The size spectrum represents a powerful approach for quantifying the effects of environmental changes from individuals to communities in aquatic ecosystems. However, our understanding of its temporal stability in freshwater ecosystems is still limited. In the present study, we used a size spectrum approach to investigate the responses of 126 lake fish communities to changes in the intensity of three common anthropogenic stressors (i.e., global warming, nutrient loading and biological invasions) in French natural lakes and reservoirs over an average 5‐year time period. Using a backward selection on a full model including all possible effects of stressors on the size spectrum slope, we demonstrated that (i) increasing summer temperature shifted fish abundance towards the largest size classes, resulting in a flatter size spectrum slope and (ii) nutrient loading and biological invasions were associated with a shift towards smaller size classes in natural lakes, while the opposite effect was observed in reservoirs. In addition, these two stressors interacted in determining changes in the size structure of fish communities, complicating what the size spectrum can reveal about changes in stressor intensity during monitoring programs. All predictors accounted for a limited part of the observed changes in size spectra, and further investigations are needed to fully apprehend the interplay between natural and human‐induced drivers of the temporal changes in size spectra in contrasting environmental conditions.