A mathematical model for the simulation of the removal of hydrophilic compounds using biotrickling filtration was developed. The model takes into account that biotrickling filters operate by using an intermittent spraying pattern. During spraying periods, a mobile liquid phase was considered, while during non-spraying periods, a stagnant liquid phase was considered. The model was calibrated and validated with data from laboratory- and industrial-scale biotrickling filters. The laboratory experiments exhibited peaks of pollutants in the outlet of the biotrickling filter during spraying periods, while during non-spraying periods, near complete removal of the pollutant was achieved. The gaseous outlet emissions in the industrial biotrickling filter showed a buffered pattern; no peaks associated with spraying or with instantaneous variations of the flow rate or inlet emissions were observed. The model, which includes the prediction of the dissolved carbon in the water tank, has been proven as a very useful tool in identifying the governing processes of biotrickling filtration.