Long-term column studies with ozonated secondary effluent were conducted to evaluate the removal of dissolved organic carbon (DOC) and to assess formation and stability of the oxidation by-product bromate in combined ozonation and managed aquifer recharge (MAR) systems. DOC removal during simulated MAR was continuously increased from approximately 20 to 40% by pretreatment with ozone indicating the high potential of this combination to remove disinfection by-product (DBP) precursors. This improvement in DOC removal was likely caused by transforming DOC into fractions that are more amenable to biodegradation, as well as the supply of dissolved oxygen favouring aerobic degradation processes. Bromate formation during ozonation of secondary effluent from the Berlin-Ruhleben WWTP exceeded the limit of the EU Drinking Water Directive at a specific ozone consumption of >0.9–1.0 mg O3/mg DOC0. During oxic infiltration, no significant removal of bromate could be observed. Under anoxic conditions, bromate concentration was efficiently reduced. Additional biodegradation tests in small-scale columns indicated a simultaneous consumption of nitrate and bromate as electron acceptors.