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Integrated water resource management in transboundary basins requires participatory frameworks that bridge technical modeling with stakeholder knowledge. This study presents a participatory Water-Energy-Food (WEF) nexus assessment methodology applied to the Ewaso Ng’iro North Basin (ENNB), Kenya, spanning five counties with 3.4 million inhabitants. Combining the UNECE Nexus Assessment methodology with WEAP (Water Evaluation and Planning) modeling and GIS-based spatial analysis, we engaged stakeholders through structured workshops to co-develop decision-making scenarios. The methodology integrated qualitative participatory processes— including problem identification, hotspot mapping, priority matrices, and trade-off analysis—with quantitative hydrological modeling across 12 sub-catchments. Seven scenarios were co-created: baseline/reference, increased water productivity, wastewater reuse, transboundary cooperation, integrated strategies, technology adoption, and water supply improvements. Results demonstrate that the Integrated Nexus scenario reduces unmet water demand from 78 Mm³/year (business-as-usual) to 18 Mm³/year, stabilizes groundwater levels (0.1 m/year vs. 1.5 m/year depletion), increases agricultural productivity by 24%, and reduces energy requirements by 35%. The participatory approach achieved 78% spatial correspondence between stakeholder-identified and technicallyassessed hotspots, validating local knowledge integration. This framework transformed passive consultation into active co-creation, providing a replicable model for nexus-based governance in data-scarce transboundary contexts.