This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 LicenseModern methodological approaches were applied to analyze the zooplankton community spatial distribution (with the example of the middle river part of the Cheboksary Reservoir). Zooplankton communities were sampled in the middle river part of the Cheboksary Reservoir (from the city of Nizhny Novgorod to Vasilsursk town) in the summer low-water period in 2018. The boundaries between the communities in the Cheboksary Reservoir were gradually changing during the history of the Cheboksary Reservoir from the time of its construction to present. In the middle river part of the Cheboksary Reservoir there are two distinct spatially stable zooplankton communities associated to the Oka and Volga streams. The distinction between these two zooplankton communities was demonstrated by hierarchical cluster analysis. Redundancy analysis has shown that chlorophyll-a and pH were the main factors influencing the specific zooplankton structure.Chlorophyll-a concentration reflects the meso-scale heterogeneity of the horizontal phytoplankton distribution and hence the distribution of the zooplankton's food sources. The relation of zooplankton to pH level reflects the high sensitivity of the species of the genus Brachionus Pallas, 1766 to high acidity. The influence of pH as an environmental factor was less evident. However, this variable is well known as one of the leading factors determining the structure of zooplankton communities. Its role in zooplankton community assembly of lowland reservoirs deserves further investigation.