Wastes of the ore cyanide process are prone to oxidation and acid leaching that cause mobilization, migration, and precipitation of elements, including noble metals. The issues of waste oxidation, as well as release and transport of oxidation products, are of principal environmental concern and a focus of active geochemical research. We study the behavior of Au and Ag in the natural–industrial system “sulfide wastes–surface/pore waters–particulate matter–bottom sediments” in the presence of different elements (Na, Mg, K, Ca, Al, Fe, Cu, Zn, Se, Ag, Au, Hg, Pb, REE, etс.), at the Novo-Ursk auriferous pyritic deposit (Salair, Kemerovo region, Russia).The wastes include processed primary ore (wastes I) and ore from the gold-bearing weathering profile (wastes II) that store, respectively, 0.5ppm Au, 18ppm Ag and 0.26ppm Au, 13ppm Ag. Gold in wastes I occurs in the native form with Cu and Ag impurities and also Au exist as invisible species in pyrite. In wastes II, gold is adsorbed onto the surfaces of secondary mineral particles (kaolinite, montmorillonite, hydromica, and Fe(III) compounds) while silver is an isomorphic impurity in alunite–jarosite minerals. The oxidation of wastes produces acid mine drainage (AMD) water, with рН=1.9 and high concentrations of sulfate, Fe, Al, Cu, Zn, Pb, As, Se, Te, Hg, Сd, and REE, which flows into the Ur River (a tributary of the Inya).The stream transports gold and silver existing in dissolved+colloidal and particulate forms. Dissolved+colloidal gold and silver have similar distribution patterns with their contents inversely proportional to рН. Dissolved+colloidal gold in the AMD water is more abundant than silver (0.4–1.2ppb Au against 0.1–0.3ppb Ag). Gold changes from the dissolved+colloidal (in AMD) to particulate (till 0.03ppb) forms and precipitates in progressively larger amounts with distance from the tailings. Silver in most of the analyzed natural and tailings-impacted waters exists as suspended particles (to 1ppb). The concentrations of gold and silver are the highest (1.8–2.1ppb Au and 4.5–5.7ppb Ag) in peat pore waters within the geochemical trains of the tailings, apparently as a result of re-precipitation on organic barriers.