Florida Bay is nearly 1000 square miles of shallow water basins, grass-covered mud banks, and dense mangrove islands. It begins at the base of the peninsula where the freshwater Everglades meets the salty waters of the Gulf of Mexico and the Atlantic Ocean. These brackish waters create a highly productive estuary which fosters a diverse assemblege of tropical and temperate marine and terrestrial life. Spiny lobster, pink shrimp, snook, and redfish are bay inhabitants which have commercial or recreational value. Other inhabitants such as West Indian manatee, loggerhead sea turtle, and the American crocodile are endangered or threatened species. Because of its importance as nurseryground and its proximity to the Florida Keys with its nearby coral reef tract, Florida Bay plays an important ecological role in the entire South Florida ecosystem.

The Bay is bordered to the east by the Florida Keys, a chain of limestone islands which extends about 100 miles southwest of the Florida mainland. Tidal flow between the Straits of Florida in the Atlantic Ocean and the bay occurs through the channels between the keys in the southeastern bay. This area in the southeastern bay, designated the Atlantic transition zone, is characterized by patches of dense turtle grass beds and soft coral hard-bottom communities.

Basins are a key feature in Florida Bay. Basins are shallow areas generally with a homogenous bottom composition surrounded by more elevated flats or land masses.

Scientists studying Florida Bay have divided the area into six zones which reflect the different environmental conditions seen in these different parts of the bay. The Eastern Zone is located in the northeast section of the bay adjacent to the upper Keys. Basins in this zone experience relatively little tidal exchange with the Atlantic Ocean because the channels between the keys in this area are narrow and few in number.

In addition, many openings between the islands have been filled-in to create causeways which effectively block tidal exchange. Basins of the Western zone, which are surrounded by miles of grass-covered banks, are exposed regularly to tidal flow from the Gulf. The more open, deeper waters of the Gulf transition zone are adjacent to the shallow banks of the western bay on the margin of the continental shelf. Basins in the Central zone which are sheltered by narrow well-defined banktops experience little, if any, of the tidal flow from the Gulf or Atlantic. Under certain environmental conditions, waters in these shallow interior basins can become quite saline. Calm weather, low rainfall, high evaporation rates, high surface temperatures and low circulation can drive salinities to levels well beyond that of normal seawater.