This study identified biotransformation products formed from three anthropogenic trace organic compounds (TOrCs) (benzotriazole, triclosan, and trimethoprim) in aerobic and anoxic sludge from a biological nutrient removal (BNR) wastewater treatment system. Liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-QTOF) was used to identify intermediate transformation products. A user-defined compound library was used to target unknowns in samples with a mix of TOrCs without requiring chemical standards and developed using EAWAG-BDD predictive software, which included 37 potential transformation products. Biotransformation batch experiments were conducted using activated sludge from anoxic and aerobic redox regimes of a BNR treatment plant located in Southern Nevada, United States. Four intermediates were observed for benzotriazole in both aerobic and anoxic activated sludge, which consisted of two isomers of hydroxy benzotriazole and two isomers of methoxy benzotriazole. Four intermediates were observed for trimethoprim under aerobic conditions, which formed 2,4-diaminopyrimidin-5-yl)(3,4,5-trimethoxyphenyl)methanol (TMP 306) and 2,6-diamino-5-hydroxy-5-(3,4,5-trimethoxybenzyl)-5,6-dihydropyrimidin-4(1H)-one (TMP 324) and two demethylation isomers of desmethyl trimethoprim. Triclosan had one confirmed transformation product, triclosan-o-sulfate, formed in both conditions. The identification of these transformation products will allow for more thorough risk assessments to be performed for the target TOrCs.