The need for an integrated approach to sustainable resources management to achieve the Sustainable Development Goals has become widely recognized. Population growth, climate change, environmental degradation, and scarcity of resources have been identified as the major factors affecting society’s future. Given the fundamental societal needs for food, energy, and water, the Water–Energy–Food (WEF) nexus has emerged as a useful sustainable resource management framework and has been widely applied. However, in the Middle East and North Africa (MENA) region, there have been relatively few studies that adopt a nexus approach. In this study, the Ain Temouchent region in Algeria is used as a WEF Nexus case study. The region has a strong agricultural-based economy and the increased intensity of agricultural production in the region has resulted in the overuse of groundwater resources. Establishing a reverse osmosis desalination plant with a daily production capacity of 200,000 m³ significantly alleviated the resulting water crisis, yet its energy consumption and environmental impact raise several questions. This study identifies the critical links between the WEF sectors and using this understanding, the dynamics between them are assessed using System Dynamics Modelling. The study reveals that any further increase in agricultural production in Ain Temouchent may lead to excessive use of groundwater resources. Although desalination can help alleviate the water crisis, its high energy consumption raises concerns. The analysis shows that the use of surface water and recycled wastewater for irrigation could be possible alternatives. The study emphasizes the value of adopting a WEF nexus approach to achieve a balance between agricultural development, energy sustainability, and water resource management in the Ain Temouchent region.