The main university campus in Tallahassee is a one-hour drive north of the laboratory on State Road 319. The laboratory is located on the shores of Apalachicola Bay, a part of the Alligator Harbor Aquatic Preserve, which lies between the Apalachicola River to the west, the Ochlocknee River to the east and bounded offshore by barrier islands and sand bars. Low-energy beaches, small bays, salt marshes and the Big Bend seagrass meadows dominate the coastal area. Due to the tidal action and wind conditions of Apalachicola Bay, inshore waters vary greatly in salinity, turbidity, and temperature. Water clarity, temperature and salinity are much more stable to the east.
Bottom sediments range from sand to mud.
Substrates include limestone outcroppings, springs, and drowned karst features dispersed across an open sand and shell bottom. A diverse array of marine, estuarine and freshwater habitats lie within easy access of the laboratory. Development along the adjacent coastal areas for several hundred miles is minimal and waters, even inshore, are pristine. The environment in this area supports a remarkable variety of organisms. More than 1,600 animal and plant species occurring within easy reach of the laboratory have been identified.