A method is presented for the online measurement of methane in aquatic environments by application of membrane inlet mass spectrometry (MIMS). For this purpose, the underwater mass spectrometer Inspectr200-200 was applied. A simple and reliable volumetric calibration technique, based on the mixing of two end member concentrations, was used for the analysis of CH4 by MIMS. To minimize interferences caused by the high water vapor content, permeating through the membrane inlet system into the vacuum section of the mass spectrometer, a cool-trap was designed. With the application of the cool-trap, the detection limit was lowered from 100 to 16 nmol/L CH4. This allows for measurements of methane concentrations in surface and bottom waters of coastal areas and lakes. Furthermore, in case of membrane rupture, the cool-trap acts as a security system, avoiding total damage of the mass spectrometer by flushing it with water. The Inspectr200-200 was applied for studies of methane and carbon dioxide concentrations in coastal areas of the Baltic Sea and Lake Constance. The low detection limit and fast response time of the MIMS allowed a detailed investigation of methane concentrations in the vicinity of gas seepages.