St. Joseph Bay is located in Gulf County along Highway 98 near the community of Port St. Joe, approximately 35 miles southeast of Panama City and 100 miles southwest of Tallahassee.

St. Joseph Bay is bound in the eastern shoreline by the city of Port St. Joe and the St. Joseph Bay State Buffer Preserve and on the west by the St. Joseph Peninsula. The bay is approximately 15 miles long and 6 miles at its widest part, and opens north to the Gulf of Mexico.

The aquatic preserve encompasses 55,000 acres of state-owned sovereign submerged lands below the mean high water line. Uplands and manmade canals are excluded from the preserve. Other exclusions include of privately owned submerged lands along the eastern shore, private in-holdings that occur along the southern and western shore, the area of the bay north of the Port St. Joe navigation channel and the immediate area of the channel.