Long-term observations of the rates and pattern of changes in flora and vegetation contribute to understanding of one of the most important contemporary global problems, the eutrophication of water bodies. In this study, using classical floristic methods, we attempt to determine (for a period of almost 80 years) the nature and possible causes of changes in the floristic composition of the lakes of karst origin, Velikoe and Parovoe (Pustinskaya lake-river system, the right bank of Nizhny Novgorod oblast). The paper shows that over a long period of observations a significant transformation of the vegetation cover has occurred in the lakes. The process was accompanied by the disappearance of a number of native species and appearance of others, including adventitious ones (for example, Elodea canadensis Michx., Zizania latifolia (Griseb.) Stapf, Bidens frondosa L. and Epilobium adenocaulon Hausskn.). The weak saturation of the flora with adventive species indicates that the reservoirs are subject to moderate anthropogenic transformation. This is also indicated by the presence of characteristic indicator species, for example, Najas minor All., Glyceria fluitans (L.) R. Br., Hydrocharis morsus-ranae L. and Stratiotes aloides L. in the plant communities. In addition, the studied water bodies are subject to a further increase in the degree of eutrophication. This can be judged by scattered records of Potamogeton trichoides Cham. et Schlecht., the disappearance of a number of species (such as Elatine alsinastrum L. and Callitriche hermaphroditica L.), as well as the presence of a significant number of macrophyte indicators of the eutrophic state of water bodies. We suggest that a gradual increase in the trophicity of the studied water bodies is due to a combination of anthropogenic impact (water withdrawal for economic needs, recreational load), natural and climatic features of the region (alternation of high and low water periods) and the natural succession processes associated with the current fundamental changes in the conditions of the runoff formation in the Volga River basin. As a result of studies conducted by authors in 2014–2015, it has been shown that in general the taxonomic and ecological structures of the flora of both lakes are quite diverse and traditional for the territory and the European part of Russia. Meanwhile, the flora of these two reservoirs insignificantly differs in taxonomic composition, which is due to their individual morphometric characteristics, the physical and chemical properties of the aquatic environment, and the nature of the anthropogenic load. At the same time, the equilibrium balance of coastal and aquatic plants in the flora of Lake Parovoe (in contrast to Lake Velikoe) indicates a degree of successional stability of its floristic complex.