Short answer
A plan or project affecting a Natura 2000 site may proceed through one of three routes under Article 6 of the Habitats Directive 92/43/EEC. First, a reasoned screening may objectively exclude any likelihood of significant effects, alone or in combination. Measures designed to avoid or reduce project harm cannot be used to reach that screening conclusion. Second, if appropriate assessment is required, ordinary consent is possible only where the competent authority is certain that the proposal will not adversely affect site integrity. The assessment must use the best scientific knowledge, address the site's conservation objectives and leave no reasonable scientific doubt.
If adverse effects cannot be ruled out, Article 6(4) provides a strict exceptional route. The authority must establish that no alternative solution exists, that imperative reasons of overriding public interest require the project, and that all necessary compensatory measures will protect the overall coherence of Natura 2000. Sites hosting priority habitats or species have a narrower public-interest test.
Evidence must be site-specific and reasoned. It should identify protected features and pathways, examine cumulative effects, support mitigation with sufficiently certain design and delivery, explain expert disagreement and compare alternatives. An EIA or future compensation cannot substitute for Article 6 analysis.
Which sites and proposals are covered?
Article 6(3) covers any plan or project not necessary to site management that is likely to have a significant effect. “Project” is broad and not confined to construction; each new authorisation of a recurring activity may be a distinct project.
The procedure protects Habitats Directive sites. Article 7 extends Article 6(2)-(4) to special protection areas classified under the Birds Directive 2009/147/EC. Off-site effects matter where pathways reach conservation objectives.
Stage one: screening uses a low trigger
Screening asks whether objective information excludes a significant effect, alone or in combination, against the site's conservation objectives. A probability, risk or reasonable doubt triggers assessment; uncertainty cannot be dismissed as merely small.
In People Over Wind, C-323/17, the Court drew a firm line around the evidence used at screening:
Article 6(3) of Council Directive 92/43/EEC must be interpreted as meaning that, in order to determine whether it is necessary to carry out, subsequently, an appropriate assessment of the implications, for a site concerned, of a plan or project, it is not appropriate, at the screening stage, to take account of the measures intended to avoid or reduce the harmful effects of the plan or project on that site. —
That rule prevents mitigation from concealing the risk that should trigger detailed assessment. A screening decision should identify its evidence, conservation objectives, pathways, in-combination projects and reasons.
Eco Advocacy, C-721/21 adds a narrow distinction. Standard features inherent in every project of that type may be considered at screening even if they incidentally reduce harm. But features incorporated to avoid or reduce this project's effects remain mitigation and belong in the appropriate assessment. A decision dispensing with assessment must explain, despite contrary opinions or expressed reasonable doubts, why no reasonable scientific doubt remains about possible significant effects.
Stage two: appropriate assessment must remove scientific doubt
Article 6(3) sets both the assessment task and the consent threshold:
Any plan or project not directly connected with or necessary to the management of the site but likely to have a significant effect thereon, either individually or in combination with other plans or projects, shall be subject to appropriate assessment of its implications for the site in view of the site's conservation objectives. —
The authority may give ordinary consent only after ascertaining that the project will not adversely affect the site's integrity. In Waddenzee, C-127/02, the Court expressed the required certainty:
That is the case where no reasonable scientific doubt remains as to the absence of such effects. —
Using the best scientific knowledge, the assessment must identify every aspect capable, alone or in combination, of affecting conservation objectives. Its complete, precise and definitive findings must dispel reasonable scientific doubt; monitoring cannot fill a pre-consent gap.
The conservation objectives must exist before the assessment. In joined Cases C-27/25 and C-356/25, decided on 16 July 2026, the Court held that an authority cannot validly assess implications for a special protection area if site-specific conservation objectives have not first been adopted. Objectives may be unnecessary merely to delimit the geographical area potentially affected, but they are indispensable when deciding whether a protected site within that area faces a probability or risk of significant effects.
What evidence should the assessment contain?
The record should ordinarily cover:
- the site's conservation objectives and a current baseline for every habitat and species for which it is protected;
- construction, operation and decommissioning parameters;
- direct, indirect and off-site pathways, including hydrology, emissions, disturbance, fragmentation and lost ecological function;
- seasonal surveys, methods, limitations, data gaps and the scientific basis for predictions;
- effects in combination with other relevant plans and projects;
- precise mitigation, with evidence of efficacy, timing, responsibility, enforceability and delivery; and
- a reasoned conclusion connecting the predicted effects to site integrity.
In Holohan, C-461/17, the Court required assessment of protected features and unlisted or off-site features capable of affecting conservation objectives. Parameters may be deferred only if consent conditions guarantee no adverse integrity effect.
The authority must evaluate the science. If it rejects expert advice for more information, Holohan requires:
an explicit and detailed statement of reasons capable of dispelling all reasonable scientific doubt concerning the effects of the work envisaged on the site concerned. —
Site integrity concerns lasting preservation of the characteristics connected to the conservation objectives. In Sweetman, C-258/11, permanent and irreparable loss of part of a priority limestone-pavement habitat was an adverse effect on integrity.
Mitigation is not compensation
In Briels, C-521/12, a motorway would damage protected habitat while the plan proposed creating an equal or larger area of that habitat elsewhere in the site. The future creation could not be counted as mitigation to support a no-adverse-effect finding. It was compensatory and could be considered only if every Article 6(4) condition was satisfied. Similarly, uncertain future ecological gains cannot be netted against definite habitat loss at the Article 6(3) stage.
Stage three: the Article 6(4) exception
Where adverse effects cannot be ruled out, Article 6(4) is a strict derogation:
If, in spite of a negative assessment of the implications for the site and in the absence of alternative solutions, a plan or project must nevertheless be carried out for imperative reasons of overriding public interest, including those of a social or economic nature, the Member State shall take all compensatory measures necessary to ensure that the overall coherence of Natura 2000 is protected. —
The sequence matters.
First, the assessment must identify the harm. Second, the authority must exclude less damaging feasible locations, routes, scales or designs and, where relevant, not proceeding. In Commission v Portugal, C-239/04, Portugal failed to show that alternative motorway routes were unavailable.
Third, the reason must be both public and overriding: important enough to be weighed against the directive's conservation objective. In Solvay, C-182/10, the Court held that infrastructure merely intended to accommodate a management centre was not sufficient. A project of private character can qualify only exceptionally where its nature and social or economic context establish an overriding public interest and no alternatives exist.
If the site hosts a priority habitat or species, only human health, public safety or beneficial consequences of primary importance for the environment may be relied on directly. Other imperative reasons require a prior Commission opinion.
Compensation must protect Natura 2000's overall coherence. Evidence should connect the damaged contribution to replacement or restoration and establish location, scale, timing, feasibility, legal security and funding. The Member State must inform the Commission; notification is not compliance.
Conclusion
A development may proceed ordinarily only if objective evidence excludes likely significant effects at screening, or assessment rules out adverse integrity effects without reasonable scientific doubt. Mitigation may support only the second conclusion; uncertain future habitat creation cannot erase damage.
If that certainty is unavailable, the project must stop or pass the strict exception: no alternative solution, a genuinely overriding public reason and effective compensation. A defensible decision follows the stages in order and records its evidence and reasoning.
Sources
This article provides general legal information, not advice for a specific matter. Laws, facts and procedural deadlines may change the result. Follow the linked primary sources and obtain local advice before acting.