In article the improvement model of forming the biofilm structure taking into account on the heterogeneity along its thickness with steady and changeable porosity in the constant and transient conditions at the aerobic wastewater treatment and taking into account on the influence of different hydrodynamical factors on its operation, availability of the other substances in particular inert biomass and polymeric ones is proposed. To a great extent the attention was allotted on investigation of the influence of the biofilm heterogeneity on the mass transport processes. Besides the analysis of the main factors the correlations for building of the mathematical model of the wastewater treatment with using of biofilms was carried out. It was shown that for the practical calculations of wastewater treatment the one-dimensional model of homogeneous biofilm is proposed taking into account on the obtained valuations and limitation of its using. Comparisons the calculation results with experimental data were shown that such homogeneous model in many cases has a good agreement with experimental ones. The some recommendations relative determination of the form of the biofilms surface are proposed. It can to say that the effectiveness of biological methods of removing pollutants of various origins in particular organic compounds (OC) and nitrogen (N) in various bioreactors may be improved by means of the arrangement on the surface of the additional loading a fixed biocenosis with a high concentration of microorganisms (biofilm).