The Baltic Sea, a brackish basin characterised by significant organic matter deposition, presents a crucial area for climate change research. This study examines the long-term evolution of methane geochemistry in sediments from four sites within the Gotland basins of the Baltic Sea, spanning the past 14,000 years since deglaciation. This timescale enables us to capture the full transition from lacustrine to marine conditions and link past organic matter accumulation with present-day methane dynamics. Using a transport-reaction model, we also explore future scenarios (2020−2100), aligned with climate projections, to assess how changes in bottom water temperature, organic matter loading, and freshwater input may influence methane production and emission from sediments. Our findings reveal that a 2 °C rise in bottom water temperature could increase free gas formation, though without directly impacting methane release into the sea. However, elevated organic matter loading significantly influences methane diffusion through the seafloor. Additionally, anticipated freshwater influx and subsequent reductions in sulphate concentrations will substantially enhance methane diffusion into seawater. The model projects that rising temperatures, eutrophication, and freshwater input will together drive increased methane emissions into the Baltic Sea, with potential consequences for climate change amplification.