The water-energy complex of Central Asian countries represents a tightly interconnected system in which river flow allocation, hydropower operation regimes, generation structure, irrigation water use, and food security jointly shape a unified dynamic of risk and resilience. The region is experiencing increasing climate variability (rising frequency of droughts, desertification processes, extreme floods, and glacier retreat), alongside simultaneous growth in electricity and food demand. Fragmented interstate governance further creates conditions in which decisions taken within one sector systematically generate cross-sectoral externalities in others. This study proposes an ecosystem-based management framework for the Central Asian water-energy complex within the logic of the Water-Energy-Food (WEF) Nexus. The framework integrates: i) the physical and hydrological foundations of water resources; ii) energy infrastructure and dispatch optimization; iii) agricultural production functions and irrigation efficiency; iv) climate risks and uncertainty; and v) institutional constraints and governance gaps. Methodologically, the research is grounded in an integrated mathematical model combining system dynamics (stock-flow balances), multi-objective optimization (water-energy-food trade-offs), scenario modeling (2030-2040-2050 horizons), policy simulation (tariff-subsidy schemes, investments in renewable energy and storage, irrigation modernization, seasonal regulation rules), and a climate risk module (probabilistic flow and temperature shocks, stress testing, and robust adaptive optimization). To address the institutional dimension, a “mandates-responsibilities-data-incentives” matrix is introduced, enabling quantitative assessment of governance gaps in transboundary water allocation mechanisms and coordinated energy operation regimes. The study generates a set of quantitative Nexus efficiency and resilience indicators, including a systemic coherence index of decision-making, water-energy-food deficit metrics, economic losses from uncoordinated dispatch, socio-environmental externalities, and a ranking of policies based on Pareto improvement criteria. The findings provide an applied foundation for designing coordinated reservoir operation rules, investment portfolios, and interstate agreements that enhance Central Asia’s resilience to climate shocks while preserving basin ecosystem functions and reducing resource allocation conflicts.