Hydrological processes in permafrost regions are very sensitive to climate change. Siberia is affected in particular, as it experiences a stronger warming trend than the global average. We use data from the Gravity Recovery and Climate Experiment (GRACE) satellite mission to study inter-annual water mass variations in the Siberian permafrost between 2003 and 2010. 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. The lake level rise can explain about half of the mass increase observed by GRACE. Other potential reasons for water storage variations such as changes in lake surface extension, soil moisture and the talik formation are discussed.