While meteoric water recharge is known to stimulate biogenic methane formation in shale and coal seams, the underlying mechanisms are currently unresolved. To this end, we conducted fieldwork in the Tempoku Coal Field, Japan. Pore water in core samples and well water in boreholes were analyzed for dissolved components and isotopic compositions. The hydraulic gradient was determined using values of borehole hydraulic head. Cl- concentrations (38 mg L-1 to 16,600 mg L-1), delta O-18(H2O) values (-10.5 parts per thousand to -2.4 parts per thousand), and delta D(H2O) values (-71.6 parts per thousand to -17.8 parts per thousand) increased with depth ( < 200 m), indicating meteoric water recharge. The positive correlation between delta C-13(CH4) values (-74.9 parts per thousand to -42.7 parts per thousand) and delta C-13(CO2) values (-27.5 parts per thousand to + 13.3 parts per thousand), as well as between delta D(H2O) and delta D(CH4) values (-264 parts per thousand to -200 parts per thousand), in the core samples and groundwater, indicted in situ methanogenesis in the zone of mixing and migration of meteoric water and saline groundwater. Some of the pore water samples contained biogenic acetate, propionate, and succinate at remarkably high concentrations (similar to 200 mg L-1), implying: (i) the thermodynamic inhibition of fermentation at fermentation sites, and (ii) spatial separation between the fermentation sites and methanogenesis sites. Planar fracture modeling indicates that at distances greater than a millimeter between fermentation and methanogenesis sites, the advective transport of fermentation products dominates rather than diffusive transport of those. Hence, meteoric water recharge would stimulate biogenic methane formation by inducing advective transport of the fermentation products, thus (i) relaxing the thermodynamic inhibition of fermentation at the site of the fermentation, and (ii) enhancing the rate of transport of the fermentation products to the site of methanogenesis.