AbstractFloodplains are highly productive environments that provide critical rearing habitat and increased growth for diverse native fishes, including juvenile Chinook salmon (Oncorhynchus tshawytscha). Yet, stranding during the flood recession is a potential negative outcome in restored ecosystems where environmental cues are not always present as they were under historical conditions. Outmigration cues of native and non‐native fishes from a restored floodplain were evaluated along the Cosumnes River, CA, USA. This river is the only remaining major unregulated river in the Sierra Nevada that flows into the Central Valley. It remains unclear how native and non‐native fishes utilize spatiotemporally heterogeneous habitats in the Cosumnes River; however, a better understanding of these dynamics could yield insight into how degraded river ecosystems in the region could be rehabilitated to benefit native fishes. In 2018 and 2019, daily fyke net surveys of fish assemblages were conducted within the floodplain and in outmigration corridors, along with the collection of environmental data to identify possible cues. Bayesian modeling showed that temperature increases, along with the rate of floodplain drawdown and the average flow over a rolling seven‐day period, were important triggers for cuing native fishes to exit the floodplain. We conclude that the numerous benefits to the aquatic food web and growth of native fishes justify the risk of stranding that floodplain restoration poses, particularly when supplemented with outmigration cues.