Water environment security (WES) is defined in terms of three aspects: first, that it meets basic demands due to industrial and domestic usage; second, that it protects public health from acute and chronic threats; and third, that measures are adopted to ensure sustainable ecological functioning of freshwater resources. Limitations associated with current water environment security indicators in China — including inefficiency in terms of environmental monitoring, inappropriate indicators and parameters that do not take sufficient account of local water characteristics, and a lack of management targets — leads to a failure of effective water management. To achieve better water environment management, a systematic approach, encompassing several steps including establish ideal indicator system and narrow down the scope, screen priority pollutants, identify local characteristics and organize discussion workshop, should be followed to establish a comprehensive water environment indicator system. A case study in Suzhou is included to demonstrate the detailed operational procedures used to assess the risks associated with poor management practices relating to water environment security as well as design an appropriate water environment security indicator system.