We investigated environmental variables associated with spawning migration behavior for a dual spawning population of endangered Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus in the Great Pee Dee River, South Carolina. From 2016 to 2021, 147 Atlantic Sturgeon were captured, implanted with acoustic transmitters, and monitored using a stationary array of 40 receivers located every 5‐20 km along a 302‐km section of the Great Pee Dee River from the river mouth at Winyah Bay to the first movement barrier at Blewett Falls Dam, North Carolina. We observed 47 Atlantic Sturgeon attempt 74 spring migrations and 39 Atlantic Sturgeon attempt 76 fall migrations across four years of telemetry observations (2018‐2021). Mixed effects models indicated that discharge interacted with water temperature to affect both migration initiation and upriver movement, and these interactions differed between spring and fall runs. Spring runs were cued by rising temperatures and high river discharge, whereas fall runs were cued by falling temperatures and low discharge. Within migrations, spring‐run fish migrated further upriver when discharge was falling, and fall‐run fish moved further upriver when discharge was rising. Overall, fall‐run sturgeon migrated significantly further upriver than spring‐run sturgeon. Differences in migratory behavior among runs suggest potentially unique adaptations to ambient river conditions during respective spawning seasons. Identifying the environmental factors that drive, and thereby limit, Atlantic Sturgeon migrations in the Great Pee Dee River informs regional recovery efforts and highlights the importance of studying and managing this species at the population level.