We study the contents of elements and group composition in natural organic matter (NOM) that interacts with acid mine drainage (АMD) and high-sulfide tailings at the Ursk site (southwestern Siberia, Russia). AMD causes biomass changes in NOM, related changes in the composition of fractions, and hydrolysis of hydrolyzable compounds; it increases the water-soluble fraction and maintains depolymerization of humic acids to fulvic acids, but exerts no effect on substances soluble in organics (bitumen) or on poorly hydrolyzable compounds. Accumulation of inorganic elements and precipitation of minerals obscure the true fraction composition of NOM: the superposed mineral component contributes significantly to the water-soluble, humic acid, hydrolyzable and non-hydrolyzable fractions, and may reach 26.4% per total of all fractions. Rock-forming and potentially toxic elements partition among NOM fractions and predominate in the water-soluble fraction. The contents of Au and Ag are the highest in the fractions of humic acids and hydrolyzable compounds but are lower in the non-hydrolyzable residue. The obtained data have implications for possible migration of potentially toxic elements and noble metals and thus for remediation of polluted areas. The observed fractionation of Ag and Au in NOM helps us to understand the mechanisms of their distribution in organic-bearing environments, such as peatlands or coal basins.