A biofilm model was developed to describe the simultaneous NO3- and SeO42- reduction in a H-2-based membrane biofilm reactor (MBfR). Model calibration and validation was conducted using the experimental data of a reported H-2-based MBfR. With a good level of identifiability, the SeO42- affinity constant and the SeO32- affinity constant were estimated at 9.80 +/- 0.51 g Se m(-3) and 1.83 +/- 0.38 g Se m(-3), respectively. The model was then applied to evaluate the effects of key operating conditions on the single-stage H-2-based MBfR and the role of reactor configuration through comparing two-stage to single-stage MBfR systems. The results showed that (i) high SeO42- or low NO3- concentration in the influent favored the growth of selenate-reducing bacteria (SeRB) and therefore benefited the Se removal, (ii) the influent dissolved oxygen slightly inhibited the Se removal through enhancing the aerobic microbial respiration on H-2, (iii) the H-2 supply should be controlled at a proper level to avoid SeRB suppression and H-2 wastage, (iv) thin biofilm should be avoided to ensure a protected niche for SeRB and therefore a promising Se removal, and (v) the two-stage MBfR configuration offered relatively higher efficiency in removing Se and NO3- simultaneously under the same loading condition. (C) 2018 Elsevier Ltd. All rights reserved.