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This paper presents a new methodology for optimal operation of inter-basin water transfer systems by conjunctive use of surface water resources in water donor basin and groundwater resources in water receiving basin. To incorporate the streamflow uncertainty, an integrated stochastic dynamic programming (ISDP) model is developed. In the ISDP, the monthly inflow to the reservoir in the water donor basin, the water storage of the reservoir, and the water storage of the aquifer in the water receiving basin are considered as state variables. A water allocation optimization model is embedded in the main structure of ISDP and a new ensemble streamflow prediction model based on K-nearest-neighbourhood algorithm is also developed and linked to the ISDP. By using a new reoptimization process, the ISDP model provides monthly policies for water allocation to users in water donor and receiving basins. As …