Treatment of polluted air stream with toluene in a biofilter under quasi-steady-state condition is described with a three-dimensional (3-D) pore network model. The efficiency of the process depends on the pore structure of the biofilter media. The previous models for the process, considered transport and reaction equations mostly in the continuum systems. They cannot show the effect of pore spaces' morphology, different pore size distributions and connectivity types. We used the 3-D pore network model to simulate the pore structure and to study the effects of biofilm growth on pore size distribution and pore connectivity on the biofilter performance. This model predicts the toluene conversion, pressure drop profiles, biofilm thickness and clogging in the biofilter. Our developed model assumes a nonlinear kinetic for the biodegradation reaction of toluene in the biofilm. The differential equations of the model are solved numerically. Model results indicated that biofilter media with smaller mean pore size and higher connectivity have a higher toluene conversion. To investigate the validity of the model, we compared the model results with experimental data and found satisfying similarities. (C) 2010 Elsevier Ltd. All rights reserved.