The construction of water transfer projects brings new challenges to water resources management, especially in water supply security with the use of multiple water sources. However, the operations of water diversion and water supply have been considered in separation in practice. In particular, there are few decision support systems (DSS) designed to tackle the challenges in emergency planning of water transfer operation. This paper describes a generic DSS which is designed for the operation of multiple water sources supply and complex water supply targets. Emergency management is incorporated in the DSS to provide more effective water supply under extreme conditions. Specifically, the emergency scheduling plans regenerate the water supply strategy of Biliuhe Reservoir and Yingnahe Reservoir, and then reduce the impact of severe drought year on Dalian. The scheduling results of the case study reveal that this DSS makes good use of mutual compensation functions among multiple water sources when it is applied to the water supply emergency management of Dalian in a severe drought year. The results indicate that this developed DSS can be easily generalized and further applied to similar cities in China and other countries in the world.