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This paper discusses a methodology where geo-spatial analysis tools are used to quantify risk derived from anthropic activities on habitats and species. The method has been developed with a focus on simplification and the quality of standard procedures set on flora and fauna protected by the European Directives. In this study case, the DPSIR (Drivers, Pressures, State, Impacts, Responses) is applied using spatial procedures in a geographical information system (GIS) framework. This approach can be inserted in a multidimensional space as the analysis is applied to each threat, pressure and activity and also to each habitat and species, at the spatial and temporal scale. Threats, pressures and activities, stress and indicators can be managed by means of a geo-database and analyzed using spatial analysis functions in a tested GIS workflow environment. The method applies a matrix with risk values, and the final product is a geo-spatial representation of impact indicators, which can be used as a support for decision-makers at various levels (regional, national and European).