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Arctic and subarctic rivers are warming rapidly, with unknown consequences for migratory fishes and the human communities dependent on them. To date, few studies have provided a comprehensive assessment of possible climate change impacts on the hydrology and temperature of Arctic rivers at the regional scale, and even fewer have connected those changes to multiple fish species with input and guidance from Indigenous communities. We used climate, hydrologic, and fish-growth simulations of historical (1990–2021) and future (2034–2065) young-of-year (YOY) growth potential of Chinook salmon (Oncorhynchus tshawytscha) and Dolly Varden (Salvelinus malma) for seven river basins in the Arctic-Yukon-Kuskokwim (AYK) region of Alaska, USA and Yukon Territory, Canada. Historically, summer water temperatures of all river basins remained below thresholds regarded as deleterious for Chinook salmon (14.6 °C) and Dolly Varden (16 °C), even in the warmest years. However, by the mid-century, Chinook salmon growth was limited, with declines in the warmest years in most river basins. Conversely, Dolly Varden are expected to benefit, with a near-doubling in growth projections in all river basins. This suggests that there may be an increase in suitable habitat for Dolly Varden by mid-century. The results highlight species-specific consequences of climate change and can guide future research on refugia for these species of cultural and subsistence importance to Indigenous communities in the AYK region and throughout the Arctic.