Temporal and spatial distributions of Gulf of Mexico (Gulf) sturgeon Acipenser oxyrinchus desotoi were assessed in the Pensacola bay system, Florida, using stationary ultrasonic telemetry. Fifty‐eight Gulf sturgeon were tagged within the Escambia (n = 26), Yellow (n = 8), Blackwater (n = 12) and Choctawhatchee Rivers (n = 12) in June, July, September and October, 2005. Fifty‐four Gulf sturgeon were detected at least once during the study. Migration of sturgeon occurred throughout the bay system in fall, to various winter habitats in the Gulf of Mexico and Santa Rosa Sound. In spring, tagged sturgeon migrated back through the bay system to summer habitats in rivers. Based on the duration and number of detections, Gulf sturgeon primarily used the upper portions of East and Escambia Bays as migration routes in and out of all rivers during spring and summer and inhabited the lower portion of Pensacola Bay for longer durations in fall and winter. Specific areas within the Pensacola bay system were used in summer and winter that were not previously documented as essential sturgeon habitat. Areas in southeastern Pensacola Bay were heavily used during winter by a large portion of the population. Gulf sturgeon also exhibited long‐term winter residency in Santa Rosa Sound for two consecutive years. An area in northeastern Escambia Bay supported Gulf sturgeon during the summer, which was unexpected and can not be explained by the data from this study. However, the discovery that Gulf sturgeon remain in the bay during the summer has important ecological and management implications that need further investigation.