<p>Numerous countries face water crises due to population growth, shifting climatic patterns, limited water resources, rapid industrialization, societal changes, and poor resource governance, which pose challenges to the supply of water, food, and energy. This study develops a Water–Food–Energy Nexus (WFE) model using the System Dynamics (SD) approach to capture the complex interactions among domestic, industrial, and agricultural sectors while incorporating environmental protection policies. The proposed model is developed and applied to assess the water crisis in the Zayandeh-Roud River basin, which plays a strategic role in ensuring water, energy, and food security in central Iran. Climate change alters hydroclimatic patterns and directly and indirectly affects the subsystems of the water–food–energy nexus. Precipitation and temperature outputs from three Atmosphere–Ocean General Circulation Models (AOGCMs), obtained from the Intergovernmental Panel on Climate Change Sixth Assessment Report (AR6), were used to evaluate the impacts of climate change on river flow under the SSP1 (optimistic) and SSP5 (pessimistic) emission scenarios. The simulation results indicate: (i) a reduction of 7.2% and 15.7% of the river flow under the optimistic and pessimistic emissions scenarios, respectively, (ii) a severe decline in groundwater levels, (iii) an increasing trend in agricultural water demand in most years, (iv) reduced crop yields, and (v) the drying of the Gavkhouni wetland in the future period (2025–2034). Several policy options for mitigating water deficits were evaluated. The most effective strategy involved fallowing 40% of rice cultivation areas, reducing groundwater extraction by 50%, and securing 70% of the environmental water rights of the Gavkhouni Wetland to restore water balance within the basin.</p>