Alligator Harbor Aquatic Preserve very much represents the natural beauty of North Florida. The relatively undeveloped lands surrounding Alligator Harbor aid in preserving the peaceful idyllic conditions encountered on its waters. Its shallow sand bars and Phipps Preserve, located at the tip of Alligator Point, provide essential habitat for a number of migratory nesting shorebirds.

Along with the Guana Buffer Preserve, the Guana River Marsh Aquatic Preserve serves as the hub and headquarters of the Guana Tolomato Matanzas National Estuarine Research Reserve (GTM Research Reserve). The estuary and uplands of the Guana River has been a valued resource for centuries of human populations with many changes taking place over time.