The combination of CH4 venting and gas hydrate occurrence on the seafloor was observed by a remotely operated vehicle (ROV) offshore Joetsu, on the eastern margin of the Japan Sea. The intensity and location of venting varied within a few days, suggesting the potential for short-term gas hydrate formation and rapid geochemical changes. To investigate temporal variations in gas hydrate dynamics, we deployed a long-term in situ water sampling system (OsmoSampler), consisting of a pump and a sampling coil, next to the vent to collect interstitial water continuously for a year. However, the volume recovered from the sample was only a quarter of the expected amount. The presence of gas hydrate was confirmed in the OsmoSampler during its recovery by ROV. This unexpected event was attributed to a CH4 intrusion into the system—either by direct intake through the tip of sampling coil or by a structurally vulnerable connections—followed by gas hydrate formation with the prefilled distilled water. The resulting blockage reduced the rate of sampling. Despite this technical limitation, OsmoSampler geochemical data revealed dynamic variations. Cl− concentrations sporadically fluctuated from 50 to 900 mM repeatedly until 40 m of coil length, indicating alternately saline and fresh conditions likely due to repeated cycles of gas hydrate growth and dissociation. At 40 m, a distinct geochemical transition—marked by an increase in Cl− and SO42- concentrations to 440 mM and 26 mM, respectively, and a sharp decline in CH4 to 0 mM—closely resembled to the composition of surface interstitial water. This suggests that seawater infiltration into the sampling system was likely triggered by the collapse of the gas hydrate due to buoyancy. The topographic depression observed by the ROV during the recovery supports this interpretation. These findings provide new insights into short-term gas hydrate instability near the seafloor and the sudden release of CH4 from sediments into the overlying water column.