Abstract Conservation efforts for endangered Snake River sockeye salmon (Oncorhynchus nerka) have been hindered by high en route adult mortality during their ∼1450 km freshwater spawning migration. Identifying causal factors for this mortality has been difficult given very small (often <10 fish) annual returns in recent decades. However, several hundred hatchery-bred fish returned in 2000 and we intercepted and radio-tagged 31 in mid-migration to monitor behaviours and survival. All fish initially migrated at similar rates, but later-timed fish eventually slowed migration and were far more likely to be unsuccessful. Late-season mortality was strongly associated with water temperatures near tolerance thresholds (21–24 °C). The data also suggest increased risk for fish in poor initial condition (i.e., with injuries or parasites) and probable recent selection against late-timed salmon. Results parallel temperature- and condition-related adult mortality in Columbia and Fraser River sockeye salmon populations and demonstrate the potential vulnerability of marginal southern populations to regional climate warming.