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East Siberian Arctic Shelf, the widest and the shallowest shelf of the World Ocean, covering greater than two million square kilometers, has recently been shown to be a significant modern source of atmospheric methane (CH4). The CH4 emitted to the water column could result from modern methanogenesis processes and/or could originate from seabed deposits (pre-formed CH4 preserved as free gas and/or gas hydrates). This paper focuses primarily on understanding the source and transformation of geofluid in the methane seepage areas using ions/trace elements and element ratios in the sediment pore-water. Six piston cores and totally 42 pore-water samples were collected in the East Siberian Sea and the Laptev Sea at water depths ranging from 22 to 68 m. In the active zones of methane release, concentrations of vanadium, thorium, phosphorus, aluminum are increased, while concentrations of cobalt, iron, manganese, uranium, molybdenum, copper are generally low. The behavior of these elements is determined by biogeochemical processes occurring in the pore-waters at the methane seeps sites (sulfate reduction, anaerobic oxidation of methane, secondary precipitation of carbonates and sulfides). These processes affect the geochemical environment and, consequently, the species of these elements within the pore-waters and the processes of their redistribution in the corresponding water–rock system.