Rivers play a key role in the water cycle on the earth via integrating all hydrological channels to return terrestrial precipitations back to the oceans. In addition, rivers, together with groundwater, are powerful transformers of the surface lithosphere, responsible for chemical weathering of rocks and the removal of solute into the ocean. Tracing the dynamics of surface water and groundwater versus atmospheric feeding of rivers presents important issues in Arctic regions due to the ongoing change of the structure of hydrological runoff. In this study, stable water isotopes were used to reveal the temporal dynamics of water sources and to predict their possible change under the conditions of ongoing climate warming of the largest European Arctic river, the Severnaya Dvina, and adjacent groundwater. The isotopic composition of the river waters of the studied region is formed by the mixing of atmospheric precipitation with groundwater. The isotopic depletion in the springtime is mainly due to the recharge of thawed snow waters. A less pronounced effect in the autumn-winter period is provided by the discharge of groundwater into rivers, including the meltwater of the Last Glacial Period. This depletion is partially offset due to discharge of isotopically light thawed snow waters and is linked to evaporation in headwater streams, reservoirs, and wetlands. The isotopic composition of groundwater with low mineralization was formed throughout the Holocene and to a large extent depends on paleoclimatic conditions in the study area. In addition to fresh groundwater, brackish groundwater also takes part in the river’s recharge. These brackish waters are associated with ancient and modern marine transgressions on the estuarine site and with the dissolution of Ca sulfate rocks in a karst region located in the middle reaches of the river. According to isotope data, the average annual input of the underground source to the total river flow is 25%. The results of this work will serve as the basis for continuing monitoring of the isotopic composition of river waters with an assessment of hydrological processes and observation of short as well as long-term climatic and anthropogenic impacts.