The article discusses the results of studies of the Amur River left-bank tributary on the example of the Zavitaya River during the flood in the summer of 2021. The river is exposed to anthropogenic pressure as it flows through the territory of the cultivated landscape of the Zeya-Bureya plain. The waters of the Zavitaya River are characterized by high oxygenation and rich in organic matter due to high values of permanganate oxidizability (PO). In July after the flood the BOD5 value increased. A small number of heterotrophic, ammonium-, nitrite- and phosphorus-oxidizing bacteria during the flood period was associated with water dilution and, accordingly, reflected the violation of the river’s self-purification and self-regulation mechanisms. The results obtained from the study of hydrochemical and microbiological indicators of the Zavitaya River make it possible to reveal the patterns of interaction between natural and anthropogenic components and to assess the possibility of preserving the biodiversity of the river ecosystem.