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Permafrost-affected region in Russian Arctic is an important study area for investigating fate of trace metals in soils by geological processes and human-induced trace metals through atmospheric deposition. Two plots of soils in Yamal region were selected: Northern Trans-Urals area (PU1, PU2, PU3) adjacent to urban areas and Gydan Peninsula representing reference groups as natural landscapes (Yavai, Gyda, Enysei). The levels of most metals in Urals area were more than those in Gydan Peninsula. In soil profile, Histic horizon revealed the accumulation of most metals. Cd and Pb were classified as metals, which were transported by atmosphere from urban areas and accumulated in surficial organic layers. Gleying processes and cryogenic mass exchanges transported metals from bottom to top layers in mineral horizons. Moreover, gleying horizon functioned as a geochemical barrier for metal transporting below permafrost table. The levels of As, Mn, and Fe were obliviously higher than threshold limit values of Russian Siberia. However, these values cannot represent the natural hydromorphic soils in Arctic tundra. The Geoaccumulation Index (I-geo) were determined for assessing surface soil samples regarding to metals' pollution. The results suggested local geology pollution for Gydan Peninsula and atmospheric transport pollution for Urals area. More investigations with respect to trace metals behavior in permafrost-affected soil profile needed to be studied for understanding levels of trace metals with changes of active layer depth due to climate changing.