In large parts of Western Europe agricultural intensification after World War II has led to an increased use of fertilisers. The resulting nutrient enrichment (=eutrophication) has a huge impact on the occurrence and distribution of plant species and is one of the main pressures on native plant communities. We used the distribution maps (grid size: 16 km(2)) of individual plant species, obtained through two consecutive survey projects (1939-1971 and 1972-2004) in Flanders (northern Belgium), to estimate the relative change in their distribution area. The comparison of changes in range size among groups of taxa classified according to habitat preference and Ellenberg indicator values, demonstrated a marked decline in distribution area in species that are characteristic for nutrient-poor habitats. To assess geographic patterns in the change of species assemblages, we calculated the mean Ellenberg N- and R-values for every grid cell during each of both survey periods. Differences between these values were analysed in relation to soil type and estimates of atmospheric nitrogen deposition. The largest shifts in Ellenberg N-values, reflecting a decline of species from nutrient-poor conditions and/or an increase of nitrophilous plants, were observed in areas with nutrient-poor, acid sandy soils and high nitrogen deposition rates. Hence, shifts in species composition were modulated by geographic variation in soil type and levels of nitrogen deposition. As the levels of atmospheric nitrogen deposition are still very high in Flanders, it is likely that species from nutrient-poor habitats such as heathlands, will further decline in the near future.