The use of phototrophic biofilms in wastewater treatment has been recognized as a potential option for development of new reactor configurations. For better understanding of these systems, a numerical model was developed including relevant microbial processes. As a novelty, this model was implemented in COMSOL Multiphysics, a modern computational environment for complex dynamic models. A two-dimensional biofilm model was used to study the spatial distribution of microbial species within the biofilm and along the length of the reactor. The biofilm model was coupled with a one-dimensional plug-flow bulk liquid model. The impact of different operational conditions on the chemical oxygen demand (COD) and ammonia conversions was assessed. The model was tuned by varying two parameters: the half-saturation coefficient for light use by phototrophs and the oxygen mass transfer coefficient. The mass transfer coefficient was found to be determining for the substrate conversion rate. Simulations indicate that heterotrophs would overgrow nitrifiers and phototrophs within the biofilm until a low biodegradable COD value in the wastewater is reached (organic loading rate <2.32 gCOD/(m2 d)). This limits the proposed positive effect of treating wastewater with a combination of algae and heterotrophs/autotrophs. Mechanistic models like this one are made for understanding the microbial interactions and their influence on the reactor performance.