Sponge carrier media provide a large surface area for biofilm support; however, little information is known about how to model their dual nature as a moving bed and as porous media. To investigate the interaction of mass transfer and detachment with bio-clogging, a novel biofilm model framework was built based on individual-based modelling, and hydrodynamics were modelled using the lattice Boltzmann method. The combined model structure enabled the simulation of oxygen and biomass distribution inside the porous network as well as inside the biofilm. In order to apply the model to moving bed biofilm reactors (MBBR), biofilm detachment due to abrasion (carrier collisions) was modelled to be dependent on intracarrier distance. In the initial growth stage, biofilm grew homogeneously on the internal skeleton after which a more discontinuous growth developed which significantly increased permeability. Low detachment rates caused clogging in the outer pores which limited growth of biofilm to the surface region of the sponge. High detachment rates on the surface enabled deeper oxygen penetration with higher internal biomass activity. The degree of clogging was also sensitive to the presence of extracellular polymeric substances because of its large spatial occupancy.