Ice-wedge polygons often accommodate small and shallow periglacial surface waters. They provide suitable habitats for freshwater ostracods (Crustacea, Ostracoda) in Arctic Siberian tundra landscapes, and are well known from Pleistocene and Holocene permafrost successions. Freshwater ostracods are sensitive to environmental conditions, and have been widely used as biological indicators for past and present environmental changes in temperate regions. In Arctic environments, habitat conditions of ice-wedge polygon ponds are barely constrained, and the abundance and diversity of ostracods is currently documented in scattered records with incomplete ecological characterizations. In order to further develop the ostracods potential as biological indicators from ice-wedge polygon tundra landscapes, the taxonomic and ecological range of ostracod assemblages and habitat conditions in polygon ponds in the Indigirka Lowland (north-east Siberia, Russia) were determined. Furthermore, we focused the seasonal variability of a selected pond site, its ostracod population, and the geochemical properties of ostracod valve calcite. Well-oxygenated and dilute ponds with slightly acidic pH hosted an abundant and diverse ostracod fauna. A total of 4849 identified ostracods from 8 species and 3 taxa represent the first record of the ostracod fauna in the Indigirka Lowland. Fabaeformiscandona krochini and Fabaeformiscandona groenlandica were documented for the first time in continental Siberia. Fabaeformiscandona sp. I and Fabaeformiscandona sp. II were newly found taxa holding a strong indicative potential for hydrochemical parameters. Repeated sampling of a typical low-center polygon pond revealed detailed insights in the population dynamics of Fabaeformiscandona pedata. Substrate properties, physical and hydrochemical conditions in the polygon ponds offered the ostracods largely homogeneous habitats. However, river flooding and differences in pond morphology resulted in variations in substrate, vegetation, hydrochemical and stable water isotope composition. Air temperature and precipitation were identified as the main external drivers of water temperatures, water levels, ion concentrations, and stable water isotope composition in polygon ponds on diurnal and seasonal scales. Freshwater ostracods inhabiting polygon ponds have the potential to store environmental information on a seasonal scale in their population structure and valve geochemistry. In particular, ostracod valve calcite recorded seasonal variations in stable oxygen isotopes of the ambient waters. This information needs to be interpreted carefully with regard to species-specific ecology, the pond´s water supply, and meteorological conditions. A better understanding of seasonal dynamics of ice-wedge polygons and their freshwater ostracod assemblages supports the paleoenvironmental interpretation of fossil records in response to climate change, and allows detecting changes in modern Arctic environments.