Determination of 24 semi-volatile organic compounds (SVOCs) and 24 trace elements in water samples was conducted in order to investigate the quality of the Nanjing source of drinking water taken from Yangtze River. The total concentrations of SVOCs and trace elements were in the range of 1,951-11,098 ng/l and 51,274-72,384 microg/l, respectively. No significant seasonal changes were found for the pollutants' concentrations. A primary health risk assessment was carried out to evaluate potential health effects. Risk quotients involving carcinogenic effects for benzo(a)anthracene, benzo(a)pyrene, benzo(b)fluoranthene, dibenz(a,h)anthracene, bis(2-ethylhexyl)phthalate and arsenic were >1 under the worst-case scenario. The results of this study demonstrate the importance of further studies on the environmental health effects of exposure to the source water.