In a heavily dammed Californian river, lower, less variable stream flows were associated with reduced salmon production, and suppressed winter flow cues with reduced early emigration of fry. Otolith records in the returning adults revealed strong selection against early and late migrants, likely resulting from degradation of downstream habitats and increasingly hot summers. Conversely, managed reservoir releases appeared to benefit spring migrants. Yet even with this weakened portfolio, maintaining a broad migratory window increased adult production and reduced variance. This study highlights the importance of freshwater flow and habitat management to recover salmon populations in an increasingly unpredictable climate.