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Management of Natura 2000 sites

Links between the Nature Directives and Water Framework Directive, Marine Strategy Framework Directive and Floods Directive

Commission notes

Article 6.3 permit procedure - implementation

The Commission has funded a fact finding study to gather and review information on the perceived nature, extent and significance of the problems and burden associated with the Article 6.3 permitting procedure and to formulate recommendations for improving the efficiency of the procedure. The final report provides a first snap shot of how Article 6.3 operates in different parts of the EU. It also offers a wide range of good practice techniques and examples that have been used up to now to improve the efficiency of the procedure. The final report is accompanied by a more in-depth analysis of a number of case studies on the practical implementation of Article 6.3 under a range of different circumstances.

  • Final report (Dec 2013) - summarising the findings of the study


Article 6 - Managing and protecting Natura 2000 sites

Article 6 is one of the most important articles in the Habitats Directive as it defines how Natura 2000 sites are managed and protected.

Paragraphs 6(1) and 6(2) require that, within Natura 2000, Member States:

  • Take appropriate conservation measures to maintain and restore the habitats and species for which the site has been designated to a favourable conservation status;
  • Avoid damaging activities that could significantly disturb these species or deteriorate the habitats of the protected species or habitat types.

Paragraphs 6(3) and 6(4) lay down the procedure to be followed when planning new developments that might affect a Natura 2000 site. Thus:

  • Any plan or project likely to have a significant effect on a Natura 2000, either individually or in combination with other plans or projects, shall undergo an Appropriate Assessment to determine its implications for the site. The competent authorities can only agree to the plan or project after having ascertained that it will not adversely affect the integrity of the site concerned (Article 6.3)
  • In exceptional circumstances, a plan or project may still be allowed to go ahead, in spite of a negative assessment, provided there are no alternative solutions and the plan or project is considered to be justified for imperative reasons of overriding public interest. In such cases the Member State must take appropriate compensatory measures to ensure that the overall coherence of the N2000 Network is protected. (Article 6.4)

Article 6 – General Commission Guidance


To assist in the understanding and correct application of this Article 6 procedure, the Commission has produced a number of general interpretative and methodological guidance documents on specific provisions of the Article:

Guidance document: Managing Natura 2000 sites

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Updated version November 2018

Assessment of Plans and Projects significantly affecting Natura 2000 sites

Methodological guidance on the provisions of Article 6 (3) and (4) of the Habitats Directive 92/43/EEC

Court rulings related to Article 6

A compilation of the most important rulings of the European Court of Justice related to Article 6 of the Habitats Directive is available here.

Article 6(4) Commission Opinions

The second subparagraph of Article 6(4) provides for a special treatment whenever the plan or project concerns a site hosting priority habitats and/or species. The realisation of plans or projects likely to adversely affect these sites can be justified only if the evoked imperative reasons of overriding public interest concern human health and public safety or overriding beneficial consequences for the environment, or if, before granting approval to the plan or project, the Commission expresses an opinion on the initiative envisaged.


Commission guidance document on streamlining environmental assessments conducted under Article 2(3) of the Environmental Impact Assessment Directive

Article 6 - Sector Specific Guidance

The Commission is also in the process of developing sector-specific guidance in the following policy areas: non-energy extractive industries, wind farm development, ports and estuaries, inland waterway transport, aquaculture. The overall objective of these guidance documents is to establish a better understanding of how to apply the Article 6 procedure to developments plans and projects in each of these sectors and to provide further advice on how to carry out an Appropriate Assessment in particular.

These guidance documents, which are developed in close cooperation with the stakeholders concerned, will be uploaded on the present webpage once they have been finalised.

Energy transmission facilities and EU nature legislation

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Official Journal link

Energy transmission facilities and EU nature legislation

Hydropower and EU nature legislation

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Official Journal link

Hydropower and EU nature legislation

Guidance on Natura 2000 and forests

Guidance Natura 2000 and Forests

Guidance document "Farming for Natura 2000"

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Annexes A - D with A) Key habitat types of Community interest that are dependent on agricultural management, B) Key species of Community interest associated with farmland, C) Main habitats of Community interest dependent on agriculture in each Member State and D) Management recommendations for each Annex I habitat type dependent on agricultural management

Annex E with case studies en cs el fr de pl it es

Guidance on Aquaculture and Natura 2000 - Sustainable aquaculture activities in the context of the Natura 2000 Network

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wind farms
Inland waterway transport and Natura 2000 - sustainable inland waterway development and management in the context of the EU Birds and Habitats Directives
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wind farms

The implementation of the Birds and Habitats Directives in estuaries and coastal zones
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Leaflet presenting the guide:
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For the policy context, see the Commission Staff Working Document:
Integrating biodiversity and nature into port development (58Kb)

wind farms

Wind energy developments and Natura 2000
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Leaflet presenting the guide:
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wind farms

Non-energy mineral extraction and Natura 2000

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Leaflet presenting the guide:
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NEEI brochure
Other Guidance

Guidance document on Climate change and Natura 2000


all documents downloadable from this page are in pdf format