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Eutrophication is a major problem currently impacting many surface water ecosystems. Impacts of increased nutrient concentrations on biodiversity may differ between different scales, different organism groups, and different trophic states. Surveys at different spatial scales have suggested that biodiversity of different taxa may exhibit significant cross-taxon congruence. In our study, we examined the diversity of zooplankton and zoobenthos across 261 lakes in the Lake Taihu watershed, an area that is undergoing a severe eutrophication process. We tested the cross-taxon congruence in species richness and Shannon-Wiener diversity between zooplankton and zoobenthos along a nutrient gradient across the lakes. Our findings were consistent with the intermediate disturbance hypothesis, considering nutrient input as the disturbance. Also, we found significant cross-taxon congruence between zooplankton and zoobenthos diversities. Our results confirmed that excess nutrient levels resulted in diversity loss and community simplification. Zoobenthos were more sensitive to nutrient increases compared with zooplankton, which decreased cross-taxon congruence because these organism groups did not respond similarly to the anthropogenic disturbance.