Large plain reservoirs are water bodies of a slow water exchange with Кw less than 10 year-1 contributing to multi-year (annual) flow regulation. All reservoirs of the Volga-Kama cascade belong to this type of reservoirs, except the Cheboksary and Saratov reservoirs with Кw about 20 year-1. Weekly and daily fluctuations of the runoff are observed in these reservoirs. This mode of operation of hydraulic constructions leads to an increase in the flow rate and fluctuations of the level, which determines the specific conditions for the formation and accumulation of bottom sediments characteristic of river systems. It is shown that the areas of coarse-grained sediments are 55 and 70%, respectively. The reservoirs under consideration are transit reservoirs for suspended substances and aerators for the oxidation of chemical pollutants and their neutralization, so they play a crucial role in the natural self-purification and management of natural water quality. Methods. The aim of the study is to characterize the spatial and temporal transformation of the lower layer of the ecosystem in reservoirs with high water exchange (by the example of the Cheboksary and Saratov reservoirs) and to identify its role in water self-purification taking into account biomarkers. It is known that river systems or systems similar to them are more efficient and are characterized as potentially saturated with food organic/mineral resources for hydrobionts. The assessment of water quality and bottom sediments of different hydro-morphometric characteristics, dynamics of water masses and operating conditions is presented using methods of bioassay and toxicology by the example of chironomid larvae and antioxidant defense system of benthic fish. Results. Based on the data of the integrated hydrobiological cruises during the growing season 2014–2020, it is difficult to say that the quality of water and bottom sediments, biotic and toxicological parameters depend on the flow rate, so further studies are required. The work is original, because there are no analogues in the world for monitoring of bottom sediments in reservoirs and quantitative assessment of sedimentation processes in space and time. The results of the biogeochemical analysis indicate, that in terms of the degree of deterioration of the eco/toxicological state, the Volga reservoirs are in a series: Volgograd = Saratov > Kuibyshev > Cheboksary > Gorky.