Recent studies have demonstrated the role of biofilms on the stability of drug residues in wastewater. These factors are pertinent in wastewater-based epidemiology (WBE) when estimating community-level drug use. However, there is scarce information on the biotransformation of drug residues in the presence of biofilms and the potential use of transformation products (TPs) as biomarkers in WBE. The purpose of this work was to investigate the formation of TPs in sewage reactors in the presence of biofilm mimicking conditions during in-sewer transport. Synthetic cathinones (methylenedioxypyrovalerone, methylone, mephedrone) and phenethylamines (4-methoxy-methamphetamine and 4-methoxyamphetamine) were incubated in individual reactors over a 24 h period. Analysis of parent species and TPs was carried out using liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-QToFMS). Identification of TPs was done using suspect and non-target workflows. In total, 18 TPs were detected and identified with reduction of β-keto group, demethylenation, demethylation, and hydroxylation reactions observed for the synthetic cathinones. For the phenethylamines, N- and O-demethylation reactions were identified. Overall, the experiments showed varying stability for the parent species in wastewater in the presence of biofilms. The newly identified isomeric forms of TPs particularly for methylone and mephedrone can be used as potential target biomarkers for WBE studies due to their specificity and detectability within a 24 h residence time.