This study examined the complex relationship between hydropolitics and strategic security in post-conflict South Sudan, emphasizing the critical role of water resource management within the Nile Basin. Given South Sudan’s recent independence after decades of civil war, the research explored how water scarcity, infrastructural deficiencies, and regional geopolitical tensions influenced internal stability and regional diplomacy. Employing a pragmatic research philosophy, the study adopted a mixed-methods design, integrating qualitative stakeholder interviews, policy analysis, and quantitative data to provide a comprehensive understanding of water governance challenges. The data collection followed a concurrent embedded approach, allowing for the simultaneous gathering and analysis of multiple data sources, which enhanced the validity of the findings through triangulation. The target population comprised approximately 200 stakeholders, including government officials, community representatives, technical experts, NGOs, and international actors, selected through purposive and snowball sampling techniques to ensure diverse and relevant representation across geographic and institutional lines. Quantitative data encompassed infrastructure conditions, governance indicators, and conflict metrics, which were analyzed using descriptive statistics, regression models, and principal component analysis to explore relationships between water infrastructure, policy frameworks, and security outcomes. Qualitative data from semi-structured interviews, focus group discussions, and document reviews underwent thematic content analysis, capturing stakeholder perceptions, institutional narratives, and social dynamics. This mixed-methods approach facilitated a nuanced understanding of how governance deficiencies, ethnic identities, and regional geopolitics contributed to water-related conflicts.