Wastewater contains a high number of organic micropollutants and transformation products of environmental concern. Recent approaches, combining methodologies based on target and suspect screening (for suspected substances based on prior information but with no reference standard) are important for the comprehensive characterization of environmental samples. Nevertheless, samples still contain many chromatographic peaks which do not correspond to substances included in target and suspect screening lists. These substances may be potentially relevant (e.g. due to their concentration or potential effects) and thus the identification of selected non-targets is important. However, full identification of unknown compounds is often difficult and there is no guarantee of a successful outcome. The aim of this work is to show some specific examples on the identification of unknown compounds in real wastewater (collected from the WWTP of Athens). Identifications were conducted using a developed integrated workflow based on LC–QToF-MS to detect formerly unknown organic contaminants in wastewater.