Fouling of membrane bioreactor (MBR) has been studied intensively. Because of the high concentration of carbonates, scaling can be a serious problem in anaerobic bioreactor, which attracts little attention. In this study, the wastewater was treated with an anaerobic process followed by either a submerged or a sidestream aerobic membrane reactor. The wastewater was spiked with calcium to investigate the effect of scaling on membrane filtration. Very little scaling was detected in the external membrane system (the sidestream MBR). Results from chemical cleaning of internal membrane system indicated that the flux decline caused by membrane scaling was far more severe than that by membrane fouling. However, the flux decline from membrane scaling can be effectively recovered by the chemical cleaning of EDTA and NaOCl.