Comparative experiments were conducted under different water level heights and methane concentration conditions using a self-designed explosion experiment pipeline. The results showed that, in comparison with the scenario without water storage, when the water level was 2 cm and methane concentration was 6.5–12.5%, there was a dual effect including a pressure decrease caused by the endothermic cooling of liquid water and a pressure increase caused by the expansion of water vapour. These effects caused the pressure time history curve to exhibit a double-peak or multi-peak structure, and the average decrease in the peak deflagration pressure was 23.76%. The heat of vaporisation absorbed by the stored water and barrier effect of water vapour on the transfer of the heat slowed down the increase in the deflagration temperature. The average decrease in the peak deflagration temperature of methane was 13.82%, and the time to reach the peak deflagration temperature was extended as a whole, with an average delay of 0.22 s. Water storage also changed the shape of the deflagration flame front, which exhibited ‘knife’, ‘V’, and ‘crescent’ structures. Moreover, the flame propagation speed was significantly reduced, with the peak and average flame propagation speeds decreased by 83.3% and 83.6%, respectively. The research results can provide a certain reference for preventing gas explosions in typical confined spaces, and also help to explore new anti-explosion methods, which can be applied to marine equipment such as ships.