Simultaneous monitoring of the gas concentration and water level in groundwater was achieved at the Omaezaki open well. Coaxially arranged pipes inserted into the well enabled us to pump groundwater directly from an aquifer and to return it the aquifer without disturbing the groundwater level. Concentration of methane, as one subsurface-origin gas, was monitored using a quadrupole mass spectrometer equipped with a gas separation tube. The methane concentration intermittently showed spike-like increases during the observation period. The temporal change of the methane concentration was independent of the seismic activity around the station, the groundwater temperature, the ambient temperature, and the pumping rate, with the exception of the groundwater level. The methane concentration was associated with the difference of the groundwater level, of which the amplitude of a barometric response is greater than that of a tidal one. Spike-like increases of the methane concentration were explained using a logistic model as a function of the groundwater level change.