In the Western High of the Sea of Marmara, where pervasive gas hydrate and hydrocarbon gas seepage occurs, late Pleistocene-Holocene sediments are composed of a lower lacustrine and an upper marine unit. The sedimentary evolution, gypsum formation and carbonate anomaly, under the complex sedimentary environment at cold seep sites on the Western High, have not been systematically well explained. The transition from the lacustrine to marine unit occurs at around 7.5 m below the sea floor (mbsf), with a sulfidization front present in the lacustrine sediments just below it, and the marine unit includes a sapropel layer between 5.20 and 7.20 mbsf. The sedimentary sequence is characterized by authigenic minerals including pyrite, carbonates, and gypsum in the upper 0.50 mbsf, corresponding to the present-day sulfate-methane transition zone (SMTZ) near the seafloor. Mineralogical, chemical and isotopic compositions (13C, 18O, 34S, 26Mg) of the sediments in the core studied show their close relationship with intensive sulfate-driven anaerobic oxidation of methane (AOM) and other hydrocarbons. The dissolution of carbonate, related to the gas and oil migration, and organic matter enrichment might be the main cause of carbonate deficiency in the sapropel unit. Heavy carbon isotopic composition (δ13CCarb = 6.98‰) of carbonate at 4.30 mbsf implies that the carbon might be the residual by-product of subsurface biodegradation of seeping petroleum. The formation of secondary gypsum and partial dissolution of carbonate in the Sea of Marmara is commonly considered of being associated with the aerobic oxidation of pyrite. However, the euhedral authigenic gypsum studied might be with different origins, possibly including anaerobic oxidation of Fe-sulfides, carbonate deficiency in the sapropel unit and AOM. Gypsums below SMTZ are with the size of hundreds of microns. Linear pits and grooves are developed on these gypsum surfaces, probably due to corrosion by the methane-rich fluid of latest hydrocarbon seepage. Platy hexagonal gypsum in SMTZ, without any corrosion on crystal surface, might be associated with the changing flux of the acidic composition (e.g. CO2) in the seepage. Depleted-26Mg by about 1‰ in the SMTZ might be caused by the upward seepage of hydrocarbons. Magnesium isotope of authigenic carbonate could be a valid proxy for the recognition of SMTZ in a hydrate geo-system.