Segregation studies have mainly focused on urban structures as a whole or have discussed specific (gentrifying or renewing) neighbourhoods. The literature suggests that changes in segregation occur primarily through selective migration. In this paper, we follow up on recent work that has questioned these orthodoxies, suggesting that in situ social mobility, and entries to and exits from the city population should be taken into account as well, and that dynamics in all neighbourhoods should be considered. The paper traces the processes by which segregation changes for the cities of Amsterdam and The Hague for 1999–2006, using a longitudinal individual‐level database covering the entire population. It extends previous work by looking at income rather than socio‐economic status and by drilling down to the neighbourhood level. Applying an existing measure of segregation (Delta) in a novel way, the analysis focuses on changes in the spatial distribution of household income, measuring the relative contribution of a range of processes to changes in segregation. Results show that segregation rises in both cities but that different processes drive changes in each case. Furthermore, the aggregate change in segregation for each city masks a diversity of changes at the neighbourhood level, some of which tend to increase segregation while others tend to reduce it. Mapping these changes and the individual processes contributing to them shows that they have a distinct geography, which seems to be structured by historically specific trends in state and housing market context. © 2016 The Authors. Population, Space and Place. Published by John Wiley & Sons, Ltd.