Kayaking and canoeing are excellent ways to explore Biscayne National Park's mangrove-fringed shorelines and the Biscayne Bay's shallow waters. A popular starting point for visitors wanting to explore the waters south of Caesar Creek is Adams Key. More experienced kayakers, however, might enjoy crossing the seven mile expanse of Biscayne Bay to camp at Boca Chita Key or Elliott Key. Using the islands as a base camp will allow visitors to explore the channels, creeks, and lagoons south of Caesar Creek. It's likely that kayakers and canoeists will have these waters to themselves due to many areas being much too shallow for motorized vessels.

Shallow Jones Lagoon offers a chance for visitors to spot large wading birds, large schools of fish, upside-down jellies, rays, and sharks. Within the lagoon is a bird rookery that kayakers and canoeists should be careful not to disturb. Another great spot is Hurricane Creek, providing amazing snorkeling underneath mangrove roots to view crabs, sea squirts, and anemones among other marine life. Giant sponges and rocky ledges offer hiding spots for spiny lobsters.

Visitors with their own kayaks or canoes can launch them at the Dante Fascell Visitor Center for free. Kayak and paddle board rentals are available at Convoy Point, where the visitor center is located, on the weekends. Paddling trail guides are available online and at the visitor center for the Black Point, Crocodile Creek, Deering, Elliott Key, Mowry Canal and Jones Lagoon trails. Website, Map