Intensification of the Arctic hydrologic cycle and permafrost melt is expected as concentrations of atmospheric greenhouse gases increase. Quantifying hydrologic cycle change is difficult in remote northern regions; however, monitoring the stable isotopic composition of water runoff from Arctic rivers provides a means to investigate integrated basin-scale changes. We measured river water and precipitation δ18O and δD to partition the river flow into snow and rain components in the Kolyma River basin. On an annual basis, we found water leaving the basin through the river consisted of 60% snow and 40% rain. This is compared with annual precipitation inputs to the watershed of 47% snow and 53% rain. Despite the presence of continuous permafrost, and fully frozen soils in the spring, our analysis showed not all spring snowmelt runs off into the river immediately. Instead, a substantial portion is retained and leaves the basin as growing season evapotranspiration.