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The objective of this article is to define and validate a mathematical model that desribes the physical and biological processes occurring in a trickle‐bed air biofilter for waste gas treatment. This model considers a two‐phase system, quasi‐steady‐state processes, uniform bacterial population, and one limiting substrate. The variation of the specific surface area with bacterial growth is included in the model, and its effect on the biofilter performance is analyzed. This analysis leads to the conclusion that excessive accumulation of biomass in the reactor has a negative effect on contaminant removal efficiency. To solve this problem, excess biomass is removed via full media fluidization and backwashing of the biofilter. The backwashing technique is also incorporated in the model as a process variable. Experimental data from the biodegradation of toluene in a pilot system with four packed‐bed reactors are used to validate the model. Once the model is calibrated with the estimation of the unknown parameters of the system, it is used to simulate the biofilter performance for different operating conditions. Model predictions are found to be in agreement with experimental data. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 583–594, 1997.