The Whitney Laboratory is located in the town of Marineland, on the border between St. Johns and Flagler counties in northeast Florida. The eight-acre campus is situated on a narrow barrier island, bounded by the Atlantic Ocean and the Intracoastal Waterway, both of which are just a few hundred feet away.
The area provides a great variety of habitats: acres of salt marsh and mangroves with countless tidal creeks and other estuarine areas; a shoreline of sand beach and shallow surf including a unique and extensive outcropping of coquina rock. The nearby Matanzas Inlet connects the intracoastal estuarine basin with the benthic and pelagic habitats of the Atlantic. This habitat diversity ensures that many species of marine organisms, both invertebrates and fishes, will be available locally throughout the year. Several additional habitats, though distant, are accessible: the great grassflats of the Mosquito Lagoon near Cape Canaveral, and the rich animal resources of the Gulf coast and the subtropical Florida Keys.
Although the Laboratory is situated in a rural seaside area, most of the cultural and educational amenities of northeast Florida are close by. To the north are St. Augustine (18 miles) and Jacksonville (60 miles); Daytona Beach is to the south (45 miles); and the main campus of the University of Florida in Gainesville is only 78 miles to the west.