In this study, a spatiotemporal disaggregated simulation model was developed based on water–food–energy (WFE) nexus approach to assess water and food supply security considering ecosystem provisioning services. The main components of the developed model in this study (SD-WFE model) are population, water, agriculture, and energy modules. The model, which was developed using system dynamics (SD) approach, was utilized to simulate effectiveness of sectoral municipal, industrial, and agricultural water and energy consumption management and environmental protection policies in improving ecosystem provisioning services during a 20-year period. Through sensitivity analysis utilizing the Monte Carlo model, the study addresses the formulation of sustainable water resource policies across four main categories: water demand management, water supply management, food resource management, and energy resource demand management. Additionally, it explores the integration of policies within an optimal framework. The simulation of proposed solutions revealed that a combination of water demand management and food resource management yielded the most promising outcome. Specifically, the recommended solution entails enhancing water irrigation efficiency by 18% through the expansion of pressurized irrigation network coverage, adjusting cropping patterns by 14%, reducing agricultural product losses by 8% via improved food supply management, minimizing food demand by 9% due to reduced food consumption losses, and achieving an annual 10% increase in crop performance. These selected policies form the foundation for sustainable water resource management strategies.