The chlorophenol elimination potential of two identically designed fixed bed biofilm reactors was compared. One of the reactors was operated continuously, and the other in sequenced batch mode. In the continuous flow biofilm reactor (CFBR) a stratification of biomass occurred, whereas biomass in the sequencing batch biofilm reactor (SBBR) developed uniformly due to the use of an advanced fill strategy. Recirculation was needed to overcome biosorption during filling and to achieve equal biomass distribution. Under shock loading, degradation in SBBR was better than in CFBR. However, even the CFBR showed a high flexibility, i.e. it performed better than expected. Sorption properties in both reactors seem to be responsible for the flexibility in terms of break through. Experimental studies and modelling of sorption properties are necessary to describe the response of biofilm reactors to unsteady state conditions.