Long-term effects of ZnO nanoparticles on the system performance of an MBR were investigated together with their removal behavior in the system. Continuous operation over 242 days showed that ZnO NPs at both 1.0 and 10.0 mg/L caused moderate deterioration in the removal of COD, nitrogen and phosphorus. Denitrification was affected upon the exposure but recovered subsequently. Although no significant acute effect on ammonia-oxidization was observed, permanent inhibition occurred after long-term exposure. Nitrite-oxidization was not affected even with 10.0 mg/L ZnO NPs. Significant changes were observed in activated sludge properties which resulted in severe membrane fouling. Although ZnO NPs caused changes in the bacteria community structure, the diversity however remain unchanged. ZnO NPs was removed effectively in the MBR (>98%) with biosorption being a major removal mechanism. Membrane filtration also played an important role (20% of the total removal) especially at high ZnO NPs concentrations (around 10.0 mg/L). (C) 2015 Elsevier Ltd. All rights reserved.