Heavy metal and NH4+-N co-contaminated wastewater are frequently found, and the presence of NH4+-N makes it extremely difficult to treat. In the present study, bench-scale and pilot-scale experiments were conducted to investigate the simultaneous removal of beryllium and NH4+-N from smelting wastewater by biological aerated filter (BAF) reactors. The results of the five-stage BAF reactors showed that the system could endure shock loadings. The average removal efficiency for beryllium and NH4+-N was 92.6% and 95.0%, respectively. Sequence extraction indicates that the primary removal mechanism in the first two reactors was precipitation, whereas the organic-bound fraction was predominant in the last three reactors due to the high accumulation rates of beryllium inside the microbial cells. Polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) and sequence analysis of 16S rDNA gene fragments showed that N-oxidizing bacteria (Nitrosomonas sp. and Beta proteobacterium CH24i) were primarily detected in the first two BAF reactors, in accordance with their high NH4+-N removal efficiencies, and metal-resistant bacteria (Actinobacteria sp.) were found in all BAF reactors. (C) 2012 Elsevier B.V. All rights reserved.