Membrane inlet sensor techniques allow online, real-time and in situ analyses of gases during the investigation of aquatic environments. Of specific interest for research and applied objectives are quantifications of gases like methane, higher hydrocarbons, carbon dioxide, nitrogen, volatile organic compounds, and pollutants. For these objectives, membrane inlet systems are coupled to optical or solid state sensors as well as mass spectrometers. Besides the gases of interest, large quantities of water vapor are passing through the membrane and are thus introduced into the sensor system. This downgrades the detection limit, affects the ionization efficiency of mass spectrometers, or could cause the condensation of water within infrared sensors. In this study, we describe a novel robust, low-power cryotrap coupled to a membrane inlet system (CT-MIS), which is suitable to be used in harsh environments, including underwater applications. The entire system is of small size and weight, is operated at –85°C, and requires an energy consumption of less than 10 Watt. By using the cryotrap, we are able to reduce water vapor in the analytical line by more than 98%. The detection limits for major and trace gases are considerably improved this way. For the trace gas methane (CH4), the detection limit was lowered from 100 to 16 nmol/L, which allows the measurement of methane in surface and bottom waters of coastal areas and lakes. In case of membrane failure, the CT-MIS acts as a security system by shock-freezing the water, thus blocking the capillary connection to the analyzer unit.