The conjunctive use of surface and subsurface water is one of the most effective ways to increase water supply reliability with minimal cost and environmental impact. This study presents a novel stepwise optimization model for optimizing the conjunctive use of surface and subsurface water resource management. At each time step, the proposed model decomposes the nonlinear conjunctive use problem into a linear surface water allocation sub-problem and a nonlinear groundwater simulation sub-problem. Instead of using a nonlinear algorithm to solve the entire problem, this decomposition approach integrates a linear algorithm with greater computational efficiency. Specifically, this study proposes a hybrid approach consisting of Genetic Algorithm (GA), Artificial Neural Network (ANN), and Linear Programming (LP) to solve the decomposed two-level problem. The top level uses GA to determine the optimal pumping rates and link the lower level sub-problem, while LP determines the optimal surface water allocation, and ANN performs the groundwater simulation. Because the optimization computation requires many groundwater simulations, the ANN instead of traditional numerical simulation greatly reduces the computational burden. The high computing performance of both LP and ANN significantly increase the computational efficiency of entire model. This study examines four case studies to determine the supply efficiencies under different operation models. Unlike the high interaction between climate conditions and surface water resource, groundwater resources are more stable than the surface water resources for water supply. First, results indicate that adding an groundwater system whose supply productivity is just 8.67 % of the entire water requirement with a surface water supply first (SWSF) policy can significantly decrease the shortage index (SI) from 2.93 to 1.54. Second, the proposed model provides a more efficient conjunctive use policy than the SWSF policy, achieving further decrease from 1.54 to 1.13 or 0.79, depending on the groundwater rule curves. Finally, because of the usage of the hybrid framework, GA, LP, and ANN, the computational efficiency of proposed model is higher than other models with a purebred architecture or traditional groundwater numerical simulations. Therefore, the proposed model can be used to solve complicated large field problems. The proposed model is a valuable tool for conjunctive use operation planning.