Abstract.-The relationships between lower Columbia River water temperatures and migration rates, temporary tributary use, and run timing of adult fall Chinook salmon Oncorhynchus tshawytscha were studied using historical counts at dams and recently collected radiotelemetry data. The results from more than 2,100 upriver bright fall Chinook salmon radio-tagged over 6 years (1998,(2000)(2001)(2002)(2003)(2004) showed that mean and median migration rates through the lower Columbia River slowed significantly when water temperatures were above about 208C. Slowed migration was strongly associated with temporary use of tributaries, which averaged 2-78C cooler than the main stem. The proportion of radio-tagged salmon using tributaries increased exponentially as Columbia River temperatures rose within the year, and use was highest in the warmest years. The historical passage data showed significant shifts in fall Chinook salmon run timing distributions concomitant with Columbia River warming and consistent with increasing use of thermal refugia. Collectively, these observations suggest that Columbia River fall Chinook salmon predictably alter their migration behaviors in response to elevated temperatures. Coolwater tributaries appear to represent critical habitat areas in warm years, and we recommend that both main-stem thermal characteristics and areas of refuge be considered when establishing regulations to protect summer and fall migrants.