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We present the chemical and isotope compositions of the water and gas phases of the unique Mukhen cold high-pCO2 spa. Estimated δ18O, δD, and δ13CTIC values and data on geology and hydrogeology of the studied area indicate that the source of the groundwaters is meteoric waters, whereas carbon dioxide is of deep genesis and numerous regional faults are gas-feeding channels. Calculations of equilibrium reactions in the water–rock system show that the upper-aquifer waters (HCO3–Ca–Mg) with low TDS are undersaturated with carbonate minerals, montmorillonites, and aluminosilicates but are oversaturated with kaolinite, whereas the lower-aquifer waters (HCO3–Na) with high TDS are oversaturated with calcite, dolomite, and clay minerals but are undersaturated with main aluminosilicates. We propose a new concept of the formation of these groundwaters, demonstrating that long interaction between rocks and groundwaters in the presence of CO2 and considerable precipitation of secondary minerals are responsible for the high TDS of the lower-aquifer waters (up to 14 g/L) and their geochemical type (HCO3–Na) and unusual isotope composition (δ18O = −25.2‰, δD = −69.0‰).