This article examines the governance of water security as a critical factor in conflict prevention, drawing on a comparative analysis of institutional frameworks in the Horn of Africa and Gabon. Employing a qualitative, process-tracing methodology, the study analyses documentary evidence and scholarly literature to uncover the causal pathways linking governance to water-related tensions. It finds that the risk of conflict is determined less by absolute water scarcity than by the strength and legitimacy of governing institutions. In the Horn, fragmented and exclusionary frameworks exacerbate local disputes. In Gabon, despite abundant resources, centralised and opaque management creates pockets of scarcity and grievance, demonstrating how institutional weakness can generate conflict risk irrespective of hydrological endowment. The study concludes that effective conflict prevention requires a shift from technical solutions to institutional reforms that prioritise transparency, equity, and community participation. These insights offer evidence-based guidance for policymakers seeking to enhance water security as a foundation for stability in diverse regional contexts.