It was located near north of Mobile at Mount Vernon Landing on the Mobile River, close to the confluence of the Tombigbee and Alabama Rivers. It served as the western terminus of the Federal Road which ran through Creek lands to Fort Wilkinson, Georgia.
Aaron Burr was held here after his arrest in 1807 for treason against the United States.
Fort Stoddert served as the outpost for the Mississippi Militia during the Creek War (1813–1814).