Wastewater-based epidemiology (WBE) is considered to be a useful tool for monitoring chemical consumption in the population. However, the lack of information on potential transformation of biomarkers in the sewer system can compromise the accuracy of the consumption estimation. The present study contributes to addressing this issue by investigating the in-sewer stability of biomarkers from a number of commonly used drugs using laboratory sewer reactors that can mimic different sewer conditions. A stable and an unstable chemical (carbamazepine and caffeine) were also used as benchmarking chemicals to reflect the chemical degradation potential in different sewer conditions. The results suggested that ketamine and norketamine were unstable in gravity and rising main sewers, ketamine was unstable in bulk liquid while norketamine was stable under the same condition. Similarly, mephedrone and methylone were unstable in sewer conditions with considerable deviation. Significant loss of buprenorphine, methadone, oxycodone and codeine was observed in the rising main sewer. Morphine and codeine glucuronide were found to be deconjugated from their glucuronides quickly in the presence of biofilms. This study indicates that it is important to evaluate the stability of biomarkers in the sewer system before using them in WBE for estimating consumption/exposure to reduce uncertainties.