The concentrations of some important endocrine disrupting chemicals and pharmaceuticals after various stages of wastewater treatment were investigated. The endocrine disrupting chemicals included natural and synthetic estrogenic and androgenic steroids. The pharmaceuticals included a series of sulfonamide antibiotics and trimethoprim. The removal efficiency of a membrane bioreactor (MBR) was investigated and compared with a conventional activated sludge (CAS) system. Samples were analysed by liquid chromatography tandem mass spectrometry. Results showed that the MBR and CAS systems effectively removed steroidal estrogens and androgens, but only partially eliminated the target antibiotics from wastewater. The MBR was shown to be more effective than the CAS system which was possibly attributed to the high solid retention time and concentration of biosolids in the MBR. The results highlight the potential wider application of MBRs for the removal of trace chemical contaminants in wastewater and their potential for use as decentralised wastewater treatment systems.