Widespread declines among Atlantic salmon (Salmo salar) and brown trout (Salmo trutta) over recent decades have been linked to pollution, exploitation and catchment modification, but climate change is increasingly implicated. We used long-term, geographically extensive data from the Welsh River Wye, formerly a major salmon river, to examine whether climatically mediated effects on juveniles (>0+) might contribute to population change. Populations of Atlantic salmon and brown trout fell across the Wye catchment, respectively, by 50% and 67% between 1985 and 2004, but could not be explained by pollution because water quality improved during this time. Stream temperatures, estimated from calibrations against weekly air temperature at eight sites, increased by 0.5–0.7 °C in summer and 0.7–1.0 °C in winter, with larger tributaries warming more than shaded headwaters. Rates of winter warming were slightly greater after accounting for the effect of the North Atlantic Oscillation (1.1–1.4 °C). However, warming through time was smaller than measured variations among tributaries, and alone was insufficient to explain variations in salmonid density. Instead, population variations were best explained in multilevel mixed models by a synoptic variate representing a trend towards hotter, drier summers, implying interactions between climate warming, varying discharge and fluctuations in both brown trout and salmon. Taken alongside recent data showing effects of warming on survival at sea, these data suggest that Atlantic salmon might be jeopardized by future climatic effects in both their marine and freshwater stages. Effects on nondiadromous brown trout also imply climatically mediated processes in freshwaters or their catchments. Climate projections for the United Kingdom suggest that altered summer flow and increasing summer temperatures could exacerbate losses further in these species, and we advocate management actions that combine reduced abstraction with enhanced riparian shading.