The paper provides information on the composition, structure and dynamics of phytoplankton of three morphologically different tributaries of the Cheboksary reservoir (the Vetluga, the Kerzhenets and the Vishnya rivers). The species composition of algae includes 826 species and intraspecific taxa, the flora was formed by diatom, green and euglena algae. It reflects the watercourses particularities of the southern taiga zone. Based on long-term studies of phytoplankton a change in the composition of algoflora by more than half was noticed, especially in the groups of Charophyta, Cryptophyta, Miozoa, Ochrophyta and Euglenophyta. An increase in quantitative indicators of algocoenoses from oligotrophic to oligotrophic-mesotrophic level in the middle reaches of rivers by mesotrophic-eutrophic level in estuarine areas is shown. In a fifty-year research series a tendency of phytoplankton reduction in size by more than 3,5 times has been established. It reflects the impact of eutrophication and gradual warming of the climate. The period of abnormally hot summer of 2010 led to increased vegetation in the middle reaches of rivers of diazotrophic blue-green algae and dinophytes. Since the early 2000s, gradual penetration and naturalization of both planktonic invasive algae species and representatives of benthic algocoenoses have been noticed. The mentioned changes reflect the nature of phytoplankton rearrangements as the essential component of the biota and emphasize the importance of long-term research with a possibility to predict negative consequences.