Refuge waters include 2,000 acres of man-made pools open to bank fishing year-round and to boats (outboard motors not larger than 10 hp), March 15-October 15, in the St. Marks Unit. Otter Lake (120 acres), Alligator Lake (100 acres), Lake Renfro (20 acres) and other small lakes and ponds less than five acres are open year-round to boats (outboard motors not larger than 10 hp) and bank fishing. Aucilla, St. Marks and Wakulla Rivers lead into Apalachee Bay (approximately five miles of each river within or near refuge boundaries) Approximately 32,000 acres of bay/estuary are within refuge executive closing boundary; saltwater boat launch provides access to the bay. Saltwater fishing is allowed year-round. Available species include largemouth bass, sunfish and catfish. Saltwater species are bluefish, spotted seatrout, flounder, red drum, Spanish mackerel, mullet, shark and black sea bass.
The St. Marks NWR is open to fishing all year long and provides opportunities for both fresh and salt water fishing. In addition to many lakes, ponds, creeks and rivers, the refuge has boat launching sites (see maps) for access to Apalachicola Bay.
Bank fishing is permitted in refuge impoundments along Lighthouse Rd. (Co. Rd. 59) all year; hand-launch boats are permitted March 15 - October 15 with electric trolling motors only.
Boats are permitted with motors up to 10 h.p. in the lakes along S.R. 372 and Otter Lake off S.R. 372A.
Crabbing is only permitted in tidal waters at the lighthouse. Crabbing is not permitted in refuge pools or impoundments.