Integrated management of water, energy, and food (WEF) systems requires governance approaches that account for biophysical interdependencies while remaining grounded in the institutional arrangements through which decisions are made and implemented. Despite the widespread appeal of the WEF nexus, its operationalization remains limited, particularly in data and capacity-constrained contexts. This study presents a sequenced diagnostic framework to assess WEF nexus governance, explicitly linking biophysical interactions to institutional and policy processes. The approach begins with a basin-level analysis of subsystem interactions to characterize a clearly defined nexus challenge. It then situates this challenge within the broader governance landscape, before proceeding to detailed analyses of policy coherence and governance architecture, including proposal and approval procedures, formal implementation arrangements, and guiding principles. Applied to the Tana River Basin in Kenya, the framework identifies 50 explicit synergies and 7 trade-offs across national sectoral policies, alongside uneven coordination mechanisms between sectors. The findings show how land-use, water allocation, agricultural priorities, climate adaptation, and ecosystem protection are shaped by the interaction between biophysical constraints and sectoral mandates. By linking policy alignment with institutional design, the framework identifies actionable entry points for improving cross-sector coordination. Designed for both preliminary assessments and stakeholder-engaged processes, the approach provides a practical pathway for operationalizing WEF nexus governance in real-world settings.

This comprehensive state-of-the-art literature review explores recent scientific developments in climate, land, energy, and water systems (CLEWs) modelling by systematically analysing 41 peer-reviewed studies published between 2020 and 2024. This research uncovered insights into the evolving interdisciplinary landscape, revealing various trends, such as approximately 74% of studies publishing their data as open-access and 50% employing an open-source analytical tool, or tools, in combination with open-access data. This study identified four areas of significance: (1) the connections between CLEWs and the sustainable development goals, (2) how the CLEWs framework is linked to capacity development, (3) the critical interplay between energy and water systems, and (4) the transformative potential for comprehensive system integration using the CLEWs modelling framework. By pinpointing promising research directions such as soft-linking CLEWs models with geographic information systems, applying robust decision making methodologies, adapting the CLEWs framework to the city level, and highlighting the need to assess real world impact of CLEWs research, the review provides a strategic roadmap for future interdisciplinary research. Notably, the analysis emphasised the urgent need for enhanced institutional coordination and collaborative communities of practice, particularly for open-source modelling tools like the open-source energy modelling system, to further accelerate knowledge dissemination and foster innovative, integrated approaches to complex systemic challenges.