The removal of pharmaceuticals (PhACs) present in urban wastewater by membrane bioreactors (MBRs) followed by reverse osmosis (RO) or nanofiltration (NF) membranes has been frequently addressed in the literature. However, data regarding the removal of their main human metabolites and transformation products (TPs) is still scarce. In this study, the presence of 13 PhACs and 20 of their metabolites and TPs was monitored during 2 consecutive years in the different treatment steps of urban raw wastewater (sewer, primary treatment, MBR and RO/NF). Rejection of the selected contaminants when using low pressure NF membranes (NF-90) or RO membranes (ESPA 2) after the MBR step was also investigated. The analgesic acetaminophen, which was found at the highest concentrations in the sewer and influent samples (18–74 µg L−1) over the two experimental periods, was fully eliminated during MBR treatment. Those PhACs that were only partially removed after the MBR, were almost completely removed (>99%) by the RO membrane working under different process conditions. At a similar average permeate fluxes (18 L m−2 h−1), the NF membrane showed high removal efficiencies (>90%) for all of the PhACs and their metabolites, though lower than those achieved by the RO membrane. When the flux of the NF90 membrane was increased to 30 L m−2 h−1 (while still operating at a feed pressure lower than the RO membrane at 18 L m−2 h−1) the performance of the membrane increased, achieving 98% rejection of PhACs.