The effluent activity from a well-known pockmark structure in Eckernforde Bay was monitored for methane, salinity, and temperature signals in the water column intermittently over three years between 1991, 1993 and 1994. Groundwater discharge from an aquifer into the brackish waters of the western Baltic, dilutes bottom water satinities to values as low as 2.9‰ Seasurface height and the amount of precipitation preceding sampling periods by 5 days correlated significantly with the rate of groundwater discharge. Concentrations of methane in bottom water at the pockmark site were strongly influenced by seepage intensity. At two sampling sites (control and pockmark site) distinctly lower methane concentrations were observed towards the sea surface, although the entire water body of Eckernforde Bay appears to be affected by methane seeping from the sediments. This is supported by high methane concentrations above equilibrium with atmospheric methane throughout most of the year. Maximum concentration above the equilibrium value in surface waters was 2800‰. Methane flux from surface waters into the atmosphere follows strong seasonal variations, with maximum values in the winter (200-400 μmol m-2 d-1). The study reveals the important role of coastal oceans in the global methane cycle, as an intense but variable source of methane of largely unknown magnitude.