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The discharge of acid mine drainage from abandoned high sulfur (S) coal mines has caused serious pollution in the Shandi River, Yangquan, Shanxi Province. To determine the impact of long-term acid mine drainage on the microorganisms in the river, we collected river sediments from a polluted tributary (Group P) and the mainstream of Shandi River (Group R) to study the bacterial diversity and community composition. The results showed that the tributary was seriously polluted by acid drainage from abandoned coal mines, with the pH value of the sediment being < 2.5, resulting in the low bacterial richness and diversity of the tributary samples. Acidophillic Fe- and S-metabolizing bacteria, such as Metallibacterium, Acidiphilium, and Acidithiobacillus, were the dominant genera in Group P samples, while the Group R was dominated by the neutral anaerobic iron-reducing bacteria Geothrix and Geobacter. Results of principal co-ordinates analysis (PCoA) revealed that the bacterial communities are significantly different between groups P and R, and the significant different species were mainly attributed to phylum Proteobacteria, Actinobacteria, and Acidobacteria. The distribution of the microbial community is mainly influenced by pH, and the Fe and Cd concentrations. Metallicactrium, the dominant genus, is negatively correlated with pH (R2 = − 0.95) and positively correlated with Fe (R2 = 0.99), while Geothrix and Geobacter, are mainly affected by the heavy metals. This study determined the impact of river pollution caused by abandoned coal mine drainage, especially on the microbial diversity and community composition within the river sediment. [ABSTRACT FROM AUTHOR]