<p>This paper develops a transparent approach to diagnose cross-sector interactions in the water, energy, food, and ecosystems (WEFE) nexus and to support intervention prioritization. We introduce two directional metrics, the Nexus Synergy Index (<i>NSI</i>) and the Nexus Conflict Index (<i>NCI</i>), that score ordered interactions between sectors through three mechanisms, efficiency, reliability, and safeguards. Positive and negative effects are reported separately, ensuring that benefits do not mask risks. Scores are adjusted by an evidence quality factor <i>q</i> and an impact-scale factor <i>m</i>, which together reflect how credible the evidence is and how widely and persistently the effects occur. The method combines structured rubric with traceable anchors for expert judgment and integrates observed data where available, supporting both qualitative and quantitative assessment modes. It outputs mechanism level diagnostics and summary indices (<i>NSI</i>, <i>NCI</i>) and an optional Net Nexus Interaction Index (<i>NII</i>). The approach is demonstrated with nationally determined contribution relevant options in Lebanon, including wastewater reuse, irrigation modernization, solar pumping, and ecosystem restoration. The application shows how the framework distinguishes high synergy options, reveals nontrivial ecosystem or reliability risks, and identifies where safeguards or design adjustments are needed before scale up. The method is reproducible, low cost to apply, and adaptable to data rich or data scarce settings. It is designed to help planners, regulators, and financiers compare alternatives on consistent terms, align portfolios with climate and development goals, and make tradeoffs explicit so that resources are allocated where they deliver the most durable co-benefits with the fewest unintended consequences.</p>