The study concerns modeling and simulation of the growth of biofilms with heterogeneous structures with a discrete mathematical model based on theory of cellular automata. The article presents two-dimensional density distributions of biofilms for microbial processes: oxidation of ammonium by Nitrosomonas europaea bacteria and glucose utilization by Pseudomonas aeruginosa bacteria. The influence of limiting substrate concentration in the liquid phase on biofilm structure was determined. It has been shown that the value of death rate coefficient of microorganisms has the qualitative and quantitative influence on the density and porosity of the biofilm.