Anthropogenic pressures are the main drivers of freshwater biodiversity loss. Lakes can act as sentinels of both local and regional changes and experience increased anthropogenic disturbances. Functional traits have been developed to elucidate the consequential functional progression of community changes, yet only a few studies on rotifer functional approaches exist compared with other biotic community attributes. Here, we investigate the responses of rotifer taxonomic and functional diversity metrics to an environmental gradient representing changing lake morphology, land use and physicochemical conditions in 30 lakes along the Yangtze River, China. Based on the distinct lake morphological gradient, land use patterns and environmental conditions, the 30 lakes were clustered into three groups with decreasing anthropogenic stress from Group 1 to Group 3. Our findings indicated that both species and functional richness decreased from Group 1 to Group 3 and that functional richness exhibited better correspondence with multiple stressors than did taxonomic richness. Moreover, we found that the rotifer assemblages varied significantly among the three lake groups along land use and environmental gradients, and the community-weighted means (CWM) of trait expression of the corresponding communities changed simultaneously. Types of trophi and corona were considered as the most variable traits among the three lake groups. We highlight that trait-based approaches are more sensitive, responsive and informative than taxonomic approaches in indicating human-induced environmental alterations in freshwater ecosystems.