Freshwater bioindicators have been developed to assess ecosystem health and responses to human-induced stressors. To date, most bioindicators primarily rely on the species identity of plant and animal communities and do not account for interactions among organisms and fluxes of energy between trophic levels. Body size is one of the most important ecological traits in aquatic ecosystems because it governs interactions among organisms and is affected by environmental conditions but, surprisingly, many of assessment approaches do not use individual body size. The community size spectrum is defined as the linear relationship between the abundance and the body size of organisms and reflects several important ecological features including ecosystem carrying capacity, predation-prey interactions, and trophic energy fluxes. In this study, we explored the potential of using the size spectrum parameters (slope, elevation and linearity) of fish community as a complementary bioindicator in 51 natural lakes and 102 reservoirs distributed across France. We determined how the fish size spectrum and other common bioindicators based on fish, macrophyte and phytoplankton communities responded to the water quality degradation, littoral habitat alterations and fish invasions. Results demonstrated that: (i) the size spectrum was driven by water quality degradation both in lakes and reservoirs, while size spectrum was affected by habitat loss in natural lakes and by fish invasion in reservoirs and (ii) the size spectrum was more sensitive to habitat loss than common bioindicators in natural lakes. This study highlights that the use of fish community size spectrum could provide additional insights into our understanding of the responses of freshwater ecosystems to global changes and could serve to improve the efficiency of management programs. This can be done at very limited additional cost because fish body size is commonly measured in biomonitoring protocols.