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Abstract Across the world, conflicts have disrupted dam operations, leading to water mismanagement and increased disaster potential. This study uses water balance modelling and scenario analysis to present a replicable framework for assessing flood risks in inaccessible, data-scarce conflict-affected areas. The methodology is demonstrated through the case of the Jebel Aulia Dam in Sudan, where an ongoing conflict since April 2023 has rendered the dam non-operational. Following an attack on the dam in November 2023, operators fled, leaving the gates in fixed positions. The dam remained non-operational from November 2023 to January 2025, significantly increasing flood risks. Model simulations indicate that, under various climatological scenarios, water levels would have exceeded the dam full supply level, posing a risk of uncontrolled flooding. Even though community interventions temporarily mitigated the danger, an unexpected flood in December 2024, occurring outside the usual flood season, underscores the necessity of proactive and structural operational forecasting using this framework in such unsteady environments. This study highlights the compounded threats posed by armed conflict and climate variability on critical infrastructure. In times of war, communities face dual risks, not only from direct violence such as bombs and gunfire but also from the cascading effects of mismanaged infrastructure, which can trigger devastating consequences. The methodology followed for this study is applicable to other regions where water infrastructure faces similar risks due to war and/or collapse of the governance structure. To enhance resilience and facilitate timely interventions, real-time monitoring, in particular with remote sensing techniques and adaptive forecasting tools, should be integrated into disaster risk management strategies for water infrastructure in conflict-prone areas worldwide.