This article develops a novel theoretical framework for analysing water security governance in the Horn of Africa, a region characterised by transboundary hydrological interdependence and political fragility. It critiques the limitations of existing state-centric and basin-wide institutional models, arguing they often exacerbate rather than mitigate conflict. Drawing on polycentric governance theory and insights from the unique hydro-political context of São Tomé and Príncipe—a small island state facing distinct but instructive water security challenges—the framework proposes a multi-scalar, adaptive institutional architecture. This architecture integrates sub-national, national, and regional governance nodes to enhance resilience and collaborative capacity. The article concludes by outlining the framework's theoretical contributions to political science and its practical implications for conflict-sensitive water policy design in the Horn and analogous fragile contexts.