The Mosquito Lagoon runs as far North as New Smyrna Beach and runs South into Titusville, which is adjacent to part of the Canaveral National Seashore and Merritt Island Wildlife Sanctuary. Mosquito Lagoon is known world wide for its large redfish and gator trout and has been named "Redfish Capital of the World." You may not see it at first, but this estuary is full of life. Many of the fish, shrimp, clams and oysters spend part or all of their lives in this estuary.

The shallow waters, salt marshes, sea grasses and mangrove roots provide excellent hiding places from larger predators. Some species grow in estuaries for a short time and depend on the waters for various reasons. Sea turtles spend their adolescent years growing up in the lagoon. Manatee come to eat the tender grasses that grow on the lagoon's floor. Birds nest in the mangrove trees. Dolphin feed on the schools of fish. Schools of Redfish over 40 pounds are not uncommon during certain times of the year. Most of the Lagoon is tide free.

The Mosquito Lagoon is a long, narrow, estuary that is bordered on the east by a barrier island and on the west by the mainland and is connected to the Indian River Lagoon via the Haulover canal near Titsuville. Mosquito Lagoon has been designated an Outstanding Florida Water by the State of Florida and, as part of the Indian River Lagoon, an Estuary of National Significance by the Environmental Protection Agency. It is renown for its outstanding biological diversity, recreational fishery and as habitat for several federally-protected animals. Lagoon waters are classified as Class II which is suitable for shellfish (clam and oyster) propagation and harvesting.

Since the lagoon ecosystem is based heavily on healthy seagrass beds, water clarity is essential. Grass beds require light to conduct photosynthesis. Water that is clouded with silt or organic matter, including algal blooms caused by high levels of nutrients, prevent light penetration and limit the growth of seagrass. Water clarity in Mosquito Lagoon is very good in the winter and early spring but decreases in the summer and fall.