Dynamic fluctuations in water table elevation cause the entrapment of air, which affects the hydraulic properties of the porous medium in the capillary fringe as well as the biogeochemical status of the underlying, potentially O2–depleted groundwater. In this study, we conducted quasi two-dimensional flow-through experiments at the laboratory bench scale to investigate in detail the mass transfer of O2 in a fluctuating capillary fringe. We evaluated the effects of different boundary conditions such as single drainage and imbibition events as well as periodic fast and slow water table fluctuations. High-resolution vertical profiles of O2 concentration, measured at two distances in the horizontal groundwater flow direction, and mass fluxes, determined in the effluent of the flow-through chamber, were used to quantify O2 transfer under the different boundary conditions applied. The results show that the partitioning between the aqueous and the gaseous phases plays a significant role in the supply of O2 to groundwater at medium time scales. In the case of fast water table fluctuations, the specific yield has to be considered. The experiments with a periodically changing boundary condition demonstrate that highly dynamic fluctuations of the water table enhance the mass transfer of O2 from the atmosphere into the groundwater when compared with steady-state conditions. Moreover, the characteristics of the water table fluctuations determine a specific dynamic response of the system: we observed an approximately double amount of O2 transferred to the groundwater when applying slow fluctuations compared with the case of cyclic, abrupt changes in the water table elevation.