It was demonstrated that simultaneous removal of ammonia and manganese could be accomplished by biological aerated filter (BAF) with low-cost lava as media. Long-term operation performance and impact factors were systematically studied. DGGE analysis demonstrated that ammonia oxidizing bacteria (AOB), manganese oxidizing bacteria (MOB) and simultaneous ammonia and manganese oxidizing bacteria (SAMOB) co-existed in the bio-film. Ammonia and manganese concentration profiles along the height of BAF column, including that in the influent and effluent, were investigated with varying hydraulic loadings, aeration intensities and feed ammonia concentrations. It was inferred that AOB and MOB may have different spatial distribution in vertical direction, and AOB and MOB may compete for oxygen capture or be present on different layers of the bio-films. Further work should focus on the distribution of AOB, MOB and SAMOB in the reactor and optimize it for more efficient mass transfer and better system performance. (c) 2013 Elsevier Ltd. All rights reserved.