Advanced wastewater treatment such as powdered activated carbon (PAC) reduces the load of organic micropollutants entering the aquatic environment. Since mobile and persistent compounds accumulate in water cycles, treatment strategies need to be evaluated for the removal of (very) polar compounds. Thereby, non-targeted analysis gives a global picture of the molecular fingerprint (including these very polar molecules) of water samples. Target and non-target screening were conducted using polarity-extended chromatography hyphenated with mass spectrometry. Samples treated with different types and concentrations of PAC were compared to untreated samples. Molecular features were extracted from the analytical data to determine fold changes, perform a principal component analysis and for significance testing. The results suggest that a part of the polar target analytes was adsorbed but also some byproducts might be formed or desorbed from the PAC.