We use national scale data to test the hypothesis that nitrogen (N) deposition is strongly negatively correlated with plant species richness in a wide range of ecosystem types. Vegetation plots from a national ecological surveillance programme were drawn from heathland, acid, calcareous and mesotrophic grassland habitats. Mean species number and mean plant traits were calculated for each plot and related to atmospheric N deposition. There was a significant reduction in species richness with N deposition in acid grassland and heathland even after fitting covarying factors. In acid grassland and heathland, evidence from trait changes suggested that acidification rather than increased fertility was responsible for species loss. In contrast, calcareous grassland showed evidence of eutrophication in response to increasing N deposition. Loss of species richness from chronic N deposition is apparent in infertile grasslands and heathland. Mechanisms associated with loss of species richness differ between habitats so mitigation of N deposition should be targeted to habitat type.