Increasing anthropogenic influence and climate change are leading to significant transformations in living conditions for indigenous representatives of aquatic communities. The problem of alien species invasions is actively discussed in the example of large rivers and water reservoirs, but medium and small rivers with weak anthropogenic influence have been insufficiently studied in this aspect. With the help of analysis of literary data and the results of our own long-term observations of phytoplankton using morphological and molecular genetic methods in some left-bank Volga tributaries, we identified six invasive species of different taxonomic groups of algae, with a predominance of diatoms. The relevance of using both traditional and modern approaches to identifying invasive algae species is revealed. Such invasive species as Thalassiosira incerta, T. faurii, Skeletonema subsalsum, Unruhdinium kevei, and Gonyostomum semen were part of planktonic communities; the benthic species Plagiotropis lepidoptera var. proboscidea sometimes reached a significant level of development (up 6 to 44% from total biomass) in plankton. It was demonstrated that some algae species have firmly taken the position of dominants and subdominants in planktonic algae communities. The expansion of alien representatives of microphytobenthos was noted in the Volga River basin for the first time. For Gonyostomum semen, its European origin was revealed, for plankton and benthic diatom-Ponto-Caspian. Our study showed that the processes of invasion and subsequent development of alien species take place in habitats with weak anthropogenic influence, which is likely determined by the hydrological, hydrochemical, and climatic changes in river basins and the high adaptive capabilities of invasive species.