Biofiltration has proved to be a useful system to treat combined sewer overflow (CSO). The study presented uses numerical simulation to detect the critical operating conditions of the filter. The multi-component reactive transport module CW2D was used for the simulation study. Single-event simulations of lab-scale-column experiments with varying boundary conditions regarding the throttle outflow rate were carried out. For the calibration of the CW2D model measurement results of four experiments in two lab-scale columns were used. The model was validated by simulating four events of two further columns filled with the same filter material. These columns were operating with higher throttle outflow rates than the columns used for calibration. For ammonium (NH4-N) a good fit between measured and simulated data could be achieved. However, the comparison of simulated and measured effluent concentrations of nitrate (NO3-N) showed that there is a need for further investigations mainly due to the uncertainties in the degradation process during dry periods between the loadings.