We evaluate the variability of carbon dioxide and methane in the surface layer of the north-eastern basins of the Baltic Sea in 2018. We show that the shallower coastal areas have considerably higher spatial variability and seasonal amplitude of surface layer pCO₂ and cCH₄ than measured in the offshore areas of the Baltic Sea. Despite this high variability, caused mostly by coastal physical processes, the average annual air–sea CO₂ fluxes differed only marginally between the sub-basins.