Double-reservoir-and-double-pumping-station systems are commonly used for irrigation water supply in hilly regions of southern China. An optimization model for this water supply system is proposed to minimize water shortage. The model features few coupling constraints, including available water in the system and pumping volume limited by regional water rights. Dynamic programming was adopted to solve the subsystem and aggregation models. The results with the model and that with the standard operation policy were compared; the total water shortage was reduced by 87.7%, total water replenishment from outside was reduced by 2.2%, and total water spill was reduced by 60.6% for a system in Nanjing, China. The method may provide a reference for optimal operation of water supply systems comprising reservoirs and pumping stations.