Global warming is likely to transform Siberian environments. Recent eco-hydrological evidence indicates that water and carbon cycles have been changing rapidly, with potentially serious effects on the Siberian flora and fauna. We have comprehensively analysed dendrochronological, hydrological, and meteorological data and satellite remote sensing data to track changes in vegetation and the water and carbon cycles in the Lena River Basin, eastern Siberia. The basin is largely covered with larch forest and receives little precipitation. However, from 2005 to 2008 the central part of the basin experienced an extraordinarily high level of precipitation in late summer and winter. This resulted in the degradation of permafrost, forest, and hydrological elements in the region. Dendrochronological data implied that this event was the only incidence of such conditions in the previous 150 years. Based on data collected before and after the event, we developed a permafrost-ecosystem model, including surface soil freeze-thawing processes, to better represent the heat, water, and carbon fluxes in the region. We focused on the surface soil layer, in which an increased thawing depth is now apparent, surface soil moisture, and net primary production. An analysis of observed and model-simulated data indicated that the annual maximum thawing depth (AMTD) had increased gradually on a decadal scale and deepened abruptly after 2005. Climatological analyses of atmospheric water circulation over the region indicated that the recent increases in precipitation over the central Lena River Basin were partly related to cyclone activity. Consequently, the increased precipitation from late-summer to winter resulted in increases in soil moisture, soil temperature, and AMTD in the region.