The characteristics of the composition, ecological-geographical, and functional structure of the phytoplankton dominant complexes of three different types of lakes in the Nizhny Novgorod Volga region (Klyuchik, Svetloyar, and Svyatoye Dedovskoye) are given. Lake Klyuchik is a rare type of gypsum, highly mineralized “blue” lake; unique in terms of its supply source, the role of which is played by the underground river with high water consumption, and has a weakly expressed stratification. Lakes Svyatoye Dedovskoye and Svetloyar are dimixic, light-water, low-mineralized, of hydrocarbonate class, and with neutral pH values that are fed by rainwater. All lakes belong to specially protected natural areas. Analysis of the algal flora of the studied lakes showed the taxonomic significance of the divisions of Cyanobacteria, Chlorophyta, Bacillariophyta, Ochrophyta, and Euglenophyta, constituting more than 70% of the total species richness. The composition of the dominant species contained 114 taxa of algae (26.38% of the total composition): in Lake Svyatoye Dedovskoye, greens and diatoms predominated (50%), in Lake Svetloyar, euglenids predominated (25%), in Lake Klyuchik, diatoms predominated (more than 40%). Among 13 dominants (from 5 divisions) with high values of DF>10, Dt>10, and pF>20, dinoflagellates from the functional group L0 (Ceratium hirundinella, Peridinium cinctum) were noted in all lakes, with maximum development in the summer stratification. In the group of diatoms, representatives of centric diatoms of codon B (species of the genus Cyclotella) predominated in each water body, reaching maximum development rates under conditions of water mixing. The composition of the remaining dominant groups in each reservoir was determined by its limnological features. Using the method of multivariate analysis of variance (PERMANOVA), a statistically significant (P-value=0,001) low degree of similarity of the dominant and functional phytoplankton complexes was shown, which may indicate the uniqueness of algae cenogenesis in each of the studied lakes due to the influence of a certain combination of factors.