Charlotte Harbor, covering 86,747 acres, is a bay situated in Charlotte County, with the associated WBID(s): 2065A, 2065B, 2065C, 2065D.

Charlotte Harbor is the second-largest estuary in Florida and the largest, deepest and most diverse of the five Charlotte Harbor Aquatic Preserves, encompassing the Gasparilla Sound-Charlotte Harbor Aquatic Preserve. Fresh water from the Peace and Myakka rivers mixes with salt water coming through Boca Grande Pass from the Gulf of Mexico. The Charlotte Harbor Watershed includes Charlotte Harbor as well as the Peace River and the Myakka River basins.

Note that this waterbody is impaired for one or more parameters including Mercury. All recreational marine waters in Florida are impaired for Mercury based on fish tissue assessments and a statewide Total Maximum Daily Load (TMDL) pollutant limit for Mercury has been adopted in response. The largest sources of Mercury are from air pollution generated from local and global power plants.