The Nile River Basin, spanning eleven countries and supporting over 300 million people, faces escalating hydro-political tensions driven by climate change, infrastructure development, and regional power asymmetries. South Sudan, which contains approximately 2.5% of the basin's water resources, remains highly vulnerable due to internal conflict, institutional weaknesses, and limited influence in regional negotiations. Understanding how hydro-conflicts impact water governance is critical for promoting sustainable development and climate resilience in this fragile context. This study examines the influence of hydro-conflicts on water governance effectiveness in South Sudan, emphasizing institutional capacity, regional power dynamics, and environmental policy. It aims to identify strategic pathways for strengthening governance frameworks, fostering cooperation, and addressing the root causes of water insecurity. Using a qualitative comparative case study approach, the research integrates semi-structured interviews with 75 stakeholders including government officials, regional organizations, and local communities and systematic document analysis of policy frameworks and institutional reports. Thematic content analysis, supported by NVivo software, was employed to identify patterns and relationships. Theoretical frameworks such as hydro-hegemony, institutional theory, and social-ecological systems guide interpretation. Comparative insights from successful basin models like the Rhine were also incorporated. Historical colonial treaties, such as the 1929 and 1959 agreements, continue to favor upstream states like Ethiopia and Egypt, marginalizing South Sudan. Institutional fragmentation, with over seven overlapping agencies operating on just 2.3% of the national budget, hampers effective management. Regional power asymmetries, exemplified by Ethiopia’s construction of the Grand Ethiopian Renaissance Dam (GERD), which aims to generate 6,450 MW of electricity,