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Freshwater organisms are disproportionately impacted by climate change and human disturbance, resulting in shifts in species' distributions and life histories. We coupled contemporary and historical datasets documenting physical and ecological variables over four decades to quantify changes in the abundance, emergence timing, and body size of salmonflies (Pteronarcys californica) in the Madison River in southwest Montana. In contemporary surveys, water temperature was the main driver of salmonfly abundance, emergence timing, and body size. Salmonfly densities were negatively correlated with summer water temperature, which explained 60% of variation in larval density among sites, whereas substrate type played a negligible role. Emergence occurred 20 days earlier, and male and female exuvia length were 13.8% and 11.3% shorter, respectively, at the warmest site relative to the coolest site (4 degrees C difference). These patterns were supported by historical data. For example, a 1.2 degrees C increase in mean annual water temperature in the Madison River between 1977 and 2017 coincided with evidence for upstream range contraction. Between 1973 and 2017, emergence timing varied widely among years, occurring up to 41 days earlier in years when spring water temperatures were relatively warm. As climate change progresses, we predict that salmonflies could be extirpated from an additional 28 km of currently occupied habitat, representing a 22.6% reduction in suitable habitat along the Madison River. This study provides evidence of long-term biological change of an aquatic insect and highlights the importance of combining spatial and historical datasets to better understand species' responses to environmental stressors across both space and time.