This study uses multilayer minimum spanning tree analysis to develop a model for student retention from a complex system perspective, using data obtained from first-year engineering students at a large well-regarded institution in the European Union. The results show that the elements of the system of student retention are related to one another through a network of links and that some of these links were found to be strongly persistent across different scales (group sizes). The links were also seen to group together in different clusters of strongly related elements. Links between elements across a wide range of these clusters would have system-wide influence. It was found that there were no elements that are both persistent and have system-wide effects. This complex system view of student retention explains why actions to enhance student retention aimed at single elements in the system have had such limited impact. This study therefore points to the need for a more system-wide approach to enhancing student retention.