A dynamic model of forest ecosystems was used to investigate the effects of climate change, atmospheric deposition and harvest intensity on 48 forest sites in Sweden (n = 16) and Switzerland (n = 32). The model was used to investigate the feasibility of deriving critical loads for nitrogen (N) deposition based on changes in plant community composition. The simulations show that climate and atmospheric deposition have comparably important effects on N mobilization in the soil, as climate triggers the release of organically bound nitrogen stored in the soil during the elevated deposition period. Climate has the most important effect on plant community composition, underlining the fact that this cannot be ignored in future simulations of vegetation dynamics. Harvest intensity has comparatively little effect on the plant community in the long term, while it may be detrimental in the short term following cutting. This study shows: that critical loads of N deposition can be estimated using the plant community as an indicator; that future climatic changes must be taken into account; and that the definition of the reference deposition is critical for the outcome of this estimate.