Stocking streams with hatchery produced fishes is an increasingly common practice to restore native populations but the fate of these fish is uncertain due to low survival or high emigration rates. Monitoring these vital population rates is needed to assess stocking and translocation of rare and endangered fishes to identify approaches that maximize persistence and survival and ultimately result in established populations. We quantified survival, emigration, movement directionality, and long term (24 months) trends in apparent survival of stocked and wild caught fish implanted with passive integrated transponder (PIT) tags. We PIT tagged and tracked 1,419 individuals, consisting of direct comparisons between two species of hatchery and wild fish, as well as four other wild captured species, from 2020 to 2022 in three desert streams in Arizona and New Mexico. We found that hatchery fish had high (>98%) estimates of survival after being released (<40 days), that was similar to all tagged wild fish. But hatchery fish had a five‐fold higher emigration rate than wild conspecifics shortly (<40 days) after being released. Emigrating hatchery fish also tended to move downstream, whereas wild fish were more likely to move upstream. Additionally, apparent survival estimates were about ten times higher for tagged wild fish than hatchery conspecifics six months after release; hatchery fish apparent survival approached zero after about 165 days but did not approach zero for wild fish until 690 days following tagging and release. Our results suggest emigration, rather than reduced survival might limit the success of stocking efforts. Thus, choosing optimal stocking locations and the time of year of the stocking, such as upstream reaches during times near the species reproduction season, might improve retention and establishment of stocked fish.