Purpose <p>Tailwater discharged into rivers can affect microbial diversity and community structure in river sediments. Most previous studies have focused on a single type of wastewater treatment plant. Six sewage-based rivers were selected for this experiment to investigate how different types of wastewater treatment plants affect the structure and diversity of microbial communities in sewage-based rivers. The objective of this study is to understand how industrial wastewater treatment plants and municipal wastewater treatment plants alter microbial biogeochemical function to different degrees.</p> Materials and methods <p>A total of 36 sediment samples were collected from six wastewater treatment plants. High-throughput sequencing of the 16S rRNA gene's hypervariable V3-V4 regions was conducted to analyze bacterial communities in the sediment, enabling a comparative assessment of the differences between upstream and downstream sites of each outfall. Correlations were assessed between environmental factors and community structure and identify key drivers through community analysis, functional prediction, and random forest analysis. This provides technical support for precise pollution control and helps to realize the goal of sustainable development of water environment in the basin. Results elucidate the tripartite relationship between industry-specific disparities, microbial community responses, and subsequent ecological feedback mechanisms.</p> Results and discussion <p>We found differences in the response of downstream sediments to tailwater, the abundance and diversity of microbial communities downstream of municipal WWTPs decreases with the discharge of tailwater, whereas the opposite is occurring in industrial WWTPs. Downstream microbial communities were less stable compared to upstream sediments. Contrary to previous reports of homogenization of WWTP impacts, our multi-omics approach reveals that municipal and industrial WWTPs can have different impacts on downstream sediment diversity.</p> Conclusions <p>The dominant phylum in all samples were <i>Proteobacteria, Acidobacteria, Chloroflexi,</i> and <i>Bacteroidetes</i>, however, the proportion in different river sediments varies. <i>Gemmatimonadetes</i> and <i>Verrucomicrobia</i> are key species affecting microbial communities in upstream and downstream sediments and in industrial and municipal WWTPs. NO₂-N and TKN were the most significantly affected environmental factors. Our research will provide data to support the protection of river ecosystems.</p>