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Regardless of the efforts of the European Union, freshwaters are in a state of environmental crisis. The Water Framework Directive has established a basis for the protection and restoration of European inland and coastal waters. In parallel, the Birds and Habitats Directives protect, maintain or restore, at favourable conservation status, selected species and habitats under a representative network of protected areas. Hence, the interplay between the EU regulations is of high scientific interest and practical relevance. In this article, Greece is used as a case study to explore whether anticipated synergies between the Water Framework Directive and the Nature Directives result in a better ecological status in the protected areas than in the non-protected ones. We investigated whether the ecological qualities that are defined by three biological quality elements (BQEs) differ between the WFD monitoring sites that are located within the Natura 2000 protected areas and those that are not. We identified a total of 148 river monitoring sites that are located within the Natura 2000 network, which corresponds to 30% of the WFD monitoring network. By employing ordered logit models for each BQE, we found that the ecological quality has the same likelihood to fail the WFD target of “good” quality for sites that are located within and outside the Natura 2000 protected areas. Our results confirmed our hypothesis that the EU directives have little synergy when it comes to restoration of ecological status of Greek running waters, according to the WFD.

Do Water Bodies Show Better Ecological Status in Natura 2000 Protected Areas Than Non-Protected Ones?—The Case of Greece