National emission inventories for UN FCCC reporting estimate regional soil nitrous oxide (N2O) fluxes by considering the amount of N input as the only influencing factor for N2O emissions. Our aim was to deepen the understanding of N2O fluxes from agricultural soils, including region specific soil and climate properties into the estimation of emission to find targeted mitigation measures for the reduction of nitrogen losses and GHG emissions. Within this project, N2O emissions and nitrate (NO3−) leaching were modelled under spatially distinct environmental conditions in two agricultural regions in Austria taking into account region specific soil and climatic properties, management practices and crop rotations. The LandscapeDNDC ecosystem model was used to calculate N2O emissions and NO3− leaching reflecting different types of vegetation, management operations and crop rotations. In addition, N input and N fluxes were assessed and N2O emissions were calculated. This approach allowed identifying hot spots of N2O emissions. Results show that certain combinations of soil type, weather conditions, crop and management can lead to high emissions. Mean values ranged from 0.15 to 1.29 kg N2O–N ha−1 year−1 (Marchfeld) and 0.26 to 0.52 kg N2O–N ha−1 year−1 (Grieskirchen). Nitrate leaching, which strongly dominated N-losses, often reacted opposite to N2O emissions. Larger quantities of NO3− were lost during years of higher precipitation, especially if winter barley was cultivated on sandy soils. Taking into account the detected hot spots of N2O emissions and NO3− leaching most efficient measures can be addressed to mitigate environmental impacts while maximising crop production.