The Water-Energy-Food Nexus (WEFN) has gained international attention as an approach for managing water more holistically, building on the progress made by the Integrated Water Resources Management (IWRM) approach. However, modelling the availability of water, energy, and food and their interconnections is complex, with major barriers that include the availability of both data and modelling platforms capable of assessing the interconnected systems of the WEFN. There have been attempts to model resource availability in each sector generally, but few attempts to consider the WEFN in complex transboundary basins, especially considering Sustainable Development Goals (SDGs). Here, a water, energy, and food availability model was developed using a combination of remotely sensed, national government reported, and global datasets. The model explores the complex interactions between the physical availability and production of water, energy, and food for several subbasins representing different states. Results showed the potential impacts of socioeconomic development, population changes and transboundary cooperation on resources. Transboundary cooperation in the case study Ma Basin in Southeast Asia, under existing resources and operations could improve monthly food security and reduce coal power operations using excess hydropower in the basin during the dry season. These findings show that transboundary cooperation improves access to energy and food, whilst potentially reducing demands for water. Furthermore, the research has highlighted ways in which transboundary cooperation can further assist in attaining SDGs 12 and 13 on responsible production and climate action, respectively. The modelling framework is easily transferable and can support similar analysis in other basins, contributing to global attainment of several SDGs.