The release of persistent and mobile organic chemicals (PMOCs) into the aquatic environment puts the quality of water resources at risk. PMOCs are challenging to analyze in water samples, due to their high polarity. The aim of this study was to develop novel analytical methods for PMOCs and to investigate their occurrence in surface and groundwater samples. The target compounds were culled from a prioritized list of industrial chemicals that were modeled to be persistent, mobile, and emitted into the environment. Analytical screening methods based on mixed-mode liquid chromatography (LC), hydrophilic interaction LC, reversed phase LC, or supercritical fluid chromatography in combination with mass spectrometric detection were successfully developed for 57 target PMOCs and applied to 14 water samples from three European countries. A total of 43 PMOCs were detected in at least one sample, among them 23 PMOCs that have not been reported before to occur in environmental waters. The most prevalent of these novel PMOCs were methyl sulfate, 2-acrylamino-2-methylpropane sulfonate, benzyltrimethylammonium, benzyldimethylamine, trifluoromethanesulfonic acid, 6-methyl-1,3,5-triazine-diamine, and 1,3-di-o-tolylguanidine occurring in ≥50% of the samples at estimated concentrations in the low ng L−1 up to μg L−1 range. The approach of focused prioritization combined with sensitive target chemical analysis proved to be highly efficient in revealing a large suite of novel as well as scarcely investigated PMOCs in surface and groundwater.