Three different hydraulic retention times (HRTs) were investigated for NH4+-N and Mn2+ removal using an upflow biological aerated system (BAF) as a new approach in drinking water treatment system. Currently in Malaysia, there is no specific treatment for NH4+-N and Mn2+ in drinking water treatment plant. BAF is a well known system in biological treatment for wastewater but not for drinking water treatment. This study showed that at 24 hours operation of BAF system, about 91.3% of COD, 94.4% of NH4+-N and 83.4% of Mn2+ were efficiently removed. When HRT was decreased to 12 and 6 hours, there was insignificant removal difference in COD and NH4+-N removal. Instead, the Mn2+ removal significantly showed an increasing trend (p<0.05) as the HRT was decreased with the removal percentages of 92.1% (12 hours) and 94.8% (6 hours). Real-time monitoring through pH, ORP and DO profiles confirmed that completed simultaneous NH4+-N and Mn2+ removal occurred within 6 to 7 hours HRT.