The Lena River Delta in Northern Yakutia forms one of the largest deltas in the Arctic and its catchment area (2 430 000 km2) is one of the largest in the whole of Eurasia. The study site is one of the coldest and driest places on Earth, with a mean annual air temperatures of about -13 °C, a large annual air temperature range of about 44 °C and summer precipitation usually less than 150 mm. Permafrost plays a major role for storage and release of water to rivers and surface and subsurface water bodies. Very cold continuous permafrost of about −8.6°C underlays the area between about 400 and 600 m below the surface and since 2006 the permafrost has warmed more than 1°C at 10.7 m. Roughly half of the land surface is dominated by wet surfaces, such as polygons, thermokarst lakes and ponds. Ponds are generally well mixed and experience high water temperatures up to 23°C during the summer and therefore are hotspots for biological activity and CO2 emission. Compared to the gaseous emissions, however, the lateral export of dissolved carbon from the polygonal tundra was negligible due to the small volumes of runoff. The ponds in the study area freeze completely in winter, whereas the deeper thermokarst lakes do not freeze to the bottom. These deep thermokarst lakes are thermally stratified during winter and reach maximum water temperatures of up to 19°C during summer. There are distinct differences in the zooplankton community between ponds and lakes, depending on their hydrological and chemical characteristics. Most productive ecosystems are thermokarst ponds with a high abundance of zooplankton and biomass. The summer water balance at the catchment scale was found to be mainly controlled by vertical fluxes (precipitation and evapotranspiration). Overall, the long-term summer storage (precipitation minus evapotranspiration) in the polygonal tundra from 1958-2011 is reasonably balanced with an average surplus of 5 mm. But it is also characterized by high inter-annual variability due to changes in precipitation. During negative water balance years where evapotranspiration exceeds precipitation, shallow water bodies dry out. This indicates that the extent of wetlands and water bodies will shift with changes in vertical water fluxes as well as permafrost warming and thaw.