Mosquito Lagoon is located in the northern part of the Indian River Lagoon system and the Atlantic Intracoastal Waterway. It extends from Ponce de León Inlet in Volusia County, Florida, to the north end of Merritt Island, and connects to the Indian River via the Haulover Canal. The Lagoon divides the city of New Smyrna Beach. It also runs next to the Canaveral National Seashore on Cape Canaveral and the Merritt Island National Wildlife Refuge.