The implementation of Natura 2000 is causing difficulties in the EU’s Member States, including Slovenia. In addition to the positive environmental it also results in the negative economic, social, and governance-administrative effects. To prevent similar quandaries in adopting and implementing EU policies, the project ESPON EATIA developed a participatory process for the territorial impact assessment. Testing the Habitat Directive has shown that in addition to the positive effects regarding the conservation of biodiversity, the directive represents a major obstacle for the economy and the delivery of investments. At the same time it represents the potential of the area for tourism and opportunity for the development of new industries. The regulation contributes to a better quality of life, but also extends the spatial planning procedures and conflicts between investors and the local community. This approach has proven to be an appropriate medium for the exchange of experiences of various stakeholders who are involved in either the preparation or the implementation of the rules and as the proper tool for the global assessment of the effects of selected EU regulation