The effects of climate change on oligotrophic rivers and their communities are almost unknown, albeit these ecosystems are the primary habitat of the critically endangered freshwater pearl mussel and its host fishes, salmonids. The distribution and abundance of pearl mussels have drastically decreased throughout Europe over the last century, particularly within the southern part of the range, but causes of this wide-scale extinction process are unclear. Here we estimate the effects of climate change on pearl mussels based on historical and recent samples from 50 rivers and 6 countries across Europe. We found that the shell convexity may be considered an indicator of the thermal effects on pearl mussel populations under warming climate because it reflects shifts in summer temperatures and is significantly different in viable and declining populations. Spatial and temporal modeling of the relationship between shell convexity and population status show that global climate change could have accelerated the population decline of pearl mussels over the last 100 years through rapidly decreasing suitable distribution areas. Simulation predicts future warming-induced range reduction, particularly in southern regions. These results highlight the importance of large-scale studies of keystone species, which can underscore the hidden effects of climate warming on freshwater ecosystems.