The variability of hydrochemical parameters, the heterogeneity of the habitat, and a low level of anthropogenic impact, create the premises for conserving the high biodiversity of aquatic communities of small water bodies. The study of small water bodies contributes to understanding aquatic organisms’ adaptation to sharp fluctuations in external factors. Studies of biological communities’ response to fluctuations in external factors can be used for bioindication of the ecological state of small water bodies. In this regard, the purpose of the research is to study the structure of zooplankton of small lakes in South-East Kazakhstan in connection with various physicochemical parameters to understand the role of biological variables in assessing the ecological state of aquatic ecosystems. According to hydrochemical data in summer 2019, the nutrient content was relatively high in all studied lakes. A total of 74 species were recorded in phytoplankton. The phytoplankton abundance varied significantly, from 8.5 × 107 to 2.71667 × 109cells/m3, with a biomass from 0.4 to 15.81 g/m3. Shannon diversity index of phytoplankton in the lakes at high altitude varied from 1.33 to 2.39 and from 0.46 to 3.65 in the lakes at lower altitudes. The average weight of the cells of algae species varied from 0.2079 to 1.5076 × 10−6 mg in the lakes at lower altitudes, the average weight of the cells of algae species changed from 0.6682 to 1.2963 × 10−6 mg in the lakes at higher altitudes. Zooplankton was represented by 58 taxa. The total abundance of zooplankton varied from 0.05 to 169.00 thousand ind./m3 with biomass of 0.51-349.01 mg/m3. Shannon diversity of zooplankton in the lakes at lower altitude fluctuated from 0.42 to 2.32 and it was 0.66–1.77 in the lakes at higher altitudes. The average individual mass of specimens in zooplankton in mountain lakes ranged from 0.021 to 0.037 mg and varied from 0.002 to 0.007 mg in other lakes. The main factors in the development of the structure of zooplankton communities in small lakes were temperature, TDS, the content of nitrates, phosphates, and the composition and biomass of planktonic algae. The hydrochemical and biological data of the investigated lakes indicated their organic pollution. Our results once again confirmed the applicability of structural variables of zooplankton in assessing water quality.