The phytoplankton and vascular aquatic plants have been studied in small lakes Vashutinskoe, Chashnitskoe, Ryumniki, and Zaozer’e, located in the southern part of the Yaroslavl Region, Russia. The taxonomic composition of phytoplankton comprised 137 species of algae belonging to 8 divisions, 18 orders, and 76 genera. The studied water bodies were characterized by high biomass of cyanobacteria. Aphanizomenon flos-aquae (L.) Ralfs ex Born et Flah. and the species of the genus Anabaena had a significant contribution to the phytoplankton biomass in the lakes Zaozer’e, Chashnitskoe, and Ryumniki, Limnothrix planctonica (Wołosz.) Meff. and Microcystis aeruginosa (Kütz.) Kütz, in the Lake Vashutinskoe. In terms of phytoplankton biomass, the pelagial and shallow areas of the Lake Vashutinskoe belonged to eutrophic reservoirs, of the Lake Ryumniki, to oligotrophic. The phytoplankton biomass in the pelagial zone of the lakes Chashnitskoe and Zaozer’e indicated the mesotrophic status of these water bodies, in the littoral zone, eutrophic. The study of the phytoplankton of the lakes was carried episodically and was often performed at different periods of the growing season. Therefore, the obtained data did not allow one to assess the direction of the successional changes in the algal flora. The flora of vascular plants of lakes was represented by 118 species belonging to 4 divisions, 5 classes, 22 orders, and 37 families. Thirty-four species were common to all studied water bodies. The differences in the The differences in the flora of vascular aquatic plantsof the studied lakes were associated with differences in their trophic status, the presence of various biotopes, the nature of anthropogenic load, and the degree of eutrophication. During a hundred years of observations, some species have disappeared, but some have appeared, including adventive species (such as Elodea canadensis Michx., Bidens frondosa L., Epilobium adenocaulon Hausskn, Zizania latifolia Griseb., and Juncus tenuis Willd.). The study of the current state of rare and protected species of vascular plants made it possible to reveal the eventual causes and period of disappearance of some species from the lakes. The taxonomic and ecological structure of phytoplankton and vascular plants of lakes was quite diverse and usual for the water bodies of the European part of Russia.