Over the years, sectoral analysis has overlooked the complex relationships between water and energy systems in development. Allowing silo policies silos to thrive. Yet, the complexities of development require an appreciation of the theoretical and methodological link between water and energy systems and policy implications. This chapter explores the contemporary theoretical frameworks and methodologies for analysing water and energy systems to provide a comprehensive understanding of the multifaceted relationships for sustainable development. It integrates insights from the environmental, economic, and social sciences—transdisciplinary approaches, such as nexus, multi-level perspective, system-based analysis, flow analysis, and the Sustainable Development Goals (SDGs). Transdisciplinary approaches enable diverse actors and institutions to engage in collaborative innovations beyond discipline-specific boundaries in water and energy policy. It provides a holistic perspective for knowledge and skills sharing and applications to achieve water and energy policy goals while bringing to the fore the competing interests in such complex systems.