This paper discusses key methodological issues with nodalising interaction data of urban networks to produce a state‐of‐the‐art settlement geography of the Netherlands. We operationalise the three‐systems model that analyses functional settlement geographies through the interaction between the daily urban system, the central place system and the export base system. We utilise theoretically‐informed selections of spatial interactions derived from travel survey data at the finely‐grained postcode level. After examining the methodological challenge of the node‐inclusivity dilemma, we estimate the causal mechanisms that geographically structure each system and determine which spatial interactions should be assigned to nodes (containment) and edges (connectivity). The three systems produce different regionalisations that are neither mutually exclusive nor perfectly nested. Further analysis of the multiplexity of the three systems reveals the importance of the imbricated boundaries between the urban subsystems. We argue that these interplaces deserve more attention as they are particularly sensitive to changes in urbanisation trends.