# 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, 2010Draft ii August 2010 

### Table of Contents

Executive Summary

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

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

.............................................................................................. 8 Biological Summary

............................................................................................................. 10 Biological Res ources
..................................................................................................................... 12 

### Water Quality Studies

......................................................................................................... 13 Court Decision Regarding Proposed Approach

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

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

..................................................................................... 20
References

.......................................................................................................................... 21Draft 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 T MDL assessment (from FDEP 2008).

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

................................................................................................ ........................................ 11Draft 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 Perdi do 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 i n Perdido Bay, 1995

– 2009.

................ 19Draft 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 impac ts 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 p rimary 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 phyto plankton blooms occurred from 1993 to 19 94 , 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 toxin

producing diatom)

, were first noted from 1996 to 19 97. 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 20 03, 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 plankto n 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 t hese algal blooms and significant changes in the b ay’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 impl e mented , 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 f or 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 e nrichment symptoms in Perdido Bay

- = Empty cell/no data

Response variable Observed H istorically ? Observed C urrently ? 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 ph enomenon associated with storm events (Heck 1996 ). Increased chlorophyll a concentrations Yes No C hlorophyll a exceeded 11 micrograms per liter ( **μ** g/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

.

Problemati c macroalgal growth No No Problematic macroalgal growth has not been observed.
S ubmerged aquatic vegetation (S AV ) 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 affec ted 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 (OF W), is located in extreme western Florida and is contiguous with the Alabama border (Figure s 1a and 1b )

. The Perdido River and Bay are interstate waters that form the boundary between Alabama and Florida (t he 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 Eleven m ile 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 t o 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 E levenmile Creek southwest to a constriction in the bay created by Grassy and Double Points. Bayou Marcus dischargesDraft 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 bou nded 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 Mexic o 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 las t segment is the west bay, defi ned 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 1 a . 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 20 th century adverse ly 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 volum e of its tidal prism (Niedoroda 1992), Perdido Bay is a highly stratified estuary (Table 2) . The steep density gradient (pycnocline) effective ly suppresses vertical mixing. The relatively short fetch relative to
p revailing wind currents enhances stratification in deeper parts of the bay. Warm summer temperatures , which caus e 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 average s 0.15 meters [m] ), contribute to the high stratification of the bay (Figure s 2 and 3; Table 3 ).

The d ownward 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 inDraft 5 August 2010 the bottom layer of the lower bay. DO in e ach part of the bay (river

- estuary , upper bay, and lower bay) is specifi cally related to its geographic position in the bay and corresponding water depth. S tepwise
regr ession indicate s 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 a ssociated reduction of DO

. The highly stable stratification conditions usually are directly related to these hypoxic conditions.

T he hypoxia at depth is statistically associated with the reduction of several biological indices , including the Fish/Invert ebrate/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 f ee t [ft] ) Silty mud bottom Strong stratification Circulation

– surface fast but bottom stagna nt 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 T idal 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 inputDraft 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 [ km 2 ]) 129 N ational Oceanic and Atmospheric Administration (N OAA) Watershed area (km 2 ) 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 [ m 3 ]) 197
, 370
, 000 NOAA Tidal range (m) 0.15 NOAA Tidal freshwater inflow (1 , 000 cubic meters per day [m 3 d -1 ]) 3, 910
, 000 NOAA

Mean water residence time /tidal exchange (days) 29 NOAA

Average s alinity ( Practical Salinity Units [ PSU ]) 

### 13 NOAA

Annual l oading of total nitrogen ( TN ) and total phosphorus ( TP ) TN= 2,534,000 kilograms per year ( kg/yr )

or 19,643.4 kilogra m s per square kilometer per year ( kg/km 2 /yr )

TP= 98,890 kg/yr or 766.59 kg/km 2 /yr NOAA



### Sources and Fates of Nutrients
As part of the ongoing Total Maximum Daily Load ( TMDL ) rotat ing basin assessment, FDEP (2006 ) summarized the existing nutrient data for Perdido Bay (Table 4). A water quality model was developed by Hydroqual for the I nternational Paper Mill for the purpose of establishing Water Qual ity

– Based Effluent Limits (WQBELs) for the pulp mill’s discharge to Elevenmile Creek. The model included the mill d ischarge 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 n utrient

- 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 n itrogen (N) to p hosphorus (P) r atios for T MDL assessment (from FDEP 2008).
Median and Ratio Value
TN m edian 0.592 (m illigrams per liter [m g/L ])
TP m edian 0.042 (mg/L)
N to P r atio m edian 16.346
N to P r atio m inimum 7.586
N to P r atio m aximum 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 B ridge (Hagy 20 10 ). 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/km 2 /y. TP loading at th e same location averaged 22,000 kg y -1 , from which the average yield was computed to be 17 kg P/km 2 /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 watershe d (Figure 7 ).



### Biological Sum mary 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 c ommunities in the Perdido watershed , including su r face area occupied (FDEP 2008)

. Description Acres Mi 2 % 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 0.10Draft 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 u s e the coastal areas for feeding and resting during migration between the tropic s 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 ( Chelo nia mydas )—us e 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 pat ches of scrub and coastal strand

.

P erdido Bay has three species of seagrasses: turtle grass ( Thalassia testudinum ), shoal grass ( Halodule wrightii ) , and widgeon grass ( Ruppia maritim a )

. Eel grass ( Vallisneria americana ) is also present in the freshwater and brackish portions of the bay. Seagrasses provide habitat for many commercially and recreational ly 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). B ased on an analysis of 1992 data
, s eagrasses 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 freshwat er , 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 fi sh 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 golds tripe darter ( Etheostoma parvipinne )

. The Florida Fish and Wildlife Conservation Commission (FWCC) confi rmed 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 ) us es the Perdido River, as documented by the Ala bama 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 web s (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 [ > 10 6 cells L -1 ])

. The numerically dominant species included the diatom Cycl otella 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. Cry ptophytes and nannoplankton were most numerous in mid

- bay areas.

During 1997 and 1998 , subsequent to two years of increased nutrie nt loading to the bay through Elevenmile Creek , there were major changes in the phytoplankton assemblages in the bay

. P hyto plankton abundance was highest in the upper bay , where t he 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 i norganic phosphorus (IP) loading f rom Eleven m ile 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)

. -200 0 200 400 600 800 10001988/101989/041989/101990/041990/101991/041991/101992/041992/101993/041993/101994/041994/101995/041995/101996/041996/101997/041997/101998/041998/101999/041999/102000/042000/102001/042001/102002/042002/102003/042003/102004/042004/102005/042005/102006/042006/102007/04

year/month 0.001 0.010 0.100 1.000 10.000 100.000 1000.000μgL-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 phyt oplankton 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 , it s abundance was reduced

. In 2002 a nd 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 drainag e 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 signific antly 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 (R 2 = - 0.36, P< 0.05). Annual averages of Cyclotella peaked with the downward trend of Hete rosigma 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 (R 2 = 0.38, P< 0. 05) and salinity stratification (R 2 = 0.45, P<0.05). T here 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 nutrien t 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 th ese 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

se asonal 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 20 1 0). The b iomass 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 f or 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, well

balanced 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/m 2 ) of herbivores, omnivores, and three levels of carnivores (primary= C1, secondary= C2, and tertiary=C3). Figure 10 depicts the p attern and distribution of the various F ish/Infauna/Invertebrate Index trophic levels in Perdido Bay over the 19

-Draft 15 August 2010 year study period

. H erbivore biomass was present mainly in the seagrass beds of upper Perdido Bay
, but herbivores were reduced during the period of increased nutrient loading

. H erbivore biomass increased during periods of low nutrient loading and when Heterosigma concentrations were low (1998

– 1999; 2003

– 2004; 2006). O mnivore biomass increased during periods of high nutrient loading and when Heterosigma concentrations were high (1995

– 2000 ; 2003

– 2005).



## Dominant bloom species

10000 100000 1000000 10000000OctoberNovemberDecemberJanuaryFebruaryMarchAprilMayJuneJulyAugustSeptember



## month CYCCHOn-av HETAKAn-av MERTENn-avDraft 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 l oading 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 H ABs , 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 b iomass decreased in the upper bay , and from 2004 to 2006, C1 carnivores were primarily restricted to a station near Grassy Point . H owever, the recovery of C1 carnivores was noted at the end of the study period. Secondary, L evel 2 carnivores ( C2 carnivore s) 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. T here was a general decrease of C2 carnivore biomass with t ime. T ertiary, 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 recover y, potentially due to a delayed response associated with the earlier HAB events. Because ecosystem recovery i s ongoing and d oes not yet appear to be complete, a reasonable decision would be to establish nutrient criteria based upon the conditions that occ urred 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 aDraft 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
**μ** g/L, is relatively low compared with many other southeast ern U.S. estuaries (Hagy 2009). Note that the main point source discharge into the bay (paper mill) had implemented nutrient reduct ions by 1998.

Annual geometric mean T N 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 Escamb ia Bay (Figure 13).

Since 1995 , the annual geometric mean chlorophyll a for the entire Perdido Bay system ranged from 1.1
to 6.0 **μ** g/L (Figure 14), demonstrating that chlorophyll

- induced transparency reductions are generally not an issue in the bay.

Fig ure 11. Annual averages of the Fish/Infauna/Invertebrate Index trophic organization across station s 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 1.00001988-891989-901990-911991-921992-931993-941994-951995-961996-971997-981998-991999-002000-012001-022002-032003-042004-052005-062006-07



### year avFIIherb avFII0mniv avFIIC1 avFIIC2 avFIIC3Draft 18 August 2010 Figure 12. Annual geometric mean T P concentrations in Perdido Bay , 1995

– 2009.

Figure 1 3. Annual geometric mean T N 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 TNDraft 19 August 2010 Figure 1 4. 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 it s discharg e to Perdido Bay was the subject of recent litigation ( Division of Adminis trative Hea r ings [ DOAH ] 2010). During the proceedings, FDEP argued that the conditions in Perdido Bay that occurred prior to the onset of HABs represented the historical ly healthy, well

- balanced biological expectation for the bay. FDEP also argued that t he 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 defensib le. 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 f

ollowed 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 aDraft 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 th e 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, a nnual mean chlorophyll a values have generally been below the 303(d) impairment threshold for estuaries (11 **μ** g/L) in the I WR (Chapter 62

- 303, F.A.C.), with annual mean values of 12.83 **μ** g/L (1994), 7.7 **μ** g/L (1998), 7.310 **μ** g/L (1999), 8.316 **μ** g/L (2000), 7.449 **μ** g/L (2001),
7.887 **μ** g/ L (2002), and 6.41 **μ** g/L (2003). Livingston (2010) noted blooms of H. akashiwo (a toxin

producing diatom) occurred during the same period (2004) that chlorophyll a exceeded 11 **μ** g/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 nutri ent loading to Perdido Bay, whic h 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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