Sulfate, halogen, and radioactive 129I concentrations were determined in pore waters associated with massive gas hydrate deposits in shallow sediments along the boundary between the Amurian and Okhotsk plates in the Okhotsk Sea and Japan Sea. Because of the strong biophilic behavior of iodine and weaker behavior of bromine, in contrast to conservative chlorine, in the marine system and the presence of a long-lived radioisotope of iodine (129I), these analyses are useful for determining the age and nature of source organic materials responsible for hydrocarbons, mostly methane, in gas hydrates. Rapid sulfate decreases with depth reflect active methane migration toward the seafloor, particularly around gas hydrate-bearing sites at both locations. While salt exclusion from gas hydrates during crystallization is likely to have resulted in the downward increase of Cl, and potentially Br and I concentrations, gas hydrate dissociation at depth caused a gentle dilution of pore waters. Biophilic Br and I concentrations rapidly increase with depth, reaching 1500 and 400 μM at the core bottom, respectively, indicating that upwelling fluids are enriched in Br and I derived from marine organic materials degraded in deep sediments. The 129I/I ratios thus reflect the potential ages of source formations of iodine and associated methane, providing ∼35 Ma northeast off Sakhalin Island in the Okhotsk Sea and ∼30 Ma in the Umitaka Spur-Joetsu Knoll region in the eastern margin of the Japan Sea. These ages correspond well with the initial activities of the Amurian and Okhotsk plates and the subsequent opening of the Japan Sea, which formed the present geological setting of the northeastern margin of the Eurasian continent. Active plate motions led to the rapid accumulation of organic-rich sediments that are responsible for iodine and methane in gas hydrate occurring along the plate boundary.