To observe long time changes of the greenhouse gas methane great efforts are made to determine its sources and sinks within a global atmospheric methane budget. Methane emissions from marine environments encounter large uncertainties due to the lack of data and adequate measuring facilities. In this thesis a new system is presented, which allows the continuous and autonomous measurement of methane and carbon dioxide in surface waters of the Baltic Sea. It permits measurements with an unrivaled spatio-temporal resolution and the identification of influencing parameters and processes.