To improve the water resource management of the inland river basins of northwestern China, a Decision Support System (DSS) is developed to provide an operative computer platform for decision makers. The DSS is designed according to actual water resource management problems and is seamlessly integrated into a user-friendly interface implemented in the Visual C# programming language. The DSS comprises an information management system that performs data collection, verification, management, and visualization, and models estimated crop water demand and water allocation for different levels of water use units. The objective of this study is to aid in the decision-making process related to water allocation scheme planning and implementation and to aid real-time responses to changes in water supply, allowing a new water allocation scheme to be developed based on the actual relationship between the supply and demand for water. The system is tested to allocate water to different levels of water use units as a standard decision support tool by means of the actual total available water from rivers, reservoirs, and groundwater. More than 60 water decision makers use the system at more than 40 locations along the middle reaches of the Heihe River Basin.