The paper presents the results of a comparative analysis of planktonic algae structure in the Volga and Kama rivers at the confluence of the Kuibyshev reservoir. The author has also assessed the trophic state of the studied river sections in 2012. The hydrochemical regime of the Kuibyshev reservoir is heterogeneous and is determined by the chemical composition of the Volga and Kama waters, which differ in the ratio of ions and mineralization. The ionic composition of the Kama waters is often dominated by sulfates. The salinity depending on the season and water content of the year ranges from 168 to 674 mg/l. The Volga waters contain calcium bicarbonate and have a lower mineralization (120130 mg/l). The variability of the incoming water, the amount of runoff, the degree of volume drawdown within water bodies and groundwater inflows primarily affect the conditions for planktonic algae existence. In the phytoplankton of the Volga and Kama rivers (areas before their confluence in the Kuibyshev Reservoir), 123 taxa of algae were identified during the 2012 growing season. The waters of the Volga River have a higher species diversity (107 species). The phytoplankton of the Kama River is less diverse (76 species). In the seasonal dynamics of phytoplankton in the studied river sections, two peaks of abundance and biomass are observed by the middle of summer and at the end of it, when the maximum values of abundance and biomass are reached. The waters of the investigated sections of the Volga River is characterized by a complex of phytoplankton of blue-green, diatoms and green algae, while the Kama River is dominated by diatom phytoplankton. In summer and autumn the blooming of water in both rivers is due to the massive development of blue-green algae of the genera Microcystis, Aphanizomenon, Anabaena, Oscillatoria. The waters of the Volga and Kama rivers in 2012 during the study period corresponded to the mesasaprobic type and moderately polluted zone; the waters of the Kama River had higher saprobity indices. The trophic status of the rivers under consideration in the study area was mostly related to the eutrophic type; during the periods of maximum reproduction of blue-green algae to the hypereutrophic type.