The biological aerated filter (BAF) system, a new alternative in drinking water treatment, was designed to remove NH4+-N and Mn2+ simultaneously. This study aimed to control the aeration time in the BAF system for simultaneous NH4+-N and Mn2+ removal to achieve the Malaysian effluent quality regulation for drinking water. The experiment was conducted under four strategies of Si, S2, S3 and S4. The results demonstrated that acceptable levels of NH4+-N and Mn2+ were achieved over a 6 h aeration period (S1), producing effluent concentrations of 0.7 mg/L (93.2% removal) and 0.08 mg/L (79.6% removal), respectively. At the initial treatment of Si and S2, the dissolved oxygen (DO) level rapidly increased until it reached a saturated concentration (6.8 mg/L DO) after 2 h period. Automatic on-off aeration time to maintain 3 mg/L DO set point (S4) resulted with a good effluent quality of NH4+-N and Mn2+ compared with the 2 mg/L DO set point (S3) which did not meet the regulated standard limits. Through the automatic on-off aeration time, the saturated and excessive DO levels in the BAF system can be avoided consequently reduce the wastage of energy and electrical consumption for simultaneous NH4+-N and Mn2+ removal from drinking water treatment. (c) 2012 The Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.