Abstract. Methane and carbon dioxide were measured with an autonomous and continuous running system on a ferry line crossing the Baltic Sea on a 2-3 day interval from the Mecklenburg Bight to the Gulf of Finland in 2010. Surface methane saturations show great seasonal differences in shallow regions like the Mecklenburg Bight (103-507 %) compared to deeper regions like the Gotland Basin (96-161 %). The influence of controlling parameters like temperature, wind, mixing depth and processes like upwelling, mixing of the water column and sedimentary methane emissions on methane oversaturation and emission to the atmosphere are investigated. Upwelling was found to influence methane surface concentrations in the area of Gotland significantly during the summer period. In February 2010, an event of elevated methane concentrations in the surface water and water column of the Arkona Basin was observed, which could be linked to a wind-derived water level change as a potential triggering mechanism. The Baltic Sea is a source of methane to the atmosphere throughout the year, with highest fluxes occurring during the winter season. Stratification was found to promote the formation of a methane reservoir in deeper regions like Gulf of Finland or Bornholm Basin, which leads to long lasting elevated methane concentrations and enhanced methane fluxes, when mixed to the surface during mixed layer deepening in autumn and winter. Methane concentrations and fluxes from shallow regions like the Mecklenburg Bight are predominantly controlled by sedimentary production and consumption of methane, wind events and the change in temperature-dependent solubility of methane in the surface water. Methane fluxes vary significantly in shallow regions (e.g. Mecklenburg Bight) and regions with a temporal stratification (e.g. Bornholm Basin, Gulf of Finland). On the contrary, areas with a permanent stratification like the Gotland Basin show only small seasonal fluctuations in methane fluxes.