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The South Sakhalin mud volcano (Sakhalin Island, Russia) emits HCO3-Cl/Na-Mg water, emanates CO2 prevailing over CH4 in the gas phase, and extrudes mud bearing five carbonate mineral species. The study focuses on the distribution, diversity, and origin of the carbonate minerals from the mud volcano (MV) ejecta, in terms of carbon cycle processes. The data presented include a synthesis of field observations, compositions of MV gases and waters, chemistry of carbonate minerals, as well as stable isotope geochemistry of MV waters (δ13C, δD, and δ18O) and carbonates (δ13C and δ18O). The sampled MV waters are isotopically heavy, with δ18O = +5.7‰ to +7.5‰ VSMOW, δD = −18.0‰ to −11.0‰ VSMOW, and 13C (δ13CDIC = +6.9‰ to +8.1‰ VPDB). This composition may be due to the dilution of basinal water with dehydration water released during the diagenetic illitization of smectite. Carbonates in the sampled mud masses belong to three genetically different groups. Mg-rich siderite, (Fe0.54–0.81Mg0.04–0.30Ca0.05–0.23Mn0.00–0.08)CO3, disseminated in abundance throughout the mud masses, coexists with common calcite and sporadic ankerite. The trace-element chemistry of Mg-siderite, as well as the oxygen (δ18O = +34.4‰ to +36.8‰ VSMOW) and carbon (δ13C = −1.3‰ to +0.6‰ VPDB) isotopic signatures, confirms its authigenic origin. Siderite formed during early diagenesis of the Upper Cretaceous sandy and clayey marine sediments mobilized by mud volcanism in the area. Another assemblage, composed of dawsonite, siderite, and vein calcite (±kaolinite), represents altered arkose sandstones found as few fragments in the mud. This assemblage may be a marker of later CO2 flooding into the sandstone aquifer in the geological past. The trace-element chemistry, particular morphology, and heavy C (δ13C = +5.5‰ to +7.0‰ VPDB) and O (δ18O = +39.1‰ to +39.5‰ VSMOW) isotope compositions indicate that aragonite is the only carbonate species that is related to the current MV activity. It crystallized in a shallow reservoir and was maintained by CO2 released from rapidly ascending liquefied mud and HCO3-Cl/Na-Mg-type of MV waters.