This study examines the influence of the increased atmospheric nitrogen (N) deposition observed in central Russia between 1960 and 2010 (with a peak in 1990) on biodiversity and the availability of N in soil in pine forests. Shifts in N availability in soils of 3 pine plots were analyzed using presence/absence chronosequence records of the dynamics of ground vegetation plants and a set of specialist plant species with a narrow range of tolerance as bioindicators of soil richness. We assumed that changes in plant communities might be caused by increased atmospheric N input. To examine this assumption, (i) the species composition of forest ground vegetation was analyzed using the Ellenberg N scale and the Tsyganov N scale, which was developed for forest vegetation in European Russia, and (ii) the dynamics of the main N pools were examined using simulation models of forest growth and elements cycling in the forest—soil system. Our results confirm that changes in the ground vegetation communities experiencing eutrophication occurred in all plots. The number of indicators of N-rich conditions for these plots reached a maximum in 1990, the year N deposition reached its maximum in this area. The decline in the number of oligotrophic species indicated that N-poor soils decreased over the monitoring period. Model simulations showed an increase in labile N compounds in the soil and in the total N pool in forest ecosystems. Our results demonstrate an acceleration of natural succession due to atmospheric nitrogen deposition in this region.