A pilot-scale membrane bioreactor (MBR) was installed and operated for one year at a Swiss hospital. It was fed an influent directly from the hospital’s sanitary collection system. To study the efficiency of micropollutant elimination in raw hospital wastewater that comprises a complex matrix with micropollutant concentrations ranging from low ng/L to low mg/L, an automated online SPE-HPLC-MS/MS analytical method was developed. Among the 68 target analytes were the following: 56 pharmaceuticals (antibiotics, antimycotics, antivirals, iodinated X-ray contrast media, antiinflamatory, cytostatics, diuretics, beta blockers, anesthetics, analgesics, antiepileptics, antidepressants, and others), 10 metabolites, and 2 corrosion inhibitors. The MBR influent contained the majority of those target analytes. The micropollutant elimination efficiency was assessed through continuous flow-proportional sampling of the MBR influent and continuous time-proportional sampling of the MBR effluent. An overall load elimination of all pharmaceuticals and metabolites in the MBR was 22%, as over 80% of the load was due to persistent iodinated contrast media. No inhibition by antibacterial agents or disinfectants from the hospital was observed in the MBR. The hospital wastewater was found to be a dynamic system in which conjugates of pharmaceuticals deconjugate and biological transformation products are formed, which in some cases are pharmaceuticals themselves.