It is widely accepted that climate change constrains biota. Yet, because of the lack of consistent multisite and multitaxon surveys, few studies have addressed general rules about how climate change impacts on structure and diversity of animal communities. Especially, the relative influence of nonclimatic anthropogenic disturbances on this impact is fairly unknown. Here, we present for the first time a meta-analysis assessing the effect of global warming on stream organisms. Fish communities of large rivers in France undergoing various anthropogenic pressures showed significant increase in proportions of warm-water species and of specific richness during the last 15–25 years. Conversely, the equitability decreased, indicating a gradual decrease of the number of dominant species. Finally, the total abundance increased, coupled with rejuvenation and changes in size-structure of the communities. Interestingly, most of these effects were not depressed by the strength of nonclimatic anthropogenic disturbances. Conversely, geographical location of communities and especially closeness of natural barriers to migration could influence their response to climate change. Indeed, increase in the proportion of southern species seemed hindered at sites located close to the southern limit of the European species' geographical ranges. This work provides new evidence that climate change have deep impacts on communities which, by overtaking the effects of nonclimatic anthropogenic disturbances, could be more substantial than previously thought. Overall, our results stress the importance of considering climate change impacts in studies addressing community dynamics, even in disturbed sites.