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Biodiversity, which strengthens ecosystem stability, ecosystem function, and ecosystem services, is threatened by anthropogenic perturbation and climate change worldwide. However, despite the study of the role of biodiversity in multiple facets of freshwater ecosystems, the linkages between macroinvertebrates diversity and ecosystem functioning have not yet been well‐assessed in eutrophication gradients of lowland river‐floodplain systems. In this study, we have examined the relationship between macroinvertebrates diversity (species diversity, functional diversity, phylogenetic diversity) and macroinvertebrates biomass across the three typically featured eutrophication gradients: "MACROPHYTE," "TRANSITION," and "PHYTOPLANKTON," of floodplain lakes in the middle and lower reaches of the Yangtze River (China). Our results suggest that macroinvertebrates diversity in three different lacustrine conditions, biomass, and the relationship between diversity and biomass varied along eutrophication gradients. Functional richness and variance (divergence in taxon community) were the two important macroinvertebrate diversity indices, which accounted for the largest amount of variation in the biomass (63% in PHYTOPLANKTON lakes and 57% in MACROPHYTE lakes, respectively). We also found that the macrophyte coverage is more important than the relative abundance in maintaining the macroinvertebrates diversity and biomass in lowland Yangtze floodplain lake systems, while the relative abundance of macrophyte would change the BEF relationship. Our results demonstrate the functional performance of Yangtze River lakes, which would change with increased nutrient loading and decreased macrophyte coverage and would highlight the significance of the restoration of macrophytes to reduce nutrient loads. [ABSTRACT FROM AUTHOR]