Trap-and-haul programs can maintain connection among habitats for migratory salmonids in fragmented systems. To conserve diversity within and among life history strategies, downstream trap and transport of juvenile salmonids could ideally mimic the natural, underlying out-migration dynamics of the population. A two-way trap-and-haul program is implemented in the lower Clark Fork River, Montana, to conserve adfluvial Bull Trout Salvelinus confluentus. We used PIT technology to assess whether downstream trapping efforts are effectively capturing variation in the out-migration dynamics of juvenile Bull Trout in Graves Creek, a key spawning and rearing tributary in the system. We tagged 821 juvenile Bull Trout in Graves Creek and used these tagged Bull Trout in conjunction with stationary PIT antennas to monitor out-migration and evaluate efficiency of the downstream trapping program. Capture efficiency in Graves Creek varied substantially from autumn to spring, with 89–96% of autumn out-migrating Bull Trout captured and 5–10% of spring out-migrating Bull Trout captured. Overall, we found that Bull Trout transported during the autumn out-migration periods generally reflect the natural out-migration dynamics of the population; however, Bull Trout that out-migrate in the spring are currently underrepresented in the downstream transport program. By understanding the underlying out-migration dynamics of the Bull Trout population in Graves Creek, management of the downstream trapping efforts can focus on minimizing potential selection for or against out-migrants based on timing and age at out-migration. Minimizing selection will conserve variation within the adfluvial life history strategy and therefore maximize resilience of the adfluvial Bull Trout populations.