Managed aquifer recharge (MAR) systems are an efficient barrier for many contaminants. The biotransformation of trace organic chemicals (TOrCs) strongly depends on the redox conditions as well as on the dissolved organic carbon availability. Oxic and oligotrophic conditions are favored for enhanced TOrCs removal which is obtained by combining two filtration systems with an intermediate aeration step. In this study, four parallel laboratory-scale soil column experiments using different intermittent aeration techniques were selected to further optimize TOrCs transformation during MAR: no aeration, aeration with air, pure oxygen and ozone. Rapid oxygen consumption, nitrate reduction and dissolution of manganese confirmed anoxic conditions within the first filtration step, mimicking traditional bank filtration. Aeration with air led to suboxic conditions, whereas oxidation by pure oxygen and ozone led to fully oxic conditions throughout the second system. The sequential system resulted in an equal or better transformation of most TOrCs compared to the single step bank filtration system. Despite the fast oxygen consumption, acesulfame, iopromide, iomeprol and valsartan were degraded within the first infiltration step. The compounds benzotriazole, diclofenac, 4-Formylaminoantipyrine, gabapentin, metoprolol, valsartan acid and venlafaxine revealed a significantly enhanced removal in the systems with intermittent oxidation compared to the conventional treatment without aeration. Further improvement of benzotriazole and gabapentin removal by using pure oxygen confirmed potential oxygen limitation in the second column after aeration with air. Ozonation resulted in an enhanced removal of persistent compounds (i.e., carbamazepine, candesartan, olmesartan) and further increased the attenuation of gabapentin, methylbenzotriazole, benzotriazole, and venlafaxine. Diatrizoic acid revealed little degradation in an ozone–MAR hybrid system.