Atmospheric nitrogen (N) deposition across Europe increased substantially from the 1950s to the 1990s. Targeted surveys suggest a negative correlation between N deposition and species richness within quadrats in sensitive habitats. However, it remains unclear whether plant species losses at national recording scales are correlated with nitrogen deposition. We relate plant species losses before 1987 in Great Britain to reduced and oxidized N deposition, land use change and climate change. The mean Ellenberg fertility (N) indices of plant species lost in each 100 km2 cell before 1987 was compared with those of species that were recorded between 1987 and 1999. In 45% of squares, indices of species lost were significantly lower than those for species present after 1986. For 17%, primarily upland, squares, the opposite effect was found. A generalized least squares regression model, with difference in the mean Ellenberg N index between samples as the dependent variable, showed that higher deposition of reduced N was significantly associated with selective loss of species with a lower index. Arable land use and change in arable land use also demonstrated this positive relationship. Rough grazing, change in rough grazing, change in pasture and change in annual precipitation showed negative effects. Difference in Ellenberg R index was highly correlated with difference in Ellenberg N and was negatively correlated with oxidized N deposition, suggesting that the lack of a significant effect of oxidized N deposition on Ellenberg N was because it had effects through both acidification and eutrophication, while the effect of reduced N deposition was primarily through eutrophication. Our results suggest that N deposition, along with land use and precipitation changes, has been a significant driver of local plant extinctions. With N deposition increasing in many parts of the world, local extinctions of plant species may be experienced in other regions.