The recent figures on the conservation status of EU protected habitats and species underscore the obvious need for a more stringent application of the protection rules included in Article 6 of the Habitats Directive on ongoing activities, such as dredging, recreation and forestry, with adverse effects on Natura 2000-sites. However, all too often the Member States refrain from scrutinizing harmful forms of existing use in already heavily degraded Natura 2000-sites. The economic concerns tied to the continuation of existing use often prevail over restoration considerations. This paper showcases that, despite submissions to the contrary, legitimate interests and legal certainty cannot, as such, preclude the application of the protection rules contained in Article 6 of the Habitats Directive in relation to ongoing activities. Whilst granting the Member States some leeway as to the application of the ex ante assessment rules to ongoing activities, the Court of Justice puts forward the protection duty enshrined in Article 6(2) of the Habitats Directive as bottom-line in relation to all possible ongoing activities which could lead to deterioration and/or significant disturbance of a Natura 2000-site. However, the recent case-law illustrates that many Member States are struggling with the effective implementation of the latter obligation.