Eutrophication alters the trophic dynamics in lakes and may result in biotic homogenization. How nutrient enrichment drives patterns of taxonomic and functional (i.e., trait‐based) homogenization of macroinvertebrate assemblages at within‐lake (local) and among‐lake (regional) scales is, however, not well understood. Taxonomic and functional compositions of macroinvertebrate assemblages in 41 lakes of the middle and lower reaches of the Yangtze River and Huaihe River were analyzed at within‐lake and among‐lake scales. Our results indicated that there was a significant difference in macroinvertebrate assemblages among lakes under different trophic status, and that total phosphorus was the major environmental factor that regulated both taxonomic and functional beta diversity of macroinvertebrate assemblages. That the abundances of pollution‐tolerant species (e.g., Limnodrilus hoffmeisteri and Microchironomus tabarui) increased with trophic state contributed the most to among‐lake dissimilarity. Functional beta diversity was significantly positively correlated with taxonomic beta diversity, while functional beta diversity was on average lower than taxonomic beta diversity. A combination of univariate and multivariate techniques revealed that nutrient enrichment homogenized taxonomic and functional diversity of benthic macroinvertebrate assemblages in shallow lakes at within‐lake and among‐lake scales, and that there was an overall trend toward taxonomic homogenization that exceeded the trend of functional homogenization. Thus, taxonomic and functional compositions should be considered simultaneously to improve understanding of the response of aquatic communities to anthropogenic disturbance, as the loss and gain of species may be influenced by species‐specific features, and functional composition may exhibit a relatively high correspondence with changes in environmental conditions.