Unintentional indirect potable water reuse, where wastewater effluent is used as a part of a downstream drinking water source, has become a great concern. In this case, a variety of organic micro-pollutants contained in wastewater effluent could create problems. Membrane bioreactors (MBRs) have gained significant popularity as an advanced wastewater treatment technology and might be effective in removing such organic micro-pollutants. Available information on the performance of MBRs regarding removal of micro-pollutants, however, is currently limited. This study examined the ability of submerged MBRs to remove pharmaceutically active compounds (PhACs). Experiments were conducted at an existing municipal wastewater treatment facility, and the performance of the MBRs was compared with that of the conventional activated sludge (CAS) process. Six acidic PhACs (clofibric acid, diclofenac, ibuprofen, ketoprofen, mefenamic acid, naproxen) and one acidic herbicide (dichloprop) were investigated. Compared with CAS, MBRs exhibited much better removal regarding ketoprofen and naproxen. With respect to the other compounds, comparable removal was observed between the two types of treatment. Removal efficiencies of the PhACs were found to be dependent on their molecular structure such as number of aromatic rings or inclusion of chlorine.