This study was conducted to evaluate the kinetics of simultaneous removal of COD, NH4+-N and Mn2+ in a biological aerated filter (BAF) system. The evaluation was performed in a BAF system under various conditions of organic loading rates (OLRs) (0.2–1.0kgCOD/m3d), aeration rates (ARs) (0–2L/min) and hydraulic retention times (HRTs) (6–24h). Increasing the OLR and AR in the BAF system increased simultaneous COD, NH4+-N and Mn2+ removal. Meanwhile, decreasing the HRT resulted in an insignificant impact on COD and NH4+-N removal, but Mn2+ removal was significantly affected. The Monod model was used to estimate the kinetic coefficients of μmax and KS for the three substrates, i.e. COD, NH4+-N and Mn2+. The kinetic coefficients were found to be 0.28d−1(μmax,COD) and 5.1mg-COD/L (KS,COD) for COD, 0.17d−1 (μmax,NH4+-N) and 0.03mg-N/L (KS,NH4+-N) for NH4+-N, and 0.28d−1 (μmax,M2+) and 0.03mg-Mn2+/L (KS,M2+) for Mn2+. From the Monod parameter estimation, the specific growth rate of biomass cells was adequately predicted for high quality effluent of simultaneous COD, NH4+-N and Mn2+ removal.