The removal of bromate (BrO3−) as a by-product of ozonation in subsequent managed aquifer recharge (MAR) systems, specifically in anoxic nitrate (NO3−)-reducing zones, has so far gained little attention. In this study, batch reactors and columns were used to explore the influence of NO3− and increased assimilable organic carbon (AOC) due to ozonation pre-treatment on BrO3− removal in MAR systems. 8 m column experiments were carried out for 10 months to investigate BrO3− behavior in anoxic NO3−-reducing zones of MAR systems. Anoxic batch experiments showed that an increase of AOC promoted microbial activity and corresponding BrO3− removal. A drastic increase of BrO3− biodegradation was observed in the sudden absence of NO3− in both batch reactors and columns, indicating that BrO3− and NO3− competed for biodegradation by denitrifying bacteria and NO3− was preferred as an electron acceptor under the simultaneous presence of NO3− and BrO3−. However, within 75 days’ absence of NO3− in the anoxic column, BrO3− removal gradually decreased, indicating that the presence of NO3− is a precondition for denitrifying bacteria to reduce BrO3− in NO3−-reducing anoxic zones. In the 8 m anoxic column set-up (retention time 6 days), the BrO3− removal achieved levels as low as 1.3 μg/L, starting at 60 μg/L (98% removal). Taken together, BrO3− removal is likely to occur in vicinity of NO3−-reducing anoxic zones, so MAR systems following ozonation are potentially effective to remove BrO3−.