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Wastewater effluents contain a multitude of organic contaminants and transformation products, which cannot be captured by target analysis alone. High accuracy, high resolution mass spectrometric data were explored with novel untargeted data processing approaches (enviMass, nontarget, and RMassBank) to complement an extensive target analysis in initial “all in one” measurements. On average 1.2% of the detected peaks from 10 Swiss wastewater treatment plant samples were assigned to target compounds, with 376 reference standards available. Corrosion inhibitors, artificial sweeteners, and pharmaceuticals exhibited the highest concentrations. After blank and noise subtraction, 70% of the peaks remained and were grouped into components; 20% of these components had adduct and/or isotope information available. An intensity-based prioritization revealed that only 4 targets were among the top 30 most intense peaks (negative mode), while 15 of these peaks contained sulfur. Of the 26 nontarget peaks, 7 were tentatively identified via suspect screening for sulfur-containing surfactants and one peak was identified and confirmed as 1,3-benzothiazole-2-sulfonate, an oxidation product of a vulcanization accelerator. High accuracy, high resolution data combined with tailor-made nontarget processing methods (all available online) provided vital information for the identification of a wider range of heteroatom-containing compounds in the environment.