Indonesia is an archipelago with significant variations in natural resources, infrastructure, socioeconomic, culture, human resource capacity, accessibility, and access to financial and technical assistance. In this situation, integrated and unique efforts are needed to manage natural resources and build synergy between their protection and utilization to achieve water, energy, and food (WEF) security in accordance with the SDG targets. This paper analyzes the implementations of the WEF nexus in rural Indonesia by examining existing legal frameworks and other related policies, journals, textbooks, and publications. We explore factors influencing the success and failure of the implementation of the WEF nexus approaches from technical, socioeconomic, cultural, political, and institutional perspectives of the rural development framework.