Notwithstanding the dispersed nature of the water, energy and food (WEF) nexus scholarship in the African continent, its strategic importance to the African agenda has gained widespread attention in research and planning circles. In this regard, the bibliometric science mapping and content analysis of the WEF nexus scientific publication trends, the conceptual, intellectual and social structures, as well as the inherent paradigmatic shifts in the WEF nexus body of knowledge in the African continent have been undertaken, using the nexus body of literature accessed from the Web of Science and Scopus core collection databases. The review results confirmed that, whilst the WEF nexus scholarship has expanded since 2013, there is also evidence of growth in the conceptual, intellectual and social structures of the WEF nexus in the African continent. These shifts have resulted in the emergence of hot topics (subfields) including modelling and optimization, climate variability and change, environmental ecosystem services sustainability, and sustainable development and livelihoods. The review further determined that these structures have evolved along two main perspectives of WEF nexus research development, i.e., the interdisciplinary and transdisciplinary domains. In support of the interpretation of the visual analytics of the intellectual structure and changing patterns of the WEF nexus research, the shifts in positivist, interpretivist and pragmatic paradigmatic perspectives (these are underpinned by the ontology, epistemology, and methodology and methods) are considered when explaining WEF nexus research shifts: (a) From the unconnected silo paradigms that focus on water, energy and food (security concerns) to interconnected (and sometimes interdependent or nested) linkages or systems incorporating environmental, social-economic and political drivers (also viewed as subfields) in a bid to holistically support the Sustainable Development Goals (SDGs) across the African continent; and (b) in the evaluation of the WEF nexus scholarship based on novel analytical approaches. We contend that whilst the theories of science change underpin this apparent expansion, the macro-economic theory will find use in explaining how the WEF nexus research agenda is negotiated and the Integrative Environmental Governance (IEG) is the duly suited governance theory to bridge the inherent disconnect between WEF nexus output and governance processes uncovered in the literature. Overall, operational challenges and opportunities of the WEF nexus abound, transitioning the WEF nexus research to practice in Africa, motivating the need to take advantage of the scholar–practitioner research underpinnings, as contemplated in the transdisciplinary research approach, which is characterised by the dual quest for new knowledge and considerations of use. Yet, there is need for more coordinated and collaborative research to achieve impact and transition from WEF nexus thinking to WEF nexus practice.