Anadromous fishes often use various survival tactics while migrating through main stem rivers to successfully reach spawning grounds and reproduce. Mixed-stock assemblages of anadromous adult summer steelhead Oncorhynchus mykiss re-enter the Columbia River from late spring through fall including the period of peak summer water temperatures, and previous studies suggest that stocks alter migratory behaviour in response to warm temperatures by seeking cool water refuges. We combined parentage-based tagging with mixed stock analyses to test whether steelhead use a non-natal tributary (Deschutes River, OR, USA) as a thermal refuge and if this migratory behaviour is associated with stock-specific run-timing. Results collected over two migration years indicated that out-of-basin fish in the Deschutes River were disproportionately from specific stocks in the Snake River (Salmon and Grande Ronde) that had migrated through the main stem Columbia River when water temperatures exceeded 21 °C. Stocks migrating through the main stem river during cooler temperature periods were either less frequent (Clearwater River), or not encountered (lower Snake River) in the Deschutes River. This study facilitates an improved understanding of stock-specific migratory characteristics associated with environmental conditions in this system. Results potentially affect fisheries management, hatchery protocols, cool-water refuge maintenance, and conservation of wild Deschutes River populations.