Understanding the fundamental aspects of transport through biomaterials is a necessity for a vast range of bio-related studies. Biofilm formation on the surface of adsorptive media such as granular activated carbon (GAC) has been extensively used to remove organic materials, nitrogen species, heavy metals, and other contaminants in wastewater treatment. In this study, a multilayer mass transfer system consisting of the reactor's bulk fluid, diffusion layer, biofilm, and GAC is modeled. In order to consider the equilibrium at the interface of biofilm and activated carbon, Freundlich adsorption method is applied. The interfacial interactions are taken into account in the biodegradation process. The results of model prediction are compared with the available experimental data and show a very good agreement. The effect of biofilm formation on the reactor porosity is considered through a porous media approach. Furthermore, the influence of variation in particle diameters on the removal efficiency is studied. It can be seen that porosity alteration as a result of biofilm formation within the carbon bed has a noticeable effect on the removal efficiency.