A conventional evaluation methodology for drinking water pollution focuses on analysing hundreds of compounds, usually by liquid chromatography–tandem mass spectrometry. High-resolution mass spectrometry allows comprehensive evaluation of all detected signals (compounds) based on their elemental composition, intensity, and numbers. We combined target analysis of 192 emerging micropollutants with nontarget (NT) full-scan/MS/MS methods to describe the impact of treatment steps in detail and assess drinking water treatment efficiency without compound identification. The removal efficiency based on target analytes ranged from − 143 to 97%, depending on the treatment section, technologies, and season. The same effect calculated for all signals detected in raw water by the NT method ranged between 19 and 65%. Ozonation increased the removal of micropollutants from the raw water but simultaneously caused the formation of new compounds. Moreover, ozonation byproducts showed higher persistence than products formed during other types of treatment. We evaluated chlorinated and brominated organics detected by specific isotopic patterns within the developed workflow. These compounds indicated anthropogenic raw water pollution but also potential treatment byproducts. We could match some of these compounds with libraries available in the software. We can conclude that passive sampling combined with nontargeted analysis shows to be a promising approach for water treatment control, especially for long-term monitoring of changes in technology lines because passive sampling dramatically reduces the number of samples and provides time-weighted average information for 2 to 4 weeks.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10661-023-11348-w.