The assessment of water resources plays an important environmental and economic role, since it allows developing an effective program of regional development with regard to the environmental load. The hydro-chemical regime of lakes includes water temperature, content of biogenic elements, total mineralization, oxygen regime, and other parameters (transparency, color, and smell). However, this assessment cannot be considered full, since it does not take into account the effect of human activity. Therefore, various systems of water monitoring have been developed, one of which is the assessment of zooplankton. The state of zooplankton is a universal marker. The quantitative and qualitative assessment allows monitoring the physical and chemical state of water resources and assessing their bio-production potential. This research investigated zooplankton communities in lakes Aksuat, Altybai and Taly (Kostanay Region, Kazakhstan). The qualitative composition and dominant species of zooplankton was determined; their population dynamic was monitored. The oxygen regime of lakes remained stable; no oxygen deficiency was found. The lakes have favorable conditions for the development of zooplankton. This also provides favorable conditions for commercial fish farming if the main diet of fish is zooplankton.