The predicted increase of ground temperatures in the Arctic results in the deepening of the active layer and intensification of geochemical processes. Determining the responses of riparian soil systems to surrounding hydrological flows is important for understanding seasonal changes in hydrological processes. In this study, one soil core from a polygon rim (close to the Taz River, TA) and two soil cores from a riverine terrace (close to the Syoyakha River, SY and Murtyyakha River, MU) in Western Siberia, Russia, and their suprapermafrost water, adjacent surface flows, and river water were sampled for analysis of geochemical elements. Results showed that most elements above their respective detection limits began accumulating in the underlying gleyed layer during September-October in response to the deepest thaw in the active layer. This study focused on the highly mobile elements in the deepest layer; and found that the transport of organic matter in the upper layer carried these elements to both surface water ponds/flows and suprapermafrost water, and further, to the rivers. The efflux of released elements from surface soil to surrounding surface water appeared to be low. The best linear correlation for both surface flows and river water was with Mn; therefore, Mn may be a proxy for predicting the processes occurring within the active layer during the annual summer-autumn thaw. Moreover, landscapes with different ice contents may experience changes in the elements transported to surface waters. A general conceptual model for the response of elements to the thawing-freezing process of the active layer is established.