The paper presents the results of zooplankton research in June, July and September 2017 in eight floodplain lakes of the middle reaches of the Kerzhenets River located in the Kerzhinski Nature Reserve. The studied water bodies are shallow lakes with weakly acidic pH (5, 40–6, 23) and low mineralized water (46, 90–68, 40 mg/l), with increased chromaticity (202, 00–1048, 20 deg.) and content of suspended substances (4, 40–22, 90 mg/l). As a result of a carried out hydrobiological research, 106 species of zooplankton were identified. According to the zoogeographical characteristics, the zooplankton fauna of floodplain water bodies is typical for the European part of Russia, with the exception of two invasive species: the North American rotifers Kellicottia bostoniensis (Rousselet, 1908) and the Caspian branching diocese of southern origin Diaphanosoma orghidani (Negrea, 1982). In addition, in a number of lakes, the Arctic relict crustacean Holopedium gibberum (Zaddach, 1855) was found. The crustacean is listed in the Red Data Book of the Nizhny Novgorod Region. Alien rotifers in a number of floodplain reservoirs were the dominant species and had a high abundance. The Caspian southern crustacean was found only in two reservoirs, its number was not high, and it did not play a significant role in the zooplankton communities of these reservoirs. New findings of the Arctic relict species Holopedium gibberum (Zaddach, 1855) make it possible to recommend the introduction of a number of floodplain reservoirs into the Red Book of the Nizhni Novgorod Region as habitats of this rare species. Redundancy analysis (RDA) has revealed four factors that significant related with development of zooplankton in a number of floodplains, such as water temperature, hydrogen index, dissolved oxygen content and suspended solids.