Based on results of study of fluid inclusions, we have established the specific fluid regime of formation of the Kalguty Mo–W(Be) deposit (Gorny Altai). Using classical thermobarogeochemistry (cryo- and thermometry) and modern microprobing methods (Raman spectroscopy and LA-ICP-MS), we studied fluid inclusions in quartz of quartz–wolframite veins (ore formation stage I), specific “quartz core” (quartz lens), and pyrite-chalcopyrite-molybdenite paragenesis (ore formation stage II). The results of study show that the quartz–wolframite veins of the Kalguty deposit formed with the participation of reduced W-Sb-bearing fluids with a salt content of up to 5.9 wt.%. Their gas phase consisted of CO2, N2, and CH4. Formation of pyrite-chalcopyrite-molybdenite mineralization involved oxidized hot (530–420 °C) fluids with the average salt content of 9.3 wt.%. Their gas phase was of high density (up to 0.55) and consisted of CO2, N2, and H2S. The pressure of the mineral-forming environment varied from 50 to 25 MPa. The fluids contained Cu, Mo, Bi, and S. The productive greisen-vein Mo–W(Be) mineralization of the Kalguty deposit resulted from the superposition of greisen molybdenite-chalcopyrite mineralization on parageneses of earlier formed quartz-wolframite veins. Oxidized metal-bearing fluids that formed the Mo mineralization of the Kalguty deposit have high contents of S and are geochemical analogs of magmatic metal-bearing ore-forming fluids of the Central Aldan porphyry Cu-Au-Mo deposits, which are genetically related to alkaline massifs. This suggests the significant influence of the mantle source on the formation of the Kalguty rare-metal ore-magmatic system. The same is evidenced from the sulfur isotope composition of chalcopyrite, molybdenite, and pyrite from ore parageneses, falling in the narrow range of δ34S‰ from –1.2 to +2.9 corresponding to the isotope composition of mantle sulfur.