A recently developed multimethod for the determination of 150 pesticide metabolites was exemplarily applied to 58 samples of groundwater and surface water. 37 of these metabolites were detected in at least two samples with a concentration ≥0.025 μg/L. The detected metabolites were ranked according to their concentration and frequency of detection. Findings are clearly dominated by metabolites of chloroacetanilide herbicides, but metabolites of sulfonylurea and thiocarbamate herbicides and other herbicides (dichlobenil) together with metabolites of some fungicides (tolylfluanid, chlorothalonil, trifloxystrobin) were also prominent. A number of 17 of the ranked metabolites are denoted as emerging metabolites because no reports on their previous detection in groundwater or surface water were found. Most of them, however, were correctly predicted to occur in the summary reports of the European pesticide approval process. Median total concentrations of the analysed pesticide metabolites summed up to 0.62 μg/L in groundwater and 0.33 μg/L in surface waters. While the concentration of the individual metabolites is usually low (<0.1 μg/L) the diversity of metabolites found in one sample can be large; between two and six metabolites were detected most frequently (maximum of 12 metabolites). Runoff from urban surfaces was investigated in this study and also here previously undetected pesticide (biocide) metabolites were detected. The emerging pesticide metabolites detected in environmental water samples in this study require more extended monitoring.