Spatiotemporal characterisation of the soil redox status within the capillary fringe (CF) is a challenging task. Air-filled porosities (ε), oxygen concentration (O2) and soil redox potential (EH) are interrelated soil variables within active biogeochemical domains such as the CF. We investigated the impact of water table (WT) rise and drainage in an undisturbed topsoil and subsoil sample taken from a Calcaric Gleysol for a period of 46 days. We merged 1D (EH and matric potential) and 2D (O2) systems to monitor at high spatiotemporal resolution redox dynamics within self-constructed redoxtron housings and complemented the data set by a 3D pore network characterization using X-ray microtomography (X-ray μCT). Depletion of O2 was faster in the organic matter- and clay-rich aggregated topsoil and the CF extended >10 cm above the artificial WT. The homogeneous and less-aggregated subsoil extended only 4 cm above the WT as indicated by ε–O2–EH data during saturation. After drainage, 2D O2 imaging revealed a fast aeration towards the lower depths of the topsoil, which agrees with the connected ε derived by X-ray μCT (εCT_conn) of 14.9% of the total porosity. However, small-scaled anoxic domains with O2 saturation <5% were apparent even after lowering the WT (down to 0.25 cm2 in size) for 23 days. These domains remained a nucleus for reducing soil conditions (EH < −100 mV), which made it challenging to characterise the soil redox status in the CF. In contrast, the subsoil aeration reached O2 saturation after 8 days for the complete soil volume. Values of εCT_conn around zero in the subsoil highlighted that soil aeration was independent of this parameter suggesting that other variables such as microbial activity must be considered when predicting the soil redox status from ε alone. The use of redoxtrons in combination with localised redox-measurements and image based pore space analysis resulted in a better 2D/3D characterisation of the pore system and related O2 transport properties. This allowed us to analyse the distribution and activity of microbiological niches highly associated with the spatiotemporal variable redox dynamics in soil environments.