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Waters of mud volcanoes in Azerbaijan have been characterized chemically and isotopically. Anomalously heavy stable carbon isotope compositions in bicarbonate component (up to +19.8‰) are interpreted to have a secondary biogenic history. Correlation between CO2 of gases and water bicarbonate support that 13C-enrichment of the HCO3 ions is attributed to anaerobic degradation occur at shallower depths. High content of HCO3 component along with the presence of low-rate mineralized alkaline waters explained that formation occur in open hydrogeological conditions. Groundwater of mud volcanoes most probably interacts with hydrocarbon phases by processes such as gas dissolution, oil “water washing” bringing microorganisms caused intensive bacterial oxidation processes. Microbial degradation processes are more typical for highly fractured geological regions with high water permeability and presence of shallower oil-and-gas fields (in particular, Shamakha-Gobustan oil-and-gas bearing area).