Structural and microbial heterogeneity occurs in almost any type of biofilm system. General approaches for the design of biofilm systems consider biofilms as homogeneous and of constant thickness. In order to improve the design of biofilms systems, models need to incorporate structural heterogeneity and the effect of inert microbial mass. We have improved a 2D biofilm model based on cellular automata (CA) and used it to simulate multidimensional biofilms with active and inert biomass including a self-organizing development. Results indicate that the presence of inert biomass within biofilm structures does not change considerably the substrate flux into the biofilm because the active biomass is located at the surface of the biofilm. Long-term simulations revealed that although the biofilm system is highly heterogeneous and the microstructure is continuously changing, the biofilm reaches a dynamic steady-state with prediction of biofilm thickness and substrate flux stabilizing on a delimited range.