Understanding mechanisms of controlling the bacteria growth and degradation of pollutants is critical for effective improvements in water treatment and bioremediation in porous media. In this study, we developed an integrated model of individual‐based model and multicomponent lattice Boltzmann method to study interactions of oxygen, bioclogging, chemical oxygen demand (COD) removal, and their influence on growth and permeability of microbial biofilms. We found biofilm growth to be very heterogeneous on the surface of the solid matrix and pores. There is a biofilm porosity threshold. Beyond this threshold, the porosity of biofilm has no obvious influence on the flow rate and COD removal. We also studied the influence of initial cell populations, bulk oxygen concentration and biofilm permeability on the flow rate and COD removal. It demonstrated the capability of the present model to investigate biofilm growth, clogging and contaminants degradation in porous media, and its potential applications in water treatment.