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Permafrost plays an important role in the balance of greenhouse gases, functioning of Arctic ecosystems and hydrology of the northern regions. To investigate the role of climate change on permafrost degradation and hydrology, the extensive field work was conducted in a series of small watersheds located in the discontinuous permafrost zone of lower Yenisei River near the Igarka, and in continuous permafrost zone of Kolyma River near Cherskii. Climatic, hydrologic and permafrost characteristics were monitored at both locations over three year period and extended using historical data at both sites. Stable isotope composition of rain, snow, and various types of ground ice was used to determine various inputs and runoff pathways to a river flow in several watersheds. The study found that water flow of smaller creeks following precipitation closely, while flow of larger rivers is affected by evaporation effects related to water storage in thermokarst lakes. Epigenetic permafrost near Igraka has similar isotopic composition to the Holocene permafrost and contemporary late summer precipitation. Syngeneic Pleistocene permafrost (Ice Complex) near Cherskii has significantly lighter isotopic composition than pore water of the active and transient layer. Increases in air temperature resulted in thickening of the active-layer and melting of ice reach transient layer in continuous permafrost. Progressive decrease in the seasonal freezing layer and lower permafrost table promoted more groundwater storage and redistribution of summer precipitation towards winter baseflow in discontinuous permafrost region. The major contribution of permafrost at both locations is not through the melting of ground ice, but through changes in soil properties affecting the water flow.