This study aims to enlighten the geometric changes at the pore scale of filtering media of Vertical Flow Treatment Wetlands (VFTW) and their influence on oxygenation during the rest period. A 3-day ex-situ drying of six samples of a VFTW was carried out at controlled temperature, and relative humidity simulating the rest period. Samples (16-cm long) were taken at the end of the feeding period of a filter in the first stage and let dry. Three of the samples were sterilized before drying using gamma rays to differentiate oxygenation without bacterial activity. At 0, 1 and 3 days of drying, X-ray scans of the samples were performed to observe changes in the samples structure. After each scan, the oxygen transport within the sample was studied by measuring vertical oxygen concentration profiles. Although X-ray tomography allows small structure changes to be detected, it is necessary to modify the drying conditions perform a more realistic drying. The complexity of the results of oxygen profiles lead us to suggest the use of CFD tools to understand how oxygenation occurs.