Efforts to ameliorate negative effects of diversion dams on aquatic species of concern are important in rivers where water withdrawal supports agricultural economies and are likely to become increasingly important with impending climate change. A multiyear study was conducted to evaluate the survival consequences of diversion dam passage for juvenile Chinook Salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) in the highly managed Yakima River, Washington. Canal entrainment and passage were evaluated at four diversion dams encountered by seaward migrating juvenile salmon and steelhead. Fish pass dams via spillbays or enter canals with downstream fish-screening facilities designed to collect entrained fish and return them to the mainstem river. Percent entrainment into canals was substantial (6–59%) at three of the four diversion dams studied, and entrainment probability was positively associated with the proportion of streamflow diverted into canals. Survival probability estimates for groups of tagged fish that were entrained into canals were lower than survival probability estimates for tagged fish that passed through spillbays on the dams. Absolute differences in survival probabilities between routes ranged from 0.099 to 0.369, demonstrating that canal entrainment reduced survival of outmigrating juvenile Chinook Salmon and steelhead. We also found that entrainment resulted in migration delays, which could further affect survival because fish are increasingly exposed to predation and decreased water quality as water temperature increases throughout the migration season. These results highlight the need to limit entrainment of juvenile salmon and steelhead at diversion dams in rivers where salmon recovery is important.