The Water Energy Food nexus is a powerful topic in agricultural systems to elucidate threats to biodiversity conservation and culture. This paper aimed to recapitulate nexus thinking research, focusing on social-ecological transitions of agriculture systems and biodiversity management within the Water-Energy-Food nexus. We developed a systematic review and a bibliometric analysis derived from 529 documents in the Scopus database. The ToS method identified a total of 81 relevant information in the sample of documents (529) categorised into roots (10), trunks (9) and leaves (62). This review paper situates types, focus, and highlights regarding biodiversity and prevalent thematic research areas such as “Food Nexus”, “Environmental Flows”, “Sustainability”, “Transitions”, and “Governance”. Our results suggest that future research should focus on the nexus of “Water-Energy-Food-Biodiversity” and propose a transdisciplinary approach to elucidate the state of sustainability transitions in the agricultural systems at the landscape level. It could increase stakeholder interest in conservation, and sustainability management, to reverse biodiversity losses in ecosystems.