A requirement for developing desalination in coastal regions suffering water scarcity is proposed to address the increased water demand and limited traditional water supply. The determination of plant capacity and water allocation scheme in a multiple-source water supply system, the first problem in planning desalination under stream flow and water demand uncertainties, remains a challenge. To address this gap, an interval-parameter two-stage stochastic programming model is developed in this study. The first-stage problem is to determine a proper desalination plant capacity, and the second is the water allocation scheme under uncertainties of natural stream flows, water demands, benefits and economic losses. The objective function is to maximize the net benefit of the system, and the cost function of desalination, including capital and operational costs, implying environmental impact, is linearized within a range of plant capacities to solve the model. The proposed approach is applied to an urban area of Weihai city in China to illustrate the validity of the model. The results suggest a capacity of 46 103 m3/d in 2030 and 56 103 m3/d in 2040. Sensitivity analyses of the parameters indicate that the unit price of electricity influences the utilization level of desalinated seawater, and a complementary relationship is observed between reclaimed water and desalinated seawater.