The water, energy and food nexus (WEF nexus) is currently quite popular in environmental management. The concept found a fertile ground in science and policymaking, but there is no consistent view on the meaning of integration within the nexus. Here, a wealth of publications is reviewed in an endeavour to: (1) reveal the lines of justification for the need of the WEF nexus debate and (2) identify the range of tools for analysing the interdependent resource issues of the nexus using an integrated framework of science and policy. There are three drivers behind the emergence of the nexus thinking. These are a) increasing resource interlinks due to growing scarcities, b) recent resource supply crises, and c) failures of sector-driven management strategies. Evaluation of the WEF nexus integrative debate can be carried out using four key criteria, namely ability to change current policy debates, issue and thinking novelty, practicability and measurability, and clearness and implementation roadmap. It is clear that, although the nexus has been quite successful in changing policy debates, issue prioritization is missing and seems to be left to specific case studies and policymakers' choices. There is a high need for ‘incorporation’ and ‘cross-linking’ of issues between the three resources. In this regard, nexus governance is the missing link in the nexus debate.