The Fort Pickens State Park Aquatic Preserve is located in the southwestern corner of the Florida panhandle. This 34,000 acre preserve surrounds the western end of Santa Rosa Island and the eastern end of Perdido Key which are both typical examples of undeveloped barrier islands. The submerged lands along the northern sides of these islands are characterized by shallow saline waters, continuous and patchy seagrass beds, and salt marshes. These communities provide habitat for wildlife and birds such as nesting sea turtles and shorebirds. Several species are listed as endangered or threatened.

Due to the proximity to the Gulf Intracoastal Waterway and the Pensacola Ship Channel, the preserve experiences some of the heaviest boat traffic (industrial, military, and recreational) in northern Florida. Such intense use poses threats to the area, and integrated management between state, federal, and local governments is crucial.

The proximity of the Gulf Islands National Seashore facility provides many recreational possibilities within the preserve. Fishing, swimming, diving, boating, and sight seeing are regular activities. There is an underwater archaeological preserve within the preserve, the USS Massachusetts that provides excellent diving and fishing opportunities.

The barrier islands provide a crucial stop over spot for migrating birds coming from South America. The Audubon Society monitors this activity annually. The Pensacola Pass centered in the middle of the preserve allows flushing of the surrounding bays, keeping water quality in good condition. The pass also allows for the required life-cycle migration of some fish and invertebrate species. The salt marshes and seagrasses serve as critical habitat and nursery areas for aquatic species, birds and other wildlife. The undisturbed sandy beaches provide nesting habitat for several endangered birds and sea turtle species.