Natural organic matter (NOM) within the dispersion train of Novo-Ursk tailings (Salair Ridge, Kemerovo region, Russia) is composed of remnant sedge peat mounds and is located either on the surface or is buried under cyanide wastes. The organic material interacts with AMD and with the wastes, which leaves imprint on its composition. This interaction produces geochemical anomalies (g/t: 1582 Cu, 41,300 Zn, 6060 Se, 11,700 Hg, 114–155 Au, 534 Ag, 416 I). The contents of elements depend on Fe in three groups of NOM samples that contain <10 wt% Fe (group I), 10–22 wt% Fe (group II), and >22 wt% Fe (group III). NOM with higher Fe enrichment contains less Cu, Zn, Se, Hg, Ag and I, as well as Cd, Ba, Sr and Rb, Y, Zr, Nb, Mo, Sn, Sb, and Te but more As. Yet, gold may reach high concentrations in NOM with any Fe contents. Accumulation of elements by NOM during its prolonged interaction with wastes and AMD is maintained by physical, chemical, biochemical, and mineralogical processes. They are, respectively, migration of waters controlled by permeability of material in the dispersion train depending on its grain sizes and by AMD flow direction; oxidative dissolution of sulfides, complexing, and adsorption on organic matter and Fe(III) hydroxides; microbial mediation; and secondary mineralization. The chemistry of waters interacting with NOM at the time of its deposition can be reconstructed with regard to several factors, including microbial mediation. Namely, local geochemical anomalies with ultrahigh element concentrations may arise because microorganisms can immobilize Hg to make it less toxic; sulfate-reducing bacteria can maintain precipitation of Zn, Cu, and Cd sulfides; microbial activity can mediate redistribution of elements between clastic and organic materials, etc. The inferred inheritance of AMD geochemical signatures by NOM has implications for the conditions and mechanisms of element accumulation.