The vertical transport of methane from the deep water body towards the redox zone as well as differing hydrographic conditions within the redox zone were identified as major factors that determine the pelagic methane oxidation. The deep water methane inventory of the eastern Gotland Basin showed a seasonal pattern, with concentrations increasing during spring/summer and decreasing during fall/winter as a direct result of the seasonal varying vertical turbulent diffusivity. The western Gotland Basin showed no clear correlation between the seasons and the observed deep water methane variability.