Banana River Aquatic Preserve is entirely within Brevard County in east central Florida and was designated on June 3, 1970. It contains approximately 30,000 acres.

Banana River Aquatic Preserve is sandwiched between Merritt Island on the west and a beach barrier island on the east. It is part of the Indian River Lagoon system and extends from SR 528 (the Bennett Causeway) nearly down to the southern end of Merritt Island and includes Newfound Harbor and Sykes Creek. It is a relatively shallow body of water with little water exchange from the sea or freshwater inflow which classifies it as a lagoon. The lagoon contains several spoil islands which are also part of the preserve. Most of the natural shoreline is fringed by mangroves, but much of the shoreline near and adjacent to the preserve is heavily developed.