Addressing complex interactions within water, energy, and food (WEF) resources, innovative tools for in-depth analysis and decision-making are imperative. This study introduces chorematic focus maps (CFMs) as a groundbreaking method to visualize and tackle the WEF nexus’s complexities, focusing specifically on the Danube Delta Biosphere Reserve (DDBR). By merging geospatial analysis with on-site validation, this research reveals intricate interdependencies within the nexus and positions CFMs as an effective tool for stakeholders. This study adopts a methodological approach that focuses on identifying human activities and evaluating their impacts on the WEF nexus, with the goal of developing practical and grounded strategies for managing these essential resources. By testing this approach within the DDBR, the potential for wider application is demonstrated, offering a promising framework for addressing similar socio-environmental challenges across various regions. Future research directions include refining CFMs’ precision and practicality through extended fieldwork and stakeholder engagement, testing the framework’s adaptability across various locations and nexus dynamics. Additionally, incorporating cutting-edge technologies such as machine learning could provide deeper insights and reinforce CFMs’ role in decision support for the WEF nexus. Conclusively, this investigation into the WEF nexus through CFMs emphasizes the critical need for strategies that navigate the complexities of environmental management and resource optimization, marking CFMs as a significant tool for both decision-makers and researchers.