Arctic precipitation (PG) that occurs as rainfall (Pr) or snowfall (Ps) depending on the prevailing climatic conditions results in seasonally specific hydrological events. Climate change can affect the PG- and permafrost-originated water (Pi) regimes, resulting in change to ecohydrological processes. However, the relative influences of source waters (i.e., Pr, Ps, and Pi) on terrestrial hydrological processes have not yet been fully established. Here, we report the development and implementation of a numerical water tracer model designed to quantify changes in the storages and fluxes of the source waters and the hydrogen and oxygen isotopic tracers associated with hydrometeorological events. The presented tracer model was used to illustrate the spatiotemporal variability of the tracers in the surface–subsurface system of a deciduous needleleaf boreal forest, and to separate the contribution rates of the tracer waters to evapotranspiration (ET). Although Ps accounted for 14%–40% of ET and the subcomponents, the contribution rates to soil evaporation and transpiration were significant only during the spring season. The major source water for soil moisture was Pr, which accounted for 80.1% of ET and showed an increasing trend. Additionally, Pr also accounted for 85.7% of transpiration. Under the present conditions of warming permafrost, Pi demonstrated negligibly low impact on ET. The tracer model was shown capable of quantifying the contribution rates of tracer waters to ET, highlighting the advantages of the tracer model for similar quantitative separation regarding future climate change.