Apalachee Bay is a broad, shallow coastal bay in Florida's Big Bend region, bounded by the Ochlockonee River to the west and the Econfina River to the east. It covers a surface area of 412 square kilometers with an average depth of only 3.0 meters. The bay's coastline is largely protected as part of the St. Marks National Wildlife Refuge, characterized by vast seagrass beds, marshes, and clear, shallow waters without industrial development. Paddling here involves navigating a network of embayments, rivers, creeks, and islands, with conditions heavily influenced by wind and tide. The bay is rife with oyster bars, shallow water, rocks, and submerged pilings, requiring careful navigation and a detailed, current chart.

Primary access for paddlers is through the Apalachee Bay Maritime Heritage Paddling Trail System, which consists of ten designated trails. Most trails are located in Wakulla County between the communities of Panacea and St. Marks and are designed to be completed in two to three hours. Specific launch points include the Shell Point Public Boat Ramp and the Levy Bay (Circle Point) Public Boat Ramp near Panacea, as well as the St. Marks Riverfront Park and Launch. The Mashes Sands Recreational Facility serves as a put-in for the 6.6-mile Mashes Sands Paddling Trail, which circles Mash Island and proceeds to the Levy Bay Boat Ramp. These are public launches, with some charging a five-dollar fee and offering amenities like parking, docks, and restrooms.

The paddling experience is defined by significant tidal influence and open water exposure. Paddlers are advised to time trips around slack tide for the easiest conditions and to be prepared for coastal winds that can quickly build chop across the bay's open stretches. While some launches like Shell Point offer calmer, sheltered water suitable for beginners, venturing into the main bay or crossing channels requires awareness of boat traffic, especially from motorboats during scallop and fishing seasons. Wildlife viewing is a major highlight, with frequent sightings of manatees, dolphins, bald eagles, osprey, pelicans, a wide variety of wading birds, and, along the shore, species like black bear and white-tailed deer. The area holds historical significance, with evidence of ancient shell middens and more recent Apalachee Indian settlements, as well as the Spanish fort at St. Marks.