We present new and more complete information than previously available on the pelagic fauna of the Lena River Delta, eastern Siberia. Zooplankton samples collected between 2000 and 2011 from 11 varied aquatic habitats on Samoylov Island have been examined and clear differences noted between the zooplankton communities in different types of tundra waterbody. Well-marked synchronism in the development of common species populations was, however, revealed by analysis of their life cycles. The pelagic fauna of the investigated aquatic ecosystems is heterogeneous in origin, consisting mainly of aboriginal Arctic species but also including invasive species from more temperate latitudes and relicts of ice-age fauna. One hundred and twenty-five zooplankton taxa belonging to Rotifera (67) and Arthropoda (58) phyla were identified. Five Copepoda species and seven Cladocera species were recorded for the first time in the Lena River Delta; the presence of most of these species in the delta’s aquatic ecosystems is associated with Lena River water influx during spring flood. Two calanoid copepods, Eurytemora arctica Wilson and Tash and Eurytemora foveola Johnson, are new species to Palearctic pelagic fauna, previously known only from the Nearctic. The data obtained provide new confirmation that the last glaciation had a marked influence on microcrustacean distributions within the Arctic.