In contrast to enhanced biological phosphorus removal (EBPR) in activated sludge systems mass transfer processes have a major influence on overall phosphorus removal in biofilm reactors. Based on results from a laboratory scale sequencing batch biofilm reactor (SBBR) and from a mathematical model the influence of the following processes on EBPR in biofilms was evaluated: (1) mass transfer limitation for oxygen, (2) mass transfer limitation for organic substrate, (3) lack of controlled removal of biomass from the system. It was shown that mass transfer of soluble components (oxygen and organic substrate) had only a minor effect on overall phosphorus removal. Soluble components fully penetrate the biofilm at certain times during the SBBR cycle as a consequence of SBBR operation with large concentration variations over the cycle time. The limiting processes for EBPR is the efficient removal of phosphorus rich biomass from the reactor. Biomass at the base of the biofilm that is not removed during backwashing will release accumulated phosphorus due to lysis or endogenous respiration and will not contribute to net phosphorus removal. For efficient operation of EBPR in biofilm systems regular and intensive backwashing resulting in thin biofilms is suggested.