Pore waters collected from the eastern margin of the Japan Sea including gas hydrate fields off Joetsu were analyzed for concentrations of major and minor dissolved species in order to characterize fluid migration in high methane potential area. Rapid decreases of sulfate concentration and accompanying increases of alkalinity and hydrogen sulfide concentrations point to active diagenesis of organic matter such as anaerobic methane oxidation at the sulfate-methane interface, indicating high methane flux and subsequent gas hydrate formation near the seafloor on the Umitaka Spur and Joetsu Knoll. Gas hydrate occurrences are inferred generally by ion dilution and enrichment in 18O and deuterium of pore waters, ion enrichment and depletion in 18O and deuterium, to the contrary, indicate rapid growth of massive gas hydrate exceeding ion/water diffusion. Alkalinity increase also results in the precipitation of carbonates near the seafloor, corresponding to rapid decrease of Ca concentration. Pore water geochemistry changes remarkably in the shallow interval, induced mainly by active methane flux to the water column. Concentration of Cl and isotopic compositions of oxygen and hydrogen reflect inputs of deep fluids as well, deep-sourced material can be delivered to the shallow interval. Long-termed fluid migration is also evident in the research area.