Two typical rural water utilities in Beijing, China were chosen to describe the principles and applications of water safety plans (WSP), to provide a methodological guide for the actual application and improve the quality of rural drinking water quality, and to establish an appropriate method for WSP applied in rural water supply. Hazards and hazardous events were identified and risk assessment was conducted for rural water supply systems. A total of 13 and 12 operational limits were defined for two utilities, respectively. The main risk factors that affect the water safety were identified in water sources, water processes, water disinfection systems and water utility management. The main control measures were strengthening the water source protection, monitoring the water treatment processes, establishing emergency mechanisms, improving chemical input and operating system management. WSP can be feasibly applied to the management of a rural water supply.