After consumption, pharmaceuticals are excreted as parent compounds and/or metabolites in urine and faeces. Some are not completely removed during wastewater treatments, forcing sewage treatment plants (STPs) to apply alternative technologies to guarantee quality of treated water. To monitor the removal efficiency of STPs, not only unchanged compounds and metabolites have to be taken into account, but also formation of possible transformation products (TPs). In this work, QTOF MS has been used for screening metabolites/TPs of pharmaceuticals in effluent wastewater from Athens. A customised database was built with the exact masses of metabolites reported in literature for the parent drugs found in an initial screening. Additionally, TPs identified in previous degradation experiments performed at our laboratory were included. Up to 34 metabolites/TPs were detected for omeprazole, venlafaxine, clindamycin, clarithromycin, clopidogrel or dipyrone, among others. Seven corresponded to TPs whose reference standards were available at our lab, seven were TPs previously identified in laboratory degradation experiments, eight were TPs tentatively identified by QTOF MS without reference standards, and twelve TPs were discovered after using the common fragmentation pathway approach. Tentative identification of TPs was supported by prediction of their chromatographic retention time based on the use of advanced chemometric QSRR models. ; The authors acknowledge the financial support from Plan Nacional de I+D+i, Ministerio de Economía y Competitividad (Project ref CTQ2012-36189), and from Generalitat Valenciana (Group of Excellence Prometeo 2009/054; Collaborative Research on Environment and Food Safety, ISIC/2012/016). This research has also been co-financed by the European Union and Greek national funds through the Operational Program “Education and Lifelong Learning” of the National Strategic Reference Framework (NSRF)—ARISTEIA 624 (TREMEPOL project). Richard Bade acknowledges the European Union for his Early Stage Researcher (ESR) contract as part of the EU-International Training Network SEWPROF (Marie Curie—PEOPLE Grant #317205).