In order to strengthen the management of risk sources and guarantee the security of drinking water source areas, the drinking water source area of the Taizhou Third Waterworks was used as a case study. A risk identification system for risk sources (such as plants discharging wastewater without treatment, sewage treatment plants, and wharfs) was developed considering factors including the hazard degree of risk sources themselves, the control mechanisms of risk sources, and the hazards caused by risk accidents. Furthermore, the water environmental integrated risk assessment system for drinking water source areas was improved by enhancing the environmental regulation ability and emergency response capability. Grading standards and weights of indices, as well as risk grade dividing standards of risk sources and drinking water source areas, were obtained from surveys and expert panel acts. On the basis of evaluation systems, the evaluation results were obtained: (a) there are eight middle-risk sources and no high-risk source around the Taizhou Third Waterworks, and (b) the risk level of the water source area of the Taizhou Third Waterworks is low.