The Gravity Recovery and Climate Experiment (GRACE) satellite mission has proven as valuable tool to observe hydrological mass variations, e.g., in the Amazon basin, groundwater depletion in Northwest India, inland glacier mass losses. The long time span of more than 10 years of GRACE observations now allows also the detection of smaller inter-annual mass variations. In our study, we address the permafrost-regime in Siberia, Russia. We use GRACE data to study water mass variations in the Lena basin between 2003 and 2011. The observed mass changes indicate long-term changes in the hydrological budget of the large Siberian watersheds. For selected lakes in the Lena basin, we employ satellite radar altimetry observations to estimate water storage changes related to lake level variations. Large parts of Siberia are covered by thousands of lakes. As consequence of a strong wetting trend in this region lake levels are rising. We compare the total mass variation derived from GRACE and the mass variations related to changes in lake level. The lake level changes can explain between 15% to 40% of the water storage changes observed by GRACE. Other potential reasons for water storage variations could be related to changes in lake surface extension, soil moisture changes, increase in sub-permafrost ground-water storage and talik formation.