Abstract. Coastal areas contribute significantly to the emissions of methane (CH4) from the ocean. In order to decipher its temporal variability in the whole water column, dissolved CH4 was measured on a monthly basis at the Boknis Eck Time Series Station (BE) located in Eckernförde Bay (SW Baltic Sea) from 2006 to 2017. BE has a water depth of about 28 m, and dissolved CH4 was measured at six water depths ranging from 0 to 25 m. In general, CH4 concentrations increased with depth, indicating a sedimentary release of CH4. Pronounced enhancement of the CH4 concentrations in the bottom layer (15–25 m) was found during February, May–June and October. CH4 was not correlated with Chlorophyll a or O2 over the measurement period. Unusually high CH4 concentrations (of up to 696 nM) were sporadically observed in the upper layer (0–10 m; e.g., in November 2013 and December 2014) and coincided with major Baltic inflow (MBI) events. Surface CH4 concentrations were always supersaturated throughout the monitoring period, indicating that Eckernförde Bay is an intense but highly variable source of atmospheric CH4. We did not detect significant temporal trends in CH4 concentrations or emissions, despite ongoing environmental changes such as warming and deoxygenation in Eckernförde Bay. Overall, the CH4 variability at BE is driven by a complex interplay of various biological and physical processes.