Frequent spatial reorganization of administrative units is common in many countries. It may comprise the merging or division of spatial units, or boundary changes between units. These reorganizations prevent the effective assessment of longer-term population dynamics at a detailed spatial level. To deal with this problem in the Netherlands, we developed a new temporal correction method for the populations of municipalities. Rather than estimating the affected population, we used existing data on the number of persons affected by each spatial change. We assumed that before any boundary changes took place, population development was spatially uniform within a municipality. Systematically transferring proportions of the population from original to newly defined target municipalities back in time provided a corrected time series for 1988-2011, based on the 2011 municipal boundaries. Overall, our results correspond well with a detailed reconstruction for 1999-2009 based on data for individual households. Our procedure may be applicable in other countries with effective population registration systems.