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A detailed study of cement and matrix of ooidal ironstones of the Bakchar deposit (Western Siberia) was carried out to assess the factors influencing ore-forming processes. This research focusses on a debated issue about iron sources for Phanerozoic ooidal ironstone. Siderite, the main cementing mineral in the ironstones, is of two varieties that differ in morphology, chemical and isotopic composition, and types of fluid inclusions. The first variety of siderite occurs either as veinlet or as anhedral cement, consisting of isotopically light carbon and oxygen (δ13C from −39.5 to −29.7‰ and δ18O from −15.2 to −5.1‰). Fluid inclusions show a relatively high homogenization temperature (170–320 °C) and methane in the gas phase, corresponding to methane-bearing hydrothermal fluids. The second variety of siderite occurs as aggregates of small crystals in the ironstone matrix and is relatively enriched in heavier stable carbon and oxygen isotopes (δ13C from −28.1 to −12.2‰ and δ18O from −28.4 to −2.1‰), suggesting its formation on the seafloor under the combined influence of methane flux and seawater. The zone of the ooidal ironstone most proximal to the most intense ore-mineralization, an area of intense diffusion of metals and methane through marine sediments, is marked by the first variety of siderite, with rare authigenic minerals, a low clay content (kaolinite, chlorite, nontronite) and a high Fe content of the smectites. The authigenic mineral associations reflect the transition from methanic (sulfate-methane transition zone) to ferruginous (iron reduction zone) through sulfidic environment. The intermediate zone is dominated by montmorillonite-illite-saponite-nontronite and the second variety of siderite. The distal zone of the ore deposit is relatively unaltered, and is marked by illite-montmorillonite (illite-smectite), with rare second variety of siderite. The ratio of 1 M phyllosilicates (kaolinite) to the main swelling 2 M phyllosilicates in the clay fraction (K/M mineral index) decreases from the proximal zone of the intense iron-mineralization to the distal zone. The trend of clay mineral changes reflects the decreasing alteration of sediment matrix away from the main iron-rich and/or carbonate-bearing fluid influx. This study shows the expected lateral and vertical variation in authigenic minerals associated with marine Phanerozoic ironstone deposits, related to variable flux of metal- and methane-bearing fluids. [Display omitted] • The siderite in ironstones bears signatures of hydrothermal methane fluids. • Changes in the composition of the phyllosilicate matrix are consistent relative to the hydrothermal influx. • The proximal zone of the ore deposit shows the nontronite-kaolinite-chlorite matrix. • The distal zone, dominated by illite-montmorillonite (illite-smectite), is the least altered. • The mineral associations of the ironstone cements record the transition between multiple different diagenetic zones. [ABSTRACT FROM AUTHOR]