Factors such as climate change, economic development, population growth, pandemics, and geopolitical instability threaten water, energy, and food (WEF) security, which consequently put sustainability at risk. However, studies that simultaneously consider WEF security and sustainability aspects still need improvement. This research aimed to build a sustainable WEF nexus framework and analyze the interrelationships among water consumption, electricity demand, food production, and ecological footprint, considering the Environmental Kuznets curve (EKC) hypothesis and external factors of the WEF nexus. For the empirical analysis, this study employed the three-stage least squares method to identify synergies and trade-offs in the sustainable WEF nexus in South Korea using panel data from 2005 to 2019. The results indicated that rice production causes excessive use of agricultural water, thereby deteriorating water availability and quality. This phenomenon leads to scarce water resources and environmental degradation, which negatively impact energy production and sustainability. Although increased agricultural productivity through automation “improves food security,” it can pose a threat to energy security by increasing electricity demand and energy imports. The EKC hypothesis test revealed that environmental problems cannot be solved through economic development. However, the indicators related to WEF security influence environmental sustainability rather than economic growth. These results indicate that WEF security and sustainability can be improved simultaneously by maximizing synergies and minimizing trade-offs within a sustainable WEF nexus. Therefore, this research provides a roadmap for policymakers regarding efficient ways to improve environmental quality and WEF security.