Site-Specific Information 

in Support of 

Establishing Numeric Nutrient 

Criteria for Perdido 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 .............................................................................................. 8

Biological Summary............................................................................................................. 10

Biological Resources.....................................................................................................................12

Water Quality Studies ......................................................................................................... 13

Court Decision Regarding Proposed Approach ..................................................................... 19

Waters on the 303(d) List..................................................................................................... 20

Proposed Numeric Nutrient Targets..................................................................................... 20

References .......................................................................................................................... 21
Draft iii August 2010

List of Tables

Table 1. Checklist of nutrient enrichment symptoms in Perdido Bay........................................................... 2

Table 2. Summary of physical properties, including depth, sediment type, stratification, and 

circulation regimes of Perdido Bay (after Niedoroda 2010)....................................................... 5

Table 3. Summary of physical/chemical information for Perdido Bay......................................................... 8

Table 4. Perdido Bay Basin nitrogen (N) to phosphorus (P) ratios for TMDL assessment (from 

FDEP 2008).................................................................................................................................. 9

Table 5. Natural communities in the Perdido watershed, including surface area occupied (FDEP 

2008).........................................................................................................................................11
Draft iv August 2010

List of Figures

Figure 1a. Perdido Bay watershed. .............................................................................................................. 4

Figure 1b. Map of Perdido Bay showing the grid system used for water quality modeling. ....................... 4

Figure 2. Bathymetry and orientation of Perdido Bay (after Niedoroda 2010). .......................................... 6

Figure 3. Tidal regime of Perdido Bay. ......................................................................................................... 7

Figure 4. Cross sectional view of Perdido Bay showing freshwater output/saline input pattern. ............... 9

Figure 5. Conceptual aspects of Perdido model........................................................................................... 9

Figure 6. Grids and depths for three-dimensional (3-D) hydrodynamic model..........................................10

Figure 7. Yield of TN delivered to Perdido Bay from subwatersheds of the Perdido Bay 

watershed. ................................................................................................................................11

Figure 8. The percent differences in the sum of inorganic nitrogen (IN) and inorganic phosphorus 

(IP) loading from Elevenmile Creek to upper Perdido Bay (red line), compared with the 

mean H. akashiwo biomass averaged over all Perdido Bay stations (blue line), 1988–

2007. Data are presented as six-month moving averages (from Livingston 2010).................13

Figure 9. Seasonal abundance peaks of C. choctawhatcheeana (blue), H. akashiwo (red), and M. 

tenuissima (green) in Perdido Bay following a period of increased ammonia and 

orthophosphate loading from Elevenmile Creek. .....................................................................16

Figure 10. Biomass of three consumer trophic levels at selected north Florida bays, including 

data for Perdido Bay before and after the occurrence of HABs, and data for 

Apalachicola Bay, before and after a drought decreased available nutrients. ........................16

Figure 11. Annual averages of the Fish/Infauna/Invertebrate Index trophic organization across 

stations from 1988–89 through 2006–07.................................................................................17

Figure 12. Annual geometric mean TP concentrations in Perdido Bay, 1995–2009.................................. 18

Figure 13. Annual geometric mean TN concentrations in Perdido Bay, 1995–2009. ................................18

Figure 14. Annual geometric mean chlorophyll a concentrations in Perdido Bay, 1995–2009. ................19
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, to support the development of 

numeric nutrient criteria for Perdido Bay.

1

Historically, Perdido Bay has sustained a general loss of benthic production due to salinity stratification 

and hypoxia, both of which directly resulted from dredging and subsequent saltwater intrusion from the 

Gulf of Mexico. Perdido Bay has also been impacted by anthropogenic sources of nutrient enrichment, 

with impacts documented in a long-term (19-year) study of the Perdido River and Bay system. The study 

evaluated the impact of anthropogenic sources of nutrients on the food web organization of the 

estuary, with an emphasis on the interaction of nutrient loading, plankton response, and induced 

changes of food webs due to algal bloom generation (Livingston 2010). 

 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. 

A relatively natural, well-balanced plankton community was observed in Perdido Bay from 1988 to 1991. 

However, a series of phytoplankton blooms occurred from 1993 to 1994, attributable to drought 

conditions and increased nutrient loading by a pulp mill into Elevenmile Creek (Livingston 2010). Blooms 

of the blue-green alga, Merismopedia tenuissima, and the raphidophyte, Heterosigma akashiwo (a toxinproducing diatom), were first noted from 1996 to 1997. Merismopedia blooms, mainly in Elevenmile 

Creek, were associated with high levels of nutrients during drought periods. The Merismopedia blooms 

were statistically associated with severely altered food webs and a significant loss of biological 

productivity in Elevenmile Creek. Heterosigma blooms in the upper bay occurred primarily during 

periods of increased rainfall and increased loading of ammonia and orthophosphate from the pulp mill. 

From 2002 to 2003, additional loading from a sewage treatment plant in the upper bay was associated 

with considerable Heterosigma blooms. Hurricane Ivan (September 2004) had minimal effects on the

plankton blooms. Repeated blooms of Heterosigma resulted in severe damage to formerly productive 

parts of the upper bay and the loss of biological components of the lower bay (Livingston 2010). FDEP 

interprets these algal blooms and significant changes in the bay’s food web dynamics, which led to 

reductions in beneficial productivity, as nutrient-induced imbalances in flora and fauna, violating 

Paragraph 62-302.530 (47)(b), Florida Administrative Code (F.A.C.). 

After 2003, reductions in nutrient loadings to the bay were implemented, and biological recovery was 

observed, although there was evidence that the previous damage made biological communities less 

resilient to further anthropogenic nutrient enrichment. FDEP proposes that the nutrient loading that 

was characteristic of the bay prior to the harmful algal blooms (HABs) be adopted as protective numeric 

criteria. This specific nutrient loading, which was associated with healthy, well-balanced aquatic 

communities, would protect the designated use of Perdido Bay. This concept was recently upheld 

during court proceedings.

The proposed criteria will be available after model runs have been completed. 

Table 1 summarizes the potential nutrient-related responses for Perdido Bay.

 

1 Contributors to this report include Skip Livingston, Tom Gallagher, Alan Niedoroda, Jim Hagy, Just Cerbian, Ken Heck, and Russel Frydenborg.
Draft 2 August 2010

Table 1. Checklist of nutrient enrichment symptoms in Perdido Bay - = Empty cell/no data

Response variable Observed 

Historically?

Observed 

Currently? 

Explanation 

Low dissolved oxygen 

(DO) (hypoxia/anoxia)

Yes Yes Low DO concentrations have been observed 

historically, and current periodic low DOs are 

associated with natural salinity stratification and 

natural organic material delivered by river systems

(Niedoroda 1992, Livingston, 1984a, 1989; 

Livingston et al. 2000).

Reduced clarity No No Turbidity is a temporary phenomenon associated 

with storm events (Heck 1996).

Increased chlorophyll a 

concentrations

Yes No Chlorophyll a exceeded 11 micrograms per liter 

(μg/L) only once during a period of HABs (FDEP 

2006). 

Phytoplankton blooms 

(nuisance or toxic)

Yes Recovering Problematic algae blooms were historically 

observed, but recovery is ongoing, associated with 

nutrient reductions from point sources (Livingston 

2010).

Problematic epiphyte 

growth 

No No Epiphyte growth was not found to be an issue.

Problematic macroalgal 

growth

No No Problematic macroalgal growth has not been 

observed.

Submerged aquatic 

vegetation (SAV) 

community changes or 

loss

Yes No SAV reductions occurred due to salinity changes 

associated with dredging a pass, not from nutrient 

enrichment (Kirschenfeld et al. 2006). 

Emergent or shoreline 

vegetation community 

changes or loss 

No No -

Coral/hardbottom 

community changes or 

loss 

No No Not present.

Impacts to benthic 

community

Yes No HABs affected benthic communities in 1990s, but 

present communities improving (Livingston 2010).

Fish kills Yes No None reported.

Geographic and Physical Description

Perdido Bay, classified as an Outstanding Florida Water (OFW), is located in extreme western Florida and 

is contiguous with the Alabama border (Figures 1a and 1b). The Perdido River and Bay are interstate 

waters that form the boundary between Alabama and Florida (the state line bisects the middle of the

river and bay). The Perdido River is the major freshwater tributary to the bay, with additional 

freshwater input from Elevenmile Creek, Bayou Marcus, Soldier Creek (Alabama), and Palmetto Creek 

(Alabama). The bay is separated from the Gulf of Mexico by Perdido Key, a sand-based barrier island. 

Perdido Bay is connected to Big Lagoon and Pensacola Bay via the dredged Gulf Intracoastal Waterway

(GIWW), and to the Gulf of Mexico via a dredged pass near Orange Beach, Alabama. The bay has several 

distinct areas. The upper bay extends from the mouth of the Perdido River and Elevenmile Creek 

southwest to a constriction in the bay created by Grassy and Double Points. Bayou Marcus discharges 
Draft 3 August 2010

into the upper bay. The lower limit of the middle bay is at the bay constriction created by Manuel and 

Dupont Points. The main bay is bounded at the lower end by a line from Mill Point to Inerarity Point and 

another line south across the GIWW from Hatchet Point. Tarkiln Bayou, Soldier Creek, and Palmetto 

Creek drain to the main bay. The lower bay connects the main bay to the Gulf of Mexico through 

Perdido Pass and includes Bayou St. John. This segment extends east to join the Big Lagoon at the State

Road 292 Bridge. The Big Lagoon and GIWW connect Perdido Bay to Pensacola Bay. The last segment is 

the west bay, defined as the open expanse of water from Hatchett Point west to the Alabama Canal. 
Draft 4 August 2010

Wolf Bay enters the west bay segment. Mobile Bay is connected to Perdido Bay by way of Bay La 

Launch, Wolf Bay, and the Intracoastal Canal (FDEP 2008). 

Figure 1a. Perdido Bay watershed. 

Figure 1b. Map of Perdido Bay showing the grid system used for water quality modeling.

The opening of Perdido Bay to high-salinity water from the Gulf in the early 20th century adversely 

affected the secondary productivity of the system (Livingston 2010). Prior to dredging of the marine 

passes, Perdido Bay was oligohaline, with freshwater biota inhabiting the upper bay. Due to the bay’s 

current physiographic characteristics and a relatively large freshwater inflow compared with the volume 

of its tidal prism (Niedoroda 1992), Perdido Bay is a highly stratified estuary (Table 2). The steep density 

gradient (pycnocline) effectively suppresses vertical mixing. The relatively short fetch relative to 

prevailing wind currents enhances stratification in deeper parts of the bay. Warm summer 

temperatures, which cause lower surface densities; the (northeast to southwest) orientation of the bay, 

which is parallel to the direction of frequent strong winds; and the small tidal range, which averages 

0.15 meters [m]), contribute to the high stratification of the bay (Figures 2 and 3; Table 3). 

The downward diffusion of oxygen is arrested at the pycnocline, and bottom waters become relatively 

depleted at the deeper, more-salinity-stratified stations. DO profiles indicate reduced oxygen supply in 
Draft 5 August 2010

the bottom layer of the lower bay. DO in each part of the bay (river-estuary, upper bay, and lower bay) 

is specifically related to its geographic position in the bay and corresponding water depth. Stepwise 

regression indicates that 44% of the variability in DO distribution in Perdido Bay is a function of 

temperature, depth, salinity concentration, and the level of stratification. With an increase in bottom 

salinity during warm periods of the year, there is an associated reduction of DO. The highly stable 

stratification conditions usually are directly related to these hypoxic conditions. 

The hypoxia at depth is statistically associated with the reduction of several biological indices, including 

the Fish/Invertebrate/Infauna Index (Livingston 2010). This loss of production is similar to findings in 

other bay systems (Livingston, 1984a, 1989; Livingston et al. 2000). 

Table 2. Summary of physical properties, including depth, sediment type, stratification, and 

circulation regimes of Perdido Bay (after Niedoroda 2010). 

Bay Regime Physical Properties 

Lower Perdido River Deep (~7 m or ~ 23 feet [ft]) 

Silty mud bottom

Strong stratification

Circulation–surface fast but bottom stagnant

Upper Bay Shallow (2 m or 6 ft)

Sand-silt-clay

Low to moderate stratification

Tidal circulation–sluggish

Advective flushing (1 to 2 days)

River, creek, and bayou inputs

Middle Bay Intermediate depth (~3 m or ~10 ft)

Clayey silt

Stratification–persistent

Tidal circulation–moderate

Advective flushing–(1⁄2 to 1 day)

Lower Bay Significant depth (~4-5 m or ~13-16 ft) 

Clayey silt to sand 

Stratification–persistent 

Tidal circulation–good 

Advective flushing (1 to 3 days) 

Gulf water input
Draft 6 August 2010

Figure 2. Bathymetry and orientation of Perdido Bay (after Niedoroda 2010). 
Draft 7 August 2010

Figure 3. Tidal regime of Perdido Bay.
Draft 8 August 2010

Table 3. Summary of physical/chemical information for Perdido Bay.

Physical/Chemical Information Value Source

Estuarine surface area 

(square kilometers [km2])

129 National Oceanic 

and Atmospheric 

Administration 

(NOAA)

Watershed area (km2) 2,928 NOAA

Land use % in watershed Forest 64.2%

Agriculture 23.6%

Wetland 3.6%

Urban 8.6%

NOAA

Mean depth (m) 1.53 NOAA

Volume (cubic meters [m3]) 197,370,000 NOAA

Tidal range (m) 0.15 NOAA

Tidal freshwater inflow 

(1,000 cubic meters per day 

[m3d-1])

3,910,000 NOAA

Mean water residence 

time/tidal exchange (days)

29 NOAA

Average salinity (Practical 

Salinity Units [PSU])

13 NOAA

Annual loading of total nitrogen 

(TN) and total phosphorus (TP)

TN= 2,534,000 kilograms per year (kg/yr) 

or 19,643.4 kilograms per square 

kilometer per year (kg/km2

/yr)

TP= 98,890 kg/yr or

766.59 kg/km2/yr

NOAA

Sources and Fates of Nutrients

As part of the ongoing Total Maximum Daily Load (TMDL) rotating basin assessment, FDEP (2006) 

summarized the existing nutrient data for Perdido Bay (Table 4). A water quality model was developed 

by Hydroqual for the International Paper Mill for the purpose of establishing Water Quality–Based 

Effluent Limits (WQBELs) for the pulp mill’s discharge to Elevenmile Creek. The model included the mill 

discharge to Elevenmile Creek and to Perdido Bay through wetlands (Figures 5 and 6). WQBELs were 

developed to address nutrient and DO issues. Major areas of the bay system addressed by the model 

include the Perdido River, Elevenmile Creek (impaired for low DO), and Perdido Bay. The model was 

calibrated for steady-state periods during the summers of 1989 and 1990. It includes a nutrient-algal 

model (Pritchard-WASP). The model includes a time-variable period (1990) coupled with hydrodynamic 

modeling (circulation and color).
Draft 9 August 2010

Table 4. Perdido Bay Basin nitrogen (N) to phosphorus (P) ratios 

for TMDL assessment (from FDEP 2008).

Median and Ratio Value

TN median 0.592 (milligrams per liter [mg/L])

TP median 0.042 (mg/L)

N to P ratio median 16.346

N to P ratio minimum 7.586

N to P ratio maximum 37.5

Figure 4. Cross sectional view of Perdido Bay showing freshwater output/saline input pattern.

Figure 5. Conceptual aspects of Perdido model. 
Draft 10 August 2010

Figure 6. Grids and depths for three-dimensional (3-D) hydrodynamic model.

TN loading was estimated by the U.S. Geological Survey (USGS) using Florida water quality data for the 

Perdido River at the U.S. Highway 90 Bridge (Hagy 2010). The average for 1992 to 2004 was 561,000 kg 

N y-1, from which the average yield was computed to be 443 kg N/km2

/y. TP loading at the same 

location averaged 22,000 kg y-1, from which the average yield was computed to be 17 kg P/km2

/y. The 

TN:TP (atomic) loading ratio was 57. Hagy (2009) calculated the yield of TN delivered to Perdido Bay 

from subwatersheds of the Perdido Bay watershed (Figure 7).

Biological Summary

Perdido Bay and its watershed contain a wide diversity of habitats and aquatic biological resources. 

Table 5 lists the natural communities that characterize the watershed.
Draft 11 August 2010

Figure 7. Yield of TN delivered to Perdido Bay from subwatersheds of the Perdido Bay watershed.

Table 5. Natural communities in the Perdido watershed, including surface area occupied (FDEP 2008). 

Description Acres Mi2 % area

Coastal strand 379.18 0.592 0.15

Sand/beach 1,146.22 1.791 0.45

Xeric oak 147.45 0.230 0.06

Sand pine scrub 281.77 0.440 0.11

Sandhill 93.85 0.147 0.04

Mixed hardwood 

pine forest

12,801 20.002 5.02

Hardwood 

hammock forest

5,911.9 9.237 2.32

Pineland 87,154.45 136.179 34.21

Freshwater 

marsh/wet prairie

1,105.08 1.727 0.43

Shrub swamp 133.88 0.209 0.05

Bay swamp 5,968.39 9.326 2.34

Cypress swamp 709.44 1.108 0.28

Mixed wetland 

forest

14,213.2 22.208 5.58

Hardwood swamp 14,046.85 21.948 5.51

Salt marsh 267.1 0.417 0.10
Draft 12 August 2010

Biological Resources

The following description of biological resources is paraphrased from FDEP 2006. The basin’s coastal 

beaches, scrub, and strand communities provide important habitat for many species listed as 

threatened or endangered. Scrub and strand communities west of Perdido Key State Recreation Area 

are important to migratory birds that use the coastal areas for feeding and resting during migration 

between the tropics and North America. From March to August, sandy beaches provide nesting habitat 

for the royal tern (Sterna maxima), state-listed snowy plover (Charadrius alexandrinus), black skimmer 

(Rynchops niger), least tern (Sterna antillarum), and federally listed endangered piping plover

(Charadrius melodus). The Perdido Key beach mouse (Peromyscus polionotus trissyllepsis) is a federally 

endangered species limited in range to sand dunes located on Perdido Key. Four species of marine sea 

turtles—loggerhead (Caretta caretta), leatherback (Dermochelys coriacea), Ridley (Lepidochelys kempii), 

and green sea (Chelonia mydas)—use coastal beaches for nesting from May to September, though the 

most common sea turtles are loggerheads and green sea turtles. Godfrey’s golden aster (Chrysopsis 

godfreyi) can be found on patches of scrub and coastal strand. 

Perdido Bay has three species of seagrasses: turtle grass (Thalassia testudinum), shoal grass (Halodule 

wrightii), and widgeon grass (Ruppia maritima). Eel grass (Vallisneria americana) is also present in the 

freshwater and brackish portions of the bay. Seagrasses provide habitat for many commercially and 

recreationally important species, including shrimp (Penaeus sp.), crabs (Callinectes sp.), scallops 

(Argopecten sp.), speckled trout (Cynoscion sp.), redfish (Sciaenops sp.), and mullet (Mugil sp.). 

A comparison of the SAV acreage between 1941 and 1992 revealed that the total bay acreage had 

decreased by 74% to 307.1 acres (Kirschenfeld et al. 2006). Based on an analysis of 1992 data, 

seagrasses were not detected in middle Perdido Bay, and the lower Perdido Bay declined to about 303.8 

acres (Kirschenfeld et al. 2006). More recent data (2003) indicate that approximately 300 acres of shoal 

grass remain in Perdido Bay. Most of this acreage is located around or near Ono Island and Big Lagoon. 

Note that the presence of seagrass is highly influenced by salinity regime, and that the salinity regime in 

Perdido Bay is dynamic (due to river inflows) and has been altered by the saline influence of the dredged 

passes. The former, primarily freshwater, regime would not have been expected to support marine 

seagrasses. FDEP has concluded that these complications limit the utility of using seagrass as a nutrient 

response variable for the bay. 

The Perdido River and Bay Basin provides habitat for several rare and threatened fish species. Three 

rare fish species were historically noted from the Perdido River: one listed species of special concern, 

the saltmarsh topminnow (Fundulus jenkinsi), as well as the crystal darter (Crystallaria asprella) and 

goldstripe darter (Etheostoma parvipinne). The Florida Fish and Wildlife Conservation Commission

(FWCC) confirmed the presence of the saltmarsh topminnow during field sampling in 2001 and 2002 in 

tributaries of the Perdido Bay watershed. Striped bass also use the Perdido River throughout its length. 

The Gulf race of the Atlantic sturgeon (Acipenser oxyrinchus desotoi) uses the Perdido River, as 

documented by the Alabama Geological Survey in 2004. 

Based on the 19 years worth of data from Livingston (2010), it has been determined that the most direct 

link between anthropogenic nutrients and adverse biological response involves HABs and their 

subsequent adverse effects on food webs (described below). 
Draft 13 August 2010

Water Quality Studies

The primary response to anthropogenic nutrient enrichment observed in Perdido Bay was the 

proliferation of HABs during a period of elevated point source nutrient loading that resulted in 

secondary effects on the bay’s trophic functioning (Figure 8) (Livingston 2010). From 1988 to 1996, the 

plankton communities indicated healthy, well-balanced conditions in Perdido Bay, with a low occurrence 

of plankton blooms (occurrences of more than 1 million cells per liter [> 106 cells L-1]). The numerically 

dominant species included the diatom Cyclotella choctawhatcheeana, with the highest numbers of 

phytoplankton noted in mid-bay areas. Miraltia throndsenii, Prorocentrum cordatum, Gymnodinium 

splendens, and Skeletonema costatum were present in the bay but were noted in relatively low 

numbers. Cryptophytes and nannoplankton were most numerous in mid-bay areas. 

During 1997 and 1998, subsequent to two years of increased nutrient loading to the bay through 

Elevenmile Creek, there were major changes in the phytoplankton assemblages in the bay. 

Phytoplankton abundance was highest in the upper bay, where the raphidophyte H. akashiwo became

dominant (and was also present in all parts of the bay. H. akashiwo is well known for ichthyo-toxic 

blooms (Honjo 1994). Concurrently, the formerly dominant diatom C. choctawhatcheeana was greatly 

reduced in the upper bay, although this taxon was still dominant in mid- and lower bay areas. 

Nannococcoids, pennate diatoms, and prymnesiophytes were no longer prevalent in the bay, and 

cryptophytes had increased in all three parts of the system. The blue-green alga M. tenuissima was first 

noted in Elevenmile Creek, although in relatively low numbers. 

Figure 8. The percent differences in the sum of inorganic nitrogen (IN) and inorganic phosphorus (IP) 

loading from Elevenmile Creek to upper Perdido Bay (red line), compared with the mean H. akashiwo 

biomass averaged over all Perdido Bay stations (blue line), 1988–2007. Data are presented as sixmonth moving averages (from Livingston 2010). 

-200

0

200

400

600

800

1000

1988/101989/041989/101990/041990/101991/041991/101992/041992/101993/041993/101994/041994/101995/041995/101996/041996/101997/041997/101998/041998/101999/041999/102000/042000/102001/042001/102002/042002/102003/042003/102004/042004/102005/042005/102006/042006/102007/04

year/month

0.001

0.010

0.100

1.000

10.000

100.000

1000.000

μgL-1

11mickDIN+DIPd%Diff HETAKA(μg/l)-av

6 per. Mov. Avg. (11mickDIN+DIPd%Diff) 6 per. Mov. Avg. (HETAKA(μg/l)-av)
Draft 14 August 2010

Because of reduced nutrient discharges from the point source (pulp mill) to Elevenmile Creek starting in 

1998, from 2001 to 2002 the phytoplankton community began to shift (Livingston 2010). M. tenuissima

became the top dominant in the upper bay, and phytoplankton abundance there largely consisted of

cryptophytes and nannoflagellates. In the mid- and lower bay areas, C. choctawhatcheeana was 

dominant, and although H. akashiwo was still present in all parts of the bay, its abundance was reduced. 

In 2002 and 2003, nutrient inputs from a discharge to Bayou Marcus (upper bay) were correlated with 

the occurrence of H. akashiwo in high numbers in this part of the upper bay. At the same time, M. 

tenuissima became a dominant taxon in the Elevenmile Creek drainage and was also found in mid-bay 

areas. This coincided with reduced numbers of H. akashiwo in the Elevenmile drainage, a direct result of 

the reduced nutrient loading in this area. However, H. akashiwo was dominant in mid-bay areas, and 

appeared to respond to nutrient loading trends in the eastern part of the upper bay. Cryptophyte 

abundance in mid- and lower bay areas had increased, and the overall numbers of phytoplankton in the 

bay increased significantly due to the above-noted changes in species representation baywide

(Livingston 2010). 

Both ammonia and orthophosphate loading from Elevenmile Creek were significantly (P<0.05) 

associated with H. akashiwo cell numbers (Livingston 2010). The number of Heterosigma blooms in the 

upper bay was inversely related to the number of C. choctawhatcheeana blooms. In the upper bay, 

these species were inversely associated (R2 = -0.36, P< 0.05). Annual averages of Cyclotella peaked with 

the downward trend of Heterosigma during the period of high but diminishing nutrient loading from 

Elevenmile Creek (1994–1999). The blue green alga, M. tenuissima, was directly associated with bottom 

salinity (R2 = 0.38, P< 0.05) and salinity stratification (R2 = 0.45, P<0.05). There were general increases in 

salinity stratification during the drought periods from 1999 to 2002 and 2006 to 2007. The cryptophytes 

and nannoflagellates in the bay near Elevenmile Creek peaked during the drought of 1999 and 2002, 

with nannococcoids reaching peak values at the end of the drought. The combination of the history of

nutrient loading and drought appeared to affect the long-term distribution of these phytoplankton 

groups. 

There were seasonal trends in both the nutrient loading characteristics and the presence of dominant 

plankton species in the bay. Elevenmile Creek ammonia loading peaked during April, and 

orthophosphate loading peaked from May through September (Figure 9). When standardized as 

percent loadings of these nutrients as a function of the overall mean, there were peaks from April 

through August. Peak numbers of H. akashiwo occurred from April through July, and C. 

choctawhatcheeana peaked during April and May. Bloom species occurrence was timed to both 

seasonal and interannnal cycles of nutrient loading in Elevenmile Creek (Livingston 2010).

The series of HABs from 2002 to 2005 described above resulted in a significant adverse effect on the 

trophic functioning of Perdido Bay’s fauna (Livingston 2010). The biomass of consumer trophic levels 

(including commercially valuable shrimp, crab, and fish species) in Perdido Bay decreased markedly after 

the occurrence of H. akashiwo blooms (Figure 9). This is evidence that the level of nutrient loading

responsible for the HABs interfered with the designated use of the bay, and that reducing nutrients to 

the level that occurred prior to the HAB proliferation would return the system to a healthy, wellbalanced state.

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). Figure 10 depicts the pattern 

and distribution of the various Fish/Infauna/Invertebrate Index trophic levels in Perdido Bay over the 19-
Draft 15 August 2010

year study period. Herbivore biomass was present mainly in the seagrass beds of upper Perdido Bay, 

but herbivores were reduced during the period of increased nutrient loading. Herbivore biomass 

increased during periods of low nutrient loading and when Heterosigma concentrations were low 

(1998–1999; 2003–2004; 2006). Omnivore biomass increased during periods of high nutrient loading 

and when Heterosigma concentrations were high (1995–2000; 2003–2005). 

Dominant bloom species

10000

100000

1000000

10000000

October

November

December

January

February

March

April

MayJune

July

August

September

month

CYCCHOn-av HETAKAn-av MERTENn-av
Draft 16 August 2010

Figure 9. Seasonal abundance peaks of C. choctawhatcheeana (blue), H. akashiwo (red), and M. 

tenuissima (green) in Perdido Bay following a period of increased ammonia and orthophosphate 

loading from Elevenmile Creek.

Figure 10. Biomass of three consumer trophic levels at selected north Florida bays, including data for 

Perdido Bay before and after the occurrence of HABs, and data for Apalachicola Bay, before and after 

a drought decreased available nutrients.

From 1988 to 1991, the biomass of primary, Level 1 carnivores (C1 carnivores) was highest in upper 

Perdido Bay compared with the remainder of the bay (Figure 11). With increased nutrient loading from 

Elevenmile Creek, C1 biomass decreased in the upper bay, and from 2004 to 2006, C1 carnivores were 

primarily restricted to a station near Grassy Point. However, the recovery of C1 carnivores was noted at 

the end of the study period. Secondary, Level 2 carnivores (C2 carnivores) were distributed over a 

number of stations during the early years, with subsequent decreased coverage following bloom 

periods. The biomass of C2 carnivores was lowest during the blooms of 2001 to 2003 and 2005 to 2006. 

There was a general decrease of C2 carnivore biomass with time. Tertiary, Level 3 carnivores (C3

carnivores) increased in the upper bay from 1998 to 2000, but decreased throughout the bay (except in 

Elevenmile Creek), with no significant subsequent recovery, potentially due to a delayed response

associated with the earlier HAB events. Because ecosystem recovery is ongoing and does not yet appear 

to be complete, a reasonable decision would be to establish nutrient criteria based upon the conditions 

that occurred from 1988 to 1991, when the bay was demonstrated to be healthy. 

Data from the Impaired Surface Waters Rule (IWR) Database were analyzed to assess baywide trends 

over time. For this analysis, FDEP required that each station have a minimum of 4 observations in a 
Draft 17 August 2010

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 Perdido Bay system (Figure 12), although the range of annual geometric means for TP, from 6 to 35 

μg/L, is relatively low compared with many other southeastern U.S. estuaries (Hagy 2009). Note that 

the main point source discharge into the bay (paper mill) had implemented nutrient reductions by 1998.

Annual geometric mean TN concentrations in Perdido Bay have ranged from 0.24 to 0.7 mg/L since 1995 

(Figure 13). Hagy (2009) found that there was a relationship between salinity (due to river inflows) and 

TN concentrations in adjacent Escambia Bay (Figure 13). 

Since 1995, the annual geometric mean chlorophyll a for the entire Perdido Bay system ranged from 1.1 

to 6.0 μg/L (Figure 14), demonstrating that chlorophyll-induced transparency reductions are generally 

not an issue in the bay.

Figure 11. Annual averages of the Fish/Infauna/Invertebrate Index trophic organization across

stations from 1988–89 through 2006–07. 

Blue=herbivores, Red=omnivores, Yellow= Level 1 consumers, Green = Level 2 consumers, black = Level 3 consumers

Annual averages across stations

0.0000

0.2000

0.4000

0.6000

0.8000

1.0000

1988-891989-901990-911991-921992-931993-941994-951995-961996-971997-981998-991999-002000-012001-022002-032003-042004-052005-062006-07

year

avFIIherb avFII0mniv avFIIC1 avFIIC2 avFIIC3
Draft 18 August 2010

Figure 12. Annual geometric mean TP concentrations in Perdido Bay, 1995–2009.

Figure 13. Annual geometric mean TN concentrations in Perdido Bay, 1995–2009.

y = -0.0009x + 1.8542

R2 = 0.3209

0

0.005

0.01

0.015

0.02

0.025

0.03

0.035

0.04

1994 1996 1998 2000 2002 2004 2006 2008 2010

Geometric Mean TP

y = -0.0021x + 4.6678

R2 = 0.0054

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

1994 1996 1998 2000 2002 2004 2006 2008 2010

Geometric Mean TN
Draft 19 August 2010

Figure 14. Annual geometric mean chlorophyll a concentrations in Perdido Bay, 1995–2009.

Court Decision Regarding Proposed Approach

The nutrient effluent limits specified in the pulp mill’s National Pollutant Discharge Elimination System 

(NPDES) permit for its discharge to Perdido Bay was the subject of recent litigation (Division of 

Administrative Hearings [DOAH] 2010). During the proceedings, FDEP argued that the conditions in 

Perdido Bay that occurred prior to the onset of HABs represented the historically healthy, well-balanced 

biological expectation for the bay. FDEP also argued that the nutrient loadings that occurred during this 

period would fully protect the designated use of the bay. 

The court decision clearly demonstrates that the numeric criteria proposed here, using an analogous 

approach, are legally and scientifically defensible. After extensive testimony, Judge Bram Canter wrote 

the following decision: 

In 1989, the Department and Champion signed a Consent Order to address water quality 

violations in Elevenmile Creek. Pursuant to the Consent Order, Champion commissioned 

a comprehensive study of the Perdido Bay system that was undertaken by a team of 

scientists led by Dr. Robert Livingston, an aquatic ecologist and professor at Florida State 

University. The initial three-year study by Dr. Livingston's team of scientists was 

followed by a series of related scientific studies. 

The Livingston studies represent perhaps the most complete scientific evaluation ever 

made of a coastal ecosystem. Dr. Livingston developed an extensive biological and 

chemical history of Perdido Bay and then evaluated the nutrient loadings from 

Elevenmile Creek over a 12-year period to correlate mill loadings with the biological 

health of the Bay. The Livingston studies confirmed that when nutrient loadings from 

the mill were high, they caused toxic algae blooms and reduced biological productivity in 

y = -0.1665x + 337.55

R2 = 0.2729

0

1

2

3

4

5

6

7

1996 1998 2000 2002 2004 2006 2008 2010

Geometric Mean Chlorophyll a
Draft 20 August 2010

Perdido Bay. Some of the adverse effects attributable to the mill effluent were most 

acute in the area of the Bay near the Lanes' home on the northeastern shore of the Bay 

because the flow from the Perdido River tends to push the flow from Elevenmile Creek 

toward the northeastern shore.

Because Dr. Livingston determined that the nutrient loadings from the mill that occurred 

in 1988 and 1989 did not adversely impact the food web of Perdido Bay, he 

recommended effluent limits for ammonia nitrogen, orthophosphate, and total 

phosphorus that were correlated with mill loadings of these nutrients in those years. The 

Department used Dr. Livingston's data, and did its own analyses, to establish WQBELs 

for orthophosphate for drought conditions and for nitrate-nitrite. WQBELs were 

ultimately developed for total ammonia, orthophosphate, nitrate-nitrite, total 

phosphorus, BOD [biochemical oxygen demand], color, and soluble inorganic nitrogen.

The WQBELs in the proposed permit were developed to assure compliance with water 

quality standards under conditions of pollutant loadings at the daily limit (based on a 

monthly average) during low flow in the receiving waters. Petitioners failed to prove 

that any new data in the December 2007 report of the Livingston team demonstrate that 

the proposed WQBELS are inadequate to prevent water quality violations in Perdido Bay.

Waters on the 303(d) List

With one exception, annual mean chlorophyll a values have generally been below the 303(d) 

impairment threshold for estuaries (11 μg/L) in the IWR (Chapter 62-303, F.A.C.), with annual mean 

values of 12.83 μg/L (1994), 7.7 μg/L (1998), 7.310 μg/L (1999), 8.316 μg/L (2000), 7.449 μg/L (2001), 

7.887 μg/L (2002), and 6.41 μg/L (2003). Livingston (2010) noted blooms of H. akashiwo (a toxinproducing diatom) occurred during the same period (2004) that chlorophyll a exceeded 11 μg/L . The 

system was N:P colimited based on median TN/TP ratio of 16.35, using 35 values (FDEP 2008).

Proposed Numeric Nutrient Targets 

Based on model calculations, the protective nutrient loading to Perdido Bay, which occurred from 1988

to 1991, associated with a healthy, well balanced community, is shown in Table XX.........

FDEP’s intent is to add this section prior to the public workshop.
Draft 21 August 2010

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