The production of methane in coastal sediments and its release to the water column is intensified by anthropogenic eutrophication and bottom water hypoxia, and it is still uncertain whether methane emissions to the atmosphere will be enhanced. Here, we assess seasonal variations in methane dynamics in a eutrophic, seasonally euxinic coastal basin (Scharendijke, Lake Grevelingen). In-situ benthic chamber incubations reveal high rates of methane release from the sediment to the water column (74–163 mmol m−2 d−1) during monthly measurements between March and October 2021. Comparison of these in-situ total benthic methane fluxes and calculated diffusive fluxes point towards a major role for ebullition. In spring and fall, when the water column was oxic, microbial removal of dissolved methane occurred aerobically in the bottom water. In summer, in contrast, dissolved methane accumulated to concentrations of up to 67 μmol L−1 below the oxycline. Shifts in δ13C–CH4 and δD-CH4 towards higher values and the abundant presence of methane oxidizing bacteria point towards removal of methane around the oxycline, likely through both aerobic and anaerobic pathways, with the latter possibly linked to iron oxide reduction. Shifts in δ13C–CH4 and δD-CH4 to lower values above the oxycline indicate that bubble dissolution contributed to dissolved methane. Methane emissions to the atmosphere were observed in all seasons with the highest, in-situ measured diffusive fluxes (1.2 mmol m−2 d−1) upon the onset of water column mixing at the end of summer. Methane release events during the measurement of in-situ water-air fluxes and model calculations point towards a flux of methane to the atmosphere in the form of bubbles, which bypass the microbial methane filter. The model calculations suggest a potential year-round ebullitive methane flux between 30 and 120 mmol m−2 d−1. We conclude that methane emissions from eutrophic coastal systems may be much higher than previously thought because of ebullition.