In this study, an integrated aerobic membrane bioreactor (MBR)-nanofiltration (NF) system has been applied for advanced treatment of Opium processing wastewaters to comply with strict discharge limits. Aerobic MBR treatment was successfully applied to high strength industrial wastewater. In aerobic MBR treatment, a non-fouling unique slot aeration system was designed using computational fluid dynamics techniques. The MBR was used to separate treated effluent from dispersed and non-settleable biomass. Respirometric modeling using MBR sludge indicated that the biomass exhibited similar kinetic parameters to that of municipal activated sludge systems. Aerobic MBR/NF treatment reduced chemical oxygen demand (COD) from 32,000 down to 2,500 and 130 mg/L, respectively. The MBR system provided complete removal of total inorganic nitrogen; however, nearly 50 mgN/L organic nitrogen remained in the permeate. Post NF treatment after MBR permeate reduced nitrogen below 20 mgN/L, providing nearly total color removal. In addition, a 90% removal in the conductivity parameter was reached with an integrated MBR/NF system. Finally, post NF application to MBR permeate was found not to be practical at higher pH due to low flux (3–4 L/m2/hour) with low recovery rates (30–40%). As the permeate pH lowered to 5.5, 75% of NF recovery was achieved at a flux of 15 L/m2/hour.