One of the best ways to explore Biscayne National Park is by boat. By boating through the park, visitors can discover living coral reefs, visit the Florida Keys, and explore Biscayne Bay's protected waters. Access for boaters is provided by four nearby country marinas.

It's possible for visitors to camp in Biscayne National Park, with campgrounds provided at Elliott Key and Boca Chita Key. Camping is on a first-come, first-serve basis, and the only way to get to these islands is by boat. The most popular island in the park is Boca Chita Key. There is an open, grassy, waterside camping area with grills and picnic tables on the island. Toilets are also provided, however, there are no showers, sinks, or drinking water.

The largest island in Biscayne National Park, Elliott Key, offers camping areas both in the forest and near the water. Grills and picnic tables are also available. Cold water showers, sinks, and toilets are also provided. Drinking water is available, however, visitors are advised to bring their own in case the system should go down. Tunneling through the tropical hardwood hammock of Elliott Key are two trails. One trail is a one-mile loop near the harbor. The other tail travels the entire length of the island, seven miles one-way or fourteen miles round-trip.