# Site

- Specific Information in Support of Establishing Numeric Nutrient Criteria in A lligator Harbor

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 Biological Summary for Alligator Harbor

................................................................................ 5

Seagrass

................................................................................................ ........................................ 5 Oyster Reef

................................................................................................ ................................ .. 10 Soft

- bottom Substrate

.................................................................................................................. 11 Salt Marsh

................................................................................................ ................................... 12 Endangered and Threatened Species

............................................................................................. 13 

### Water Quality Studies

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

..................................................................................................... 16 Numeric Nutrient Criteria Recommendations

...................................................................... 16 References

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

### List of Tables
Table 1. Checklist of nutrient enrichment symptoms for Alligator Harbor

.................................................. 2 Table 2. Physical characteristics of Alligator Harbor.

.................................................................................. 3 Table 3. FDEP

- calculated potential numeric nutrient criteria concentration recommendations. Error! Bookmark not define



### List of Figures
Figure 1. Map of AHAP.

................................................................................................ ................................ 3 Figure 2. Map of the Alligator Harbor watershed.

....................................................................................... 4 Figure 3. Land uses in the Alligator Harbor watershed.

............................................................................... 5 Figure 4. Distribution of seagrass in Alligator Harbor, 1995 Fish and Wildlife Research Institute (FWRI) layer.

............................................................................................................................... 7 Figure 5. AHAP monitoring sites.

................................................................................................................. 7 Figure 6. Frequency of occurrence of seagrass species in Alligator Harbor, 2005

– 09.

................................ 8 Figure 7. Average depth of seagrass species in Alligator Harbor, 2005, 2007

– 09.

..................................... 8 Figure 8. Mean annual TN in AHAP, 2001

– 08.

........................................................................................... 14 Figure 9. Mean annual TP in AHAP, 2 001

– 08.

........................................................................................... 14 Figure 10. Mean annual chlorophyll in AHAP, 2001

– 08.

........................................................................... 15 Figure 11. TN concentrations at Alligator Harbor Coast Watch Site 1, 2001

– 08.

...................................... 15 Figure 12. TN and TP concentrations at Alligator Harbor Coast Watch Site 6, 2001

– 08.

.......................... 16Draft 1 August 2010 

### Executive Summary
This report was prepared by the Florida Department of Environmental Protection (FDEP), in cooperation w ith local scientists, 1

Marine habitats include seagrass beds as well as oyster reefs. Submersed aquatic vegetation (SAV ) is the most nutrient

- sensitive biological community i n Alligator Harbor. Salinities are high, essentially the same as the Gulf of Mexico. A lack of riverine input and sandy sediments contribute s to very clear waters, and Alligator Harbor supports one of the densest stocks of seagrass beds in northwest Flor ida, as well as a high diversity of associated plants and animals. to support the development of site

- specific numeric nutrient criteria for Alligator Harbor. The primary purpose of the proposed numeric nutrient criteria is to protect healthy , well

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

Seagrass mapping conducted in 1995 and subsequent seagrass monitoring since the spring of 2002 indicate that seagrass coverages are robust and stable. Comprehensive studies by FDEP’s Off ice of Coastal and Aquatic Managed Areas (CAMA) concluded that biological communities in Alligator Harbor are healthy based on estimated percent coverage of seagrass, epiphyte load, and associated organisms. The m easurements of all of these attributes indicate good biological condition.
Because the evidence demonstrates that biological communities in this coastal area are healthy and well balanced (Table 1), the appropriate approach for developing numeric nutrient criteria is maintaining nutrient levels within the range of natural variability. Criteria are proposed in Table 3.

1 The following individuals contributed to this report: Kim Wren, Seth Blitch, and Jeremy Johnson.Draft 2 August 2010 Table 1. Checklist of n utrient e nrichment s ymptoms for Alligator Harbor

- = Empty cell/no data N/A = Not applicable Response V ariable Observed H istorically ? Observed C urrently ? Explanation Source

Low dissolved oxygen ( DO ) (hypoxia/anoxia) No No Because of lack of stratification, DO is currently high in the harbor and consistently meets the existing C lass III criterion. A lligator Harbor Aquatic Preserve (A HAP)

Reduced clarity No No No reduction in clar ity has been reported. T he average depth for the growth of seagrasses has actually increased in Alligator Harbor

. AHAP (2005

– 09)

Increased chlorophyll a concentrations No No No increase in chlorophyll a has been reported

. -
Phytoplankton blooms (nuisance or toxic) No No No phytoplankton blooms ha ve been reported for the system. -
Problematic epiphyte growth No No No problematic epiphyte growth has been observed. -

Problematic macroalgal growth No No No problematic macroalgal growth has been observed. -

S AV community changes or loss No No There are currently 3,661 acres of seagrass in Alligator Harbor with 4 different species represented. The density of seagrass and the depth at which it is growing continue to increase. AHAP (2005

– 09)

Emergent vegetation community changes or loss No No No emergent vegetation or community changes/losses have been reported in Alligator Harbor. -

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

Impacts to benthic community No No None reported, although not well studied. -

Fish kills No Sporadic Sporadic f ish kills have been reported in the system and are attributed to unusual freshwater runoff into the harbor

. AHAP



### Geographic and Physical Description
Alligator Harbor is a shallow, high

- salinity lagoon partially separated from the nearshore Gulf of Mexico by a barrier sand spit. Loc ated in eastern Franklin County, Alligator Harbor is near the towns of Alligator Point, St. Theresa, Turkey Point , and Lanark Village. Alligator Harbor is located entirely within an FDEP Aquatic Preserve, and is bordered by several prominent offshore shoal systems, including Dog Island Reef to the southwest, South Shoal to the southeast, and the Ochlockonee Shoal to the east (Figure 1)

. AHAP covers an area of approximately 14,366 acres , with the open water portions of the harbor itself consisting of 4,045 acres. The harbor is approximately 4 1⁄2 miles long and 1 1⁄2 miles wide. The average depth is approximately 4 mete rs (m)

. Table 2 lists the physical characteristics of Alligator Harbor.Draft 3 August 2010 Figure 1. Map of A HAP

.

Table 2

. Physical c haracteristics of Alligator Harbor.

- = Empty cell/no data Physical Characteristic Values Source Estuarine surface area ( square kilometers [ km 2 ]) 4,045 acres FDEP CAMA

pH (SU) Averages 8.0 SU FDEP CAMA Mean depth (m) About 1.5 m , but as deep as 5 m in areas. F DEP CAMA Temperature 5.8 ° C

- 31.1 ° C FDEP CAMA Tidal freshwater inflow ( 1,000 cubic meters per day [1, 000 m 3 d -1 ]) Ne gligible F DEP CAMA

Salinity and salinity zones 28 to 38 parts per thousand ( ppt ); average 34 ppt; relatively stable unless there is a large rainfall event. F DEP CAMA

Land use (Figure 3) Forested 57.96% 7,216 acres Wetl and 22.40% 2,788 acres Urban 14.16% 1,763 acres Shrub/brushland 2.30% 287 acres Disturbed/beaches 2.24% 279 acres Utilities .09% 117 acres -Draft 4 August 2010 There is typically very little freshwater inflow into the harbor ; therefore , salinity levels are essentially the same as the adjacent Gulf of Mexico. H abitat includes seagrass beds, salt marshes, coastal ecosystems , and oyster bars. In 1969 , Alligator Harbor was designated an Aquatic Preserve, and later, as a U.S. Environmental Protection Agency ( EPA ) Gulf of Mexico Ecological Management Site (GEM). The system is classified as an Outstanding Florida Wate r (OFW) and a Class II waterbody with a designated use of s hellfish h arvesting

. Water temperatures in Alligator Harbor range from 5.8 ° C to 31.1 ° C, with peak temperatures generally occurring in July through August , and the lowest temperatures occurring in December and January. pH in the bay averages 8.0 standard units ( SU )

. Salinities range from 28 to 38 ppt , with a mean of 34 ppt

. DO saturation ranges from 40 % to 100% , depending upon the time of year. The bay is well mixed and hypoxia has not been rep orted. Turbidity values range from 0 to 264 nephelometric turbi d ity units ( NTUs ) , with high values typically associated with stor m events.
The system is characterized by an extremely small watershed and has regular tidal exchange with the nearshore Gulf ( Figure 2). Only during extremely heavy rains can any appreciable amount of fresh water enter Alligator Harbor. There are no active point source discharges into the harbor ; stormwater enters the system via rainfall

- driven runoff, but this is mostly limite d to the developed southern shoreline. Currently , there are 118 indirect septic systems in the Alligator Harbor watershed (systems with in 100 feet of the shoreline) and no permitted industrial waste discharge s. Figure 3 shows land uses in the watershed.

Figure 2

. Map of the Alligator Harbor watershed

.Draft 5 August 2010 Figure 3

. Land uses in the Alligator Harbor watershed

.


### Biological Summary for A lligator Harbor
Seagrass Seagrasses are important marine foundation species and are h ighly productive plants (Hughes et al. 2009). Their extensive root systems and dense, structured leaf canopies form habitat and 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 2009). Seagrasses enhance sediment stability, decrease wave energy, increase water clarity, provide and stabilize habitats, and provide food and feeding pathw ays (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, dred ging , and development. M onitoring seagrasses has become one of the best methods for determining the overall condition of the nearshore aquatic environment because these plants are sensitive to environmental stressors

. Seagrass communities have been propo sed 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 lig ht penetration appears to be a primary driver ofDraft 6 August 2010 seagrass decline. The accepted thinking on this process is that increased inputs of nitrogen (N) and phosphorus (P) lead to the excess growth of phytoplankton and epiphytic algae, reducing available light t o the seagrasses and causing decreased seagrass productivity and ultimately the large -s cale loss of seagrasses (Duarte 1995).
This explanation, while valid, does not give a complete picture of the synergistic factors controlling seagrass production. “To p- 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) controlled the effects of nutrient enrichment on the abundance of epiphytes. It is therefore critical to consider the role of “top

- down” effects from overfishing or other food web disruptions in assessments of nutrient enrichment in Alligator Harbor.
Seagrass coverage estimates from 1995 show an estimated 3,661 acres of seagrass in Alligator Harbor (Figure 4) . C urrently , A HAP staff are anal yzing satellite images from Digital Ortho

- Quad images to map the seagrass in the harbor. SAV is considered a keystone species , provi ding valuable info rmation on the health of the entire biological c ommunity in Alligator Harbor

. According to the Alligator Harbor Management Plan, the seagrass beds at the eastern (poorly flushed) end of the h arbor are relatively sparse and composed primarily of s hoal gras s ( Halodule wrightii ). SAV growth at t he western end of Alligator Harbor (adjacent to the Gulf) is much more dense and primarily composed of t urtle grass (Thalassia testudinum ), with mixed patches of

s hoal grass and m anatee grass ( Syringodium filiforme ). These grass beds are found in the shallow areas of the harbor, usually fringing the harbor.

A HAP staff started a sea grass monitoring project in the spring of 2002. The project follows protocols from the Southwest Florida Water Management District (SWFWMD) and the Charlotte Harbor Aquatic Preserve , and u s es fixed

- transect surveys to gather baseline data on seagrass health. Seagrass sites were chosen to be widely distributed and represe ntative of seagrass conditions in specific locations and included 3 sites in Alligator Harbor (Figure 5)

. All transects were monitored biannually, at the beginning of the growing season (May/June) and towards the end of the growing season (September/Octob er). At each location , a 1

- square

- meter ( m2 ) quadrat was deployed and the following data collected: identification of seagrass species, measurement of percent coverage using Braun

- Blanquet estimates , canopy height, water depth, Se cchi depth, epiphyte cov erage (identified as clean, light, medium
, or heavy), three shoots of each species for epiphyte biomass , four core samples for determin ing above - and below

- ground biomass, and sediment s (for grain size analysis)

. DO , salinity, temperature, turbidity, pH , and photosynthetic ally active radiation (PAR) measurements were also taken at each location. Data from transect monitoring provided baseline information on what species we re present and its relative health ; however , the method proved to be very time consu ming and did not give a fair representation of the entire bay system. In 2005, AHAP began sampling fixed point s to improve the spatial coverage of the sampling effort

. Figures 6 and 7 show the frequency of occurrence and average depth of seagrass species in Alligator Harbor, respectively, from 2005 to 2009.Draft 7 August 2010 Figure 4

. Distribution of seagrass in Alligator Harbor , 1995 Fish and Wildlife Research Institute ( FWRI ) layer

.

Figure 5

. A HAP m onitoring s ites

.Draft 8 August 2010 Figure 6

. Frequency of occurrence of seagrass species in Alligator Harbor , 2005

– 09

.

TTES = Thalassia testudinum ; HWRI = Halodule w rightii ; SFIL = Syringodium filiforme ; BARE = Bare s oils

Figure 7. Average depth of seagrass species in Alligator Harbor , 2005, 2007

– 09.

TTES = Thalassia testudinum ; HWRI = Halodule w rightii ; SFIL = Syringodium filiforme 0 10 20 30 40 50 60 70 80

2005 2006 2007 2008 2009% Occurrence

Year Frequency of Occurrence for Seagrass Species and No Cover in Alligator Harbor Aquatic Preserve 2005

- 2009

TTES HWRI SFIL BARE

0 0.2 0.4 0.6 0.8

1 1.2 1.4

2005 2007 2008 2009Average Depth (m)

YEAR Average Depth of Species in Alligator Harbor Aquatic Preserve 2005, 2007

- 2009

TTES HWRI SFILDraft 9 August 2010 Marine grass beds stabilize sediments, entrap silt, recycle nutrients, and provide shelter, habitat and substrate for animals and other plant forms. These grass beds serve as important nursery grounds and are important direct food sources (Odum et al. 1974; Wood et al. 1969). They are important not only for their productivity but also for the animal life associated with the community. SAV serves as an important nursery area for juvenile forms of shellfish and a substrate for many species of algae. Many commercial fishes spend at least part of their lives in these grass beds (Zieman 1982).

Common ly found s pecies associated with the s eagrass beds of Alligator Harbor include the following:

Bird s—

**•** Common Loon

**•** Brown Pelican

**•** Double

- breasted Cormorant

**•** Green

- winged Teal

**•** American Widgeon

**•** Northern Shoveler

**•** Lesser Scaup

**•** Bufflehead

**•** Ruddy Duck

**•** Red

- breasted Merganser

**•** Osprey

**•** Am erican Coot

**•** Black Skimmer

**•** Belted Kingfisher

**•** Gulls

**•** Terns
Invertebrate species —

**•** Tunicates

**•** Sea Urchins

**•** Sea Cucumbers

**•** Polychaete Worms

**•** Bryozoans

**•** Crabs

**•** Sea Anemones

**•** Gastropods

**•** Hydroids
Fish species —

**•** Pigfish

**•** Croaker

**•** Killifish

**•** Spiny Boxfish

**•** Spotted Sea Trout

**•** Silver PerchDraft 10 August 2010 **•** Mullet

**•** Gobies

**•** Pipefish

**•** Pinfish

Oyster Reef Oyster reefs are stable islands of substrate in an otherwise muddy environment. Their extensive surface area provides essential habitat for many animals, especially sessile suspension

- feeding epifauna such as barnacles and polychaetes. The crevices also provide a refuge for motile invertebrates such as crabs and amphipods. One of the functions of the reef inhabitants is to mineralize organic carbon and release N and P in forms usable by the pri mary producers (phytoplankton and benthic algae). The community may also affect local turbidity levels through the process of filtration and biodeposition.
Oysters have generally adapted well to a wide range of salinities, temperatures, turbidities , and

o xygen tensions (Bahr et al. 1981). However, in Alligator Harbor, high and rather stable salinities and high summer temperatures restrict oyster reef development below the intertidal

zone. High temperatures limit the upper level at which oysters can live. The high salinities allow predation on the oysters by whelks, stone crabs , and polychaetes , which predominate in the subtidal region of relatively constant salinity. Other predators on the community include blue crab, sheeps head minnow, raccoon s, and numerous wading birds such as the American oystercatcher and boat

- tailed grackle. C ommonly found species associated with the oyster reefs of Alligator Harbor include the following:

Birds —

**•** American Oyster Catcher

**•** Dunlin

**•** Ruddy Turn

- Stone

**•** Black Bellied Plover

**•** Willet

**•** Fish Crow

**•** Boat Tailed Grackle

Invertebrates —

**•** Hydroids

**•** Bryozoans

**•** Sponges

**•** Sea Anemones

**•** Barnacles

**•** Crabs

**•** Parasitic Gastropods

**•** Predatory Gastropods

**•** Flatworms

**•** Starfish

**•** Polychaete Worms

**•** BivalvesDraft 11 August 2010 **•** Snapping Shrimp

**•** Amphipods

Fishes —

**•** Blennies

**•** Gobies

**•** Clingfish

**•** Toadfish

Mammals —

**•** Raccoons
Dense intertidal and subtidal oyster reefs occur at the eastern end of Alligator Harbor , and scattered oyster reef communities occur throughout the rest of the harbor. In 2002 , Alligator Harbor established a program for c lam a quaculture leases ; 40 leases were implemented, and currently 10 are operational. A HAP is considered to be an excellent location for clam aquaculture due to high salinity and good water quality, and the program currently appears to be successful.
Soft

- bottom Substrate

S ubtidal , unvegetated, soft

- bottom substrate comprises the majority of the open water zone in Alligator Harbor. A variety of species are associated with this habitat type ; commonly found species include the following:

Birds —

**•** Great Blue Heron

**•** Great Egret

**•** Herring Gull

**•** Ring

- billed Gull

**•** Laughing Gull

**•** Black Skimmer

**•** Common Tern

**•** Least Tern

**•** Royal Tern

Invertebrates —

**•** Polychaetes

**•** Amphipods

**•** Pharonid Worms

**•** Blue Crabs

**•** Penaeid Shrimp

**•** Horseshoe Crabs

**•** Bivalve mollusks

**•** Gastropod mollusks

Fishes —

**•** Striped Anchovy

**•** Atlantic CroakerDraft 12 August 2010 **•** Spotted Sea Trout

**•** Inshore Lizardfish

**•** Southern Flounder

**•** Spot

**•** Pigfish

**•** Bighead Searobin

S alt Marsh Alligator Harbor contains an extensive salt marsh composed primarily of black needlerush ( Juncus roemerianus ) and smooth c ordg rass ( Spartina alterniflora ). At s lightly higher elevations , s altwort ( Batis maritime ), g lasswort ( Salicornia virginica ), s ea ox

- eye ( Borrichia frutenscens ), and

m arsh elder ( Iva frutescens ) are found

.
The animal life of the salt marsh is rich and diverse. It includes primary consumers that feed on vascular plant detritus and fresh algae, such as amphipods, fishes, shrimp, crabs, clams, oysters, snails and worms. Animals such as the rice rat and cotton mouse nest within the marsh, but others, such as the raccoon, marsh rabbit , and opossum come down to the marshes to feed during low tides. Avian species such as clapper rails, willets, red

- winged blackbirds, seaside sparrows, and marsh wrens nest in the salt marshes. Herons, egrets, ibis , and other wading birds feed on mud flats and at the edges of the marshes.

C ommon ly found s pecies associated with salt m arshes in Alligator Harbor include the following:

Birds —

**•** Willets

**•** Great Egret

**•** Clapper Rails

**•** Gulls

**•** Great Blue Heron

**•** Little Blue Heron

**•** White Ibis

**•** Spotted Sandpiper

**•** Western Sandpiper

**•** Ruddy Turnstone

**•** Dunlin

**•** Seaside Sparrow

**•** Marsh Wren

**•** Red

- winged Blackbird

Invertebrates —

**•** Penaeid Shrimp

**•** Periwinkle Snails

**•** Fiddler Crabs

**•** Barnacles

**•** Nematodes

**•** Polychaete Worms

**•** Amp hipodsDraft 13 August 2010 **•** Bivalves

**•** Gastropods

Fishes —

**•** Croakers

**•** Mullet

**•** Killifish

**•** Redfish

**•** Sand Trout

**•** Skipjack

**•** Sea Trout

**•** Tarpon

**•** Drum

**•** Sheepshead

**•** Threadfin Herring

**•** Shad
Reptiles —

**•** Diamondback Terrapin
Endangered and Threatened Species Alligator Harbor is prime habitat for several endangered species, including the Atlantic ridley turtle ( Lepidochelys k empii ) , Atlantic loggerhead turtle ( Caretta caretta caretta ) and l eatherback turtle ( Dermochelys coriacea )

. The endangered turtles emerge from the ocean to lay their eggs in t he sand surrounding Alligator Harbor. Other endangered species, including the southeastern snowy plover ( Charadrius alexandrines tenuirostris ), use Alligator Harbor as a nesting area. According to the A HAP Management Plan, threatened species that inhabit Alligator H arbor include the eastern brown pelican ( Pelecanus occidentalis carolinensis ) , southeastern kestrel ( Falco spauerius paulus ) , roseate tern ( Sterna dougallii ), and least tern ( Sterna antillarum ).


### Water Quality Studies

AHAP’s current water quality monitoring program us es several methods to examine water column characteristics. In 2001, AHAP partnered with the University of Florida’s LakeWatch/Coast Watch P rogram and began a water quality monitoring project focused on nutrient s. These data have been used to document nutrient levels, including total nitrogen (TN) and total phosphorus (TP)
, chlorophyll a , and water clarity. Water samples are collected mont h ly at seven sites in St. Joseph Bay and Alligator Harbor , and are analyz ed by the University of Florida’s water chemistry lab at the Department of Fisheries and Aquati c Sciences. The data provide a baseline record of nutrient concentrations in the bay for comparison with future measurements (see Figures 8 through 10 ).

TN show ed a geometric mean concentration of 5.90 milligrams per liter ( mg/L )
, TP showed a geometric mean concentration of 3.31 mg/L
, and chlorophyll a showed a geometric mean concentration of 1.58 mg/L from 200 1 to 2 008. TP, TN, and c hlorophyll a concentrations have generally decreased over time, although natural variability is observed at individual stations (see Figures 11 and 12). However, the short time frame in which the data ha ve been collectedDraft 14 August 2010 means that there is a higher probability of error in the results and the natural fluctuations of the system could be skewing the results.

Figure 8

. Mean annual TN in AHAP , 2001

– 08

.

Figure 9

. Mean annual TP in AHAP , 2001

– 08

. 0 100 200 300 400 500 600 700

2001 2002 2003 2006 2007 2008Total Nitrogen ug/L

YEAR Mean Annual Total Nitrogen (TN) Concentrations for Alligator Harbor Aquatic Preserve 2001

- 2008 *No data collected 2004

- 2005

TN Linear (TN)

0 10 20 30 40 50 60

2001 2002 2003 2006 2007 2008Total Phosphorus (ugL)

YEAR

Mean Annual Total Phosphorus (TP) Concentrations for Alligator Harbor Aquatic Preserve 2001

- 2008 *No data collected 2004

- 2005

TP Linear (TP)Draft 15 August 2010 Figure 10

. Mean annual chlorophyll in AHAP , 2001

– 08.

Figure 11

. TN concentrations at Alligator Harbor Coast Watch S ite 1 , 2001

– 08. 0 2 4 6 8 10 12 14 16 18

2001 2002 2003 2006 2007 2008Chlorophyll (CHLA)

YEAR Mean Annual Chlorophyll (CHLA) Concentrations in Alligator Harbor Aquatic Preserve 2001

- 2008

*no data was collected in 2004

- 2005

CHLA Linear (CHLA)

0 50 100 150 200 250 300 350 400 450 500Total nitrogen ug/L

YEAR Specific Site: AHCW1 Total Nitrogen (TN) Concentrations 2001

- 2008

AHCW1 Total Nitrogen Linear (AHCW1 Total Nitrogen)Draft 16 August 2010 Figure 12

. T N and TP concentrations at Alligator Harbor Coast Watch S ite 6, 2001

– 08.



### Waters on the 303(d) List
The only verified listing for the Alligator Harbor area is for mercury in fish tissue, and this listing is for the entire Gulf c oast . The mercury issue is being addressed by an ongoing statewide mercury Total Maximum Daily Load ( TMDL ).



### Numeric Nutrient Criteria Recommendations

The data indicate that a nthropogenic nutrient inputs are not causing adverse biological effects in Alligator Harbor. Although there are no major freshwater inputs directly carrying a terrestrial

based nutrient load, tannic water from Ochlockonee Bay sporadically is transported i nto Alligator Harbor, potentially affecting the nutrient regime. The relatively low level of inputs from l ocal point and nonpoint sources contributes to low nutrient and chlorophyll

conce ntrations in the b ay. The most sensitive biological endpoint in All igator Harbor is seagrass, and the seagrass habitat is healthy . This conclusion is based on hyperspectral imaging surveys, transect surveys, and observed epiphyte density. The bay supports a healthy assemblage of organisms, including fish and invertebrat es, scallops, and juvenile green sea turtles.
Alligator Harbor is fully meeting its designated uses, which include “ shellfish propagation or harvesting ,” and “ recreation , propagation and maintenance of a healthy , well

- balanced p opulation of fish and wildlife ” with respect to nutrients:

**•** Shellfish harvesting is consistently classified as “approved , ” indicating that waters are not adversely affected by actual or potential pollution sources.

**•** Fish and invertebrate data show high abundances in seagrass beds.

**•** Juvenile sea turtles are using seagrass habitat in high numbers throughout the year. 0 200 400 600 800 1000

0 10 20 30 40 50 60 70 80 90

6/15/1997 6/15/1998 6/15/1999 6/15/2000 6/15/2001 6/15/2002 6/15/2003 6/15/2004Total nitrogen ug/LTotal phosphorus ug/L

YEAR Site Specific: AHCW6 Total Phosphorus (TP) and Total Nitrogen (TN) Concentrations 2001

- 2008 *no data collected 2004

- 2005

TP TN Linear (TP) Linear (TN)Draft 17 August 2010 There is considerable evidence to demonstrate that existing nutrient levels in Alligator Harbor are providing for full aquatic life use support. FDEP therefore proposes nutrient concentration targets that reflect the current conditions as reported from 2001 to 2008 water quality monitoring data.
Proposed Numeric Nutrient Criteria
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 polluta nt may be above the magnitude, and frequency relates to how often the magnitude may be exceeded without adverse effects. It is preferred to derive the magnitude component of a criterion through a cause

- effect relationship (such as those measured through t oxicity 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 maintai n 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 o bserved 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 descrip tors 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 dis tribution. 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 ex pression and to control for statistical errors.
The derivation of the magnitude, frequency and duration components of the numeric nutrient criteria for Alligator Harbor 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 a t 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 dist ribution, 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 aDraft 18 August 2010 five - year period. The long

- term average condition was adjusted to a level that represents an insignific ant 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 p rone 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 (U S Sixth Circuit Court 2008). Therefore, the long

- term geometric mean limit was derived to allow for up to a ten percent increase in the long

- term geometric mean, which was calculated as the geometric mean of the annual geometric means of the long

- term dataset for each segment of the waterbody.
Because it is not always practical to assess compliance with the criteria on the same long

- term basis, FDEP also developed criteria expressed as an annual geometric mean so that estuaries could be assessed on an annu al basis. It should be noted that the duration and frequency components of the criteria must be linked to the response timeframe of the sensitive endpoint. Short

- term averaging periods (e.g., 1 to 30 days) might be appropriate for nutrient criteria where a sufficiently robust cause

- effect relationship has demonstrated that a eutrophic response occurs over such timeframes. If however, such a short

- term response cannot be demonstrated, or there is no 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 un acceptability 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 nu trient 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 captu re 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 75 th percentile of the annual geometric means from the long

- term dataset. FDEP demonstrated that setting the criteria at this percentile results in a magnitude that, whenDraft 19 August 2010 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 excee ded 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 s egment.
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 relati vely 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 geom etric mean has the benefit of assessing localized enrichment patterns. DEP has not decided whether both expressions of magnitude are needed in all cases, and we are seeking additional feedback from local experts and stakeholders.
Summary of the Proposed C riteria
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 an nual 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 Alligator Harbor, as well the annual limits f or each segment, are provided in Table 3 below

. Because of the small size and relative homogeneity of the system, segmentation was not needed, and a single set of criteria is proposed.Draft 20 August 2010 Table 3. Proposed numeric nutrient criteria for Alligator Harbor , 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 throughout the system exceed the network average more than twice in a 5 year period. The last row shows the value which single station shall not exceed, by segment, more than twice in a 5 year period. Note: FDEP is evaluating if there are currently sufficient data to promulgate numeric nutrient criteria for this system.
Proposed Criteria TP (ug/L) TN (ug/L) Chlorophyll

a (ug /L) Existing Long Term Geometric Mean 27.325 364.892 4.863501

Maximum Allowed Long Term Geometric Mean 30.058 401.382 5.350

Annual Geometric Mean for the Network of Stations (2 of 5 year exceedance rate) 41.242 495.999 8.802

Annual Geometric Mean for a Single Site (2 of 5 year exceedance rate) 45.707 534.890 9.991Draft 21 August 2010 

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