The predicted increasing ground temperatures in the Arctic results in the deepening of the active layer and intensification of geochemical processes, which could affect the geochemical composition of surface waters. Determining the responses of the riparian soil systems to surrounding hydrological flows under changing climate conditions is important for understanding the seasonal changes in hydrological processes. Therefore, in this study, one soil core from the study area polygon rim (close to the Taz River, TA) and two soil cores from the riverain terrace (close to the Syoyakha River, SY and Murtyyakha River, MU) in Russian Western Siberia and their supra-permafrost water, adjacent stream flows and river water were sampled for analysis of geochemical elements. The results showed that most elements above their respective detection limits (Mn, Sr, Fe, Mg, Cr, Co, V, Pb, Al and Ca) started to accumulate in the downwards gleyed layer during September–October in response to the deepest thaw in the active layer. This study focused on the highly mobile elements, i.e., Mn, Ca, Mg, Al and Ti, in the deepest layer; and found the transport of organic matter in the upper layer carried these elements to both surface water ponds/flows and supra-permafrost water, and further, to the rivers. The best linear correlation for both stream flows and river water were Mn, which may be a proxy for predicting the processes occurring within the active layer during the annual summer-autumn thaw. Finally, landscapes with different ice contents may experience changes in the elements transported to surface waters.