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Alligator Harbor Aquatic Preserve

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"Alligator Harbor is one of the world's largest feeding grounds for the Kemp's ridley turtle, which is the rarest and most endangered of all marine turtles. The area's abundance of blue crabs, jellyfish, shellfish and seagrass provide an important food source for all sea turtles. The unspoiled waters and beaches are valuable breeding and nesting grounds for marine sea turtles. Alligator Harbor, in addition to being a valuable natural resource, is also archaeologically rich with several Miccosukee/Seminole Indian artifacts and burial mounds surrounding the harbor."

  — Bill Wargo, Coordinator, Alligator Point Sea Turtle Patrol

  • Alligator Harbor supports a variety of commercial and recreational species of fish and invertebrates in valuable aquatic habitats including seagrasses, salt marshes, oyster bars and beaches. 
  • Clam aquaculture sites established in 2002 at Alligator Harbor are producing a very valuable product for Florida's economy. 
  • The area serves as a major forage site for migratory birds, specifically trans-gulf migrants in the fall and spring. 
  • Migratory species  — including piping plovers, semipalmated plovers, least terns, peregrine falcons and a variety of hawks — inhabit Alligator Harbor for part of the year.
  • Local species at Alligator Harbor include American oystercatchers, black skimmers, snowy plovers, royal terns and brown pelicans.

Resource Management

Alligator Harbor Aquatic Preserve staff have helped identify appropriate locations and depths to place marker buoys warning of shallow seagrass areas in an effort to protect this habitat. Staff also were involved in mapping and monitoring seagrass habitat and are correlating this information with water quality, nutrient and benthic data. Staff established partnerships with the FSU Marine Lab and Gulf Specimen Marine Lab and collaborate with both facilities to keep current a species list and identification guide for the Central Panhandle region.

Education and Outreach

Staff worked closely with the Apalachicola National Estuarine Research Reserve to participate in coastal training program workshops, local festivals, distributing local boating guides, developing educational fliers, giving presentations, writing articles for local newspapers and newsletters, and designing educational signage for local kiosks.

Research and Monitoring

Research and monitoring programs conducted through the Alligator Harbor Aquatic Preserve were developed based on the system's natural resources and vary based on issues and priorities that face the bay. Projects included seagrass, water quality and benthic monitoring and permit reviews.

Panacea, FL 32346
Managed Location Contact: 
Jon Brucker, Manager
Total Acreage: 
Receives State Funding: 
State Owned: 

Alligator Harbor Aquatic Preserve was designated in 1969. The barrier islands and spits in the area began forming 5,000 years ago when sea level had risen essentially to its present position. The region is now primarily rural with scattered concentrations of single-family beach homes, but development pressure is increasing.

Alligator Harbor Aquatic Preserve is a shallow, neutral estuary and a barrier spit lagoon. It lies just east of the Apalachicola estuary and is enclosed by the Alligator Point sand spit. The harbor is approximately 4 miles long and 1 mile wide with a mean low water depth of approximately 4 feet. There is little freshwater inflow into the harbor, and salinity levels do not vary much from those in the adjacent Gulf of Mexico. While it appears the aquatic preserve borders the Florida mainland on the north, the land mass is actually St. James Island, formed by the Ochlockonee and Crooked rivers and the Gulf of Mexico.

The Alligator Harbor area is part of a broad, sandy shore plain that is constantly being altered by wind, rainfall and sea level change, and is bordered by several prominent offshore shoal systems: Dog Island Reef to the southwest, South Shoal to the southeast and the Ochlockonee Shoal to the east.

Dog Island Reef is considered to be an example of a submerged barrier island; the South Shoal was probably deposited by the Ochlockonee River during a lower stand of sea level; and the Ochlockonee Shoal probably represents a downed barrier island or headland. 

Public Access: 

Recreational activities include fishing, boating, hiking (at Bald Point State Park), birding and beach-oriented activities such as surf-fishing, swimming and sunbathing.

Bald Point State Park borders a portion of the aquatic preserve but does not grant public access within the harbor. There is beach access and a boat ramp in St. Teresa on St. James Island and boat ramps on Alligator Point.

If you're interested in volunteering, the staff of Alligator Harbor has partnered with the Alligator Point Taxpayers Association, a network of active and concerned residents, who are interested in protecting the natural ecological diversity and functions of the harbor. This group volunteers with beach cleanup events, turtle patrol, water quality and bird surveys. The preserve staff provide the APTA newsletter with regular articles on the resources within and adjacent to the harbor and information on how citizens can stay involved in their environment.

Archaeological Resources: 

Most of the archaeological sites in the vicinity of Alligator Harbor are small and disturbed to varying degrees. However, one of the best-known examples of a ceremonial mound from the time periods of late Deptford through early Swift Creek (1,000 B.C.-500 A.D.) is the Yent Mound located on Alligator Harbor.

Another important site on the harbor is the Tucker site, which contains some Swift Creek culture phase materials but is primarily an example of the Weeden Island culture phase (500 A.D.-1,000 A.D.). This site also contained a burial mound as well as a village area.

Wildlife Habitat Description: 

Alligator Harbor's seagrass beds and salt marshes are important nursery grounds for many species of juvenile fish and invertebrates. It is an important forage area for shorebirds and migratory birds, particularly trans-gulf migrants, while Alligator Point is a vital resting spot for these birds. Alligator Harbor is one of the world's largest feeding grounds of the Kemp's ridley turtle, the world's most endangered sea turtle.

Tidal Marsh - Tidal marshes (or salt marshes) stabilize and bind sediments, protecting against erosion. They also provide significant nursery, feeding and reproductive habitat for a variety of organisms. Most of the salt marshes in Alligator Harbor are located along the tidal creek at the harbor's eastern end. The salt marsh's animal life is rich and diverse, and includes several species of invertebrates, fish, birds and even some mammals. 

Unconsolidated Substrate - Muddy, soft bottom, unvegetated substrate comprises the majority of the open water zone and is the harbor's dominant natural community. The relative composition of the sand, silt, clay and shell fractions of the sediments depends on the proximity to land, runoff conditions, water currents and biological productivity. This substrate is generally dominated by polychaetes and amphipods. 

Oyster Reefs - Oyster reefs are stable islands of substrate in an otherwise muddy environment. Their extensive surface area provides essential habitat for many animals, and the crevices provide a refuge for motile invertebrates such as crabs. They can improve water clarity through filtration. Oyster reefs comprise about 291 acres within Alligator Harbor. 

Algal Beds - More than 300 species of algae have been found in the general area of Alligator Harbor. Red algae are the most conspicuous, but green algae are also well-represented. Brown and blue-green algae are less conspicuous, but still present. These algal beds are an important food source for grazers.

Seagrass Beds - Seagrass beds are submerged flowering plants that stabilize sediments, entrap silt, recycle nutrients, provide shelter and habitat for animals, serve as nursery grounds, and are important direct food sources. They are dependent on light and have a limited range in Alligator Harbor because of turbidity. The grass beds in Alligator Harbor cover around 646 acres and are primarily shoal grass, manatee grass and turtle grass.

Habitat-Wildlife Type: 
Aquatic Preserves
Last Modified:
April 11, 2024 - 5:51pm

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