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, 2010 
Draft 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................................................................................................... 38
Draft 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 Caffery 2009). ............................................................ 7

Figure 8. Potential nitrification (micromoles per cubic centimeter per day [umol/cm3

/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/m2

/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 flowweighted 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.................................. 18
Draft 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)......................................................................................................................30
Draft 1 August 2010

 

Executive Summary

This report was prepared by the 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 endpoints in Pensacola Bay. Due to toxic 

point source discharges in the 1970s, seagrasses 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 seagrass coverage. Because physical restoration (replanting, potential sediment 

modification) will likely be required to restore the historical seagrass and oyster beds, a focus of 

maintaining the nutrient concentrations needed to achieve a chlorophyll-based, light transparency 

target is the optimal method for numeric nutrient criteria development. 

to support the development 

of numeric nutrient criteria for the Pensacola Bay system, which includes East Bay, Escambia Bay, Santa 

Rosa Sound, and Big Lagoon. 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 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 (μg/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 ability of submerged aquatic vegetation (SAV) to phytosynthesize (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 Protection Agency 2008)

concluded 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 achievable, is lacking”. 

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

Nutrient targets are summarized in Table 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 Bay. 

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 2007, 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 system is located in both Escambia and Santa Rosa Counties, with Santa Rosa Sound 

in Santa Rosa County and Big Lagoon located in Escambia County. Santa Rosa Sound is a 42.4-squaremile (mi2

) lagoon that connects Choctawhatchee Bay to the east and Pensacola Bay to 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 is deeper, with portions dredged, while Escambia and 
Draft 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 Lagoon 
Draft 4 August 2010

 

Figure 2. Relative bathymetry in Pensacola Bay (yellow indicates about 2 meters (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 (km2) and includes 3 significant watersheds—the 

Escambia, Blackwater, and Yellow Rivers—which together form several hydrodynamically linked 

subsystems and 4 major estuarine bayous. Figure 3 shows the segments with waterbody identification 

(WBID) numbers for Pensacola Bay. 

The watersheds 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 Pensacola Bay and includes low- to medium-intensity development, 

including residential, business, and industrial land uses. Land cover data suggest a relatively low 

nutrient yield from the major portions of the basin. 

Table 1 presents physical/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). Surface and bottom layer salinities may differ by up to 20 PSU. Surface DO

ranges between 80% and 105% of saturation, while bottom DO ranges between 0% and 100% 

saturation. 

Natural salinity stratification is a major factor causing hypoxia 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 explained by 

river flow and resulting salinity stratification (Figure 7).

Figure 5. Salinity cross-section of Escambia to Pensacola Bay; top 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 higher DO at night and lower 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 developed in Pensacola 

Bay despite low oxygen consumption rates in the lower water column and sediments. Total (i.e.,

2008 2009

1996

1997

1998

1999

2000

2001

2002

2004

2005

2003

R2 = 0.65

0

1

2

3

4

5

0 50 100 150 200 250 300 350

average summer flow (Jun-Aug) cms

bottom water DO mg/L
Draft 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/m2

/day) using a box model (Hagy and Murrell 2007). The model 

estimates were in reasonable agreement with average integrated oxygen consumption rates (0.94 

g/m2

/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/m2

/day 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 beach to avoid low-oxygen waters. 

Jubilees have occurred in Mobile Bay, Alabama, for more than a century (May 1973; Schroeder and 

Wiseman 1988). Hagy et al. (2008) indicated that hypoxia likely occurred in Pensacola Bay prior to 

significant human influence, but there were inadequate data to document any trend in DO during the 

past several decades.

Nitrification and denitrification rates are somewhat lower in Pensacola Bay compared with other Gulf of 

Mexico estuaries (Caffery 2009) (Figures 8 and 9). While shoals have low nitrification due to bacteria 

competing with benthic algae for ammonium, hypoxia does not appear to affect nitrification rates 

(Caffery 2009).

Figure 8. Potential nitrification (micromoles per cubic centimeter per day [umol/cm3

/d]) in Pensacola 

Bay areas compared with other Gulf of Mexico estuaries (after Caffery 2009).

0

0.5

1

1.5

2

2.5

3

Potential Nitrification μmol/cm3/d

River Shoal Channel GOM estuaries
Draft 9 August 2010

 

Figure 9. Denitrification (micromoles per square meter per day [mmol/m2

/d]) in Pensacola Bay areas 

compared with other Gulf of Mexico estuaries (after Caffery 2009).

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), respectively (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 assay 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 estuary 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 (km2) 477 km2 National Oceanic and 

Atmospheric 

Administration (NOAA) 

Watershed area (km2) 17,650 km2 NOAA 

Mean depth (m) 3.02 m NOAA 

Volume (m3) 1,440,540,000 NOAA 

Tidal range (m) 0.42 NOAA 

Tidal freshwater inflow (1,000 cubic 

meters per day (m3

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, Florida, averaged 2.8x106 kilograms 

per year (kg/y) from 1975 to 1995 (290 kg/km2

/yr with 38% interannual variation) (Hagy 2009). The TN 

loading rate for Pensacola Bay includes 5.8×106 kg N/y (watershed sources), 0.16×106 kg N/y (point 

0

1

2

3

4

5

6

Denitrification

mmol/m2/d

River Shoal Channel GOM estuaries
Draft 10 August 2010

 

sources to estuary), and 0.17×106 kg N/y (wet and dry N deposition), for a total TN load to Pensacola 

Bay of 6.1×106 kg N y-1 (12.8 g N m-2 y-1). Approximately 95% of the nutrient loading is from the large, 

primarily forested, watershed (Hagy 2009). 

Atmospheric deposition measurements 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 deposition declined over the last 

five years and that the decline was not due to different rainfall amounts (there was more rain in 2009 

than 2005 or 2006). The blue line is the approximate nitrogen deposition from the National 

Atmospheric Deposition Program (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 μg/L) is

relatively low 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 salinity and 

TN concentrations in Escambia Bay, because the river was the primary source of the N (Figure 13).

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). 
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 2009

Total Phosphorus (mg/L)

Year

Pensacola Bay Total Phosphorus
Draft 12 August 2010

 

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). 

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). 

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 2010

Total 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 Salinity

Average TN (mg/L)

Surface Water

Bottom Water
Draft 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 

directly 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 impaired 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 chlorophyll 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 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 = -0.116x + 235.42

R2 = 0.1747

0

1

2

3

4

5

6

1997 1999 2001 2003 2005 2007 2009

Geo. Mean Chlorophyll a (ug/L)

Year

Pensacola Bay Chlorophyll a
Draft 14 August 2010

 

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.

Mitigation of Point Sources

The considerable quantities of point source wastewater previously discharged into the Pensacola Bay 

system between 1955 and 1964 have been significantly 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 (Container 

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 latest information (FDEP 2007) indicates there 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 directly 

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 

issued 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 Program 
Draft 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/uses in the Pensacola Bay system:

• Fishing, including recreational fishing from boats, beaches, and fishing piers. Most 

targeted species are pelagics (e.g., redfish, king mackerel, speckled trout). 

• Commercial fishing, including shrimp-trawling activities and smaller operations that 

target mullet. 

• Oyster harvesting (via tongs and hand collection), especially in East Bay. 

• Seagrass habitats found in lower Pensacola Bay and in Santa Rosa Sound/Big 

Lagoon, 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 recreational activities that are economically important to the area. 

More than 200 species of fish and shellfish have been recorded from the Pensacola Bay Estuary (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), Alabama 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 

oysters peaked about 1970 (Macauley 2005). As much as 90% of the oyster population was lost to 

disease by 1971 and oyster beds are no longer commercially viable, although an 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 Estuary 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. 

SAV in Pensacola Bay

The Pensacola Bay system 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 highly productive plants 

(Hughes et al. 2009). Their extensive root systems and dense, structured leaf canopies form habitat and 

provide food for a wide array of organisms, including commercially and recreationally important fish and 

invertebrates, wading birds, manatees, and sea turtles (Short and Wyllie-Echeverria 1996, Williams and 

Heck 2001; 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 seagrasses come from a variety of sources, including reduced water quality and 

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

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

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

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

conditions (Orth et al. 2006). 

Seagrasses have been shown to be adversely impacted by anthropogenic nutrient enrichment (Orth and 

Moore 1983; Tomasko et al. 1996). Reduced underwater light penetration appears to be a primary 

driver of seagrass decline. One mechanism behind this process is that increased inputs of N and P lead 
Draft 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-scale 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 in 

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 

therefore 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 system. However, a 

recession and disappearance of most of Escambia Bay’s true seagrass occurred from 1950 to 1975

(Collard 1991a; Collard 1991b). A similar dramatic decline occurred in East Bay over the same period. 

Major causes for the SAV loss included toxic industrial wastewater discharges (primarily ammonia), 

dredge-and-fill activities, and beachfront alterations. Extensive fish kills occurred in Escambia Bay 

during the late 1960s and early 1970s (EPA 1971; Livingston 2005) during the same period that the 

seagrass beds were eliminated. Industrial wastewater discharges 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 SAV (Figure 17). In 

1950, incomplete 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 coverage was fully quantified, demonstrating a 

significant loss in SAV from 1960 to 1980 with no subsequent recovery (Figure 17). Most of the 

remaining SAV occurs in Santa Rosa Sound and nearby portions of lower Pensacola Bay. SAV is virtually 

absent from the remainder of the bay. 

While some may hypothesize that the failure 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 chlorophyll 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 Thalassia 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 appears to be

adequate due to metabolic 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 nature of blooms. 

Livingston conducted an extensive study of Pensacola Bay from 1990 to 1991 and from 2001 to 2002. 

No phytoplankton blooms (numbers greater than 1 million cells per liter [> 1x106 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 Prorocentrum 
Draft 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 was 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 epibenthic 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 eastern parts 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 Gulf, 

fish/infauna/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/m2

) 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 (primary) 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 data 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 (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).

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/m2
Draft 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 (sciaenids) 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 other 

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 Program (IMAP). The 

IMAP survey found that Pensacola Bay benthic abundance was the lowest of all north Florida estuaries, 

benthic invertebrate abundance increased eastward from Pensacola Bay to Apalachee Bay, and 

abundance was highest on the west Florida peninsula (Figure 20). Figure 21 shows the pattern of

benthic invertebrate abundance throughout the Pensacola Bay system. Generally low phytoplankton 

production, natural episodes of hypoxia, and habitat limitation are possible causes for low invertebrate 

abundances in Pensacola Bay. 

Figure 20. Total benthic abundance 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. 

Seagrass 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 Sound.

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 Shore
Draft 24 August 2010

 

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.

Restoration Efforts

FDEP has implemented “Project GreenShores,” a multimillion-dollar 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 city of Pensacola, Escambia 

County, Ecosystem Restoration 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 system. 

The purpose of the project is to restore the Pensacola Bay estuary to its historical state by stabilizing 

shorelines and providing essential habitat for wildlife propagation and conservation. FDEP has 

determined that the lack 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 the 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 Florida. 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 system 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 Bays north of Interstate 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 

approved 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 northwestern portion, which 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) found 

that Escambia River flooding caused high turbidity and rapid flushing in the bay, severely reducing 

phytoplankton production and biomass accumulation. Following floods, phytoplankton biomass and 

productivity sharply increased; however, the authors concluded that Escambia Bay was 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. Freshwater 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 effects 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 nutrient export from the watersheds 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 characterized 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

Escambia 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 mixing 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: chlorophyll a, Secchi 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 

(chlorophyll a, bottom light levels, and DO). 

• Determined 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 depths where historical 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 ambient particulate 

matter, color, and chlorophyll a levels. These parameters are calculated in the 

model, with chlorophyll 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 standards 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 site-specific 

alternative criterion for DO may be appropriate for Pensacola Bay. 

• Determined acceptable chlorophyll 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 

and 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 chlorophyll a levels in upper Escambia Bay were 

approximately 4 to 5 μg/L (Figure 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 forested land use. A comparison of the “current” to “natural 

background” modeling output resulted in extremely minor differences for chlorophyll 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. Calculated 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 chlorophyll a, for 1998 model calibration (Hydroqual 

2010). 

Waters on the 303(d) List

Following the methodology in the IWR, 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 historical 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. Note that coliforms are indicators 

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 information 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 often 
Draft 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 cause-effect relationship, the 

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

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

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

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

preserve the uses associated with that distribution. 

The frequency and duration components of the criteria are best established as additional descriptors of 

the reference condition data distribution. Specifically, these components should be part of a statistical 

test designed to determine whether the long-term distribution of data has shifted upward ( or in some 

cases, downward) from the reference distribution. This test would then be used to determine whether 

future monitoring data are consistent with the magnitude (long-term average) defined by the reference 

dataset. It is critical to account for the natural variability surrounding the magnitude expression and to 

control for statistical errors. 

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

for Pensacola Bay is described briefly below. More details concerning the statistical approaches used 

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

Marine Waters” (FDEP 2010).

Magnitude 

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

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

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

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

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

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

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

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

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

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

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

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

long-term dataset for each segment of the waterbody.

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

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

on an annual basis. It should be noted that the duration and frequency components of the criteria must 
Draft 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 sufficiently robust cause-effect relationship 

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

periods should be used. 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

and 

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

The two expressions of magnitude differ in the handling of within-segment spatial variability. The 

network average magnitude was calculated based on the distribution of spatially averaged annual 

geometric means, while the single site magnitude was calculated using the distribution of station annual 

geometric means. Use of the network average magnitude is appropriate for assessing overall segment 

status. However, a network average is only representative of overall segment status if it is relatively 

homogeneous. If the segment is not well mixed, is very large, or contains localized nutrient sources, 

then there is a potential that isolated areas of enrichment may be masked in the network spatial 

average. Therefore, the single station annual geometric mean has the benefit of assessing localized 
Draft 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 geometric mean concentration; b) an 

annual geometric mean of values from a network of stations over a given area, not to be exceeded more 

than twice in a five-year period; and c) an annual geometric mean of values from a single location, not to 

be exceeded more than twice in a five-year period.

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

Pensacola Bay, as well the annual limits for each segment, 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 station 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 0.615

 
Draft 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

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Draft 38 August 2010

 

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 2.1000 
Draft 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/A
Draft 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