Environmental physical and chemical factors controlling the abundance and biodiversity of zooplankton in permafrost-affected lakes are poorly known yet they determine the response of the ecosystems to on-going climate change and water warming. Here we assessed the current status of zooplankton communities of lake ecosystems in the North-West of the Bolshezemelskaya tundra (Nenets Autonomous district), and provide new information about the composition and structure of zooplankton. Results demonstrate that the structure of zooplankton communities is influenced by morphometric features of lakes and the degree of their overgrowth by macrophytes. According to the level of zooplankton development, most tundra lakes were of the oligotrophic type with an average biomass of up to 1 g/m3. The largest number of species was observed in zooplankton communities of small lakes with an area of up to 0.02 km2 and overgrown with macrophytes. The analysis of factors that influence the formation of the lakes zoocenosis demonstrated that the species composition and quantitative characteristics of zooplankton are chiefly controlled by pH and water mineralization. A comparison of the results obtained with the literature data on the lakes of this region collected 60 years ago confirms that the ecosystems of the studied lakes are in a stable state. Overall, these new insights will improve our knowledge of factors controlling the zooplankton spatial dynamics in unique but quite abundant thermokarst lakes of NE European Tundra, subjected to on-going climate warming.