Abstract Aims To discuss the need to develop ethical guidelines for researchers using sewage epidemiology to monitor drug use in the general population and specific precincts, including prisons, schools and workplaces. Method Describe current applications of sewage epidemiology, identify potential ethical risks associated with this science, and identify key means by which these risks may be mitigated through proportionate ethical guidance that allows this science to be fully developed. Results A rapidly advancing field of research is sewage epidemiology (SE) — the analysis of wastewater samples to monitor illicit drug use and other substances. Typically this research involves low ethical risks because individual participants cannot be identified and, consequently, review has been waived by human research ethics committees. In the absence of such oversight, ethical research guidelines are recommended for SE teams, peer reviewers and journal editors; guidelines will assist them to mitigate any risks in general population studies and studies of prisons, schools and workplaces. Potential harms include the stigmatisation of participants and, in the prison setting, austere policy responses to SE data that impact negatively upon inmate-participants. The risk of harm can be managed through research planning, awareness of the socio-political context in which results will be interpreted (or, in the case of media, sensationalised) and careful relations with industry partners. Ethical guidelines should be developed in consultation with SE scholars and be periodically amended. They should include publication processes that safeguard scientific rigour and be promulgated through existing research governance structures. Conclusions Guidelines will assist to promote an ethical research culture among SE teams and scholars involved in the publication process and this will work to protect the reputation of the field.