Abstract Currently available water-energy-food (WEF) modelling frameworks to analyse cross-sectoral interactions often share one or more of the following gaps: (a) lack of integration between sectors, (b) coarse spatial representation, and (c) lack of reproducible methods of nexus assessment. In this paper, we present a novel clustering tool as an expansion to the Climate-Land-Energy-Water-Systems modelling framework used to quantify inter-sectoral linkages between water, energy, and food systems. The clustering tool uses Agglomerative Hierarchical clustering to aggregate spatial data related to the land and water sectors. Using clusters of aggregated data reconciles the need for a spatially resolved representation of the land-use and water sectors with the computational and data requirements to efficiently solve such a model. The aggregated clusters, combined together with energy system components, form an integrated resource planning structure. The modelling framework is underpinned by an open-source energy system modelling tool—OSeMOSYS—and uses publicly available data with global coverage. By doing so, the modelling framework allows for reproducible WEF nexus assessments. The approach is used to explore the inter-sectoral linkages between the energy, land-use, and water sectors of Viet Nam out to 2030. A validation of the clustering approach confirms that underlying trends actual crop yield data are preserved in the resultant clusters. Finally, changes in cultivated area of selected crops are observed and differences in levels of crop migration are identified.