The first inhabitants of the island were the Timucuan Indians. Snails gathered from the shallows of the St. Johns River were a staple food of these people. Through the years, the discarded shells accumulated to form large mounds on the island, one of which may be viewed on the park’s nature trail. Three remarkable artifacts have been found in the vicinity of Hontoon Island. A large owl totem, carved from a log and two smaller carvings of wood, one of an otter holding a fish and the other of a bird which is apparently a pelican. Replicas of two of the totems stand in the picnic area as a tribute to the artistry and craftsmanship of the extinct culture.

In later years, the 1,650-acre island was a pioneer homestead, a boat yard, a center for commercial fishing and a cattle ranch before being purchased by the state in 1967.