The physicochemical modeling of mineral formation processes at the Badran subthrust gold-quartz deposit was performed, based on a study of fluid inclusions in quartz by Raman spectroscopy, gas chromatography, thermometry, and freezing. The results show that at stage I, highly productive gold-bearing quartz veins (gray quartz) of the deposit formed from heterogeneous fluid at <320 ºC and 2.0–0.1 kbar with the active participation of CO2, N2, and CH4; the salinity of this solution reached 10 wt.% NaCl-equiv. At stage II (Au-productive), milky-white quartz was produced from the homogeneous medium-chloride-sulfide solution which remained after the heterogenization of the initial fluid, at 300–100 ºC and 0.1 kbar. At stage III (with low Au production), clear quartz formed from homogeneous chloride solutions with salinity of <4.5 wt.% NaCl-equiv. at <200 ºC and <0.1 kbar. The physicochemical conditions of Au concentration within the complex geochemical system Au–Fe–Cu–Pb–Zn–As–Sb–Hg–Ag–H2O–Cl–H2S–CO2 at the Badran deposit was modeled using the Chiller software. The following models were used: (1) solution–rock interaction and (2) condensation of gas phase (for stage I); (3) simple cooling of medium-chloride-sulfide solution (for stage II); (4) simple cooling and (5) mixing of low-chloride-sulfide solution with acid meteoric waters (for stage III). The models show the sequence of vein formation in the ore-producing system and the host-rock metasomatism in the deep horizons of the deposit.