Alligator Harbor Aquatic Preserve was designated in 1969. The region is 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 ½ miles long and 1 ½ miles wide with a mean low water depth of approximately four 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 that the preserve borders the Gulf coast mainland on the north, the land mass is actually St. James Island, formed by the Ochlockonee and Crooked Rivers and the Gulf of Mexico.