Sustainable management of natural resources is a pressing global challenge that requires the prevention of loss and waste. Egypt is facing an acute water crisis due to insufficient water supplies throughout the country. To address this issue, it is essential to implement a range of solutions to improve the situation. This study aims to alleviate the stress on multiple resources and environmental impacts in one of Egypt's earliest reclaimed areas (Wadi El-Natrun, Western Desert), by applying systematic modeling to achieve sustainable development objectives and mitigate resource stress. To promote a more sustainable and resilient future, a pilot model ecovillage has been designed for a community of three thousand inhabitants, promoting integrated resource management and considering the Water-Energy-Food (WEF) nexus concept. The ecovillage design incorporates collaborative engagement of groundwater reservoirs for water supply, agricultural production for food demands, power generation, and community sensitivity. Evaluating key aspects related to water supply, power generation, agricultural production, and environmental impact within the proposed pilot design aims to provide insights into the complex interactions among these systems. A four-step methodology for evaluating and implementing the nexus at a local level, which includes identifying linkages, mapping interconnections, focusing on core foundations, and applying the findings to improve project execution was investigated. An understanding of the WEF nexus, demonstrating how such frameworks can enhance the management of scarce resources was provided. The “TORAY DS2” design is employed to analyze model parameters and quantify their values. The study’s findings aim to support decision-makers and stakeholders in developing effective strategies to navigate the complexities of the WEF Nexus, promoting optimal resource management. These findings are promising, indicating a low environmental risk while aligning with both the WEF Nexus and the Sustainable Development Goals.