The shallow seagrass beds and mangroves support large game fish, making Banana River a popular destination for fishermen. Other recreational uses of the bay include boating, sailboarding, kayaking, duck hunting and bird-watching.

There are no state parks adjacent to Banana River Aquatic Preserve or nearby, but Ulumay Wildlife Sanctuary, operated by Brevard County, offers excellent bird-watching opportunities. Boat ramps at Kiwanis Island Park, Kelly Park, Cocoa Beach Recreational Complex and Port End Park give access to the lagoon to boaters and kayakers alike.