This study deals with the measurement and analysis of the water balance of an arctic tundra site in Siberia on the island of Samoylov (Lena River Delta, Russia). The island is underlain by continuous permafrost and is characterized by polygonal tundra structures. The quantification of precipitation, evapotranspiration, runoff and storage in the annual water budget was in the focus of this research. Furthermore, it was the goal to identify the relevant processes and seasonal dynamics which characterise the water balance. In addition to the data of the existing monitoring network (e.g. precipitation and evapotranspiration), spatially distributed runoff and water level measurements were obtained. The results of the measurements indicates a negative summer water balance (–23.3 mm), in which the evapotranspiration (190.9 mm) clearly exceeded the rainfall (167.6 mm). In the annual water balance the snow cover (65 mm) was a major source of water. The spring snowmelt was the principal recharge mechanism for the tundra. The runoff (4.8 mm) in the summertime was small compared to the other components of the water balance. Storage changes (soils, lakes, cracks and polygon ponds) are mainly controlled by precipitation and evapotranspiration. The importance of lateral groundwater fluxes increases towards the end of summer due to a maximum of active layer thickness, a high amount of rain and a raising water level in lakes and polygon ponds. The annual water balance is primarily determined by rainfall and evapotranspiration. The shallow active layer limits the lateral water movement, such as groundwater flow and runoff from the island. Variations in environmental and climate conditions due to climate change may have severe impacts on the water balance. Assumed higher evapotranspiration and increased active layer thickness could multiply the water losses and enhanced the degradation of the polygonal tundra landscape. This potentially leads to increased green house gas emissions, since the availability of carbon and other nutriens for biological processes strongly depends on water flow.