Measures based on functional traits are often capable of indicating local environmental conditions and are thus considered promising tools for environmental monitoring and assessment programs. Benthic macroinvertebrates exhibit a diverse array of functional traits that can be used for assessing ecological quality of freshwater ecosystems. However, the associations between functional structure of macroinvertebrates and anthropogenic disturbances remain inadequately understood, especially for floodplain lakes. In our study, we compared the response of taxonomic and functional trait composition of macroinvertebrates to anthropogenic eutrophication in lake ecosystems of the Yangtze River floodplain. We found that the relative abundance of Mollusca, Gastropods, Bithyniidae, Bivalvia and Ephemeroptera showed significant differences among four lake groups (river-connected, macrophyte-dominated, macrophyte-algal transitional and algal-dominated lakes) subjected to different disturbance levels from mesotrophic to highly eutrophic. Using a trait-based approach, we found 13 categories, belonging to seven traits, showed significant differences observed among lake groups. Regarding influence of environmental factors on macroinvertebrate assemblages, both taxonomic measures and functional traits were mainly affected by water quality factors associated with eutrophication. However, the number and specific key environmental factors varied between measures of functional traits and taxonomic composition. The taxonomic composition responded to more environmental factors (seven factors: Chl a, CODmn, TN, area, water depth, NH4+-N and conductivity), but showed lower explained variation (24.4%) compared with functional structure (three factors: aquatic vegetation coverage, conductivity and Chl a, 36.4% explained variation). Furthermore, spatial factors only affected taxonomic composition, but they were not correlated with functional composition. In general, our study showed that functional trait structure of macroinvertebrate assemblages responded more sensitively and reliably to eutrophication than measures based on taxonomic composition in floodplain lakes. Thus, we recommend the incorporation of macroinvertebrate functional trait information into biomonitoring programs for floodplain lakes and other aquatic ecosystems, as it can be considered as a more promising approach than taxonomy-based approaches in biomonitoring programs.