs is necessary to maintain healthy populations of all bivalves, including scallops (Geiger, pers. comm. 2010 ). The optimal level has not been quantified and is likely to be variable among areas due to differences in hydrologic conditions, nutrient cycling, and habitat. Nutrient loadings that lead to excessive eutrophication are harmful to scallops if they are associated with low DO an d seagrass loss (Geiger, pers. c omm. 2010 ).

One plausible

, yet untested

, hypothesis about nutrient effects on scallops or other bivalves is that as nutrient levels rise, the phytoplankton community shifts from one dominated by diatom s to a dinoflagellate

- dominated community. This shift would decrease the abundance of phytoplankton of the correct form and size for the bivalves to filter (Geiger, pe rs. c omm. 2010 ).

Despite the limited information on the effects of nutrients on scallops, it is clear that the relatively low nutrient concentrations and chlorophyll a values in St. Andrew Bay would not limit scallop populations.

Other Key Habitats and Biological Resources The St. Andrew Bay system is one of the most diverse ecosystems in North America, rivaling Florida’s Indian River Lagoon, which is characterized as the most biologically diverse estuary in the U nited States (Brim and Handley 2002). The estuary supports approximately 3,643 species of fish, birds, mammals, reptiles, and shellfish, including a significant number of rare, endemic, and protected species (Table 6 ). St. Andrew Bay also supports a number of commercially important fish and shellfish species

, including Spanish mackerel, king mackerel, spotted sea trout, mullet, grouper, pompano, flounder, shrimp, blue crab, and scallops ( F DEP CAMA website, 2010 ).

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

- watching,
and other tourism

- related activities.Draft 17 July 2010 Table 6

. Rare/ e ndangered s pecies in the St. Andrew Bay s ystem

.

- = Empty cell/no data State listings are taken from the F WCC ; f ederal listings are taken from the U SFWS

. E = Endangered; T = Threatened; T (s/a) = Threatened due to similarity in appearance; SSC = Species of Special Concern; N/A = information not available or no designation listed
Common Name Scientific Name State Federal

Fish - - - Gulf sturgeon Acipenser oxyrhynchus SSC N/A
Salt marsh topminnow Fundulus jenkinsi SSC N/A
Reptiles - - - American alligator Alligator mississipiensis SSC T (s/a)
Atlantic loggerhead turtle Caretta caretta caretta T T Atlantic green turtle Chelonia mydas mydas E E Kemp's ridley sea turtle Lepidochelys kempi E E

Birds - - - Southeastern snowy plover Charadrius alexandrinus tenuirostris T N/A

P iping plover Charadrius melodus T T Arctic peregrine falcon Falco peregrinus tundrius E T American oystercatcher Haematopus palliatus SSC N/A

B ald eagle Haliaeetus leucocephalus T T

B rown pelican Pelecanus occidentalis SSC N/A

L east tern Sterna antillarum T N/A

Mammals - - - Choctawhatchee beach mouse Peromystus polionotus allophrys E E

Florida manatee Trichechus manatus E E



### Water Quality Studies

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

were collect ed from January 2000 to December 2009, and the spatial scale covered the entire bay system (all segments with waterbody identification [WBID] numbers characterized as “estuary”). For the IWR data, all stations were combined, and annual geometric means were calculated for total phosphorus ( TP )

, total nitrogen ( TN ) , and chlorophyll a

. Figures 8 through 10 sh ow t he distribution of
the baywide geometric means and the long

- term geometric means for each parameter

. Annual geometric means for TP were low, ranging from 12.1 to 24.8 μg/L

, with a long term geometric mean of 15.5 μg/L. Annual geometric means for TN fluctuated, but were overall relatively low

, ranging from 277.4 to 561.4 μg/L, with a long

- term geometric mean of 403.64 μg/L. Chlorophyll a concentrations were low, with annual geometric means ranging from 1.9 to 4.5 micrograms per liter (μ g/L ) and displaying a decreasing trend after 2003. The long term geometric mean was 2.8 μg/L. It is important to note that approximately one

- third of the chlorophyll a data were reported as below the minimum detect limit (mdl) of 5 μg/ L . Values reported as “belo w detect” were assigned a value equal to one

- half
of the mdl (2.5 μg/ L ).

In an additional analysis, FDEP grouped stations into the following segments: West Bay, North Bay, St. Andrew Bay, East Bay, and Grand Lagoon

. These regions are commonly used geogr aphic delineations inDraft 18 July 2010 water quality and biological studies of the system. Figures 11 through 13 show the results of a comparison of trends in the geometric means among the various bay segments from 2000 to 2009 for TP, TN, and chlorophyll a

. Geometric me ans for TP, TN, and chlorophyll a track relatively closely for each of the bay segments over the 10 year period, with the exception of North Bay, which has spikes for TP and TN in 2003 and 2007, and a spike in 2003 for chlorophyll. Data for North Bay also were limited, and were not sufficient to calculate geometric means for 6 out of the 10 years of record.

FDEP also analyzed a dissolved oxygen (DO) dataset from STORET, collected from 1967

- 2010. For analysis, t hese data were separated into an historic (1967

- 1999) and a recent (2000

- 2010) period. A summary of the DO data is shown in Table 7.

Table 7. Summary of St. Andrew Bay system dissolved oxygen (DO) data
Mg/L = Milligrams per liter
2000

- 2010 1967

- 1999 Segment N Percent
less than

5mg/L Percent
less than 4 mg/L Mean (mg/L) N Percent
less than

5mg/L Percent
less than 4 mg/L Mean (mg/L)

St. Andrew Bay 666 17% 9% 6.85 2053 17% 10% 6.75 East Bay 3769 22% 10% 6.72 6192 9% 5% 7.23 Grand Lagoon 188 13% 6% 7.01 262 15% 6% 6.74
Mouth 181 7% 3% 7.24 278 18% 11% 6.58 North Bay 2716 24% 12% 6.34 3872 8% 4% 7.18 West Bay 3094 18% 7% 6.72 2707 6% 3% 7.39

To determine if there were localized adverse water quality impacts in the West Bay “Bowl

, ” an area with

extensive historical seagrass loss and little recovery, FDEP also divided West Bay into the West Bay “Bowl” and the West Bay “Arm,” and compared TN and TP over the same 10

- year sampling period. Figures 1 4 and 1 5 show the results of t his comparison. Annual geometric means of TN for the 2 areas tracked very closely over the entire sampling period. TP did not track as closely, but the ove rall trend was similar, and the differences in mean values were small ( a maximum of 10 μg/L). Based on these results, FDEP concluded that it is appropriate to group the West Bay “Bowl” and “Arm” stations.Draft 19 July 2010 Figure 8

. Trend of annual geometric means of TP in the St. Andrew Bay system and the long

- term geometric mean for the sampling period.

Figure 9

. Trend of annual geometric means of TN in the St. Andrew Bay system and the long

- term geometric mean for the sampling period. 0 5 10 15 20 25 30

1995 2000 2005 2010TP μg/L 

## St. Andrew Bay Geometric Mean Total Phosphorus

annual geo mean

long term geo mean

0 100 200 300 400 500 600

1998 2000 2002 2004 2006 2008 2010TN μg/L 

## St. Andrew Bay Geometric Mean Total Nitrogen

annual geo mean TN Baywide

long term geo mean

TNDraft 20 July 2010 Figure 10

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

- term geometric mean for the sampling period.

Figure 11 . Comparison of geometric means of TP among bay segments. 0 0.5

1 1.5

2 2.5

3 3.5

4 4.5

5

1998 2000 2002 2004 2006 2008 2010Chlorophyll a μg/L 

## St. Andrew Bay
Geometric Mean Chl a

St. Andrew Bay
Geometric Mean Chl a

long term geo mean

0 5 10 15 20 25 30 35 40 45 50

1998 2000 2002 2004 2006 2008 2010TP μg/L 

## St. Andrew Bay System Total Phosphorus

SAB

West Bay

North Bay

East Bay

Baywide

Grand Lagoon TPDraft 21 July 2010 Figure 12

. Comparison of geometric means of TN among bay segments.

Figure 13

. Comparison of geometric means of chlorophyll a among bay segments. 0 100 200 300 400 500 600 700 800 900

1998 2000 2002 2004 2006 2008 2010TN μg/L 

## St. Andrew Bay System Total Nitrogen

SAB TN

West Bay TN

North Bay TN

East Bay TN

Baywide TN

Grand Lagoon TN

0 2 4 6 8 10 12

1998 2000 2002 2004 2006 2008 2010Chlorophyll a μg/L 

## St. Andrew Bay System Chlorophyll a

SAB Chl a

West Bay Chl a

North Bay Chl a

East Bay Chl a

Baywide Chl a

Grand Lagoon Chl aDraft 22 July 2010 Figure 1 4

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

.

Figure 1 5

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

. 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7

2000 2002 2004 2006 2008 2010TN μg/L 

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

ARM geo mean TN

BOWL geo mean TN

0 0.005

0.01 0.015

0.02 0.025

2000 2002 2004 2006 2008 2010TP μg/L 

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

ARM geo mean TP

BOWL geo mean TPDraft 23 July 2010 Water Quality Analysis and Development of a Nutrient Criteria Approach B ased on a Light Extinction Coefficient (Ke) (Hydroqual) Hydroqual, Inc.

, used data available from the IWR database and STORET from 1990 to 2008 to investigate the relationships between TN, TP, chlorophyll a , color, and S ecchi depth in West Bay (Table 8) . In additio n, a light extinction coefficient, Ke , was calculated using S ecchi depth and an empirically derived constant (1.7). Data were analyzed to determine what relationships exist between parameters and how the various parameters affect light extinction. In add ition, Hydroqual assessed the existing

seagrass coverage and the water depths associated with the seagrass beds to determinat e the water depth where seagrass es can grow in the bay. Chlorophyll a a nd various nutrient parameters were strongly correlated, except for nitrate/ nitrite ( NO2+NO3 ) (Figure 1 6 ).

Hydroqual noted that these relationships could be used to determine bay nutrient levels for a given target chl orophyll a level. For example, i f the historic minimum level of 5.54 μg/L were used as a targ et (the Impaired Waters Rule uses the historic minimum value as one of the impairment thresholds for estuaries)

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

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

geo metric mean s were 407 μg/L TN and 15 μg/L TP, and Hydroqual arithmetic means were 378 μg/L and 19 μg/L .) Hydroqual found no correlation between chlorophyll a and salinity over a range of 5 to 35 ppt, which may i ndicate that freshwater source s of nutrients do not contribute significantly to chlorophyll a levels in West Bay. Figure 1 7 presents the observed relationships between light extinction
and chlorophyll a , color, turbidity

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

Hydroqual also used multiple linear regression t o determine the relationship between light extinction
and chlorophyll a and color. Based on this relationship, e xisting algal productivity is not limiting seagrass productivity in the bay. For example, using this equation and l ight extinction coefficients for a 1.5 m water depth ( the average maximum water depth to which seagrasses extend is 1.3 m) , and an average

c olor of 28.9 platinum

- cobalt units (PCU), the resulting chlorophyll a values providing between 15 % to
25% bottom light range from 8 to 20 μg/L, which is much higher than existing levels. In addition, the
contribution of chlorophyll a to the total light ex tinction coefficient is small. At 5.54 μg/L chlorophyll a , the contribution is approximately 17%. Existing water column transparency as a function of chlorophyll

a , color

, and background conditions at this water depth, is sufficient to provide 15 % to 25% of surface
PAR at the bottom light for seagrass survival and growth in West Bay. The p ercentage of surface light required for seagrass growth varies depending on individual species requirements, epiphyte coverage, and site specific conditions, but typ ically range s between 15 and 25% (Dixon, 2000) ( Steward, et. al, 1995).

Table 8. Summary of West Bay water quality data, 1991

– 2008 (Hydroqual 2010 )

- = Empty cell/no data Mg/L = Milligrams per liter
PCU = Platinum Cobalt Unit
Year Chl orophyll a (μg/L) T N (mg/L) TP (mg/L) Color (PCU) Secchi

D epth

(m) Light
Extinction

K e (1/m)

1991 5.00 0.394 0.015 - 1.95 0.87

199 2 3.85 0.269 0.015 - 1.95 0.87

199 3 3.50 0.319 0.014 - 1.67 1.02

199 4 3.71 0.268 0.021 - 1.62 1.05

199 5 2.77 0.279 0.015 23.8 2.31 0.74Draft 24 July 2010 199 6 4.88 - 0.028 31.3 1.90 0.90

199 7 4.07 0.292 0.017 20.0 2.90 0.59

199 8 4.28 0.417 0.022 36.0 1.56 1.09

199 9 3.54 0.300 0.017 - 2.25 0.76

2000 4.93 0.275 0.019 - 1.93 0.88

200 1 6.55 0.366 0.028 30.0 1.51 1.13

200 2 5.08 0.344 0.019 26.3 2.03 0.84

200 3 5.89 0.409 0.02 42.9 2.22 0.77

200 4 4.79 0.355 0.017 30.0 2.74 0.62

200 5 4.88 0.425 0.013 38.3 2.91 0.58

200 6 5.22 0.563 0.015 22.5 3.04 0.56

200 7 5.75 0.557 0.019 21.1 1.08 1.58

2008 4.09 0.602 0.022 24.7 - - Average 4.60 0.378 0.019 28.9 2.09 0.87Draft 25 July 2010 Figure 1 6 . Chlorophyll a relationships in West Bay (Hydroqual 2010)

.Draft 26 July 2010 Figure 17. Light e xtinction c oefficient (Ke) relationships in West Bay (Hydroqual 2010)

.Draft 27 July 2010 Water Quality Monitoring by SAB

- RMA ( in partnership with the University of Florida [ UF ] Baywatch
Program )

SAB

- RMA

, in partnership with the U F Baywatch Program

, has routinely sampled water quality in the St. Andrew Bay system since 1990. Table s 9 through 11 summarize TN, TP, and chlorophyll a (uncorrected)
data in the St. Andrew Bay system from 1990 to 2006

. Total nitrogen (TN) concentrations are relatively low, with median values between 210 and 290 μg/L for each of the segments and a range of 50

- 1,000 μg/L, except for Grand Lagoon, with a me dian concentration of 410 μg/L , and a range of 110

- 1,450 μg/L. Total phosphorus (TP) concentrations are also low, with median values between 12 and 17 μg/L for all of the segments, and a range of 3

- 390 μg/L, except for Grand Lagoon, with a median

concent ration of 28 μg/L , and a range of 4

- 350 μg/L. Chlorophyll a concentrations are also low, with medians between 2 and 4 μg/L, and a range of 0

- 18 μg/L for all segments except Grand Lagoon, with a median of 5, and a range of 0

- 80 μg/L.

Table 9

. Summary of TN data for the St. Andrew Bay system from SAB

- RMA/UF Baywatch water quality monitoring program, 1990

–

2006.

TN Number of samples Mean/Med ian (μg/L) S tandard
Deviation

(μg/L) Range (μg/L)

West Bay “Bowl” 103 312/290 119 50

- 690 West Bay “Arm” 314 269/250 95 40

- 590 St. Andrew Bay 460 236/210 118 60 -1, 000 Grand Lagoon 436 458/410 215 110 -1, 450

Table 10 . Summary of TP data for the St. Andrew Bay system from SAB

- RMA/UF Baywatch water quality monitoring program, 1990

- 2006.

TP Number of samples Mean/Med ian (μg/L) S tandard
Deviation

(μg/L) Range (μg/L)

West Bay “Bowl” 103 21.5/17 14.5 8- 138 West Bay “Arm” 315 14.6/13 5.3 3- 45 St. Andrew Bay 464 16.3/12 27.5 3- 390 Grand Lagoon 437 35.8/28 30 4- 350

Table 11

. Summary of (uncorrected) chlorophyll a data for the St. Andrew Bay system from SAB

RMA/UF Baywatch water quality monitoring program , 1990

–

2006.

Chl orophyll a Number of samples Mean/Med ian (μg/L) S tandard
Deviation

(μg/L) Range (μg/L)

West Bay “Bowl” 104 4.7/4 2.8 1- 17 West Bay ”A rm ” 316 3.7/3 2.5 1- 17 St. Andrew Bay 488 2.6/2 2 0- 18 Grand Lagoon 442 8.3/5 9.4 0- 80Draft 28 July 2010 

### Waters on the 303(d) L ist

Waterbodies within the St. Andrew Bay Planning Unit that are listed for nutrient or DO impairments are shown in Table 12. These impairment listings are from an integrated assessment (Cycles 1 and 2)
verified list. Table 1 3 shows w aters proposed for delisting. In the St. Andrew Bay Planning Unit , waters are also listed as impaired for the following parameters: mercury (in fish tissue), bacteria, and fecal coliform bacteria. Mercury impairments are not related to anthropogenic nutrient inputs. The relationship between bacteria and anthropogenic nutrients is more complex, because although potential sources of bacteria may also be sources of nutrients, the presence of fecal coliform or enterococci
bacteria does not necessarily indicate the presence of anthropogenic nutrients.

The use of fecal coliforms as indicat ors of the presence of human pathogens has been under scrutiny in Florida for the past decade. One of the priorities of the Gulf of Mexico Alliance (GOMA) is to improve microbial source tracking (MST) and pathogen detection methods for use under Gulf of M exico conditions (GOMA 2009). The GOMA Pathogens Workgroup recently submitted comments regarding
the status of the U.S. Environmental Protection Agency’s ( EPA ) recreational water quality criteria (GOMA 2009). The workgroup expressed concern that the EPA recreational criteria were derived in places that do not represent Gulf of Mexico conditions, and that the use of fecal indicators was not appropriate for waters primarily influenced by animal sources. Areas in the Gulf of Mexico for which the workgroup t hought the EPA criteria might not be appropriate included low

- population

- density coastal areas, areas of heavy rainfall, subtropical latitudes, and areas where waters contain a large amount of organic detritus material and/or colored dissolved organic matt er (CDOM ) ( GOMA 2009).

Boehm et al. (2009) express similar concern about the current and proposed recreational criteria, and specifically call attention to the need for further research and revision in tropical waters and waters adversely impacted by urb an runoff and animal feces. FDEP recognizes that fecal coliform and
enterococci bacteria may indicate a human source , or may co

- occur with anthropogenic nutrient inputs

, but there is ample evidence to caution against assuming that the presence of these ba cteria automatically indicate s the presence of anthropogenic nutrients.

The following text is excerpted from a review conducted by Dr. V.J

. Harwood of the University of South Florida as part of a n MST project she is conducting for F DEP:

The main groups of indicator bacteria for recreational water quality assessment in use today include fecal coliforms, or a specific member of that group, Escherichia coli, in fresh water and the genus Enterococcus in both fresh and estuarine/marine waters. However, in orde r for the indicator concept to work optimally there are many assumptions that must hold true. One of the most important assumptions is that
indicator bacteria must co

- occur with human pathogens when pathogens are present and pose a human health risk. Unf ortunately, recent research has indicated that this assumption is often false by showing that the presence of indicator bacteria do not always correlate well with the presence of pathogens such as Salmonella, Campylobacter, Cryptosporidium, Giardia, or enteric viruses ( Anderson et al. 2005 ; Bonadonna et al. 2002 ; Harwood et al. 2005 ; Lemarchand and Lebaron 2003 ; Lund 1996 ; Rees et al. 1998 ).Draft 29 July 2010 One important reason for the lack of correlation between traditional fecal indicator bacteria and pathogens is that the indicator bacteria are not specific to humans, nor to other hosts known to shed human pathogens in their feces, but are present in the intestines of all warm

- blooded animals and some cold

- blooded animals ( Souza et al.

1999 ). Because not all animals are equally likely to carry human pathogens, contamination from all sources does not represent an equal health risk. Thus, some sources of fecal contamination in water are of greater concern than others. Furthermore, there is increasing evidence of naturalized or environmentally adapted strains indicator bacteria (both coliforms and enterococci) that are capable of persisting in a culturable form for extended periods, or even growing, in a wide variety of environmental matrices, including terrestrial soils, aquatic sediments, and attached to aquatic vegetation (Byappanahalli and Fujioka 1998 ; Byappanahalli et al. 2003 ; Ishii et al. 2006 ; Jeng et al. 2005 ; Ksoll et al. 2007 ; Solo

- Gabriele et al. 2000 ; Topp et al. 2003 ; Whitman et al. 2003 ). If indicator bacteria are persisting in environmental matrices

, their reintroduction into the water column, which may occur during storms or high recreational activity, may lead to false positive indications regarding contamination and public health risk. As a result of these two confounding factors, it is now clear that simply measuring concentrations of waterborne indicator bacteria do not offer detailed enough information to properly determine health risks associated with recreational

water use. Furthermore, this pract ice does not allow specific sources of contamination to be identified or targeted for remediation of water quality. ”

Table 12. Waterbodies in the St. Andrew Bay Planning Unit that are on the 2010 Integrated Assessment (Cycles 1 and 2) verified list for impairments for either nutrients or DO (FDEP 2010a). *Note that these waterbodies are tributaries to the bay, not segments of the bay.
Waterbody Name Type WBID Impairment(s) Direct Runoff to Bay Stream* 1060 DO (nutrients and biochemical oxygen demand [BOD]) (chlorophyll a ) Little Sandy Creek Stream* 1155 DO (nutrients

– nitrogen) Direct Runoff to Bay Stream* 1184 DO (nutrients and BOD) (chlorophyll a )

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

Table 13. Waterbodies in the St. Andrew Bay Planning Unit that are proposed for delisting from the 1998 303(d) list for either nutrients or DO (FDEP 2010b).*Note that these waterbodies are tributaries to the bay, not segments of the bay.
Waterbody Name Type WBID Impairment(s)

Peach Creek Stream* 986 Nutrients (historical chlorophyll a )

Western Lake Outlet Estuary 1009 Nutrients (historical chlorophyll a ) Direct Runoff to Bay Estuary 1053 Nutrients (chlorophyll a and historical chlorophyll a ) Parker Bay Estuary 1141 DO and nutrients (chlorophyll a and historical chlorophyll a ) Pitts Bay Estuary 1172 Nutrients (chlorophyll a )
West Bay Estuary 1061A Nutrients (historical chlorophyll a )Draft 30 July 2010 

### Numeric Nutrient Criteria Recommendations

St. Andrew Bay is fully meet ing its Class II designated uses , “ s hellfish p ropagation or h arvesting,” and
“r ecreation, p ropagation and m aintenance of a h ealthy, w ell

- balanced population of fish and wildlife, ” indicating that current nutrient levels are fully protective, as follows:

**•** Seagrasses ( the most sensitive biological endpoint) are healthy

, and coverage
increased 14% baywide from 1992 to 2003.

**•** B ay scallop populations increased in 2009, attaining “healthy” status. Recruitment
in 2009 was the strongest of all sites monitored in the state.

**•** The estuary supports approximately 3,643 species of fish, birds, mammals, reptiles, and shellfish, including a significant number of rare, endemic, and protec ted species. This diversity in St. Andrews Bay r ivals that of the Indian River Lagoon (described as
the most biologically diverse estuary in North America).

There is considerable evidence to demonstrate that existing nutrient levels in St. Andrew Bay are providing fo r full aquatic life use support . It should be noted that the West Bay “Bowl” segment experienced significant loss of seagrass following predominantly physical disturbance from a 1970s aquaculture operation. Although seagrass coverage in Wes t Bay as a whole is now increasing, seagrasses have not recovered in the West Bay “Bowl”. However, t he current nutrient and chlorophyll a concentrations in this area sh ould provide for full recovery of seagrasses

. FDEP therefore proposes

nutrient concentration criteria that would maintain the current conditions

, as reported from 2000 to 2009 water qualit y monitoring data for each segment of the bay

.

Proposed Numeric Nutrient Criteria

Methodology

For consistent appli cation 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 ad verse 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 relations hip, the magnitude may be set at a level designed to maintain the current data distribution, accounting for natural temporal variability, when the current conditions are protective of the designated uses of the waterbody. Since a criterion derived based on the existing data distribution has no direct link to any observed cause and effect relationship, it is assumed that maintaining the current data distribution will preserve the uses associated with that distribution.Draft 31 July 2010 The frequency and duration component s 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 accou nt for the natural variability surrounding the magnitude expression and to

control for statistical errors.

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

for St. Andrew Bay is described briefly below. More details concerning the statistical approaches use d

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 -t erm geometric mean never to be exceeded; and b) an annual geometric mean, not

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

- term average condition was adjusted to a level that represents an insignificant increase from the baseline. Allowing for an insignificant increase accounts for uncertainty in the estimate of the mean and partially addresses the fact that the reference based approach fails to identify a threshold of imbalance, and thus is highly
prone to excessive Type I error. For the purpose of antidegradation evaluations, EPA has established that a ten percent change in a water quality parameter represents an insignificant departure from the
historical condition, known as a de minimus change (US Sixth Circuit Court 2008). T herefore, 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 wa terbody.

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

- ef fect relationship has demonstrated that 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 beDraft 32 July 2010 above the long

- term mean. Therefore, the long

- term target must be adjusted to allow for the application to a shorter duration with an acceptable Type I error rate of no more than a 10 percent.

An annual criterion with an approximate 10 percent Type I error rate for a given frequency was derived by appropriately accounting for the annual variability above the mean. This annual target concentration was derived as an upper percentile of the distribution of the annual geometric mean concentrations. Previous proposals by EPA have utilized three

- year assessment periods to express the duration nutrient
criteria components. A lthough 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 Ni ño, La N iñ a), 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 derived 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 ma gnitude that, when expressed as an annual geometric mean not to be exceeded more than twice during a five

- year period, will achieve the targeted 10 percent error rate

. The magnitude component of the criteria (not to be exceeded more
than twice in a 5 year period) was established to allow for two separate assessments:

**•** As an annual geometric mean for a network of stations in a specified segment of the waterbody;

and

**•** As an annual geometric mean for a single station in a given segment.

The two expressions o f 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 distrib ution 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 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 thre e 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) a n annual geometric mean of val ues from a single location, not to

be exceeded more than twice in a five

- year period.Draft 33 July 2010 The proposed long

- term targets for the protection of a healthy, well

- balanced aquatic community in St. Andrew Bay as well the annual limits for each segment, are provided in Table 1 4.

Table 1 4. Proposed numeric nutrient criteria for all segments of St. Andrew Bay , including TP, TN, and chlorophyll a. For compliance purposes, the long term geometric mean shall not exceed the long term limit nor shall the average of all stations in a segment exceed the network average more than twice in a 5 year period. The last column shows the value which a single station shall not exceed, by segment, more than twice in a 5 year period.
N/A=not available. Data did not meet sufficiency requirements for analysis, so criteria not yet proposed for segment *Baywide analysis did not include Grand Lagoon or Mouth segments

Total Phosphorus ( μ g/L)

Segment Existing Long Term
Geometric

Mean Maximum
Allowed Long Term
Geometric

Mean Annual

Geometric Mean
for a Network of Stations (2 of 5 year exceedance rate) Annual Geometric Mean for a Single Site (2 of 5 year exceedance rate)

Central Bay 16.5 18.2 25.6 29.9

East Bay 13.8 15.2 20.1 25.9 Grand Lagoon 14.2 15.6 26.5 36.6
Mouth 9.0 9.9 12.5 13.7 North Bay 11.5 12.7 14.8 16.4 West Bay 16.1 17.7 22.3 26.1 Baywide * 16.1 17.8 22.7 26.4 Total Nitrogen ( μ g/L)

Segment Existing Long Term
Geometric

Mean Maximum
Allowed Long Term
Geometric

Mean Annual

Geometric Mean
for a Network of

Stations (2 of 5 year exceedance rate) Annual Geometric Mean for a Single Site (2 of 5 year exceedance rate)

Central Bay 419 461 626 651

East Bay N/A N/A N/A N/A Grand Lagoon 407 448 552 569
Mouth 322 354 508 526 North Bay N/A N/A N/A N/A
West Bay 415 456 555 582 Baywide * 415 456 575 626 Chlorophyll a (ug/L)Draft 34 July 2010 Segment Existing Long Term
Geometric

Mean Maximum
Allowed Long Term
Geometric

Mean Annual

Geometric
Mean for a
Network of Stations (2 of 5

year exceedance rate) Annual Geometric Mean for a Single

Site (2 of 5 year exceedance rate)

Central Bay 4.6 5.0 5.8 5.8

East Bay N/A N/A N/A N/A Grand Lagoon 2.5 2.7 3.2 3.4
Mouth 2.1 2.3 3.0 3.0 North Bay N/A N/A N/A N/A
West Bay 3.3 3.6 5.5 6.4 Baywide* 3.5 3.9 5.8 6.1Draft 35 July 2010 

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