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. The Kennedy Space Center is located on the lagoon as well.
Mosquito Lagoon is an acclaimed red drum fishing habitat and a well-known destination for birdwatchers and nature tours.
The Nature Conservancy is coordinating an oyster restoration project, developed by the University of Central Florida. The goal is to restore about 40 acres (160,000 m2) of oyster reef habitat within the Canaveral National Seashore.the Nature Conservancy - Indian River Lagoon
Winter, the bottlenose dolphin notable for her prosthetic tail (whose story was featured in the film Dolphin Tale and the sequel Dolphin Tale 2) was rescued from Mosquito Lagoon in December 2005.
In 2012, a brown tide bloom fouled the lagoon. The county has approval for funds to investigate this unusual bloom to see if future occurrences can be prevented.