The inland waters of Northern Kazakhstan are important components of the ecosystems of this region and have unique characteristics. Endorheic steppe lakes are important ecosystems with significant ecological value. They play an important role in maintaining biodiversity, they provide water resources for living organisms, they serve as breeding and migration sites for various animal species, and their zooplankton communities have a key role in the trophic web of these waters. Therefore, the purpose of this work is to study the diversity of zooplankton communities in some small steppe lakes in the northern part of Kazakhstan (Pavlodar, Kostanay, North Kazakhstan, and Akmola regions), which have different environmental conditions. Sampling to study the species diversity of zooplankton in the steppe water bodies of Northern Kazakhstan was carried out from 13 areas, 12 of which are plain lakes, and 1 of which is a reservoir, and sampling was performed in 2021 and 2022 during in the spring, summer, and autumn periods. Within the research period of 2021–2022, between 6 and 36 species of zooplankton were found in small steppe lakes. A total of 92 taxa were found. Rotifers (46 taxa) were found to have the richest number of species representatives. Cladocera were represented by 21 taxa, and Copepods by 25 taxa. All studied steppe lakes in the northern part of Kazakhstan are characterized by high specificity in terms of taxonomic composition, since the similarity indices did not exceed 0.632. According to cluster analysis, the studied samples of water bodies are divided into five clusters, in which lakes with a relatively similar taxonomic composition are combined. The halophile species (e.g., Arctodiaptomus salinarus) indicate water salinization. Our results confirm the applicability of the use of zooplankton in assessing water quality and the current ecological state of aquatic ecosystems.