We studied two medium size pristine rivers (Taz and Ket) of boreal and subarctic zone, western Siberia, for a better understanding of the environmental factors controlling major and trace element transport in riverine systems. Our main objective was to test the impact of climate and land cover parameters (permafrost, vegetation, water coverage, soil organic carbon, and lithology) on carbon, major and trace element concentration in the main stem and tributaries of each river separately and when considering them together, across contrasting climate/permafrost zones. In the permafrost-bearing Taz River (main stem and 17 tributaries), sizable control of vegetation on element concentration was revealed. In particular, light coniferous and broadleaf mixed forest controlled DOC, and some nutrients (NO2, NO3, Mn, Fe, Mo, Cd, Ba), deciduous needle-leaf forest positively correlated with macronutrients (PO4, Ptot, Si, Mg, P, Ca) and Sr, and dark needle-leaf forest impacted Ntot, Al, and Rb. Organic C stock in the upper 30–100 cm soil positively correlated with Be, Mn, Co, Mo, Cd, Sb, and Bi. In the Ket River basin (large right tributary of the Ob River) and its 26 tributaries, we revealed a correlation between the phytomass stock at the watershed and alkaline-earth metals and U concentration in the river water. This control was weakly pronounced during high-water period (spring flood) and mostly occurred during summer low water period. Pairwise correlations between elements in both river systems demonstrated two group of solutes—(1) positively correlated with DIC (Si, alkalis (Li, Na), alkaline-earth metals (Mg, Ca, Sr, Ba), and U), this link originated from groundwater feeding of the river when the labile elements were leached from soluble minerals such as carbonates; and (2) elements positively correlated with DOC (trivalent, tetravalent, and other hydrolysates, Se and Cs). This group reflected mobilization from upper silicate mineral soil profile and plant litter, which was strongly facilitated by element colloidal status, notably for low-mobile geochemical tracers. The observed DOC vs DIC control on riverine transport of low-soluble and highly mobile elements, respectively, is also consistent with former observations in both river and lake waters of the WSL as well as in soil waters and permafrost ice. A principal component analysis demonstrated three main factors potentially controlling the major and TE concentrations. The first factor, responsible for 26% of overall variation, included aluminum and other low mobile trivalent and tetravalent hydrolysates, Be, Cr, Nb, and elements strongly complexed with DOM such as Cu and Se. This factor presumably reflected the presence of organo-mineral colloids, and it was positively affected by the proportion of forest and organic C in soils of the watershed. The second factor (14% variation) likely represented a combined effect of productive litter in larch forest growing on carbonate-rich rocks and groundwater feeding of the rivers and acted on labile Na, Mg, Si, Ca, P, and Fe(II), but also DOC, micronutrients (Zn, Rb, Ba), and phytomass at the watershed. Via applying a substituting space for time approach for south-north gradient of studied river basins, we predict that climate warming in northern rivers may double or triple the concentration of DIC, Ca, Sr, U, but also increase the concentration of DOC, POC, and nutrients.