This is a comprehensive study of the occurrence of antibiotics, hormones and other pharmaceuticals in water sites that have major potential for downstream environmental contamination. These include residential (hospitals, sewage treatment plants, and regional discharges), industrial (pharmaceutical production facilities), and agricultural (animal husbandries and aquacultures) waste streams. We assayed 23 Taiwanese water sites for 97 targeted compounds, of which a significant number were detected and quantified. The most frequently detected compounds were sulfamethoxazole, caffeine, acetaminophen, and ibuprofen, followed closely by cephalexin, ofloxacin, and diclofenac, which were detected in >91% of samples and found to have median (maximum) concentrations of 0.2 (5.8), 0.39 (24.0), 0.02 (100.4), 0.41 (14.5), 0.15 (31.4), 0.14 (13.6) and 0.083 (29.8) microg/L, respectively. Lincomycin and acetaminophen had high measured concentrations (>100 microg/L), and 35 other pharmaceuticals occurred at the microg/L level. These incidence and concentration results correlate well with published data for other worldwide locations, as well as with Taiwanese medication usage data, suggesting a human contamination source. Many pharmaceuticals also occurred at levels exceeding predicted no-effect concentrations (PNEC), warranting further investigation of their occurrence and fate in receiving waters, as well as the overall risks they pose for local ecosystems and human residents. The information provided here will also be useful for development of strategies for regulation and remediation.