Within a short walk from Apalachicola Harbor's historic district is Scopio Creek Marina, a family-owned business catering to recreational boaters and fishers from across the country. Open seven days a week, its services include fishing guides, dry storage for boats and jet skis, lighted wet slips, a pump-out station, gas and diesel, showers, and shore power. There is an Evinrude Dealer in the Marina, and Evinrude service and repairs are also available in this Apalachicola Harbor marina.

Visitors to Apalachicola Harbor can explore the area's natural areas on Eco Explorer Cruises. Inland cruises tour the inland and coastal waterways. Inland cruises visit the Apalachicola River's marshes and swamps, and the coastal cruise includes Apalachicola Harbor and Bay and the barrier islands as well as offshore waters in the Gulf of Mexico. Docked in the Scopio Creek Marina, the cruises accommodate up to six people at a time.

The Robinson Brothers Guide Service offers fishing charters out of Apalachicola Harbor, Carrabelle, Port St. Joe, Mexico Beach, or St. George Island. Passengers range from experienced anglers to novice youngsters and families. Inshore fishing trips, mostly catch-and-release, are on 5.5-meter (18-foot) skiffs. Bay fishing takes place on boats from 6.4 to 7.6 meters (21 to 25 feet) that can accommodate four fishermen comfortably.

Captain Gill's River Cruises, designed for passengers of any age, cruise the Apalachicola Harbor and River and include picnics, sightseeing, local folklore, swimming, and fishing. Pets are welcome, too. Also based at Apalachicola Harbor's Scipio Creek Marina, the Backwater Guide Service offers half- and full-day fresh- and salt-water fishing charters as well as sightseeing on the River and at Fort Gadsden Historic Site, Cape St. George Island Lighthouse, and nature trails along the Gulf of Mexico beach.

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