To estimate drug consumption more reliably, wastewater-based epidemiology would benefit from a better understanding of drug residue stability during in-sewer transport. We conducted batch experiments with real, fresh wastewater and sewer biofilms. Experimental conditions mimic small to medium-sized gravity sewers with a relevant ratio of biofilm surface area to wastewater volume (33 m2 m–3). The influences of biological, chemical, and physical processes on the transformation of 30 illicit drug and pharmaceutical residues were quantified. Rates varied among locations and over time. Three substances were not stable—that is, >20% transformation, mainly due to biological processes—at least for one type of tested biofilm for a residence time ≤2 h: amphetamine, 6-acetylcodeine, and 6-monoacetylmorphine. Cocaine, ecgonine methyl ester, norcocaine, cocaethylene, and mephedrone were mainly transformed by chemical hydrolysis and, hence, also unstable in sewers. In contrast, ketamine, norketamine, O-desmethyltramadol, diclofenac, carbamazepine, and methoxetamine were not substantially affected by in-sewer processes under all tested conditions and residence times up to 12 h. Our transformation rates include careful quantification of uncertainty and can be used to identify situations in which specific compounds are not stable. This will improve accuracy and uncertainty estimates of drug consumption when applied to the back-calculation.