Combination of a partial nitritation process and an anaerobic ammonium oxidation process for the treatment of sludge reject water has some general cost-efficient advantages compared to nitrification–denitrification. The integrated process features two-stage autotrophic conversion of ammonium via nitrite to dinitrogen gas with lower demand for oxygen and no external carbon requirement. A nitrifying membrane-assisted bioreactor (MBR) for the treatment of sludge reject water was operated under continuous aeration at low dissolved oxygen (DO) concentrations with the purpose of generating nitrite accumulation. Microfiltration was applied to allow a high sludge retention time (SRT), resulting in a stable partial nitritation process. During start-up of the MBR, oxygen-limited conditions were induced by increasing the ammonium loading rate and decreasing the oxygen transfer. At a loading rate of 0.9 kg N m−3 d−1 and an oxygen concentration below 0.1 mg DO L−1, conversion to nitrite was close to 50% of the incoming ammonium, thereby yielding an optimal effluent within the stoichiometric requirements for subsequent anaerobic ammonium oxidation. A mathematical model for ammonium oxidation to nitrite and nitrite oxidation to nitrate was developed to describe the oxygen-limited partial nitritation process within the MBR. The model was calibrated with in situ determinations of kinetic parameters for microbial growth, reflecting the intrinsic characteristics of the ammonium oxidizing growth system at limited oxygen availability and high sludge age. The oxygen transfer coefficient (KLa) and the ammonium-loading rate were shown to be the appropriate operational variables to describe the experimental data accurately. The validated model was used for further steady state simulation under different operational conditions of hydraulic retention time (HRT), KLa, temperature and SRT, with the intention to support optimized process design. Simulation results indicated that stable nitrite production from sludge reject water was feasible with this process even at a relatively low temperature of 20°C with HRT down to 0.25 days. © 2004 Wiley Periodicals, Inc.