Transboundary water–energy–food (WEF) interactions present complex governance challenges, particularly in multi-country river basins where environmental, political, and socio-economic dynamics intersect. In such highly uncertain and interdependent systems, identifying key drivers and exploring alternative future scenarios is essential for developing a shared understanding of system behavior, reducing ambiguity, and supporting coherent and adaptive planning across national and sectoral boundaries. This study aims to identify and characterize the key drivers shaping WEF nexus dynamics within the Tigris–Euphrates basin, shared by Turkey, Syria, Iraq, and Iran, through a scenario-planning framework informed by morphological analysis. The scenarios were co-developed with stakeholders from multiple countries and sectors to ensure that diverse perspectives, priorities, and knowledge systems were explicitly represented. A systematic literature review identified 27 relevant influencing factors, from which experts selected six critical drivers for future-oriented analysis. For each driver, at least five plausible future states were defined and subsequently evaluated by basin stakeholders using structured surveys to assess both perceived likelihood and desirability. These assessments enabled the development of a set of alternative WEF scenarios—including the most probable, most acceptable, and most desirable trajectories—illustrating potential futures for the basin. The results also enable a comparative analysis of stakeholder responses across countries and sectors, revealing areas of convergence and divergence in perceptions of future risks and opportunities. By integrating morphological scenario planning with active stakeholder participation in a transboundary setting, this study offers a rigorous analytical foundation for collaborative resource management and long-term strategic planning across the Tigris–Euphrates basin. A central achievement of this research is the creation of a structured, participatory framework for assessing the WEF nexus in a shared river basin, designed to illuminate complex interdependencies and equip policymakers from multiple sectors and riparian countries with actionable insights for informed, coordinated decision-making.