The water-energy-food nexus is a topical subject for research and practice, reflecting the importance of these sectors for humankind and the complexity and magnitude of the challenges they are facing. While the nexus as a concept is not yet mature or fully tested in practice, it has already encouraged a range of approaches in a variety of contexts. This article provides a set of definitions recognizing three perspectives that see the nexus as an analytical tool, governance framework and as an emerging discourse. It discusses the implications that an international transboundary context brings to the nexus and vice versa. Based on a comparative analysis of three Asian regions—Central Asia, South Asia and the Mekong Region—and their related transboundary river basins, we propose that the transboundary context has three major implications: diversity of scales and perspectives, importance of state actors and importance of politics. Similarly, introducing the nexus as an approach in a transboundary context has a potential to provide new resources and approaches, alter existing actor dynamics and portray a richer picture of relationships. Overall, the significance of water-energy-food linkages and their direct impacts on water allocation mean that the nexus has the potential to complement existing approaches also in the transboundary river basins.