Ammonia (NH3) deposition in natural areas is a pollution problem that is suited for spatially differentiated pollution control. The heterogeneous impact of nitrogen deposition from airborne ammonia emissions could serve as the basis for differentiated policy measures. Maps were developed that show the potential impact of ammonia emissions on protected Natura 2000 sites in Flanders, Belgium. These maps link the output of atmospheric dispersion and deposition models with data on the nitrogen sensitivity of protected habitats in the Natura 2000 network. The maps demonstrate that the indicator used for impact assessment is a crucial factor in the design of the spatially differentiated policy. The currently used impact indicator in Flanders, the Significance Score, was compared with the Aggregate Deposition Score, an alternative that is a better reflection of the total damage caused by airborne ammonia emissions in nearby Natura 2000 sites. Both indicators are based on the ratio of ammonia deposition to the critical load of nitrogen of the impacted habitat. Spatial effects related to the choice of impact indicator were evaluated. The results indicate that the choice of impact indicator has a decisive role in the geographical outcome of spatially differentiated policies.