The importance of soil heterogeneity for methane emission from a wetland soil is assessed by in situ point measurements of depth-specific O2 and CH4 concentrations and simultaneous soil CH4 fluxes at contrasting water levels. Profile measurements, and associated assumptions in their interpretation, were validated in a controlled mesocosm drainage and saturation experiment applying planar O2 optodes and membrane inlet mass spectrometry. Results show that peat soil is heterogeneous containing dynamic macropore systems created by both macrofauna and flora, which facilitate preferential flow of water, O2 and CH4 and vary temporally with changes in the moisture regime. The O2 content above the water table after drainage varied horizontally from 0 to 100% air saturation within few mm. Oxic zones were observed below the water level and anoxic zones were observed in layers above the water level in periods up to days after changes in the water level. This study shows that although water table position is a competent proxy of soil CH4 fluxes at larger spatio-temporal scales, it becomes inadequate at higher spatial resolution, i.e. at the scale of the soil pedon and below. High resolution O2 measurements using planar O2 optodes have great potential to enhance our understanding of the effect of the water table position on O2 dynamics on scales of several cm to mm in wetland soils.