<p>Methane (CH<sub>4</sub>) is a climate-relevant atmospheric trace gas which is emitted to the atmosphere from coastal areas such as the Baltic Sea. The oceanic CH<sub>4</sub> emission estimates are still associated with a high degree of uncertainty partly because the temporal and spatial variability of the CH<sub>4</sub> distribution in the ocean surface layer is usually not known. In order to determine the small-scale variability of dissolved CH<sub>4</sub> we set up a purge-and-trap system with a significantly improved precision for the CH<sub>4</sub> concentration measurements. We measured the distribution of dissolved CH<sub>4</sub> in the water column of the western Kiel Bight and Eckernförde Bay in June and September 2018. The top 1 m was sampled in high-resolution to determine potential small-scale CH<sub>4</sub> concentration gradients within the mixed layer. CH<sub>4</sub> concentrations throughout the water column of the western Kiel Bight and Eckernförde Bay were generally higher in September than in June. The increase of the CH<sub>4</sub> concentrations in the bottom water was accompanied by a strong decrease in O<sub>2</sub> concentrations which led to anoxic conditions favorable for microbial CH<sub>4</sub> production in September. In summer 2018, northwestern Europe experienced a pronounced heatwave. However, we found no relationship between the anomalies of water temperature and excess CH<sub>4</sub> in both the surface and the bottom layer at the site of the Boknis Eck Time-Series Station (Eckernförde Bay). Therefore, the 2018 European heatwave most likely did not affect the observed increase of the CH<sub>4</sub> concentrations in the western Kiel Bight from June to September 2018. The high-resolution measurements of the CH<sub>4</sub> concentrations in the upper 1 m of the water column were highly variable and showed no uniform decreasing or increasing gradients with water depth. Overall, our results show that the CH<sub>4</sub> distribution in the water column of the western Kiel Bight and Eckernförde Bay is strongly affected by both large-scale temporal (i.e. seasonal) and small-scale spatial variabilities which need to be considered when quantifying the exchange of CH<sub>4</sub> across the ocean/atmosphere interface.</p>