The spatial distribution of metropolitan areas creates a complex system of competing and cooperating economic units. Understanding the size, scale and functional structure of such systems is an important topic in regional science. This paper uses commuter flow data over a 40 year period to analyse the changing structure of the Greater Manchester metropolitan area. We apply a combination of complex network analysis, residual network analysis and spatial network visualisation to detect Greater Manchester’s polycentric structure and identify intra-regional communities. This method is able to identify economic geographies in a highly complex and interdependent commuter network. We comment on the role of administrative boundaries in shaping metropolitan regions and discuss the potential of our work to inform debates on regional governance geographies and local government planning practices.