Charlotte Harbor Estuary, the second largest bay in Florida, is located on the Gulf of Mexico coast of west Florida, mostly (2/3) in Charlotte County, Florida with the remaining 1/3 in Lee County. The harbor's mouth is located behind Gasparilla Island, one of the many coastal barrier islands on the southwest coast of Florida, with access from the Gulf of Mexico through the Boca Grande Pass between Gasparilla Island on the north and Lacosta Island on the south. Charlotte Harbor covers about 270 sq mi (700 km2)
Charlotte Harbor Estuary is a natural estuary spanning the west coast of Florida from Venice to Bonita Springs on the Gulf of Mexico and is one of the most productive wetlands in Florida. The estuary has a large watershed, and includes Charlotte Harbor itself as well as the Peace River, Caloosahatchee River (via Pine Island Sound) and Myakka River basins. It covers 12,653 square kilometers (4,885 sq mi), the second largest open water estuary in the state.
It is classified as a bar-built estuary, formed when sandbars build up along the coastline. The sand bars block the waters behind them from the sea. Such estuaries tend to be shallow with minimal tidal action.
This is a threatened ecosystem because of the rapid increase of growth and development, poor land-use policies, and the overuse of natural resources. The Charlotte Harbor Aquatic Preserves, established by the state of Florida in 1975, are five contiguous aquatic preserves within the greater Charlotte Harbor estuary. It includes salt marshes, mangroves, seagrass, oyster and tidal flats. It is the preserve of many species, including the American alligator, West Indian manatee, bald eagle, wood stork, piping plover, green and loggerhead sea turtles, royal false pawpaw (Deeringothamnus pulchellus), Florida perforate cladonia (Cladonia perforata) and many more.