In order to foresee possible changes in the elementary composition of Arctic river waters, complex studies with extensive spatial coverage, including gradients in climate and landscape parameters, are needed. Here, we used the unique position of the Ob River, draining through the vast partially frozen peatlands of the western Siberia Lowland and encompassing a sizable gradient of climate, permafrost, vegetation, soils and Quaternary deposits, to assess a snap-shot (8–23 July 2016) concentration of all major and trace elements in the main stem (~3000 km transect from the Tom River confluence in the south to Salekhard in the north) and its 11 tributaries. During the studied period, corresponding to the end of the spring flood-summer baseflow, there was a systematic decrease, from the south to the north, of Dissolved Inorganic Carbon (DIC), Specific Conductivity, Ca and some labile trace elements (Mo, W and U). In contrast, Dissolved Organic Carbon (DOC), Fe, P, divalent metals (Mn, Ni, Cu, Co and Pb) and low mobile trace elements (Y, Nb, REEs, Ti, Zr, Hf and Th) sizably increased their concentration northward. The observed latitudinal pattern in element concentrations can be explained by progressive disconnection of groundwaters from the main river and its tributaries due to a northward increase in the permafrost coverage. A northward increase in bog versus forest coverage and an increase in DOC and Fe export enhanced the mobilization of insoluble, low mobile elements which were present in organo-ferric colloids (1 kDa—0.45 µm), as confirmed by an in-situ dialysis size fractionation procedure. The chemical composition of the sampled mainstream and tributaries demonstrated significant (p
< 0.01) control of latitude of the sampling point; permafrost coverage; proportion of bogs, lakes and floodplain coverage and lacustrine and fluvio-glacial Quaternary deposits of the watershed. This impact was mostly pronounced on DOC, Fe, P, divalent metals (Mn, Co, Ni, Cu and Pb), Rb and low mobile lithogenic trace elements (Al, Ti, Cr, Y, Zr, Nb, REEs, Hf and Th). The pH and concentrations of soluble, highly mobile elements (DIC, SO4
, Ca, Sr, Ba, Mo, Sb, W and U) positively correlated with the proportion of forest, loesses, eluvial, eolian, and fluvial Quaternary deposits on the watershed. Consistent with these correlations, a Principal Component Analysis demonstrated two main factors explaining the variability of major and trace element concentration in the Ob River main stem and tributaries. The DOC, Fe, divalent metals and trivalent and tetravalent trace elements were presumably controlled by a northward increase in permafrost, floodplain, bogs, lakes and lacustrine deposits on the watersheds. The DIC and labile alkaline-earth metals, oxyanions (Mo, Sb and W) and U were impacted by southward-dominating forest coverage, loesses and eluvial and fertile soils. Assuming that climate warming in the WSL will lead to a northward shift of the forest and permafrost boundaries, a “substituting space for time” approach predicts a future increase in the concentration of DIC and labile major and trace elements and a decrease of the transport of DOC and low soluble trace metals in the form of colloids in the main stem of the Ob River. Overall, seasonally-resolved transect studies of large riverine systems of western Siberia are needed to assess the hydrochemical response of this environmentally-important territory to on-going climate change.