Many habitats and species have their existence threatened, especially in densely populated areas such as Western Europe. To stop the decline of biodiversity, the Natura 2000 network is being set-up. The ultimate objective is to get all habitat types (of Annex I of the Habitats Directive) and species (of Annexes II, III and IV of the Habitats Directive and Annex I of the Birds Directive) in a favourable conservation status. In the Netherlands a national ecological network has been set up for this purpose which includes the designated Natura 2000 sites. The current amount of atmospheric nitrogen deposition, acidification and desiccation were compared with limit values per habitat type for nitrogen deposition load, soil pH and spring groundwater table respectively and subsequently presented together in one map. Fragmentation was tested for 80 species.For two-third of the examined natural surface the critical load for nitrogen deposition is exceeded, desiccation is present in over 90% of the area of groundwater dependent nature. Problems with acidification are less pronounced. Fragmentation is present causing regional problems for up to six species. When the four pressures are combined, about two third of the areas suffer from at least one pressure. Many areas suffer from a combination of nitrogen deposition and desiccation.We conclude that environmental and spatial conditions are insufficient to meet the biodiversity target set by the European Union for the Natura 2000 network, habitat types and species.