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Abstract The present study focused on 11-nor-9carboxy-Δ9-THC (THC-COOH) and Benzoylecgonine (BE), the most common metabolites of cannabis and cocaine, respectively, present in the domestic sewage entering the wastewater treatment plants. The aims of the study were: (1) to validate the analytical method of detection in wastewater and sludge; (2) to determine contribution of biodegradation and other processes to the removal in the biological reactor of the wastewater treatment plant (WWTP) and the response of biomass to different drug concentrations. The Ultra-Performance Liquid Chromatography coupled to tandem Mass Spectrometry method showed to be repeatable and reliable (recovery>75%; repeatability<10–15%; bias uncertainty<10) for measurements in wastewater; the ultrasound assisted extraction (USE) demonstrated to be reliable as pre-treatment of activated sludge solid phase. Both drugs were fully removed from the liquid phase in the lab-scale biological reactor within 24 h. Biodegradation was the main BE removal mechanism, and the first order kinetic model provided the best fitting of the experimental data. THC-COOH was mainly removed due to a combination of adsorption and biodegradation; adsorption was better described by the pseudo-second order kinetic model and the Freundlich isotherm. Both drugs at the higher concentrations caused inhibition of nitrogen oxidation and carbon removal. Graphical abstract Image 1 Highlights • BE in the range 500–4000 ng L−1 was fully removed in the biological reactor. • Biodegradation was the main removal process of BE. • THC-COOH in the range 150–2000 ng L−1 was fully removed in the biological reactor. • Removal of THC-COOH was mainly due to adsorption on sludge. • At the highest concentrations, both BE and THC-COOH caused partial inhibition. [ABSTRACT FROM AUTHOR]