Benthic diatoms are often included in bioassessment programs of river health as sensitive indicators of nutrient status and pollution. Many diatom‐based indices have been developed and are frequently used to infer conditions in water quality. However, concerns have been raised regarding the robustness of these indices in riverine systems that have natural variability in environmental conditions, including seasonal change of water quality parameters, especially in terms of physical and chemical characteristics of water, which also influence diatom community composition. Here, we used three diatom‐based indices (Diatom‐based eutrophication/pollution index, EPI‐D; Biological Diatom Index, IBD; Watanabe's Index, WAT), which have previously been validated as robust for water quality assessment in China, to explore their response to temporal changes in water quality and diatom community structure in a riverine network over time. Concentrations of total nitrogen (TN), nitrate nitrogen (NO3‐N), total phosphorus (TP), temperature (t), and turbidity in April 2010 were significantly higher than in November 2007. The 141 diatom taxa we found in April 2010 were fewer than the 194 taxa we found in November 2007. On both occasions, the three diatom indices responded to same water quality variables (phosphorus and chloride or nitrogen) as reported in previous studies. Of the three diatom indices tested, EPI‐D provided the most robust measure of natural seasonal changes in water quality and indicated the phosphorus and chloride. Our study confirms that these three diatom indices are effective for evaluating long‐term water quality in large rivers.