The Mosquito Lagoon Aquatic Preserve (MLAP) is located in east-central Florida, in southern Volusia County, south of Ponce de Leon Inlet. It is adjacent to two incorporated municipalities - New Smyrna Beach and Edgewater - and 50 miles northeast of Orlando. MLAP is part of the Indian River Lagoon (IRL) system, a long, wide, shallow estuarine lagoon bounded on the west by the Florida mainland, and on the east by a chain of barrier islands.

MLAP is in the northernmost sub-basin of the IRL system and is a bar-built type of estuary. The IRL system stretches 156 miles from Ponce de Leon Inlet at the northern end, to Jupiter Inlet at the southern end and, covers a full 40% of the length of Florida’s Atlantic Coast. Despite its name, the Indian River is not a river but is a lagoon or a shallow estuarine water body. Lagoons are estuaries characterized by restricted outlets to the sea, limiting the mixing of oceanic saltwater with terrestrially derived freshwater from rivers, streams and rainwater runoff. Three distinct bodies of water comprise the IRL system: the Indian River Lagoon, the Banana River Lagoon and Mosquito Lagoon.

MLAP is unique among the inland waters of the Atlantic Coast of Florida and a feeling of relative isolation is attainable just a short distance from nearby boat ramps. Once outside the Atlantic Intracoastal Waterway, local knowledge of water depths and channels of the Lagoon system is essential. Elevated landmarks are difficult to see at times, and it is easy to become disorientated among the winding turns and dead end waterways.