The examination of pollutants in waste-, surface- and drinking water by sum parameters like COD, BOD or TOC gives no information about their toxicity or behaviour in the drinking water treatment process. As many pollutants leaving sewage treatment plants are polar and/or thermolabile, gas Chromatographic (GC) separation coupled on-line with a mass spectrometer (MS) is not applicable to this problem. Newly established analytical methods like high performance liquid chromatography (HPLC) in on-line combination with mass- (MS) or tandem mass spectrometers (MS/MS) using soft ionization techniques like thermospray (TSP) would help to solve these problems. The comparison of GC- and LC/MS-spectra demonstrates increasing polarity beginning at the waste water treatment and ending at the drinking water treatment. It was possible to identify and quantify selected compounds, and elimination efficiency could be reviewed by comparing overview spectra. The knowledge about the existence of these compounds in waste-, surface- and drinking water requires strategies for elimination, avoidance or degradation.