# Site

- Specific Information in Support of Establishing Numeric Nutrient Criteria for Pensacola 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 Geographic and Physical Description

..................................................................................... 2
Sources and Fates of Nutrients

.............................................................................................. 9 Mitigation of Point Sources

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


### Biological Summary

............................................................................................................. 15

SAV in Pensacola Bay

................................................................................................................... 16
Nutrient Effects on Algae, Invertebrates, and Fish in Pensacola Bay

............................................... 18 Santa Rosa Sound/Big Lagoon

...................................................................................................... 22
Restoration Efforts

....................................................................................................................... 24
Shellfish Survey

............................................................................................................................ 25


### Water Quality Studies

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

..................................................................................................... 30 Proposed Numeric Nutrient Targets

............................................. Error! Bookmark not defined.
References

.......................................................................................................................... 34 Appendix A. Permitted Facilities with Discharges to Surface Water and Ground Water in the Pensacola Bay Basin

................................................................................................... 38Draft iii August 2010 

### List of Tables

Table 1. Checklist of potential nutrient enrichment symptoms in Pensacola Bay.

...................................... 2 Table 2. Summary of physical/chemical data for Pensacola Bay.

................................................................ 9 Table 3. Mean TN concentrations, TP concentrations, and N/P ratios for Pensacola Bay WBIDs (from the FDEP Impaired Surface Waters Rule (IWR) Database (after Hagy 2009).

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



### List of Figures

Figure 1. Aerial view of Pensacola Bay system.

........................................................................................... 3 Figure 2. Relative bathymetry in Pensacola Bay (yellow indicates about 2 meters (m) deep; dark blue indicates about 4 m deep).

................................................................................................ . 4 Figure 3. Segments with waterbody identification (WBID) numbers for Pensacola Bay.

............................ 5 Figure 4. Land use for the Pensacola Bay watershed.

.................................................................................. 5 Figure 5. Salinity cross

- section of Escambia to Pensacola Bay; top panel during moderate flow, bottom panel during high flow (from Hagy 2009).

..................................................................... 6 Figure 6. Salinity stratification related to Escambia River flow (from Hagy 2009).

..................................... 7 Figure 7. Bottom DO vs. Escambia River flow (from C affery 2009).

............................................................ 7 Figure 8. Potential nitrification (micromoles per cubic centimeter per day [umol/cm 3 /d]) in Pensacola Bay areas compared with other Gulf of Mexico estuaries (after Caffery 2009).

................................................................................................ .......................................... 8 Figure 9. Denitrification (micromoles per square meter per day [mmol/m 2 /d]) in Pensacola Bay areas compared with other Gulf of Mexico estuaries (after Caffery 2009).

............................... 9 Figure 10. Atmospheric deposition of nitrogen on the Pensacola Bay area (after Hagy 2009).

................ 11 Figure 11. Annual geometric means for TP, averaging all stations in the Pensacola Bay system over time. Data from the IWR Database, based on a minimum of 4 data points per station per year (n = 463)

. ........................................................................................................ 11 Figure 12. Annual geometric means for TN, averaging all stations in the Pensacola Bay system over time. Data from the IWR Database, based on a minimum of 4 data points per station per year (n = 463)

. ........................................................................................................ 12 Figure 13. Relationship between salinity and TN in Escambia Bay, 1994

– 2004. The flow

weighted mean TN concentration for the Escambia River during this period was 0.47 mg/L (after Hagy 2009).

........................................................................................................... 12 Figure 14. Annual geometric means for chlorophyll a, averaging all stations in the Pensacola Bay system over time. Data from the IWR Database, based on a minimum of 4 data points per station per year (n = 463)

. ....................................................................................... 13 Figure 15. Box plots of annual geometric means for chlorophyll a in various segments of Pensacola Bay, 1998

– present. Data from the IWR Database, based on a minimum of 4 data points per station per year.

........................................................................................... 14 Figure 16. Areas of Escambia Bay, East Bay, and Santa Rosa Sound open for oyster harvesting during part of the year.

............................................................................................................. 16 Figure 17. SAV coverage in Pensacola Bay over time: circa 1950, 1992, and 2003.

................................ . 18Draft iv August 2010 Figure 18. Trophic organization (herbivores, omnivores, primary [C1] carnivores) in the Pensacola Bay system (averaged annually over months and stations) over the 1997

– 98 study period (from Livingston 2010).

................................................................................... 20 Figure 19. Trophic organization (secondary [C2] carnivores, tertiary [C3] carnivores) in the Pensacola Bay system (averaged annually over months and stations) over the 1997

– 98 study period (from Livingston 2010).

................................................................................... 20 Figure 20. Total benthic abundance in selected Gulf of Mexico bays (from Florida IMAP).

...................... 21 Figure 21. Total abundance of benthic fauna, summer 2003 (from Florida IMAP).

.................................. 22 Figure 22. Seagrass in Big Lagoon and Santa Rosa Sound.

........................................................................ 23 Figure 23. A four

- way comparison between the deep

- edge SAV depths on the north and south shores, and between Big Lagoon and Santa Rosa Sound.

........................................................ 23 Figure 24. Effect of turbidity (caused by storm event) on PAR in Big Lagoon. Note that PAR was temporarily reduced from nonchlorophyll turbidity. When coupled with the low chlorophyll levels, this suggests that nutrient

- induced light limitation effects are less problematic than other physical factors.

.................................................................................. 24 Figure 25 . Example of efforts to reintroduce oyster hash and restore oyster beds in Pensacola Bay.

................................................................................................ ........................................... 25 Figure 26. Hydroqual estuary model study area and model grid for the Pensacola Bay system (Hydroqual 2010).

..................................................................................................................... 28 Figure 27. Calculated areas of bottom light (growing season average), > 20%, for 1998 model calibration (Hydroqual 2010).

................................................................................................... 28 Figure 28. Calculated percentage of time (summer) surface DO concentrations are > 4mg/L, for 1998 model calibration (Hydroqual 2010).

............................................................................... 29 Figure 29. Calculated percentage of time (summer) bottom DO concentrations are > 2 mg/L, for 1998 model calibration (Hydroqual 2010).

............................................................................... 29 Figure 30. Calculated growing season average of chlorophyll a, for 1998 model calibration (Hydroqual 2010).

..................................................................................................................... 30Draft 1 August 2010 

### Executive Summary
This report was prepared by t he Florida Department of Environmental Protection (FDEP), in cooperation with the U.S. Environmental Protection Agency (EPA) and local scientists, 1

Seagrass /oyster beds are the most nutrient sensitive biological endpoint s in Pensacola Bay

. Due to toxic point source discharges in the 1970s, seagrass es and oysters were largely eliminated from Pensacola Bay

. However, oysters continue to be harvested in much of the system and Santa Rosa Sound continues to have extensive seagr ass coverage

. Because physical restoration ( replanting, potential sediment modification ) will likely be required to restore the historic al seagrass and oyster beds, a focus of maintaining the nutrient concentrations needed to achieve a chlorophyll

- based

, light transpare ncy target is the optimal method for numeric nutrient criteria development. to support the development of numeric nutrient criteria fo r the Pensacola Bay system, which includes East Bay, Escambia Bay, Santa Rosa Sound, and Big Lagoon

. The primary purpose of the pr oposed numeric nutrient criteria is to protect healthy

, well

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

During the past 15 years, the annual geometric mean chlorophyll a (based on a minimum of 4 values per station per year) in Santa Rosa Sound, where healthy seagrass beds prevail, has ranged from 2 to 4.2 micrograms per liter ( **μ** g/L )

. Except for slightly higher values in certain bayous (Chico, Grande, and Texar), chlorophyll in all other portions of Pensacola Bay (Escambia Bay, East Bay, main Pensacola Bay) also had chlorophyll values in this range, suggesting that current nutrient and chlorophyll a conditions are appropriate for seagrass protection. Because chlorophyll a is not present at levels that would interfere with the abi lity of submerged aquatic vegetation ( SAV ) to phytosyn thesize (see discussion later in this report)

, maintaining current nutrient conditions is the appropriate strategy for numeric nutrient criteria development in Pensacola Bay

. Hagy et al. ( U.S. Environmental Protec ti on Agency 2008) conclude d that water quality criteria for nutrients and nutrient

- related water quality measures for Pensacola Bay “ could be based reasonably on currently observed conditions because evidence that more stringent criteria are scientifically defensible, necessary, or even achieva ble, is lacking ”.

Table 1 provides a checklist of potential nutrient enrichment symptoms in Pensacola Bay.

Nutrient targets are summarized in Ta ble 4 on page 32 of this report.

1 Contributors to this report included Skip Livingston, Tom Gallagher, Jim Hagy, and Russel Frydenborg.Draft 2 August 2010 Table 1. Checklist of potential nutrient enrichment symptoms in Pensacola B ay
. Response Variable Observed Historically? Observed Currently? Explanation

Low dissolved oxygen (DO) (hypoxia/anoxia) Yes Yes Low DO concentrations have been observed historically

, and current episodic low DOs are associated with natural salinity stratification and natural organic material delivered by river systems , not nutrient enrichment ( Caffery 2009, Hagy and Murrell 200 7, Hagy et al. 2008). Reduced clarity No No Turbidity is a temporary phenomenon associated with
storm events (Heck 1996). Increased chlorophyll a concentrations No No Although chlorophyll a levels fluctuate with hydrologic cycles, the absolute values remain at low levels which do not interfere with SAV photosynthesis (Hagy et al. 2008, Hydroqual 2010). Phytoplankton blooms (nuisance or toxic) No No Problematic algae blooms have not been observed (Livingston 2010)

. Problematic epiphyte growth No No Epiphyte growth is not an issue in Santa Rosa Sound, where SAV remains constant. Problematic macroalgal growth No No Problematic macroalgal growth has not been observed (FDEP 2007)

. SAV community changes or loss Yes Yes SAV was largely eliminated from Pensacola Bay during toxic discharge events of the 1970s and has not yet recovered, even though chlorophyll does not limit photosynthesis ( EPA 1971; Livingston 2005 , Hagy et al. 2008 )

. Emergent or shoreline vegetation community changes or loss Yes No Some shoreline vegetation was affected in urbanized bayous prior to the 1970s (FDEP 1998).

Coral/hardbottom community changes or loss No No Hard bottom not present except for small patch near Pensacola Pass.

Impacts to benthic community Yes No Industrial discharges affected benthic communities in 1970s, but present communities stable (Livingston 2010)

. Fish kills Yes No Fish kills were common in the 1970s but have not occurred in recent years.



### Geographic and Physical Description

The Pensacola Bay system includes Pensacola Bay, East Bay, Escambia Bay, Santa Rosa Sound, Big Lagoon , and several bayous (Texar, Chico, and Grande) (Figure 1)

. The bay is a generally high

- salinity system, subject to stratification, with a half

- mile

- wide pass (Caucaus Channel) to the Gulf of Mexico.

The Pensacola Bay s ystem is located in both Escambia and Santa Rosa C ounties , with Santa Rosa Sound in Santa Rosa County and Big Lagoon located in Escambia County. Santa Rosa Sound is a 42. 4- square

mile (mi 2 ) lagoon that connects Choctawhatchee Bay to the east and Pensacola Bay t o the west. The majority of Santa Rosa Sound is designated as Class II waters ( shellfish propagation or harvesting ) (see Figure 16) . A portion of Santa Rosa Sound, the Gulf Island National Seashore, is also designated as an Outstanding Florida Water (OFW ).

The Pensacola Bay system is generally shallow, with a mean depth of 3 m (excluding Santa Rosa Sound

, an adjoining “back bay” system ). Pensacola Bay i s deeper, with portions dredged, while Escambia andDraft 3 August 2010 East Bays slope to shallower depth (Figure 2)

. Tides are diurnal and have a low amplitude, ranging from 15 to 65 centimeters ( cm ).

Figure 1. Aerial view of Pensacola Bay system. Pensacola Bay Escambia Bay East Bay

Santa Rosa Sound

Big LagoonDraft 4 August 2010 Figure 2. Relative bathymetry in Pensacola Bay (yellow indicates about 2 m eters (m) deep ; dark blue indicates about 4 m deep)

.Draft 5 August 2010 Figure 3. Segments with waterbody identification (WBID) numbers for Pensacola Bay.

Figure 4. Land use for the Pensacola Bay watershed.Draft 6 August 2010 The Pensacola Bay Basin is 18,000 square kilometers ( km 2 ) and includes 3 significant watersheds

— the Escambia, Blackwater, and Yellow Rivers

— which together form several hydrodynamically linked subsystems and 4 major estuarine b ayous

. Figure 3 shows the segments with waterbody identification (WBID) numbers for Pensacola Bay.

The watershed s are primarily forested (forest cover is about 70% ) , with portions managed for timber production. Row crops (6%) occur in small areas in the lower basin (Figure 4)

. Most of the urbanized land (7%) is relatively close to P ensacola B ay and includes low - to medium

- intensity development, including residential, business

, and industrial land uses. Land cover data suggest a relatively low nutrient yield f rom the major portion s of the basin

.
Table 1 presents p hysical/chemical information for Pensacola Bay

. The system ranges from high salinity (32 practical salinity units [ PSU ] ) near the Gulf of Mexico to 0 PSU near river inputs, depending on river flow (Figures 5 and 6)

. S urface and bottom layer salinities may differ by up to 20 PSU. Surface DO ranges between 80 % and 105% of saturation, while b ottom DO ranges between 0 % and 100% saturation

.
Natural salinity stratification is a major factor causing hyp oxia in the bottom water layers in north Florida estuaries, as has been demonstrated in Escambia Bay (Caffery 2009) and in the adjacent Perdido Bay system ( Livingston 2010)

. Caffery showed that 65% of the variability in bottom DO was e xplained by river fl ow and resulting salinity stratification (Figure 7 ).

Figure 5. Salinity cross - section of Escambia to Pensacola Bay ; t op panel during moderate flow, bottom panel during high flow (from Hagy 2009)

.Draft 7 August 2010 Figure 6. Salinity stratification related to Escambia River flow (from Hagy 2009)

.

Figure 7. Bottom DO vs. Escambia River flow ( from Caffery 2009 ).

Caffery (2009) suggested that the low bottom DO in Escambia Bay was not related to photosynthesis and/or phytoplankton respiration, because there was generally h igh er DO at night and l ow er DO during the day
, due to water masses shifting with the tide

. Olinger et al. (1975) recognized that the bay often was strongly stratified and that weak circulation probably contributed to the risk of hypoxia. Hagy and Murrell (2007) quantified the stratification and circulation in Pensacola Bay to better characterize conditions that create a high susceptibility to hypoxia. They found that hypoxia develo ped in Pensacola Bay despite low oxygen consumption rates in the lower water column and sediments. Total ( i.e
., 2009 2008 1996

1997 1998

1999 2000

2001 2002

2004 2005 2003 R 2 = 0.65

0 1 2 3 4 5

0 50 100 150 200 250 300 350 average summer flow (Jun-Aug) cmsbottom water DO mg/LDraft 8 August 2010 combined) oxygen consumption for the lower water column and sediments was estimated to be 0 to 1.5 grams per square meter per day (g /m 2 / day ) us ing a box model (Hagy and Murrell 2007). The model estimates were in reasonable agreement with average integrated oxygen consumption rates (0.94 g/m 2 / day) measured during summer at several stations throughout the Pensacola Bay system

. Hagy et al. (2008) concluded that oxygen consumption in Pensacola Bay is low compared with other estuarine and coastal marine systems ( e.g ., Hopkinson 1985, Cowan et al. 1996) and is much lower than rates from a very eutrophic system such as Chesapeake Bay, where integrated metabolism below the pycnocline can exceed 10 g /m 2 /d ay of oxygen (Kemp et al . 1997).

Natural hypoxia is known to exist on the Gulf Coast, including the well

- known occurrence of “jubilee” events, in which marine animals (especially crabs) climb onto the bea ch to avoid low

- oxygen waters

. Jubilees have occurred in Mobile Bay, A labama , for more than a century (May 1973 ; Schroeder and Wiseman 1988). Hagy et al. (2008) indicated that hypoxia likely occur red in Pensacola Bay prior to significant human influence, but there were in adequate data to document any trend in DO during the past several decades.

Nitrification and d enitrification rates are somewhat lower in Pensacola Bay compared with other G ulf of Mexico estuaries (Caffery 2009) (Figures 8 and 9 ). While shoals have low nitrification due to bacteria competing with benthic algae for ammonium, h ypoxia does not appear to affect nitrification rates (Caffery 2009).

Figure 8

. Potential nitrification ( micromoles per cubic centimeter per day [ umol/cm 3 /d ] ) in P ensacola Bay areas compared with other Gulf of Mexico estuaries (after Caffery 2009). 0 0.5

1 1.5

2 2.5

3Potential Nitrification μmol/cm3/d

River Shoal Channel GOM estuariesDraft 9 August 2010 Figure 9 . Denitrification ( micromoles per square meter per day [ m mol/m 2 /d ] ) in Pensacola Bay areas compared with other Gulf of Mexico estuaries (after Caffery 200 9).



### Sources and Fates of Nutrients
Nutrients are relatively low in the Pensacola Bay system (Hagy et al . 2008), with the highest mean values in Escambia Bay, which had values of 0.59 and 0.022 mg/L for total nitrogen (TN) and total phosphorus (TP), respe ctively (Table 2). The average TN: average TP ratio suggests that phosphorus (P) is the limiting nutrient, but the system is sometimes co

- limited by nitrogen (N) and P (FDEP 2007)

. Results from algal a ssay studies are consistent with this finding, with seasonal/spatial transition from P to N limitation (FDEP 2007)

. Flemer et al. (1998) found P to be limiting in the Pensacola Bay estu ary and suggested that the co

- limitation of N and P may sometimes occur

.

Table 2. Summary of physical/chemical data for Pensacola Bay.

Data Values Source Estuarine surface area (km 2 ) 477 km 2 N ational Oceanic and Atmospheric Administration (N OAA) Watershed area (km 2 ) 17
, 650 km 2 NOAA Mean depth (m) 3.02 m NOAA Volume (m 3 ) 1,440,540,000 NOAA Tidal range (m) 0.42 NOAA Tidal freshwater inflow (1 , 000 cubic meters per day ( m 3 d -1 ) 25,800,000 NOAA

Mean water residence time (days) 26 days NOAA

The TN loading from the Escambia River, as measured at Century, F lorida

, averaged 2.8x10 6 kilograms per year ( kg/y ) from 1975 to 1995 ( 290 kg/km 2 /yr with 3 8 % interannual variation) (Hagy 2009)

. The TN loading rate for Pensacola Bay includes 5.8 × 10 6 kg N/y (watershed sources)

, 0.16 × 10 6 kg N/y (point 0 1 2 3 4 5 6Denitrificationmmol/m2/d

River Shoal Channel GOM estuariesDraft 10 August 2010 sources to estuary)

, and 0.17 × 10 6 kg N/y (wet and dry N deposition) , for a total TN l oad to Pensacola Bay of 6.1 × 10 6 kg N y -1 (12.8 g N m -2 y -1 ). A pproximately 95% of the nutrient loading is from the large

, primarily forested

, watershed (Hagy 2009)

.
Atmospheric deposition m easurements began in 2005 at three sites in the Pensacola Bay area (Figure 10). Ninety percent of deposition is in the form of nitrate. Note that d eposition declined over the last five years and that the d ecline was not due to different rainfall amounts ( there was more rain in 2009 than 2005 o r 20 06) . The b lue line is the approximate nitrogen deposition from the N ational
A tmospheric D eposition P rogram (NADP)

.
Data from the IWR Database were analyzed to assess baywide trends over time. Table 3 shows the

mean TN concentrations, TP concentrations, and N/P ratios for the Pensacola Bay WBIDs from the IWR Database

. For this analysis, each station had to have a minimum of 4 observations in a given year for data to be included in the calculation of annual geometric means. Geometric means were used because the data approximated a log

- normal distribution. From 1995 to 2009, TP has declined in the Pensacola bay system (Figure 11), although the range of annual geometric means for TP (from 16 to 35 **μ** g/L) is relatively l ow compared with many other southeast U .S. estuaries (Hagy 2009).

Annual geometric mean TN concentrations in Pensacola Bay have ranged from 0.4 to 0.95 mg/L since 1995 (Figure 12). Hagy (2009) found that there was a strong inverse relationship between sal inity and TN concentrations in Escambia Bay, because the river was the primary source of the N (Figure 13).

Table 3. Mean T N concentrations, T P concentrations, and N/P ratios for Pensacola Bay WBIDs (from the FDEP Impaired Surface Waters Rule (IWR) Datab ase ( after Hagy 2009 ).Draft 11 August 2010 Figure 10

. Atmospheric deposition of nitrogen on the Pensacola Bay area (after Hagy 2009)

.

Figure 11

. Annual geometric means for TP , averaging all stations in the Pensacola Bay system over time. Data from the IWR Database , based on a minimum of 4 data points per station per year (n = 463 ). y =

- 0.0008x + 1.6691 R2 = 0.5339

0.000 0.005 0.010 0.015 0.020 0.025 0.030 0.035 0.040

1995 1997 1999 2001 2003 2005 2007 2009Total Phosphorus (mg/L)

Year 

# Pensacola Bay Total PhosphorusDraft 12 August 2010 Figure 12

. Annual geometric means for T N

, averaging all stations in the Pensacola Bay system over time. Data from the IWR Database, based on a minimum of 4 data points per station per year (n = 463 ).

Figure 13

. Relationship between salinity and TN in Escambia Bay, 1994

– 2004. The flow

- weight ed mean TN concentration for the Escambia River during this period was 0.47 mg/L (after Hagy 2009)

. y =

- 0.0004x + 1.514 R2 = 0.0001

0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00

1994 1996 1998 2000 2002 2004 2006 2008 2010Total Nitrogen (mg/L)

Year 

# Pensacola Bay Total Nitrogen

0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50

0 10 20 30 40 Average SalinityAverage TN (mg/L) 

### Surface Water
Bottom WaterDraft 13 August 2010 Since 1998, the annual geometric mean chlorophyll a for the Pensacola Bay system has ranged from 1.8 to 5.5 ug/L (Figure 14), demonstrating that chlorophyll

- induced reductions in transparency are generally not an issue in the bay. Chlorophyll a values are commonly higher in the bayous, and chlorophyll a levels in Bayou Chico could potentially limit SAV production (Figure 15); however, SAV has not historically been found in Bayou Chico. Hagy et al . (2008) stated they were unaware of any study d irectly implicating chlorophyll a concentrations in the low range observed in Pensacola Bay with failure to support any human or aquatic life uses.

Despite the relatively low chlorophyll values, both East Bay and Escambia Bay were placed on the Verified List of impair ed waters for nutrient impairment, based on an IWR provision that tests whether chlorophyll a levels are 50% higher than the historical minimum chlorophyll (lowest 5

- year period of record). This provision does not take into account the variation in chlo rophyll related to natural hydrologic variability in estuaries. In Pensacola Bay, peaks in chlorophyll tend to occur directly after high

- flow events from the river systems (Hagy and Murrell 2007). Therefore, the information presented in this report, which demonstrates that existing chlorophyll values do not prevent seagrass photosynthesis, should take precedence over the IWR listing methodology (discussed further below).

Figure 14

. Annual geometric means for chlorophyll a , averaging all stations in th e Pensacola Bay system over time. Data from the IWR Database, based on a minimum of 4 data points per station per
year (n = 463 ). y =

- 0.116x + 235.42 R2 = 0.1747

0 1 2 3 4 5 6

1997 1999 2001 2003 2005 2007 2009Geo. Mean Chlorophyll a (ug/L)

Year 

# Pensacola Bay Chlorophyll aDraft 14 August 2010 Figure 15

. Box plots of a nnual geometric means for chlorophyll a in various segments of Pensacola Bay , 1998

–

present. Data from the I WR Database, based on a minimum of 4 data points per station
per year.

Mitigation of Point Sources
The considerable quantities of point source wastewater previously discharged into the Pensacola Bay system between 1955 and 1964 have been s ignificantly reduced and are no longer an issue (EPA 2008)

. Even by 1975, surveys by EPA and its predecessor agencies demonstrated that the combined quantity of wastewater discharged by the 4 major dischargers into the Escambia Bay drainage area (Containe r Corporation of America, Monsanto Chemical Co., American Cyanamid Co., and Air Products and Chemical Co.) was reduced by 40% for biological oxygen demand (BOD), 71% for TN , and 96% for TP (EPA, 1975).

The l atest information (FDEP 2007) indicates t here are 18 active permitted National Pollutant Discharge Elimination System (NPDES) and ground water dischargers in the Pensacola Bay Basin ( Appendix A) in Florida. Eight are NPDES industrial and domestic surface water dischargers, of which 5 discharge direct ly to the Escambia River. The largest discharger to the Escambia River is Solutia (formerly Monsanto Textiles Company), which is permitted to release up to 27 million gallons per day ( MGD ) of industrial
wastewater. Gulf Power’s James F. Crist Generating Plant, built in 1945, is permitted to use and release 18 MGD of cooling water into the Escambia River. Container Corporation has a paper mill located in Alabama near the Florida state line that also discharges industrial wastewater. Escambia County was i ssued an NPDES municipal separate storm sewer system (MS4) permit in January 1999, under Phase 1 of the federal program. The county is a copermittee with the city of Pensacola, the town of Century, and the Florida Department of Transportation (FDOT)

. Current information from the NPDES P rogramDraft 15 August 2010 indicates that there is no evidence that the remaining point source discharges are affecting chlorophyll a in the bay (see discussion below in Water Quality Studies)

. 

### Biological Summary

Hagy (2009) identified the following key biological resources/u ses in the Pensacola Bay system:

**•** Fishing , including r ecreational fishing from boats, beaches, and fishing piers. Most targeted species are pelagics ( e.g., r edfish

, k ing m acker el

, s peckled t rout ).

**•** Commercial f ishing , including s hrimp

- trawling activities and smaller operations that
t arget mullet

.

**•** Oyster harvesting (via tongs and hand collection)

, especially in East Bay

.

**•** S eagrass habitats found in lower Pensacola Bay and in Santa Rosa Sound/Big Lago on , which provide food, cover, sediment stabilization

, and other ecological services (e.g., tourism value)

.

**•** Tourism and associated marine industries, generally linked with fishing, water sports, and other recreation al activities that are economically important to the area

.

More than 200 species of fish and shellfish have been recorded from the Pensacola Bay E stuary (FDEP 2007). Common fish and shellfish species include spot (Leiostomus xanthurus), bay anchovy (Anchoa mitchilli) , Atlantic croaker ( Micropogonias undulatus) , spotted seatrout (Cynoscion nebulosus) , Gulf menhaden (Brevoortia patronus) , striped mullet (Mugil cephalus) , blue crab (Callinectes sapidus)

, American oyster (Crassostrea virginica) , and Penaeid shrimp (Penaeus spp .)

. Freshwater fish species that are tolerant of low salinities use the bay’s embayments and marshes. These include largemouth bass (Micropterus salmoides) and redear sunfish (Lepomis microlophus)

. Four anadromous fish

— Gulf sturgeon (Acipenser oxyrinchus desotoi) , Ala bama shad (Alosa alabamae) , skipjack herring (Alosa chrysochloris) , and Gulf Coast striped bass (Morone saxatilis)

— use the bay and its tributaries.

Shrimp harvests from Escambia Bay have been fairly stable since about 1983 and somewhat variable in East Bay and Santa Rosa Sound. Historically, oysters were harvested from Pensacola Bay; landings in oyst ers peaked about 1970 (Macauley 2005). As much as 90 % of the oyster populati on was lost to disease by 1971 and oyster beds are no longer commercially viable

, although a n oyster fishery still exists , accounting for 1.7% of the state’s oyster landings (Livingston 2010)

. Figure 16 depicts the portions of the Pensacola Bay E stuary classified for shellfish harvesting

.
Marsh habitat is present in the lower reaches of river floodplains and tidal creeks. In areas of higher salinity, the common marsh plant is black needlerush (Juncus roemerianus) in conjunction with saltmarsh cordgrass (Spartina alterniflora)

. More freshwater

- dominated areas contain sawgrass (Cladium jamaicense) , pickerelweed (Pontederia lanceolata) , bulrush (Scirpus validus) , and cattail ( Typha
spp

. ).Draft 16 August 2010 Figure 16

. Areas of Escambia Bay, East Bay , and Santa Rosa Sound open for oyster harvesting during part of the year.

S

AV in Pensacola Bay

The Pensacola Bay s ystem contains four species of true seagrasses

— Thalassia testudinum (turtle grass), Syringodium filiforme (manatee grass), Halodule wrightii (shoal grass), and Halophila engelmannii (star grass)

— and two brackish water species

— Vallisneria americana (tape grass) and Ruppia maritima (widgeon grass). Seagrasses are important marine foundation species and are h ighly productive plants (Hughes et al. 2009). Their extensive root systems and dense, structured leaf canopies form habitat and provid e food for a wide array of organisms, including commercially and recreationally important fish and invertebrates, wading birds, manatees, and sea turtles (Short and Wyllie

- Eche verria 1996, Williams and Heck 2001; Wren and Blitch 2009). Seagrasses enhance sediment stability, decrease wave energy, increase water clarity, provide and stabilize habitats, and provide food and feeding pathways (see reviews by Phillips and McRoy 1980 ; McRoy and Helfferich 1977 ; Zieman and Zieman 1989).

Adverse impacts to seagr asses 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 th e 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 sh own 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. One mechanism behind this process is that increased inputs of N and P leadDraft 17 August 2010 to the excess growth of phytoplankton and epiphytic algae , reducing available light to the seagrasses and causing 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 the synergistic factors controlling seagrass production. Water clarity reductions associated with tannic inputs from wetlands and “top

- down” food web effects must also be considered. In controlled, in situ experimental studies i n St. Joseph Bay, Florida, Heck et al

. (2000) found that mesograzers (amphipods, caridean shrimp, gastropods, hermit crabs) prevented excess epiphyte growth despite significant nutrient additions

. It is there fore critical to consider the role of “top

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

In 1949, seagrass beds were noted to be extensive throughout the Pensacola Bay s ystem

. However
, a recession and disappearance of most of Escambia Bay’s true seagrass occurred from 1950 to 1975 (Collard 1991 a ; Collard 1991b )

. A similar dramatic decline occurred in East Bay over the same period. Major causes for the SAV loss included toxic industrial waste water discharges (primarily ammonia)

, dredge

- and

- fill activities, and beachfront alterations. E xtensive fish kills occurred in Escambia Bay during the late 1960s and early 1970s ( EPA 1971 ; Livingston 2005) during the same period that the

s eagrass beds were eliminated

. Industrial wastewater discharge s appear to have caused the loss of vegetation in Escambia Bay

, since these effluents were in direct contact with the SAV in that area (EPA 1975).

Hagy (2009) summarized important information on changes in the distribution of S AV (Figure 17). In 1950, i ncomplete data show widespread SAV coverage , but SAV was restricted to shallow depths (about 1 m) close to shore

. In 1960, 1980, 1992, and 2003, SAV c overage was fully quantified, demonstrating a significant loss in SAV from 1960 to 1980 with no subsequent recovery (Figure 17)

. Most of the remai ning SAV occurs in Santa Rosa Sound and nearby portions of lower Pensacola Bay. SAV is virtually absent from the remainder of the b ay

.
While some may hypothesize that the f ailure of the SAV beds to recover may reflect nutrient enrichment, the current low levels of nutrients and chlorophyll in most of the bay do not support that position

. Hagy et al. (2008) determined that current nutrient and chlorophy ll levels in Pensacola Bay are not expected to impact seagrass health. Using a conservative 25% photosynthetically active radiation (PAR) target, Hagy et al. (2008) concluded that the light field in Pensacola Bay is currently adequate to support Thalassi a to a depth of approximately 2 m in the polyhaline reaches (where salinity is appropriate for Thalassia ), consistent with its present maximum colonization depth. The EPA hypothesized that SAV may be absent from many places in Pensacola Bay where light ap pears to be adequate due to m etabolic stress associated with high sulfide in sediment pore waters
, and not due to current nutrient enrichment or transparency issues.Draft 18 August 2010 Figure 17

. SAV coverage in Pensacola Bay over time : circa 1950, 1992, and 2003

.

Nutrient Effects on Algae , Invertebrates , and Fish in Pensacola Bay
Livingston (2010) emphasized that the response of a particular estuarine system to anthropogenic nutrient loading depends on many synergistic factors: long

- term drought and flood patterns ; the species composition of plankton populations ; physical factors such as depth, currents, and salinity stratification ; and the resilience of the system’s food webs to the repetitive na ture of blooms

.
Livingston conducted an extensive study of Pensacol a Bay from 1990 to 1991 and from 2001 to 2002. No phytoplankton blooms (numbers greater than 1 million cells per liter [ > 1x10 6 cells /L ] ) of the various dominant and subdominant phytoplankton populations were noted by Livingston (2010) during the sampling period in Escambia Bay. Dominant species of whole

- water phytoplankton included Cyclotella choctawhatcheeana Prasad (a common species in Perdido Bay), nannoflagellates, cryptophytes, Cryptomonas spp., Nitzschia spp ., and Navicula spp. Present in very small concentrations were Heterosigma akashiwo

, Miraltia throndsenii Marino et al

., Gymnodinium spp., and ProrocentrumDraft 19 August 2010 cordatum

. The presence of these species followed the general seasonal patterns of those in nearby bays

.
The Livingston studies of Pensacola Bay suggested no phytoplankton community imbalances

. Hagy et al. (2008) agreed, finding no clear evidence that the phytoplankton community wa s stimulated strongly by excess nutrients, or that the community was unbalanced or otherwise causing adverse ecological effects.

Livingston also found that infaunal biomass was concentrated in the upper areas of the two bay systems , with the highest biomass concentrated in the shallow shelf areas in the eastern and western parts of upper Escambia Bay and Blackwater Bay (Livingston 2010)

. Infaunal species richness was highest in the high

- salinity sections of Pensacola Bay and lower Escambia Bay. Relatively high dominance was exerted by the three top species ( Mediomastus ambiseta , Lepidactylus sp. and Streblospio benedicti ). However, there was a relatively low infaunal biomass along the eastern sections of upper Escambia Bay. In Blackwater /East Bay, there was relatively high biomass across the bay, just below the mouth of the Yellow River

. Livingston found that e pibenthic macroinvertebrate biomass was located primarily in the deeper portions of upper Escambia Bay. This distribution was dominated largely by brown shrimp ( Penaeus aztecus ) and blue crabs ( Callinectes sapidus )

. The e astern par ts of the upper bay had low invertebrate species richness in areas near point source discharges

. Fish biomass was located largely in the central parts of upper Escambia Bay

, with the numerically most dominant fish populations ( Anchoa mitchilli

, Leiostomus xanthurus

, Micropogonias undulatus ) being both plankton and benthic feeders. Another dominant fish

, Brevoortia patronus , was located in shallow areas of both Escambia Bay and East Bay. Compared with other bay systems in the northeastern G ulf, fish/infau na/invertebrate biomass levels were low in Pensacola Bay

, as were the cumulative species richness indices (Livingston 2010)

. Livingston developed a Fish/Infauna/Invertebrate Index (FII) to describe the health of estuaries based on trophic relationships. The index includes determining the biomass (g/m 2 ) of herbivores, omnivores, and three levels of carnivores (primary= C1, secondary= C2, and tertiary=C3).

Based on the results of regression analyses, a PCA

- regression analysis was carried out using a series of biological factors as the dependent variables ( Livingston 2010 ). FII herbivores were positively associated with water color and turbidity

, and negatively associated with surface salinity ( i.e., increased river flow). In addition, FII herbivores were positively correlated with increased bottom TN and surface chlorophyll

a , and FII omnivores were negatively associated with surface silica, nitrate/nitrite, and chlorophyll a

. Neither group was affected by salinity stratification or bottom DO

.

FII C1 (p rimary) carnivores were generally similar to the herbivores (negatively associated with surface salinity ; positively associated with river flow factors, nutrients

, and chlorophyll a ). Anchovies, spot

, and brown shrimp also followed this pattern. These da ta show the importance of Escambia River flow and nutrients to the biological organization of the Pensacola Bay system (Figures 18 and 19 ) (Livingston 2010)

.Draft 20 August 2010 Figure 18

. Trophic organization ( herbi vores, omnivores, primary [ C1 ] carnivores) in the Pensacola Bay system (averaged annually over months and stations) over the 1997

– 98 study period (from Livingston 2010).

Figure 19. Trophic organization ( secondary [ C2 ] carnivores, tertiary [C3] carnivores ) in the Pensacola Bay system (averaged annually over months and stations) over the 1997

– 98 study period (from Livingston 2010). Trophic Organization

0.000 0.200 0.400 0.600 0.800 1.000 1.200

Blackwat bay Up.Escambia Low. Escambia Pensacola Bay bay FIIHerbwt/m2 FIIOmnwt/m2 FIIC1wt/m2

Trophic Organization

0.000 0.015 0.030 0.045

Blackwat bay Up.Escambia Low. Escambia Pensacola Bay bay FIIC2wt/m2 FIIC3wt/m2Draft 21 August 2010 Pensacola Bay Choctawhatchee Bay St. Andrew Bay Apalachicola Bay Big Bend Tampa Bay Charlotte Harbor# Per Grab

1 10 100 1000 10000 To summarize Dr. Livingston’s findings, the main concentrations of infauna (polychaete worms), epibenthic macroinvertebrates (brown shrimp, blue crabs), and fishes (sciaenid s) that were collected in the bay system were found in the relatively shallow parts of upper Escambia Bay. This area was the center of primary and secondary production in the Pensacola Bay system due to beneficial nutrient inputs from the Escambia River ( Livingston 2010)

. The biological community in upper Escambia Bay, due
to higher primary production found there, was characterized by higher biomass of commercially important populations than elsewhere in the Pensacola Bay system

. However, compared with o ther such areas in regional river

- dominated estuaries, even the most productive area in Pensacola Bay (Escambia) contained a comparatively low biomass of infauna, epibenthic invertebrates, and fishes (Livingston 2010)

.

The Florida Fish and Wildlife Conservation Commission (FWCC) conducted a probabilistic sampling survey in Pensacola Bay as part of its Inshore Marine Monitoring and Assessment Prog r am (IMAP). The IMAP survey found that P ensacola B ay benthic abundance was the lowest of all north Florida estuaries

, benthic invertebrate a bundance increased eastward from P ensacola B ay to Apalachee Bay

, and abundance was highest on the west Florida penin sula (Figure 20 ). Figure 21 shows the pattern of benthic invertebrate ab undance throughout the Pe nsacola Bay system

. Generally low phytoplankton production, n atural episodes of h ypox ia, and habitat limitation are possible causes for low invertebrate abundances in Pensacola Bay

.

Figure 20

. Total b enthic a bundance in selected Gulf of Mexico bays ( from Florida IMAP)

.Draft 22 August 2010 Figure 21

. Total abundance of benthic fauna, summer 2003 ( from Florida IMAP)

.

Santa Rosa Sound/ Big Lagoon
The present distribution of seagrass in Santa Rosa Sound and Big Lagoon is similar to that of historical levels, which indicates that water quality has not declined below the threshold required for seagrass survival (Figure 22 )

. Heck (1996) found a constant percentage of SAV coverage over time
, but noted that non

- nutrient related issues (occasional mineral turbidity and fluctuating salinities ) were potential
stressors

.

S eagrass grows to a deeper depth on both shores of Santa Rosa Sound than in Big Lagoon. The average depth for growth in Big Lagoon is 1.4 m, with the most shallow at the far west end (around Big Lagoon State Park) and slowly increasing in depth eastward toward the pass (Figure 23)

. The average depth to SAV in Santa Rosa Sound is 2. 2 m, primarily due to lower turbidity in Santa Rosa Sound

. Figure 24 shows the relationship between turbidity caused by a storm event and PAR reaching the bottom of a Big Lagoon seagrass bed.Draft 23 August 2010 Figure 22 . Seagrass in Big Lagoon and Santa Rosa Soun d.

Figure 23. A four

- way comparison between the deep

- edge SAV depths on the north and south shores, and between Big Lagoon and Santa Rosa Sound.

Note: White = Big Lagoon North Shore, Red = Big Lagoon South Shore, Green = Santa Rosa Sound North Shore, Yellow = Santa Rosa Sound South ShoreDraft 24 August 2010 Fig ur e 24

. Effect of turbidity (caused by storm event) on PAR in Big Lagoon. Note that PAR was temporarily reduced from nonchlorophyll turbidity. When coupled with the low chlorophyll levels, this suggests that nutrient

- induced light limitation effects are less problematic than other physical factors.

Restoration Efforts
FDEP has implemented “ Project GreenShores

, ” a multimillion

- dolla r habitat restoration and creation project located in Downtown Pensacola along the urban shoreline of Pensacola Bay. This habitat restoration effort partners FDEP's Ecosystem Restoration Section with the c ity of Pensacola, Escambia County, Ecosystem Resto ration Support Organization, EPA Gulf of Mexico Program, National Fish and Wildlife Foundation, U.S. Fish and Wildlife Service, NOAA, Gulf Power, local agencies, businesses

, and volunteers in a community

- based effort to restore oyster reef, salt marsh

, and seagrass habitat within the Pensacola Bay s ystem

.
The purpose of the project is to restore the Pensacola Bay estuary to its historic al state by stabilizing shorelines and providing essential habitat for wildlife propagation and conservation. FDEP has d etermined that the l ack of suitable substrate is a major factor in the slow recovery of oyster populations in the area. Therefore, as part of this restoration, stabilized oyster hash has been placed at appropriate areas to stimulate the colonization of th e oyster, Crassostrea virginica (Figure 25).

Additional information on physical restoration efforts in Pensacola Bay is available at: ( http://internetdev/northwest/Ecosys/section/restorationoyster.htm ).Draft 25 August 2010 Figure 25

. Example of efforts to reintroduce oyster hash and restore oyster beds in Pensacola Bay.

Shellfish Survey
From 1991 through 2001, the annual reported commercial landings of shellfish in Santa Rosa and Escambia Counties averaged 34,824 pounds, with an annual dockside value of $49,365 ( F. A. Dugach Consulting Services [ FADCS ] 2005)

. This accounted for 1.7 % of shellfish landings in Florida and 1.5 % of shellfish value in Florid a. There are 3 certified shellfish processing plants in Escambia and Santa Rosa Counties. In 1999, 170 shellfish trips were reported from Escambia and Santa Rosa Counties from oystermen holding commercial Saltwater Products Licenses.

As of January 31, 1996, the Pensacola Bay s ystem has been classified separately for winter and spring/fall for shellfish harvesting (Thompson 1996). Pensacola Bay is generally prohibited throughout the year, as are Escambia and Blackwater B ays north of I n terstate 10 and Escribano Point, respectively, and East Bay Bayou. During the spring and fall, most of Escambia Bay is classified as conditionally approved, except for a portion of the northwest bay, which is restricted. East Bay is conditionally
approve d during the spring and fall. During the winter, most of Escambia Bay is conditionally restricted, except for limited areas along the eastern bay that are conditionally approved. Most of East Bay is conditionally approved during the winter, except the no rthwestern portion, whi ch is conditionally restricted.



### Water Quality Studies

Several water quality studies have been conducted in the Pensacola Bay system , including those by Wagner (2006)

, Hagy et al. (2007, 2008), Murrell et al. (2007 , 2009 )

, EPA (2008), Hydroqual (2010), and Livingston (2010)

.
Wagner (2006) concluded that the spatial and temporal variability of physical and nutrient dynamics in Escambia Bay could be explained largely by variations in freshwater input. Murrell et al. (2007) f ound that Escambia River flood ing caused high turbidity and rapid flushing in the bay , severely reducing phytoplankton production and biomass accumulation. Following flood s , phytoplankton biomass and productivity sharply increased ; however, the authors concluded that Escambia Bay wa s only a moderately productive estuary

.Draft 26 August 2010 Hagy et al

. (2007) addressed the impact of hurricanes on the Pensacola Bay system and found that wind forcing was sufficient to completely mix the water column during a hurricane

. Freshwa ter discharge from the Escambia River increased twentyfold, stimulating a modest phytoplankton bloom (chlorophyll up to 18 μg /L ) and maintaining hypoxia for several months. Although the immediate physical perturbation was extreme, the water quality effect s that persisted beyond the first several days were within the normal range of variability for this system. In terms of water quality and phytoplankton productivity effects, Pensacola Bay appeared to be quite resilient to storm activity

.
Hagy et al. (2008) analyzed current nutrient inputs from rivers, land use in the watershed, and atmospheric N deposition , and concluded that it was unlikely that anthropogenic nutrient inputs to Pensacola Bay were problematic, since the calculated n utrient export fro m the watershed s of the major rivers entering the bay was similar to that of pristine or nearly pristine watersheds. Hagy et al. (2008) noted that major causes of increased nutrient export were absent from the Pensacola bay watershed

, which was characteri zed by low population, minimal row

- crop agriculture, and low atmospheric N deposition , and concluded that reasonable management actions probably could not effect significant reductions in nutrient inputs to the bay via the major tributary rivers. Hagy et al. (2008) found good
water quality in Pensacola Bay in terms of nutrient concentrations, water clarity, and chlorophyll a , but noted that significant bottom water hypoxia existed in Pensacola Bay due to stratification (as covered previously)

. Through a weight

- of

- evidence approach, Hagy et al. (2008) ultimately determined that nutrient criteria for Pensacola Bay could reasonably be defined by maintaining the current water quality conditions

.
HydroQual (2010) developed and calibrated hydrodynamic and water quality models (estuary models) representing the processes that control the nutrient, phytoplankton

, and DO conditions in the Escambia/Pensacola Bay system. The models are three

- dimensional and time variable

, and include the
Es cambia River upstream to Molino, Escambia Bay, Pensacola Bay , Blackwater Bay, and East Bay (Figure 26)

. The models were calibrated with data collected by Woodward

- Clyde (now URS), Environmental Planning & Analysis (EP&A)

, and International Paper ( formerly Champion International). Monthly water quality data collected by EP&A and weekly water quality data collected by IP were used to calibrate the water quality model. The calibrated hydrodynamic and water quality models resulted in a reasonable representation of both the complex mix ing and circulation patterns observed in the study area and the observed nutrient, phytoplankton

, and DO dynamics of the system.

Hydroqual (2010) proposed a nutrient criteria approach for the Pensacola Bay system for three nutrient related endpoints: chl orophyll a , S ecchi depth, and DO (EPA 2008). The following were the key steps of the Hydroqual approach :

**•** Used the estuary models described above (expanded to include color as a variable and a sub

- model of sediment flux) to link nutrient loads to nutrient responses (chl orophyll a, bottom light levels, and DO ).

**•** Determine d bottom light levels sufficient to support seagrass communities in the bay. Bottom light requirements for SAV range from 15 % to 25% of surface light, and can be set as a goal in water dept hs where historic al seagrasses existed. The determination of the amount of surface light that reaches the bottom is a function of the light extinction in the water column, which is controlled by amb ient particulate matter, color, and chl orophyll a levels. These parameters are calculated in the model, with chl orophyll a programmed to be a function of nutrient loading via algal uptake and growth

.Draft 27 August 2010 **•** Determined DO levels that support a healthy bay system

, given the fact that natural vertical stratification processes cause bottom waters in the bay to be less than the state water quality standard s of 5 mg/L (daily average) and 4 mg/L (daily minimum) (see the discussion at the beginning of this document). The DO goal proposed by Hyroqual is that surface waters must meet the above water quality standards, and that bottom waters must be greater than 2 mg/L in portions of the bay based on a comparison with estimated background DO levels. FDEP believes that a s ite -s pecific

a lternative c riterion for DO may be appro priate for Pensacola Bay.

**•** Determined acceptable chl orophyll a levels using the modeling framework based on the protective nutrient loads that meet the seagrass bottom light requirement and DO goals.

Given an assessment of the current modeled conditions in the Pensacola Bay system, existing loadings support the goals of 20% bottom light and a DO standard of meeting existing criteria ( > 5 mg/L daily average and 4 mg/L daily minimum) in the surface layer and >

**•** Areas where growing season average bottom light levels are > 20% of surface light (Figure 27) compare well with bay areas where seagrass beds have historically existed. 2mg/L in the bottom layer. These conclusions are summarized as follows:

**•** DO conditions in the bay indicate that existing conditions in the surface layer meet the criterion , except in limited areas where it is attained approximately 90% of the time (Figure 28) . Bottom layer DO is greater than 2 mg/L more than 80% of the time

an d less than 2 mg/L 20% of the time in limited areas (Figure 29)

.

**•** At the existing loading conditions analyzed that met the bottom light and DO goals used, growing season average chl orophyll a levels in upper Escambia Bay were approximately 4 to 5 μg/L (Fi gure 30)

.

Current modeled conditions were also compared with “natural background conditions” that were estimated by assuming no point source discharges

, as well as the conversion of all agricultural, range, urban, and barren land uses to forest ed land us e. A c omparison of the “current” to “natural background” modeling output resulted in extremely minor differences for chl orophyll a , DO, and bottom light levels, further suggesting that current nutrient loads support an overall healthy bay system.Draft 28 August 2010 Figure 26. Hydroqual estuary model study area and model grid for the Pensacola Bay system (Hydroqual 2010)

.

Figure 27. Calculated areas of bottom light (growing season average), > 20%, for 1998 model calibration (Hydroqual 2010).Draft 29 August 2010 Figure 28. Calc ulated percentage of time (summer) surface DO concentrations are > 4mg/L, for 1998 model calibration (Hydroqual 2010)

.

Figure 29. Calculated percentage of time (summer) bottom DO concentrations are > 2 mg/L, for 1998 model calibration (Hydroqual 2010)

.Draft 30 August 2010 Figure 30. Calculated growing season average of c hlorophyll a, for 1998 model calibration (Hydroqual 2010)

.



### Waters on the 303(d) List

F ollowing the methodology in the I WR , Chapter 62

- 303 , Florida Administrative Code (F.A.C.)

, FDEP listed East Bay and Escambia Bay as impaired for nutrients because annual mean chlorophyll a levels were greater than 50% above historic al minimum levels for 2 consecutive years

. The following waterbodies were placed on the Verified List for nutrients due to 2 annual chlorophyll means exceeding 11 ug/L: Floridatown Park (coastal) and Bayou Chico Beach (coastal). Some portions of the system were also listed as impaired for mercury in fish tissue and for coliform bacteria. N ote that coliforms are indicato rs of fecal contamination (often from natural sources) , not an indicator of anthropogenic nutrient enrichment, and fish tissue mercury contamination is the result of atmospheric deposition. Unlike the IWR assessment, which is generic in nature, the inform ation presented in this report is specific to Pensacola Bay, and should precedence over the general IWR methodology.

Proposed Numeric Nutrient Targets

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 oftenDraft 31 August 2010 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 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 Pensacola Bay is descr ibed briefly below. More details concerning the statistical approaches used can be found in the document “Overview of FDEP Approaches for Nutrient Criteria Development in Marine Waters” (FDEP 2010).

Magnitude

The magnitude component can be set at a variety of values based on the frequency and duration that will be used to determine compliance. For the “healthy existing conditions” approach, FDEP established the magnitude at: a) an adjusted long

- term central tendency (geometric mean) of the distribution, expressed as a long

- term geometric mean never to be exceeded; and b) an annual geometric mean, not
to be exceeded more than two times over a five - year period. The long

- term average condition was adjusted to a level that represents an insignificant increase from the baseline. Allowing for an insignificant increase accounts for uncertainty in the estimate of the mean and partially addresses the fact that the reference based approach fails to identify a threshold of imbalance, and thus is highly
prone to e xcessive 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 C ircuit 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 components of the criteria mustDraft 32 August 2010 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 suffic iently robust cause

- effect 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 unacceptabi lity 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

app lication 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

cr iteria 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 climat ic 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 r enewal 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 perc entile results in a magnitude that, when expressed as an annual geometric mean not to be exceeded more than twice during a five

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

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

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

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

The two expressions of magnitude differ in the handling of within

- segment spatial variability. The network average magnitude was calculated based on the distribution of spatially averaged annual geometric means, while the single site magnitude was calcul ated 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
homo geneous. 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 mea n has the benefit of assessing localizedDraft 33 August 2010 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 g eometric 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 ge ometric 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 Pensacola Bay, as well the annual limits for each se gment, are provided in Table 4

.

Table 4. Proposed numeric nutrient criteria for all segments of Pensacola Bay, including TP, TN, and chlorophyll a. For compliance purposes, the long term geometric mean shall not exceed the long term limit nor shall the average of all stations in a segment exceed the network average more than twice in a 5 year period. The last column shows the value which single sta tion shall not exceed, by segment, more than twice in a 5 year period.

Total Phosphorus (mg/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)
East Bay 0.022 0.024 0.033 0.038 Escambia Bay 0.032 0.035 0.050 0.055 Pensacola Bay 0.016 0.018 0.024 0.028
Santa Rosa Sound 0.019 0.021 0.035 0.043

Total Nitrogen (mg/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)
East Bay 0.340 0.374 0.471 0.534 Escambia Bay 0.549 0.603 0.749 0.842 Pensacola Bay 0.373 0.410 0.512 0.552
Santa Rosa Sound 0.349 0.384 0.599 0.615Draft 34 August 2010 Chlorophyll a (ug/L)

Segment Existing Long Term Geometric
Mean Maximum Allowed Long Term Geometric
Mean Annual Geometric Mean for a Network of Stations (2 of 5 year exceedance rate) Annual Geometric Mean for a Single Site (2 of 5 year exceedance rate)
East Bay 3.21 3.54 5.32 5.35 Escambia Bay 5.28 5.81 10.0 11.4 Pensacola Bay 2.97 3.27 4.17 4.62
Santa Rosa Sound 3.50 3.85 5.00 5.08



### References

Caffery, J. 2009. Hypoxia and benthic processes in Pensacola Bay. Univ ersity of West Florida Center for Environmental Diagnostics and Bioremediation

. F lorida Department of Environmental Protection Nutrient Criteria Workshop.
Collard, S.B. 1991 a

. The Pensacola Bay system: Biological trends and current status. Water Resources Special Report 91

- 3. Havana , FL : Northwest Florida Water Management District.

——— . 1991 b

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### Appendix A

. Permitted Facilities with Discharges to Surface Water and Ground Water in the Pensacola Bay Basin

- = Empty cell/no data N/A = Not applicable WWTP = Wastewater treatment plant; STP = Sewage treatment plant; AFB = Air Force Base

Permit Facility Name City Type of Facility Facility Status Design Capacity (MGD) Escambia River Planning Unit - - - - -

FLG911464 Jordans Exxon Century Petroleum Cleanup Active - N/A

FLG910249 Southern Pit Stop Century Petroleum Cleanup Active - N/A

FL0032468 Town of Century Century Domestic Waste Active 0.4500

FL0102202 Pace Water WWTP Pace Domestic Waste Active 1.0000

FL0002488 Solutia Inc. Gonzalez Industrial
Waste Active 27.0000

FL0038318 Nitrous Oxide Corp. Cantonment Industrial
Waste Active 0.0006

FL0002275 Gulf Power Crist Pensacola Industrial
Waste Active 18.0000

FLRNEE173 Dana

- Couple, Inc. Pensacola Stormwater permit Active N/A

Blackwater River Planning Unit - - - - -

FLG830355 Nugget Store #33 Milton Petroleum Cleanup Active N/A

FLG110445 RMC Ewell Milton Concrete Batch Plant Active N/A

FLG110002 Pensacola Ready Mix Milton Concrete Batch Plant Active N/A

FL0021903 Milton, City of (STP) Milton Domestic Waste Active 2.5000

Yellow River Planning Unit - - - - -

FLG110441 Cemex Crestview Concrete Batch Plant Active N/A

FLA187411 Phil

- Dirt Industries
Inc. Crestview Industrial
Waste Active N/A

FLA010183 Baker High School Baker Domestic Waste Active 0.0240

FLA180017 Campbell Sand Mossy Head Industrial
Waste Active N/A

FLA180238 Cemex Mossy Head Industrial
Waste Active N/A

FLA010193 Crestview WWTF Crestview Domestic Active 2.1000Draft 39 August 2010 Permit Facility Name City Type of Facility Facility Status Design Capacity (MGD)
Waste
FLA010202 Okaloosa Correctional Crestview Domestic Waste Active 0.1750

FLA016768 Green Acres WWTP Mossy Head Domestic Waste Active 0.0250

FLA010186 Eglin AFB STP Eglin AFB Domestic Waste Active 0.1250

FLA010188 Eglin AFB STP Ft. Walton Beach Domestic Waste Active 0.0720

FLA010246 City of Paxton
WWTP Paxton Domestic Waste Active 0.0750

Shoal River Planning Unit - - - - -

FLRNEE269 FedEx Ground Crestview Stormwater Active N/A
FLG110035 RMC Ewell Crestview Concrete Batch Plant Active N/A

FLG110434 Fort Walton Concrete Crestview Concrete Batch Plant Inactive N/A

Pensacola Bay Planning Unit - - - - -

FL0002313 Air Products Inc. Pace Industrial
Waste Active 1.5000

FL0002593 Sterling Fibers, Inc. Pace Industrial
Waste Active 5.5000

FLG110210 WPR, Inc. Milton Concrete Batch Plant Active N/A

FLRNEE235 American Accessories Pensacola Stormwater Active N/A

FLG110354 Cemex Pensacola Concrete Batch Plant Active N/A

FLG110376 Cemex Navarre Concrete Batch Plant Active N/A

FL0003174 Hurlburt Field STP Hurlburt Field Domestic Waste Active 1.0000

FLG830419 Escambia Sheriffs Dept. Pensacola Petroleum Cleanup Active N/A

FLG110453 Pensacola Ready Mix Pensacola Concrete Batch Plant Active 0.2160

FLG110289 RMC Ewell Pensacola Concrete Batch Plant Active N/A

FL0002500 U.S. Naval Air Station Pensacola Domestic Waste Active 2.3500

FLRNEE145 Vehicle Facility Pensacola Stormwater Active N/A
FLRNEE085 Reddy Plant # 330 Pensacola Stormwater Active N/A
FL0021440 Main Street STP Pensacola Domestic Waste Active 20.0000

FLG911515 Grocery Supply Pensacola Petroleum Active N/ADraft 40 August 2010 Permit Facility Name City Type of Facility Facility Status Design Capacity (MGD) Cleanup
FLG911201 Double G #1 Navarre Petroleum Cleanup Active N/A

FLG110435 Fort Walton Concrete Fort Walton Beach Concrete Batch Inactive N/A

FLG911452 Navarre Beach Cabins Navarre Petroleum Cleanup Active N/A

FLG110227 Pensacola Ready Mix Gulf Breeze Concrete Batch Plant Active N/A

FL0044377 U.S. EPA Laboratory Gulf Breeze Industrial
Waste Active 0.8500

FL0024007 Pensacola Beach
WWTP Pensacola Beach Domestic Waste Active 2.4000

FLG110343 Pensacola Ready Mix o Pensacola Beach Concrete Batch Plant Active N/A

FL0023981 Navarre Beach STP Navarre Beach Domestic Waste Active 0.9000