Yukon River Chinook salmon populations are declining for unknown reasons, creating hardship for thousands of stakeholders in subsistence and commercial fisheries. An informed response to this crisis requires understanding the major sources of variation in Chinook salmon productivity. However, simple stock-recruitment models leave much of the variation in this system’s productivity unexplained. We tested adding environmental predictors to stock-recruitment models for two Yukon-drainage spawning streams in interior Alaska—the Chena and Salcha rivers. Low productivity was strongly associated with high stream discharge during the summer of freshwater residency for young-of-the-year Chinook salmon. This association was more consistent with the hypothesis that sustained high discharge negatively affects foraging conditions than with acute mortality during floods. Productivity may have also been reduced in years when incubating eggs experienced major floods or cold summers and falls. These freshwater effects—especially density dependence and high discharge—helped explain population declines in both rivers. They are plausible as contributors to the decline of Chinook salmon throughout the Yukon River drainage.