Food and water security have moved to the top of the global agenda following the food and energy price increases that started in 2007. Addressing the food, water and energy nexus is considered increasingly important for transparently and equitably meeting increasing global demand without compromising sustainability. This paper argues that given the unique regional and sector challenges of food, water and energy security, their nexus must be deconstructed to find effective, contextualized solutions. And governance challenges are at the heart of the nexus in each region. Governance is defined in various ways, but, with a few notable exceptions, the definitions have undergone relatively little analysis. In turn, governance issues are imbedded in policy, institutional, technological and financing options exercised at the global, regional, national and local levels. Furthermore, strong interactions between levels prompt policy responses to specific events and outcomes. The cu rent governance arrangements, where they exist at all, are woefully inadequate to address the challenges. They are imbedded in a lack of strategic clarity, and among stakeholders there is an unequal distribution of power, voice and access to information, resources and the capability to exercise a sound influence which will produce equitable and sustainable outcomes. Often there are huge tradeoffs between the short-term wins of individual stakeholders and long-term holistic solutions. This paper uses illustrative examples from recent global developments, as well as from China and India, to make the case for placing empirical analysis of governance issues at the top of the global agenda. At each level, governance is ues affect the choice of policies, institutions and outcomes for addressing these daunting challenges.