Modification of the hydrological cycle and, subsequently, of other global cycles is expected in Arctic watersheds owing to global change. Future climate scenarios imply widespread permafrost degradation caused by an increase in air temperature, and the expected effect on permafrost hydrology is immense. This study aims at analyzing, and quantifying the daily water transfer in the largest Arctic river system, the Yenisei River in central Siberia, Russia, partially underlain by permafrost. The semi-distributed SWAT (Soil and Water Assessment Tool) hydrological model has been calibrated and validated at a daily time step in historical discharge simulations for the 2003-2014 period. The model parameters have been adjusted to embrace the hydrological features of permafrost. SWAT is shown capable to estimate water fluxes at a daily time step, especially during unfrozen periods, once are considered specific climatic and soils conditions adapted to a permafrost watershed. The model simulates average annual contribution to runoff of 263 millimeters per year (mm yr −1 ) distributed as 152 mm yr −1 (58%) of surface runoff, 103 mm yr −1 (39%) of lateral flow and 8 mm yr −1 (3%) of return flow from the aquifer. These results are integrated on a reduced basin area downstream from large dams and are closer to observations than previous modeling exercises.