A two-dimensional, particle-based biofilm model coupled with mass transport and computational fluid dynamics was developed to simulate autotrophic denitrification in a spiral-wound membrane biofilm reactor (MBfR), where hydrogen is supplied via hollow-fiber membrane fabric. The spiral-wound configuration consists of alternating layers of plastic spacer net and membrane fabric that create rows of flow channels, with the top and bottom walls comprised of membranes. The transversal filaments of the spacer partially obstruct the channel flow, producing complex mixing and shear patterns that require multidimensional representation. This study investigated the effect of hydrogen and nitrate concentrations, as well as spacer configuration, on biofilm development and denitrification fluxes. The model results indicate that the cavity spacer filaments, which rest on the bottom membranes, cause uneven biofilm growth. Most biofilm resided on the bottom membranes, only in the wake of the filaments where low shear zones formed. In this way, filament configuration may help achieve a desired biofilm thickness. For the conditions tested in this study, the highest nitrate fluxes were attained by minimizing the filament diameter and maximizing the filament spacing. This lowered the shear stress at the top membranes, allowing for more biofilm growth. For the scenarios studied, biomass limitation at the top membranes hindered performance more significantly than diffusion limitation in the thick biofilms at the bottom membranes. The results also highlighted the importance of two-dimensional modeling to capture uneven biofilm growth on a substratum with geometrical complexity. © 2013 Elsevier Ltd.