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Aim: Over the last century, lakes all over the world have experienced significant eutrophication and become more susceptible to critical transitions. This has prompted a growing need to understand how community dynamics shift following ecological perturbations. This study aims to elucidate the present status, spatial patterns and determinants of biological diversity, and how they have changed in response to alterations driven by eutrophication. Location: Lakes of East China, mostly in the Yangtze River Basin. Taxa: Bacillariophyceae (163 species in 33 genres, see taxa names in Appendix S1). Methods: The environmental conditions of over 60 lakes were assessed based on parameters such as water quality, physical characteristics and biogeochemical constituents. Surface sediment samples and high‐resolution sediment records were collected to quantify the biodiversity of diatom communities, and principal component analysis (PCA) was used to determine the major environmental gradients. Meanwhile, linear regression, canonical correlation analysis and Mantel tests were used to quantify the correlations between variables. Results: Biodiversity metrics showed no distinct geographic patterns, although areas near large lakes showed comparatively high evenness. Smaller pairwise dissimilarities were observed among hypereutrophic lakes in comparison to lakes with a lower trophic status. The past century has witnessed a decrease in both pairwise dissimilarity and the standard deviation of evenness. A significant statistical association was found between dissimilarity and ionic concentration and composition in the surface sediment of lakes, rather than nutrient levels. Main Conclusions: Following regional eutrophication and human disturbance, a significant reduction in biodiversity differentiation was observed in lakes located in East China. Currently, the dominant factor in determining the beta diversity of diatom communities is geochemical conditions rather than nutrient concentrations. Long‐term stress caused by cultural eutrophication may also have altered the dominant determinant of regional biodiversity and diatom community dynamics. [ABSTRACT FROM AUTHOR]