Mean summer water temperatures in the Fraser River (British Columbia, Canada) have increased by ∼1.5 °C since the 1950s. In recent years, record high river temperatures during spawning migrations of Fraser River sockeye salmon (Oncorhynchus nerka) have been associated with high mortality events, raising concerns about long-term viability of the numerous natal stocks faced with climate warming. In this study, the effect of freshwater thermal experience on spawning migration survival was estimated by fitting capture–recapture models to telemetry data collected for 1474 adults (captured in either the ocean or river between 2002 and 2007) from four Fraser River sockeye salmon stock-aggregates (Chilko, Quesnel, Stellako-Late Stuart and Adams). Survival of Adams sockeye salmon was the most impacted by warm temperatures encountered in the lower river, followed by that of Stellako-Late Stuart and Quesnel. In contrast, survival of Chilko fish was insensitive to the encountered river temperature. In all stocks, in-river survival of ocean-captured sockeye salmon was higher than that of river-captured fish and, generally, the difference was more pronounced under warm temperatures. The survival–temperature relationships for ocean-captured fish were used to predict historic (1961–1990) and future (2010–2099) survival under simulated lower river thermal experiences for the Quesnel, Stellako-Late Stuart and Adams stocks. A decrease of 9–16% in survival of all these stocks was predicted by the end of the century if the Fraser River continues to warm as expected. However, the decrease in future survival of Adams sockeye salmon would occur only if fish continue to enter the river abnormally early, towards warmer periods of the summer, as they have done since 1995. The survival estimates and predictions presented here are likely optimistic and emphasize the need to consider stock-specific responses to temperature and climate warming into fisheries management and conservation strategies.