This study investigated health risk reduction in a drinking water treatment plant of Nanjing City (China) based on chemical detection of 22 semi-volatile organic compounds (SVOCs) and 24 metallic elements in source water and drinking water during 2009–2011. Chemical analysis showed that 15 SVOCs and 9 metals were present in the water. Health risk assessment revealed that hazard quotient of each pollutant and hazard index (HI) of all the detectable pollutants were below 1.00, indicating that the chemicals posed negligible non-carcinogenic risk to local residents. Benzo(a)pyrene may induce carcinogenic risk since its risk index via both oral and dermal exposure exceeded the safety level (1.00E−6), but other SVOCs induced no carcinogenic risk. Total HI of the SVOCs was 1.08E−3 for the source water and 1.56E−3 for the drinking water, suggesting that the used conventional treatment processes (coagulation/sedimentation, sand filtration and chlorine disinfection) cannot effectively reduce the non-carcinogenic risk. The source water had higher carcinogenic risk than the drinking water, but risk index of the drinking water still exceeded 1.00E−6. This study might serve as a basis for health risk assessment of drinking water and also as a benchmark for the authorities to reduce health risk arising from trace-level hazardous pollutants.