The paper presents the setting up of a mathematical model for membrane bioreactor able to simulate physical-biological wastewater organic removal. The model is basically divided into two sub-models: the first sub-model is basically devoted for the simulation of the biological features and the second one for the physical processes. In particular regarding the biological aspects, the ASM concept has been employed. On the other hand, the physical processes have been modelled considering the deep-bed theory taking into account not only the effect of the physical membrane filtration but also the cake layer effect. This latter operates as a biological membrane leading to a further reduction of the effluent COD. The model was applied to a SMBR pilot plant characterized by hollow fibre membrane module in submerged configuration. The SMBR was fed by raw wastewater collected from the Palermo (IT) WWTP and it was in operation for a total period of 130 days. During the whole experimentation the TSS was maintained meanly constant with periodic sludge withdrawal, in order to analyse the role of cake layer on organic removal. The model results are interesting and confirm the importance of cake deposition in the filtration process. The developed model can be employed as a useful tool in optimizing operation conditions as well as design issues for SMBR systems. (c) 2008 Elsevier B.V. All rights reserved.