Site-Specific Information 

in Support of 

Establishing Numeric Nutrient 

Criteria in Alligator Harbor

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

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 .......................................................................................................................... 21
Draft 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, 2001–08. ...........................................................................................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...........................16
Draft 1 August 2010

Executive Summary

This report was prepared by the Florida Department of Environmental Protection (FDEP), in 

cooperation with local scientists,1

Marine habitats include seagrass beds as well as oyster reefs. Submersed aquatic vegetation 

(SAV) is the most nutrient-sensitive biological community in Alligator Harbor. Salinities are high, 

essentially the same as the Gulf of Mexico. A lack of riverine input and sandy sediments 

contributes to very clear waters, and Alligator Harbor supports one of the densest stocks of 

seagrass beds in northwest Florida, 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 

Office 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 measurements 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 nutrient enrichment symptoms for Alligator Harbor - = Empty cell/no data

N/A = Not applicable

Response Variable Observed 

Historically?

Observed 

Currently?

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 Class III 

criterion.

Alligator Harbor 

Aquatic Preserve 

(AHAP) 

Reduced clarity No No No reduction in clarity has been reported. 

The 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 have 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. 

-

SAV 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 fish 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. Located 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 meters

(m). Table 2 lists the physical characteristics of Alligator Harbor.
Draft 3 August 2010

Figure 1. Map of AHAP. 

Table 2. Physical characteristics of Alligator Harbor. - = Empty cell/no data

Physical Characteristic Values Source 

Estuarine surface area 

(square kilometers [km2]) 

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. FDEP CAMA 

Temperature 5.8° C-31.1° C FDEP CAMA

Tidal freshwater inflow 

(1,000 cubic meters per day 

[1,000 m3d-1]) 

Negligible FDEP CAMA

Salinity and salinity zones 28 to 38 parts per thousand (ppt); average 34 ppt; 

relatively stable unless there is a large rainfall

event.

FDEP CAMA 

Land use (Figure 3) Forested 57.96% 7,216 acres

Wetland 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. Habitat 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 Water 

(OFW) and a Class II waterbody with a designated use of shellfish harvesting. 

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 reported. Turbidity values range from 0 

to 264 nephelometric turbidity units (NTUs), with high values typically associated with storm 

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 limited to 

the developed southern shoreline. Currently, there are 118 indirect septic systems in the

Alligator Harbor watershed (systems within 100 feet of the shoreline) and no permitted 

industrial waste discharges. 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 Alligator Harbor

Seagrass

Seagrasses are important marine foundation species and are highly productive plants (Hughes et 

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

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

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

1996; Williams and Heck 2001; Wren 2009). Seagrasses enhance sediment stability, decrease 

wave energy, increase water clarity, provide and stabilize habitats, and provide food and feeding 

pathways (see reviews by Phillips and McRoy 1980; McRoy and Helfferich 1977; Zieman and 

Zieman 1989). 

Adverse impacts to seagrasses come from a variety of sources, including reduced water quality 

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

Monitoring seagrasses has become one of the best methods for determining the overall 

condition of the nearshore aquatic environment because these plants are sensitive to 

environmental stressors. Seagrass communities have been proposed as “coastal canaries”—

biological indicators of changing coastal conditions (Orth et al. 2006). Seagrasses have been 

shown to be adversely impacted by anthropogenic nutrient enrichment (Orth and Moore 1983; 

Tomasko et al. 1996). Reduced underwater light penetration appears to be a primary driver of 
Draft 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 to the seagrasses and causing decreased seagrass productivity and ultimately the 

large-scale loss of seagrasses (Duarte 1995). 

This explanation, while valid, does not give a complete picture of the synergistic factors 

controlling seagrass production. “Top-down” food web effects must also be considered. In 

controlled, in situ experimental studies in St. Joseph Bay, Florida, Heck et al. (2000) found that 

mesograzers (amphipods, caridean shrimp, gastropods, hermit crabs) 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). Currently, AHAP staff are analyzing satellite images from Digital Ortho-Quad 

images to map the seagrass in the harbor. SAV is considered a keystone species, providing 

valuable information on the health of the entire biological community in Alligator Harbor. 

According to the Alligator Harbor Management Plan, the seagrass beds at the eastern (poorly 

flushed) end of the harbor are relatively sparse and composed primarily of shoal grass (Halodule 

wrightii). SAV growth at the western end of Alligator Harbor (adjacent to the Gulf) is much more 

dense and primarily composed of turtle grass (Thalassia testudinum), with mixed patches of 

shoal grass and manatee grass (Syringodium filiforme). These grass beds are found in the 

shallow areas of the harbor, usually fringing the harbor.

AHAP staff started a seagrass 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 uses fixed-transect surveys to gather baseline data on seagrass 

health. Seagrass sites were chosen to be widely distributed and representative 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/October). 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, 

Secchi depth, epiphyte coverage (identified as clean, light, medium, or heavy), three shoots of 

each species for epiphyte biomass, four core samples for determining above- and below-ground 

biomass, and sediments (for grain size analysis). DO, salinity, temperature, turbidity, pH, and 

photosynthetically active radiation (PAR) measurements were also taken at each location. Data 

from transect monitoring provided baseline information on what species were present and its 

relative health; however, the method proved to be very time consuming and did not give a fair 

representation of the entire bay system. In 2005, AHAP began sampling fixed points 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. AHAP monitoring sites. 
Draft 8 August 2010

Figure 6. Frequency of occurrence of seagrass species in Alligator Harbor, 2005–09. 

TTES = Thalassia testudinum; HWRI = Halodule wrightii; SFIL = Syringodium filiforme; BARE = Bare soils

Figure 7. Average depth of seagrass species in Alligator Harbor, 2005, 2007–09. 

TTES = Thalassia testudinum; HWRI = Halodule wrightii ; 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 2009

Average Depth (m)

YEAR

Average Depth of Species in Alligator Harbor Aquatic Preserve 2005, 2007-2009

TTES HWRI SFIL
Draft 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).

Commonly found species associated with the seagrass beds of Alligator Harbor include the 

following:

Birds— 

• Common Loon

• Brown Pelican

• Double-breasted Cormorant

• Green-winged Teal

• American Widgeon

• Northern Shoveler

• Lesser Scaup

• Bufflehead

• Ruddy Duck

• Red-breasted Merganser

• Osprey

• American 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 Perch
Draft 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 primary 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 

oxygen 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, sheepshead minnow, raccoons, and numerous wading birds such as the American 

oystercatcher and boat-tailed grackle. Commonly 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

• Bivalves 
Draft 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 clam aquaculture leases; 40 leases were implemented, and 

currently 10 are operational. AHAP 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

Subtidal, 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 Croaker
Draft 12 August 2010

• Spotted Sea Trout

• Inshore Lizardfish

• Southern Flounder

• Spot

• Pigfish

• Bighead Searobin

Salt Marsh

Alligator Harbor contains an extensive salt marsh composed primarily of black needlerush 

(Juncus roemerianus) and smooth cordgrass (Spartina alterniflora). At slightly higher elevations, 

saltwort (Batis maritime), glasswort (Salicornia virginica), sea ox-eye (Borrichia frutenscens), and 

marsh 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.

Commonly found species associated with salt marshes 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

• Amphipods
Draft 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 kempii), Atlantic loggerhead turtle (Caretta caretta caretta) and leatherback 

turtle (Dermochelys coriacea). The endangered turtles emerge from the ocean to lay their eggs 

in the 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 AHAP Management Plan, threatened species that inhabit Alligator Harbor 

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 uses several methods to examine water 

column characteristics. In 2001, AHAP partnered with the University of Florida’s 

LakeWatch/Coast Watch Program and began a water quality monitoring project focused on 

nutrients. 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 

monthly at seven sites in St. Joseph Bay and Alligator Harbor, and are analyzed by the University 

of Florida’s water chemistry lab at the Department of Fisheries and Aquatic Sciences. The data 

provide a baseline record of nutrient concentrations in the bay for comparison with future 

measurements (see Figures 8 through 10).

TN showed 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 2001 to 2008. TP, TN, and chlorophyll 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 have been collected 
Draft 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 2008

Total 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 2008

Total 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 Site 1, 2001–08.

0

2

4

6

8

10

12

14

16

18

2001 2002 2003 2006 2007 2008

Chlorophyll (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

500

Total 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. TN and TP concentrations at Alligator Harbor Coast Watch Site 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 coast. The mercury issue is being addressed by an ongoing statewide 

mercury Total Maximum Daily Load (TMDL).

Numeric Nutrient Criteria Recommendations

The data indicate that anthropogenic nutrient inputs are not causing adverse biological effects 

in Alligator Harbor. Although there are no major freshwater inputs directly carrying a terrestrialbased nutrient load, tannic water from Ochlockonee Bay sporadically is transported into 

Alligator Harbor, potentially affecting the nutrient regime. The relatively low level of inputs 

from local point and nonpoint sources contributes to low nutrient and chlorophyll 

concentrations in the bay. The most sensitive biological endpoint in Alligator 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 invertebrates, 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 

population 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 6/15/2004

Total nitrogen ug/L

Total 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 pollutant 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 toxicity testing). The magnitude would then be 

set at a level that would protect a majority of the sensitive aquatic organisms inhabiting the 

system. Absent a demonstrated cause-effect relationship, the magnitude may be set at a level 

designed to maintain the current data distribution, accounting for natural temporal variability, 

when the current conditions are protective of the designated uses of the waterbody. Since a 

criterion derived based on the existing data distribution has no direct link to any observed cause 

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

the uses associated with that distribution. 

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

descriptors of the reference condition data distribution. Specifically, these components should 

be part of a statistical test designed to determine whether the long-term distribution of data has 

shifted upward ( or in some cases, downward) from the reference distribution. This test would 

then be used to determine whether future monitoring data are consistent with the magnitude 

(long-term average) defined by the reference dataset. It is critical to account for the natural 

variability surrounding the magnitude expression and to control for statistical errors. 

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

criteria for 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 at a variety of values based on the frequency and 

duration that will be used to determine compliance. For the “healthy existing conditions” 

approach, FDEP established the magnitude at: a) an adjusted long-term central tendency 

(geometric mean) of the distribution, expressed as a long-term geometric mean never to be 

exceeded; and b) an annual geometric mean, not to be exceeded more than two times over a 
Draft 18 August 2010

five- year period. The long-term average condition was adjusted to a level that represents an 

insignificant increase from the baseline. Allowing for an insignificant increase accounts for 

uncertainty in the estimate of the mean and partially addresses the fact that the reference 

based approach fails to identify a threshold of imbalance, and thus is highly prone to excessive 

Type I error. For the purpose of antidegradation evaluations, EPA has established that a ten 

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

historical condition, known as a de minimus change (US Sixth Circuit Court 2008). Therefore, the 

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

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

geometric means of the long-term dataset for each segment of the waterbody.

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

basis, FDEP also developed criteria expressed as an annual geometric mean so that estuaries 

could be assessed on an annual basis. It should be noted that the duration and frequency 

components of the criteria 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 unacceptability high Type I failure rate 

(identifying a healthy system as being impaired) since approximately 50 percent of the individual 

yearly means are expected to be above the long-term mean. Therefore, the long-term target 

must be adjusted to allow for the application to a shorter duration with an acceptable Type I 

error rate of no more than a 10 percent.

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

derived by appropriately accounting for the annual variability above the mean. This annual 

target concentration was derived as an upper percentile of the distribution of the annual 

geometric mean concentrations. Previous proposals by EPA have utilized three-year assessment 

periods to express the duration nutrient criteria components. Although it is possible to 

construct a test that achieves the 10 percent Type I error rate target over a 3-year period, a 

slightly longer period (5 years) will provide better control for Type II error and will more fully 

capture climatic cycles (e.g., el nino, la nina), which tend to be longer than three years in Florida 

(and may actually be on a multi-decadal scale). Furthermore, a five year period is more 

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

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

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

FDEP demonstrated that setting the criteria at this percentile results in a magnitude that, when 
Draft 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 exceeded more than twice in a 5 year period) was established to allow for two 

separate assessments:

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

waterbody; and 

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

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

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

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

of station annual geometric means. Use of the network average magnitude is appropriate for 

assessing overall segment status. However, a network average is only representative of overall 

segment status if it is relatively homogeneous. If the segment is not well mixed, is very large, or 

contains localized nutrient sources, then there is a potential that isolated areas of enrichment 

may be masked in the network spatial average. Therefore, the single station annual geometric 

mean has the benefit of assessing localized enrichment patterns. DEP has not decided whether 

both expressions of magnitude are needed in all cases, and we are seeking additional feedback 

from local experts and stakeholders.

Summary of the Proposed Criteria

FDEP proposes three sets of potential criteria: a) a long-term geometric mean concentration; b) 

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

exceeded more than twice in a five-year period; and c) an annual geometric mean of values 

from a single location, not to be exceeded more than twice in a five-year period.

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

community in Alligator Harbor, as well the annual limits for 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 9.991
Draft 21 August 2010

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