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The summer heat wave in 2018 led to the highest recorded water temperatures since 1926 – up to 21°C – in bottom coastal waters of the Baltic Sea, with implications for the respiration patterns in these shallow coastal systems. We applied cavity ring-down spectrometer measurements to continuously monitor carbon dioxide (CO₂) and methane (CH₄) surface-water concentrations, covering the coastal archipelagos of Sweden and Finland and the open and deeper parts of the Northern Baltic Proper. This allowed us to (i) follow an upwelling event near the Swedish coast leading to elevated CO₂ and moderate CH₄ outgassing, and (ii) to estimate CH₄ sources and fluxes along the coast by investigating water column inventories and air-sea fluxes during a storm and an associated downwelling event. At the end of the heat wave, before the storm event, we found elevated CO₂ (1583 μatm) and CH₄ (70 nmol/L) concentrations. During the storm, a massive CO₂ sea-air flux of up to 274 mmol m^–2 d^–1 was observed. While water-column CO₂ concentrations were depleted during several hours of the storm, CH₄ concentrations remained elevated. Overall, we found a positive relationship between CO₂ and CH₄ wind-driven sea-air fluxes, however, the highest CH₄ fluxes were observed at low winds whereas highest CO₂ fluxes were during peak winds, suggesting different sources and processes controlling their fluxes besides wind. We applied a box-model approach to estimate the CH₄ supply needed to sustain these elevated CH₄ concentrations and the results suggest a large source flux of CH₄ to the water column of 2.5 mmol m^–2 d^–1. These results …