Modern hydrotherms of the Baikal Rift Zone (BRZ) are divided according to contents of ore and rare elements and gas composition into: (1) carbonaceous, forming in carbonate rocks, (2) hydrosulfuric and H2S-free nitric and methane, discharged in Cenozoic deposits, and (3) nitric, produced in granitoids. Carbonaceous hydrotherms are enriched in Sr, Ba, Y, Co, and Cr; nitric ones, in Li, Rb, Cs, Mo, W, and other granitophile elements; and hydrosulfuric hydrotherms are saturated with complex metals. High contents of U and associated elements are specific for oxidized nitric alkaline thermal waters and are atypical of carbonaceous ones, and high contents of Au are observed in methane hydrotherms. Separation of ore elements between organic and clayey matter takes place as early as the initial stage of sediment formation. During sediment accumulation, these elements pass into hydrothermal solution in the same separated associations. In oxidizing (Eh ranges from +50 to +260 mV) alkaline medium, U and, obviously, other elements of uranium association, present not only in granitoids but also in the organic matter of sediments, pass into the solution most actively. Alkaline medium (7 < pH < 10) favors the transition of Mo and W from igneous rocks and sediments into the solution. Methane hydrotherms (8 < pH < 9, Eh < –70 mV) can accumulate gold. In strongly reducing (Eh ranges from –200 to –360 mV) alkaline (pH > 8) hydrosulfuric anoxic medium, chalcophile complex metals of the clayey matter of sediments are the most active to pass into the solution. Thus, as Eh decreases and H2S concentration increases, hydrothermal solution extracts various element associations from igneous and sedimentary deposits in the sequence U–Mo, W–Au–Sn, Cu, Pb. In the solution the differentiation of elements continues. Hence, the separation of ore-element associations at the initial stage of sediment formation, long before the hydrothermal activity, is the first track in a chain of processes leading to the differentiation of ore deposits according to formational types. Hydrotherms confined to deep-fault zones contain an endogenous fluid with mantle 3He/4He values close to those in methane and carbonaceous hydrotherms of the Tunka rift depression in the BRZ. According to results of thermodynamic modeling, the fluid consists of CH4, H2O, and CO2 and obviously lacks mantle ore elements, as it was initially of hydrocarbon composition.