Abstract Ensuring water, energy, and food security with minimum damage to groundwater resources is a key challenge to achieve sustainable development in arid areas. To address this scientific and policy challenge, a Multi-Criteria Decision-Making (MCDM)-nonlinear programming approach is developed for informing debates over improved management of the groundwater, energy, and food nexus that optimally allocates resources to food production to improve economic benefit and control groundwater depletion. Furthermore, this approach is capable of evaluating management policies affecting resource planning at a regional level. The approach is applied to the Neishaboor basin in northeast Iran. The main results are: (i) economic profit and food production depend on groundwater availability and energy use, which raise environmental protection challenges; (ii) the solutions could be used to define optimal policy strategies for sustainable management of groundwater, energy, food, and simultaneously achieve economic and environmental goals; (iii) improved irrigation efficiency would be considered as an efficient strategy under conditions of growing water scarcity. The results of this research can inform policy makers on effective strategies for integrated groundwater, energy, and food planning.