•A causal characterization between nexus problems and multi-level, conflictive goals.•Conceptualization of nexus networks through the lens of relational analysis.•Formalization of nexus networks with metabolic processors and a taxonomy of relations.•An illustration of a water-food nexus network with interconnected causal mechanisms for groundwater over-draft.•A range of social-ecological patterns demanding different adaptation strategies. While a large number of descriptive studies have delineated the interlinkages between water, food and energy resources in the last decade, there is still need for systematic conceptualization of resource nexus interconnections. This paper proposes a theory of relational analysis of the nexus based on the analytical concept of nexus networks. A taxonomy of nexus interconnections, detailing sequential and hierarchical connections, is characterized between and amongst the technosphere and biosphere. We illustrate the use of a novel diagnostic tool with regard to its ability to integrate macro-, meso- and microscale drivers of nexus problems. We apply this framework to problems generated by intensive crop production for exportation in an arid landscape (driven by external markets) and sustainable management of water resources (driven by public policies) in a southern Spanish region. We elucidate interconnected causal mechanisms for groundwater overexploitation and profile different social-ecological patterns on a spatially-explicit basis. The proposed approach is capable of accounting for the water-energy-food resource nexus in an integrated and multi-level fashion, addressing the tensions generated by both multi-functionality and resource entanglement in complex social-ecological systems. Display omitted