Abstract: The enormous volumes of oil sands process-affected water (OSPW) produced during oil sands bitumen extraction have been a public concern due to the toxicity and persistence of the organic contaminants contained in the water. Among all the contaminants in OSPW, naphthenic acids (NAs) are regarded as the most problematic due to their bio-persistency and acute toxicity to aquatic life. It has been suggested that biodegradation is the most cost-effective approach for OSPW treatment. However, the in situ biodegradation half-lives of NAs in tailings ponds could be as long as 13.6 years, making it necessary to accelerate the biodegradation process through the application of engineered bioreactors. To address this need, two identical anoxic-aerobic membrane bioreactors (MBRs) with a submerged ceramic membrane were continuously operated for 742 days to treat raw and mildly ozonated (utilized ozone dose 30 O3 mg/L) process-affected water. Efforts were made to firstly evaluate their feasibility for OSPW NA degradation and then optimize their treatment performance. A > 300-day system startup/sludge acclimatization phase was performed to gradually acclimatize microorganisms in the MBRs to 100% OSPW environment, revealing the feasibility of the MBR configuration for OSPW treatment. To better understand the contribution of anoxic and nitrifying aerobic compartments to the degradation of OSPW classical NAs and oxidized NAs (oxy-NAs), a batch study was performed on biodegradation of raw and ozonated OSPWs under decoupled anoxic and nitrifying aerobic conditions. The batch study suggested that both anoxic and aerobic conditions could contribute to biodegradation of OSPW NAs though the latter demonstrated much better NA degradation. Once the MBRs were stabilized on around Day 300, a 442-day continuous operating condition optimization phase was conducted. The MBR’s performance on OSPW NA degradation was successfully improved through changing the supplemented inorganic nitrogen composition and hydraulic retention time (HRT). To assess the systems’ classical and oxidized NA degradation performance, ultra performance liquid chromatography coupled with high resolution mass spectrometry (UPLC/HRMS) analysis was performed. Among all the six examined operating conditions, the condition with an NH4-N concentration of 25 mg/L and HRT of 12 h demonstrated the best removal rates of total classical NAs (37.6%) and total oxy-NAs (23.9%) from raw OSPW. Under this particular operating condition, the MBR removed 49.7% of total classical NAs and 35.4% of total oxy-NAs from the ozonated OSPW. The hybridization of low-dose ozone pretreatment and MBR process (HRT = 12 h) degraded 94.0% of classical NAs and 43.9% of total oxy-NAs from the raw OSPW. Impacts of molecular structures of NAs on their biodegradation efficiency were discussed; and possible correlations between certain microorganisms and biodegradation of NAs with particular molecular features were found. Meanwhile, the fouling behaviors of the two MBRs for raw and ozonated OSPW treatment were closely monitored and studied over the whole operation period. By performing mathematical model fitting, it is suggested that cake layer filtration was the dominating mechanism during the long-term slow TMP growth phase. In addition, HRT might be the factor that determined the dominating fouling mechanism during the sharp TMP jump phase. Moreover, the membrane fouling cake layers were examined using techniques including scanning electron microscopy coupled with energy dispersive X-ray spectroscopy (SEM-EDX) and confocal laser scanning microscopy (CLSM). Effects of ozone pretreatment on NA biodegradation, microbial community structure, and membrane fouling development were evaluated. NAs with more alkyl branches, longer carbon chains and higher cyclicity are undoubtedly the most bio-refractory fractions in OSPW. Through preferably degrading those recalcitrant NAs, the mild ozonation pretreatment remarkably enhanced subsequent biological treatment in terms of higher NA degradation rates and lower post-biodegradation residual NAs concentrations. In addition, the ozone pretreatment substantially affected the microbial community structure in the subsequent biological systems by altering the relative abundances of the dominant microbial species and encouraging existence of numerically minor species. Moreover, a prolonged long-term slow TMP growth phase and reduced frequency of TMP jump were observed in the MBR treating ozonated OSPW. To our best knowledge, this is the very first study that combines low-dose ozone pretreatment and MBR process for OSPW treatment. In addition, this project is one of the few studies that extensively investigate the biodegradation of oxy-NAs under various operating conditions throughout the whole system operation. Out of the limited research on MBR fouling mitigation using ozone pretreatment of feed water, this study provides insightful information on how mild ozonation pretreatment impacts the MBR’s feed water quality, microbial community structure, and fouling behavior. The results obtained in this study would be illuminating for future studies on improving biological systems treating OSPW and other industrial wastewaters containing bio-persistent organic contaminants. Industries in Canada, including oil sands exploitation, refinery plants, petrochemical industry, foundry industry, pulp and paper mills, produce large quantities of wastewater containing high recalcitrant organic contents. The knowledge gained in this study could be applied to these industrial scenarios to help improve their effluent water quality, and thus minimizing the impacts on receiving water bodies including rivers, lakes and groundwaters. It is, therefore, anticipated that this study may contribute in the future to the better protection of both environment and public health in Canada.