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Jordan is among the most water-stressed countries globally, with renewable freshwater availability falling below 100 m3 per capita per year. The Jordan Valley (JV), the country’s primary irrigated agricultural corridor, faces interconnected pressures across water, energy, food, and ecosystem (WEFE) systems under intensifying climatic and demographic stressors. This study evaluates the integrated performance of the WEFE nexus in the Jordan Valley using updated evidence (2018–2023) to quantify cross-sector interactions, performance gaps, and intervention priorities. A mixed-methods empirical assessment integrated quantitative sectoral data on water supply–demand and quality, electricity supply–demand and renewable deployment, agricultural productivity, and ecosystem pressure indicators, complemented by Living Lab–based stakeholder interviews. Sectoral indices were calculated based on supply–demand adequacy and aggregated into an overall WEFE Nexus Index. Results indicate persistent water scarcity, with a domestic supply of 23.48 MCM yr−1 versus demand of 26.00 MCM yr−1 (deficit −2.52 MCM yr−1) and irrigation supply of 206 MCM yr−1 relative to approximately 400 MCM yr−1 demand (deficit −194 MCM yr−1). Water services account for 14% of national electricity consumption, while solar pumping provides approximately 40% of daytime irrigation energy. Agricultural productivity is constrained by salinity and water quality, resulting in yield gaps (e.g., greenhouse vegetables: 4.7 vs. 10.0 t/dunum). Sectoral performance is uneven (Water 0.71; Energy 1.00; Food 0.45; Ecosystem 0.50), yielding an overall WEFE Nexus Index of 0.63 (0.50 after efficiency adjustment). Climate projections indicate continued warming (+1.8 °C) and declining precipitation (−11%) by 2060. Water harvesting, integrated renewable-powered water services, wastewater reuse, salinity management, climate-smart agriculture, and ecosystem restoration are critical to enhancing climate-resilient resource security in the Jordan Valley. The WEFE index developed here offers a tool for integrated planning and underscores that achieving climate-resilient resource security in the Jordan Valley will require strategic, cross-sector interventions and adaptive governance rather than sector-specific fixes.