Recreational fishers in Mississippi are required to have a Mississippi State Saltwater Fishing License. All fishing regulations within the Seashore correspond to the state fishing regulations. Commercial fishing, including commercial shrimping and commercial crabbing, is prohibited within Seashore waters. The Seashore boundaries are one mile around Petit Bois, Horn, and Ship Islands. (Note: The Seashore does not have jurisdiction in the waters off Cat Island.) Recreational fishing is allowed in the Davis Bayou Area in Ocean Springs. The rebuilt fishing pier located near the Visitor Center is open to the public.

Charter boat operators licensed with the National Park Service are authorized to take visitors out to the Seashore to fish.  Visitors who wish to fish at West Ship Island can take the passenger ferry from Gulfport.