Since ancient times, indigenous peoples have inhabited the region surrounding Charlotte Harbor. In the 1700s and 1800s, the waters of the area were frequented by Spanish fishermen.

Following various transfers of ownership, Don Pedro Island fell into the hands of Cavanaugh Community Corp. in 1969. The corporation constructed the pavilion and docks on the southeastern part of the island.

In 1985, the state took ownership of the property. The addition of the Don Pedro Land Base in 1999 expanded the park by 100 acres, offering visitors additional recreational opportunities.