The Indian River Lagoon is the most biologically diverse estuary in North America and has been designated an Outstanding Florida Water and an Estuary of National Significance, by the EPA's National Estuary Program. The NEP program was established to protect and restore the water quality and ecological integrity of estuaries of national significance. Currently, 28 estuaries located along the Atlantic, Gulf, and Pacific coasts and in Puerto Rico are designated as estuaries of national significance. Each NEP focuses within a study area that includes the estuary and surrounding watershed.

The estuary is actually a Lagoon system 156 miles long consisting of the Mosquito Lagoon out of Volusia County, the Banana River in Brevard County, and the Indian River Lagoon which spans nearly the entire coastal extent of Brevard, Indian River, St. Lucie and Martin Counties. For the five bordering counties along the Lagoon, this very special body of water supports nearly 20 thousand jobs and around $250 million dollars in annual income.