Patterned ground of the polygonal tundra yields sensitive indicators of environmental and climate change. Polygon ponds, mires and cryosoils are typical components of Arctic Siberian wetlands underlain by permafrost. Field studies of recent environmental dynamics were carried out in the Indigirka lowland in summer 2011 and 2012. Using a multidisciplinary approach, several stages of polygonal systems were studied as modern tundra habitats in the surrounding of the WWF station Kytalyk at the Berelekh River, a tributary of the Indigirka River. The floral and faunal associations of the polygonal tundra landscape were described. Ecological, hydrological, meteorological, limnological and cryological features were analyzed in order to evaluate modern environmental conditions and their essential controlling parameters. A monitoring program was carried out to measure changes of air, water and ground temperatures as well as water conductivity, water level and soil moisture and to collect water, diatom, zooplankton, zoobenthos, tecamoebae, phytoplankton and ostracod samples. These data sets contain environmental field data, logger data, various ecological data, and analyses of sediments and water.This dataset comprises freshwater zooplankton abundance data in different water bodies from a polygonal tundra landscape, near the WWF station Kytalyk at the Berelekh River.Note: Microscopic magnification was x20 for zooplankton and x40-100 for Rotifera