Understanding the actual consumption of alcohol and tobacco in the population is important for forming public health policy. For this purpose, wastewater-based epidemiology has been applied as a complementary method to estimate the overall alcohol and tobacco consumption in different communities. However, the stability of their consumption biomarkers – ethyl sulfate, ethyl glucuronide, cotinine, and trans-3′-hydroxycotinine – in the sewer system has not yet been assessed. This study aimed to conduct such assessment using sewer reactors mimicking conditions of rising main, gravity sewer, and wastewater alone, over a 12-hour period. The results show that cotinine and trans-3′-hydroxycotinine are relatively stable under all sewer conditions while ethyl sulfate was only stable in wastewater alone and gradually degraded in rising main and gravity sewer conditions. Ethyl glucuronide quickly degraded in all reactors. These findings suggest that cotinine and trans-3′-hydroxycotinine are good biomarkers to estimate tobacco consumption; ethyl sulfate may be used as a biomarker to estimate alcohol consumption, but its in-sewer loss should be accounted for in the calculation of consumption estimates. Ethyl glucuronide, and probably most of glucuronide compounds, are not suitable biomarkers to be used in wastewater-based epidemiology due to their in-sewer instability.