This study evaluates membrane systems for the removal of the extractable organic fraction (EOF) from oil sands process-affected water (OSPW). Experiments were performed using in-situ integrated membrane units that consisted of low pressure-driven membrane (LPM) and high pressure-driven membrane (HPM) modules. LPM was prepared with a polysulfone (PSU) phase inversion casting process and HPM was fabricated by polyamide (PA) thin-film composite (TFC) interfacial polymerization. To change membrane physicochemical properties, each membrane was developed with and without multiwalled carbon nanotubes (MWNTs). The MWNTs were modified with strong acid to enhance dispersion in an organic solvent. Dispersion of the MWNTs and physicochemical properties of the membranes were characterized by microscopic and spectroscopic methods. The results showed that acid-modified MWNTs developed surface functional groups that increased their hydrophilicity, increasing the rejection of hydrophobic pollutants, increasing OSPW permeate flux, and significantly reducing membrane fouling. The LPM and HPM combinations with MWNTs were tested for the optimal organic pollutants removal from OSPW.