In recent years, researchers and policymakers have emphasised the importance of understanding the complex relationships between Water, Energy, Food and Ecosystems (WEFE). The primary reason for capturing these complexities is to understand how decisions made in the water, food and energy sectors can affect one another. Crucially, biodiversity and ecosystem services (E) play a mediating role in these relationships by making material and non-material contributions to all other sectors (W, E, F). The Nexus approach has been widely used for capturing these interdependencies and identifying opportunities for increasing efficiency, reducing trade-offs and building synergies for sustainable resource use across the WEFE nodes. One challenge in using this framework is the need to harmonise the technical and managerial dimensions of the WEFE interlinkages with the perceptions and priorities of local populations directly involved in the use and management of resources. This paper presents a methodological framework that seeks to integrate the perspectives of experts, practitioners and local stakeholders on the WEFE Nexus through the combined application of the Delphi and Focus Group methods. In this paper, the municipality of Apokoronas in Crete, Greece has served as the case in point. The combined framework allowed us to explore the Nexus understanding at the local level and was instrumental in the identification of initiatives for more integrated resource management. The triangulation of results captured the differences in priorities between practitioners and the local community at large, but also, more specifically, it pointed to discrepancies within groups and across WEFE sectors. The outcomes of this paper demonstrate that awareness and learning play a central role in Nexus actions to overcome conflicts and perceived inequalities, and to internalise solutions. The inclusion of the ecosystems node in the traditional WEF Nexus encouraged participants to contemplate the pivotal role of ecosystems in supporting the rest of the WEF sectors.