Microbiota plays an important role in the aquatic ecosystem, maintaining balance through its ability to utilize and synthesize various substances. Anthropogenic pollution affects the composition of the aquatic microbiota, thereby disrupting the stability of the system. In this work, a comprehensive analysis of the hydrochemical parameters of the rivers of Tatarstan was carried out together with the microbiome. This has enabled the identification of bacteria that can be used as bioindicators of pollution in aquatic ecosystems. It was found that the abundance of the cyanobacteria Synechococcaceae was reduced in samples with high organic matter content, and the abundance of Microcystaceae was increased with high levels of total phosphorus and phosphates. There is also evidence that members of the Proteobacteria phylum can be bioindicators of high nitrate levels in water.