The release of oil sands process-affected water (OSPW) into the environment is a concern because it contains persistent organic pollutants that are toxic to aquatic life. A modified Ludzack–Ettinger membrane bioreactor (MLE-MBR) with a submerged ceramic membrane was continuously operated for 425 days to evaluate its feasibility on OSPW treatment. A stabilized biomass concentration of 3730 mg mixed liquor volatile suspended solids per litre and a naphthenic acid (NA) removal of 24.7% were observed in the reactor after 361 days of operation. Ultra Performance Liquid Chromatography/High Resolution Mass Spectrometry analysis revealed that the removal of individual NA species declined with increased ring numbers. Pyrosequencing analysis revealed that Betaproteobacteria were dominant in sludge samples from the MLE-MBR, with microorganisms such as Rhodocyclales and Sphingobacteriales capable of degrading hydrocarbon and aromatic compounds. During 425 days of continuous operation, no severe membrane fouling was observed as the transmembrane pressure (TMP) of the MLE-MBR never exceeded −20 kPa given that the manufacturer's suggested critical TMP for chemical cleaning is −35 kPa. Our results indicated that the proposed MLE-MBR has a good potential for removing recalcitrant organics in OSPW.