With permafrost warming, the observed discharge of the Kolyma River in northeastern Siberia decreased between 1930s and 2000; however, the underlying mechanism is not well understood. To understand the hydrological changes in the Kolyma River, it is important to analyze the long-term hydrometeorological features, along with the changes in the active layer thickness. A coupled hydrological and biogeochemical model was used to analyze the hydrological changes due to permafrost warming during 1979–2012, and the simulated results were validated with satellitebased products and in situ observational records. The increase in the active layer thickness by permafrost warming suppressed the summer discharge contrary to the increased summer precipitation. This suggests that the increased terrestrial water storage anomaly (TWSA) contributed to increased evapotranspiration, which likely reduced soil water stress to plants. As soil freeze–thaw processes in permafrost areas serve as factors of climate memory, we identified a two-year lag between precipitation and evapotranspiration via TWSA. The present results will expand our understanding of future Arctic changes and can be applied to Arctic adaptation measures.