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This paper aims to preliminarily understand the structure and diversity of the bacterial community in the sediments of the Qingshui River, and analyze the differences of dominant bacteria in different river reaches, and identify the influence degree of environmental factors. In this study, surface sediments of the main stream of the Qingshui River were selected to analyze both bacterial community composition and a diversity index using the high-throughput sequencing analysis of bacterial 16S rDNA, further exploring their relationships with environmental factors. Results showed that 16,855 OTUs in the surface sediments belonged to 66 phyla, 164 classes, 274 orders, 317 families, and 501 genera of bacteria, while carbon/nitrogen-fixing bacteria were dominant at the class and genus level. There was a significant (<i>p</i> < 0.05) spatial difference between bacterial species composition and the diversity index in surface sediments. <i>Proteobacteria</i> was the most abundant phylum in the sediments of the main stream of the Qingshui River, with an average abundance of 48.15%, followed by <i>Bacteroidetes</i> (21.74%) and <i>Firmicutes</i> (5.71%). The abundance of <i>Alphaproteobacteria</i> in <i>Proteobacteria</i> was the highest (15.38%) and followed by <i>Flavobacteriia</i> in <i>Bacteroidetes</i> (11.57%). The most dominant bacteria genera were different at different areas. The most dominant genera were <i>Phyllobacterium</i> in Kaicheng, Qiying, Liwang, Tongxin and Changshantou, with relative abundances of 4.27%, 4.67%, 5.88%, 4.15% and 6.22%, respectively. <i>Flavobacterium</i> was the most dominant genus in both Dongjiao and Sanying, with a relative abundance of 5.03% and 5.84%, respectively. <i>Rhodobacter</i> was the most dominant genus in Hexi, with a relative abundance of 8.29%. Gillisia was the most dominant genus in Quanyanshan, with a relative abundance of 5.51%. Pearson correlation analysis further indicated that NH₄⁺, pH, and Cr were the main factors affecting the bacterial community structure and diversity in surface sediments. Therefore, our findings suggest that both nutrient elements (i.e., N) and toxic heavy metalloids affect the abundance and diversity of bacteria in surface sediments from the main stream of the Qingshui River. Areas of the river sampled in this study provide the biggest microbial sampling coverage to date. The results provide a preliminary understanding of bacterial communities in sediments of different reaches of the Qingshui River, and provide a reference for further research on the application of functional bacteria in pollution control of the Qingshui River.