Pharmaceuticals and selected major human metabolites are ubiquitous in Jamaica Bay, a wastewater-impacted estuary at concentrations in the low ng/L to low mu g/L range. Concentrations throughout the bay are often consistent with conservative behavior during dry-weather conditions, as evidenced by nearly linear concentration -salinity relationships. Deviation from conservative behavior is noted for some pharmaceuticals and attributed to microbial degradation. Caffeine, cotinine, nicotine, and paraxanthine were detected with the greatest analytical signal, although evidence is presented for in situ removal, especially for nicotine and caffeine. There is little evidence for significant removal of carbamazepine and sulfamethoxazole, suggesting they are more conservative and useful wastewater tracers. Immediately following heavy precipitation, which induced a combined sewer overflow (CSO) event, the concentrations of all compounds but acetaminophen and nicotine decreased or disappeared. This observation is consistent with a simple model illustrating the effect of precipitation has on pharmaceutical concentration in the wastewater stream, given the balance between dilution from rain and the bypass of treatment.