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Sites throughout Boston Harbor were analyzed for caffeine to assess its utility as a tracer in identifying sources of sanitary wastewater. Caffeine ranged from 15 ng/L in the outer harbor to a high of 185 ng/L in the inner harbor. Inner harbor concentrations were a result of combined sewage overflow (CSO) events as well as illicit discharge of sanitary sewage into municipal storm drains. Comparing current results to data from 1998 to 1999 shows reductions in caffeine levels. Reductions are attributed to termination of effluent discharge to the harbor, declines in the number of CSOs and discharge volume along with efforts to eliminate illicit discharges. Spatial distributions of caffeine identified CSOs as major contemporary sources to the inner harbor. The findings further establish the utility of caffeine as a tracer for sanitary wastewater contamination in urban estuaries and demonstrate the efficacy of pollution reduction strategies undertaken in recent decades in Boston Harbor. Published by Elsevier Ltd.