BACKGROUND: A novel membrane bioreactor (MBR) is described, employing an intermediate clarifier. Unlike the established function of a final clarifier in a conventional biological nutrient removal system, the role of an intermediate clarifier has rarely been studied. Thus, this work focused on explaining the fate of nutrients in the intermediate clarifier, as influenced by the hydraulic retention time (HRT) of the preceding anaerobic bioreactor. RESULTS: The system was tested with two different anaerobic/anoxic/aerobic biomass fractions of 0.25/0.25/0.5 (run 1) and 0.15/0.35/0.45 (run 2) using synthetic wastewater. The major findings of the study were that phosphorus (P) removal was affected by the role of the intermediate clarifier. In run 1, P was removed at a rate 0.16 g d(-1) in the intermediate clarifier while in run 2, additional P was released at 0.49 g d(-1). The nitrogen (N) removal efficiencies were 74 and 75% for runs 1 and 2 respectively, while P removal was 91 and 96%. P uptake by denitrifying phosphate accumulating organisms [DPAOs) accounted for 41 - 52% of the total uptake in the MBR. CONCLUSIONS: This study found that the intermediate clarifier assisted chemical oxygen demand (COD), N, and P removal. With respect to the fate of P, the intermediate clarifier functioned as an extended anaerobic zone when the HRT of the preceding anaerobic zone was insufficient for P release, and as a pre-anoxic zone when the anaerobic HRT was adequate for P release. (C) 2008 Society of Chemical Industry