[5] 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, smalltooth sawfish (Pristis pectinata),[6] royal false pawpaw (Deeringothamnus pulchellus), Florida perforate cladonia (Cladonia perforata), and many more.
Charlotte Harbor connects to San Carlos Bay to the south by way of Pine Island Sound and Matlacha Pass.
[7] Prior to the first Europeans, Charlotte Harbor was home to settlements of Native Americans who were part of the Calusa paramount chiefdom that occupied southwest Florida, extending from Tampa Bay in the north to the Ten Thousand Islands.
In 1539, Hernando de Soto began his journey across the Southeast by landing on the west coast of the Florida peninsula, near the chiefdom of Uzita, where he encountered Juan Ortiz, a survivor of the Narváez expedition who had been captured by the Tocobaga at Tampa Bay.
Traditional reconstructions locate Uzita at the mouth of the Manatee River in Tampa Bay, now the site of the De Soto National Memorial.
[13] This is unlikely because Mound Key in Estero Bay south of the Caloosahatchee is generally agreed to have been the location of the Calusa capital, not the Uzita chiefdom.
As the Florida continued to be explored, some fisherman from Cuba and other Spanish settlements began to set up fishing camps, or "ranchos" along the Gulf Coast, including around Charlotte Harbor.
The practice began in 1900, when the Charlotte Harbor and Northern Railway published the first written account of Jose Gaspar in a promotional brochure for its Boca Grande Hotel on Gasparilla Island.
[15][16] Charlotte Harbor is also said to have been the refuge of the pirate Brewster Baker and the site of several shipwrecks of vessels containing untold millions of Spanish gold.