The chemical status of ∼40 major and trace elements (TE) and organic carbon (OC) in pristine boreal rivers draining the basaltic plateau of Central Siberia (Putorana) and interstitial solutions of permafrost soils was investigated. Water samples were filtered in the field through progressively decreasing pore size (5 μm → 0.22 μm → 0.025 μm → 10 kDa → 1 kDa) using cascade frontal filtration technique. Most rivers and soil porewaters exhibit 2–5 times higher than the world average concentration of dissolved (i.e., <0.22 μm) iron (0.03–0.4 mg/L), aluminum (0.03–0.4 mg/L), OC (10–20 mg/L) and various trace elements that are usually considered as immobile in weathering processes (Ti, Zr, Ga, Y, REEs). Ultrafiltration revealed strong relationships between concentration of TE and that of colloidal Fe and Al. According to their partition during filtration and association with colloids, two groups of elements can be distinguished: (i) those weakly dependent on ultrafiltration and that are likely to be present as truly dissolved inorganic species (Li, Na, K, Si, Mn, Mo, Rb, Cs, As, Sb) or, partially (20–30%) associated with small size Fe- and Al-colloids (Ca, Mg, Sr, Ba) and to small (<1–10 kDa) organic complexes (Co, Ni, Cu, Zn), and (ii) elements strongly associated with colloidal iron and aluminum in all ultrafiltrates largely present in 1–100 kDa fraction (Ga, Y, REEs, Pb, V, Cr, Ti, Ge, Zr, Th, U). TE concentrations and partition coefficients did not show any detectable variations between different colloidal fractions for soil porewaters, suprapermafrost flow and surface streams. TE concentration measurements in river suspended particles demonstrated significant contribution (i.e., ⩾30%) of conventionally dissolved (<0.22 μm) forms for usually “immobile” elements such as divalent transition metals, Cd, Pb, V, Sn, Y, REEs, Zr, Hf, Th. The Al-normalized accumulation coefficients of TE in vegetation litter compared to basalts achieve 10–100 for B, Mn, Zn, As, Sr, Sn, Sb, and the larch litter degradation is able to provide the major contribution to the annual dissolved flux of most trace elements. It is hypothesized that the decomposition of plant litter in the topsoil horizon leads to Fe(III)-, Al-organic colloids formation and serves as an important source of elements in downward percolating fluids.