Water quality changes associated with the passage of aerobic reverse osmosis (RO) treated recycled water through a deep anaerobic pyritic aquifer system was evaluated in sediment-filled laboratory columns as part of a managed aquifer recharge (MAR) strategy. The fate of nine recycled water trace organic compounds along with potential negative water quality changes such as the release of metal(loid)s were investigated in large-scale columns over a period of 12 months. The anaerobic geochemical conditions provided a suitable environment for denitrification, and rapid (half-life <1–25 days) degradation of the endocrine disrupting compounds (bisphenol A, 17β-estradiol, 17α-ethynylestradiol), and iodipamide. However, pharmaceuticals (carbamazepine and oxazepam), disinfection by-products ( N-nitrosodimethylamine, N-nitrosomorpholine) and iohexol did not degrade rapidly (half-life > 100 days). High retardation coefficients (R) determined for many of the trace organics (R 13 to 67) would increase aquifer residence time and be beneficial for many of the slow degrading compounds. However, for the trace organics with low R values (1.1–2.6) and slow degradation rates (half-life > 100 days), such as N-nitrosodimethylamine, N-nitrosomorpholine and iohexol, substantial biodegradation during aquifer passage may not occur and additional investigations are required. Only minor transient increases in some metal(loid) concentrations were observed, as a result of either pyrite oxidation, mineral dissolution or pH induced metal desorption, followed by metal re-sorption downgradient in the oxygen depleted zone.