The evaluation of water treatment systems in terms of presence, fate and removal of organic micropollutants is of paramount importance for the optimal protection of both the environment and human health. In this regard, there are significant gaps in the existing data for compounds present in treated water that remain uncharacterised but are still hazardous from both a toxicological and ecological point of view. This work aims to critically summarise the existing information about the application of suspect and non-target screening approaches based on liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) to understand the behaviour of polar organic micropollutants and their corresponding transformation products during water treatment processes, focusing particularly on wastewater. Also, it includes a discussion about the novel non-target workflows whose objective is not the further structure elucidation of particular compounds but assessing changes in the molecular elemental compositions of the dissolved organic matter (DOM) during water treatment (without structural characterisation). These strategies can provide additional information and become a common step for a better understanding of treatment performance and transformation product formation.