The paper presents the results of our expedition studies of bacteriobenthos in the water area of the Kuibyshev reservoir in the autumn period of 2020 and the influence of the dynamics of currents on its spatial distribution. The relevance of the study is determined by the need to study the internal load (secondary pollution) of large reservoirs from bottom sediments. The Kuibyshev reservoir is one of the largest flowing reservoirs in the world, where features of the coastal configuration, the heterogeneity of the bed, the unsteady hydrodynamic regime, the sediment regime and its composition determine the spatial distribution of bottom sediments and the bacteriobenthos community therein, which is an important link in the circulation processes of organic and biogenic substances in the ecosystem of the reservoir. An assessment of the regime of currents and sediments was carried out by calculation on a 2D mathematical model of the Priplotinny Reach of the Kuibyshev reservoir, implemented in the software package «VOLNA». The model was verified, and a series of numerical calculations of the flow velocity was carried out taking into account the regime of water flow control at hydraulic units. The spatial geometry of the currents and the sediment flow distribution dynamics were obtained. According to the data of our expedition studies, the total numbers and biomass of bacteria were estimated, which varied in the range of (2.47–27.55)×109 cells mL-1 and 0.10–2.43 μg mL-1, respectively. As a result of the conducted studies, patterns of the spatial distribution of the bacterial community in the water area of the Priplotinny Reach of the reservoir were revealed, and the nature of the relationship between the total numbers of bacteria and the sedimentation rate, the flow velocity, and the content of organic matter in bottom sediments was established. The influence of the circulation zones of currents in shallow waters on the nature of the distribution of bottom sediments and changes in the quantitative characteristics of bacteriobenthos is shown.