The occurrence of pharmaceutical and illicit drug residues potentially arising from combined sewer overflows (CSOs) in the Central London portion of the Thames Estuary is presented. Approximately 39 million tonnes of untreated sewage enter the River Thames at 57 CSO points annually. Differential analysis of influents and effluents in a major wastewater treatment plant identified seven potential drug-related CSO markers based on removal rates. Three were present in influent at concentrations >1 μg L−1 (caffeine, cocaine and benzoylecgonine). During dry weather, analysis of hourly samples of river water revealed relatively consistent concentrations for most drugs, including CSO markers, over a tidal cycle. River water was monitored over a week in January and July and then daily across six consecutive weeks in November/December 2014. Out of 31 compounds monitored, 27 drug residues were determined in the River Thames and, combined, ranged between ~1000–3500 ng L−1. Total drug concentration generally declined during extended periods of drier weather. For CSO markers, short-term increases in caffeine, cocaine and benzoylecgonine concentration were observed ~24 h after CSO events (especially those occurring at low tide) and generally within one order of magnitude. Timings of elevated occurrence also correlated well with ammonium ion and dissolved oxygen data following CSOs. This work also represents an important study of pharmaceutical occurrence before a major 'super Sewer’ infrastructure upgrade in London aiming to reduce CSOs by 95%.