In terrestrial ecosystems, the amount and availability of water is one of the key factors affecting the net primary productivity and other biological processes of the system. At the SMEAR-II station, we have monitored the water balance of two adjacent micro-catchments since 1997. In this study, we report the long-term measurements of precipitation, throughfall, snow depth, soil water content, runoff and evapotranspiration and the annual water balances based on these measurements and discuss the uncertainties related to different measurements. The proportion of throughfall, evapotranspiration and runoff was 67%, 43% and 32% of the annual precipitation, respectively. The measured amounts of evapotranspiration and runoff were so small that the aim of closing the water balance of the studied system was not fully reached. The largest uncertainties are related to the evapotranspiration measurements and the determination of the actual surface area of the catchments used in the calculation of the runoff.