The research assesses the state of different types of lakes in specially protected natural areas of the Nizhny Novgorod Region and the anthropogenically disturbed territory of Nizhny Novgorod. The trophic status of water bodies was determined using the trophic status index (TSI_SD). It has been established that most of the lakes have eutrophic and mesotrophic status. The analysis of the species structure of zooplankton in water bodies has been carried out. The species richness of both lakes of the protected areas and urban lakes was high. Along with eurybiontic species, alien and rare species of zooplankton were identified. Significant differences in the indicators of the species structure were established, however, no critical values of the abundance, biomass, Shannon and Pielou indices were recorded. Most of the identified zooplankton species were indicative. On the basis of the Pantle-Bukk saprobity index in the Sladecek modification, the water quality class was established. The reservoirs were characterized by quality class II–III (clean-moderately polluted water). In some lakes an excess of the maximum permissible concentrations of ammonium, nitrite, iron, manganese, copper, zinc, lead has been established. However, in general, in terms of a set of indicators, water bodies are in a satisfactory condition. In order to objectively assess the ecological state of aquatic communities, to predict possible changes and develop recommendations for the conservation of species diversity, it is important to carry out regular monitoring studies.