I can think of no better way to explore the uninhabited, shallow backcountry on the Gulf side of the Keys than by kayak or canoe, since you can reach places big boats just can't get to because of their large draft. Manatees will sometimes cuddle up to the boats, thinking them another friendly species.
Many area hotels rent kayaks and canoes to guests, as do the outfitters listed here. Florida Bay Outfitters, U.S. 1 at MM 104, Key Largo (tel. 305/451-3018; www.kayakfloridakeys.com), rents canoes and sea kayaks for use in and around John Pennekamp Coral Reef State Park for $35 to $45 for a half-day, $50 to $60 for a full day. At Coral Reef Park Co., U.S. 1 at MM 102.5, Key Largo (tel. 305/451-1621), you can rent canoes and kayaks for $12 per hour; most canoes are sit-on-tops. Florida Keys Kayak and Sail, U.S. 1 at MM 75.5, Islamorada (tel. 305/664-4878), at Robbie's Pier, offers backcountry tours, botanical-preserve tours of Lignumvitae Key, historic-site tours of Indian Key, and sunset tours through the mangrove tunnels and saltwater flats. Tour rates are from $39 to $49; rental rates range from $15 per hour to $45 per day for a single kayak, and $20 per hour to $60 per day for a double kayak.