Transformation products (TPs) of organic contaminants in aquatic environments are still rarely considered in water quality and chemical risk assessment, although they have been found in concentrations that are of concern. Since many different TPs can potentially be formed in the environment and analytical standards are typically lacking for these compounds, knowledge on the prevalence of TPs in aquatic environments is fragmentary. In this study, an efficient procedure was therefore developed to comprehensively screen for large numbers of potential TPs in environmental samples. It is based on a target list of plausible TPs that has been assembled using the University of Minnesota Pathway Prediction System (UM-PPS) for the computer-aided prediction of products of microbial metabolism and an extensive search for TPs reported in the scientific literature. The analytical procedure for screening of the compounds on the target list has been developed to allow for the detection of a broad range of compounds in complex environmental samples in the absence of commercially available reference standards. It includes solid phase extraction with broad enrichment efficiency, followed by liquid chromatography and tandem mass spectrometry with high mass resolution and accuracy. The identification of target TPs consisted of extracting the exact mass from the chromatogram, selecting peaks of sufficient intensity, checking the plausibility of the retention time, and interpreting mass spectra. The procedure was used to screen for TPs of 52 pesticides, biocides, and pharmaceuticals in seven representative surface water samples from different regions in Switzerland. Altogether, 19 TPs were identified, including both some well-known and commonly detected TPs, and some rarely reported ones (e.g., biotransformation products of the pharmaceuticals venlafaxine and verapamil, or of the pesticide azoxystrobin). Overall, the rather low number of TPs detected suggests that TPs may not pose a problem of unexpected magnitude for aquatic resources.