Fall chinook salmon evolved to emigrate during the summer months. The shift in the temperature preference we observed in smolting fall chinook but not spring chinook salmon may reflect a phylogenetic adaptation to summer emigration by (1) providing directional orientation as fall chinook salmon move into the marine environment, (2) maintaining optimal gill function during emigration and seawater entry, and/or (3) resetting thermoregulatory set-points to support physiological homeostasis once smolted fish enter the marine environment. Phylogenetically determined temperature adaptations and responses to thermal stress may not protect fall chinook salmon from the recent higher summer water temperatures, altered annual thermal regimes, and degraded cold water refugia that result from hydropower regulation of the Columbia and Snake rivers. The long-term survival of fall chinook salmon will likely require restoration of normal annual thermographs and rigorous changes in land use practices to protect critical thermal refugia and control maximum summer water temperatures in reservoirs.