The continuing rise in chronic health conditions requires major changes in how healthcare is managed and delivered. While research has identified a number of factors key to bringing this about, implementing these changes requires an understanding of how the factors interact over time in different contexts. In this research study, seven senior health experts in New Zealand were interviewed, using cognitive mapping, to ascertain their thinking about major implementation challenges to enhance primary healthcare systems. The resulting cognitive maps were then consolidated and developed into a causal loop diagram, which describes a set of interlinked feedback loops representing the processes involved in implementing changes. It is concluded that these systems methods are very effective in better understanding the contextual and behavioural factors necessary for the development of a theoretical framework to support the successful implementation of innovative primary healthcare programmes.