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For the first time based on determination of the geochemical occurrence forms of trace metals the main processes that control the accumulation of elements (Al, Mn, Fe, Mo, Cr, Ni, Co, Cu, Pb, Cd, and As) in the recent sediment cores from the White Sea and Barents Sea were quantified. A high-resolution study of the bottom sediment cores allowed us to estimate the short-term variations (periodicity of 10–15 years) in the accumulation of metals to reveal the periods of maximum Fe and Mn contents in the amorphous hydroxides fraction, which serve as effective adsorbents of the trace elements majority, including heavy metals. The Mn/Fe ratio in the amorphous hydroxides phase can be considered as geochemical indicators of early diagenesis.