Effect-Directed Analysis (EDA) was used to identify bioactive compounds in surface and well water from the Upper Rhine, and to evaluate their properties against the criteria set for Persistent, Mobile and Toxic (PMT) and very persistent and very mobile (vPvM) substances. A multi-layered solid-phase extraction was implemented to enrich a broad range of polar substances from the collected samples. The extracts were fractionated into 108 fractions and tested in the transthyretin (TTR)-binding assay measuring displacement of fluorescently labeled thyroxine (FITC-T4 TTR-binding assay) and the Aliivibrio fischeri bioluminescence (AFB) bioassay. Bioactive fractions guided the identification strategy using high-resolution mass spectrometry. Chemical features were systematically annotated using library databases and suspect lists, incorporating an automated assessment of the quality of each annotation. Based on this assessment, each chemical feature was assigned a specific identification confidence level. Identification of bioactive compounds was facilitated by using bioassay specific suspect lists that were extracted from an in-house developed database of positive and negative TTR-binding compounds and from a recently published database of active inhibitors of AFB. This resulted in the identification and confirmation of ten bioactive substances, including four evaluated as PMT and vPvM substances (diclofenac, trifloxystrobin acid, 6:2 FTSA and PFOA), and one as a potential PMT substance (4-aminoazobenzene). This study demonstrates the effectiveness of EDA in the identification of PMT/vPvM substances in the aquatic environment, facilitating their prioritization for comprehensive environmental risk assessment and possible regulation.