The dominant nitrogen (N) fluxes were simulated in a mountain forest ecosystem on dolomitic bedrock in the Austrian Alps. Based on an existing small-scale climate model the simulation encompassed the present situation and a 50-yr projection. The investigated scenarios were current climate, current N deposition (SC1) and future climate (+2.5 °C and +10% annual precipitation) with three levels of N deposition (SC2, 3, 4). The microbially mediated N transformation, including the emission of nitrogen oxides, was calculated with PnET-N-DNDC. Soil hydrology was calculated with HYDRUS and was used to estimate the leaching of nitrate. The expected change of the forest ecosystem due to changes of the climate and the N availability was simulated with PICUS. The incentive for the project was the fact that forests on dolomitic limestone stock on shallow Rendzic Leptosols that are rich in soil organic matter are considered highly sensitive to the expected environmental changes. The simulation results showed a strong effect due to increased temperatures and to elevated levels of N deposition. The outflux of N, both as nitrate (6–25 kg N ha −1 yr −1) and nitrogen oxides (1–2 kg N ha −1 yr −1), from the forest ecosystem are expected to increase. Temperature exerts a stronger effect on the N 2O emission than the increased rate of N deposition. The main part of the N emission will occur as N 2 (15 kg N ha −1 yr −1). The total N loss is partially offset by increased rates of N uptake in the biomass due to an increase in forest productivity. A combination of the risk factors “elevated temperature and nitrogen inputs” will increase the rate of nitrate leaching and the emission of nitrogen oxides from a forest ecosystem in the Austrian limestone Alps.