Guidance document on

Assessment of plans
and projects in relation
to Natura 2000 sites
A summary
Environment
1
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ISBN: 978-92-76-46669-7
doi:10.2779/086397
KH-01-22-028-EN-N
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About this leaflet

This leaflet represents a summary of the European Commission’s

document on the ‘Assessment of plans and projects in relation to
Natura 2000 sites - Methodological guidance on Article 6(3) and
(4) of the Habitats Directive 92/43/EEC’. This document provides
methodological guidance on carrying out the assessments
required under Article 6(3) and (4) of the Habitats Directive, when
a project or plan is likely to have significant effects upon a Natura
2000 site.

The document is principally designed for use by developers,

consultants, site managers, practitioners, competent authorities
and national agencies in the EU Member States and in the
candidate countries. It is meant as optional support and
must be read in conjunction with the directives and national
legislations, and within the context of the Commission guidance
on ‘Managing Natura 2000 sites: The provisions of Article 6 of the
Habitats Directive 92/43/EEC’.

3
Article 6(3) and (4)
The Habitats Directive requires that EU Member States establish
the Natura 2000 network to ensure the conservation of rare and
threatened habitats and species and consider the implications of
any plan or project on the Natura 2000 sites before any decision
is made to allow them to proceed. Article 6, paragraphs (3) and
(4) state:
• 3. 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. In the light of the conclusions of the assessment of
the implications for the site and subject to the provisions of
paragraph 4, the competent national authorities shall agree
to the plan or project only after having ascertained that it will
not adversely affect the integrity of the site concerned and, if
appropriate, after having obtained the opinion of the general
public.
4
• 4. 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. It shall inform the Commission of the
compensatory measures adopted. Where the site concerned
hosts a priority natural habitat type and/or a priority species,
the only considerations which may be raised are those relating
to human health or public safety, to beneficial consequences of
primary importance for the environment or, further to an opinion
from the Commission, to other imperative reasons of overriding
public interest.
Comprehensive clarification of the concepts of Article 6(3) and
6(4) is provided in the Commission guidance on Article 6 of the
Habitats Directive.
Plans and projects
Is the plan or project necessary Yes
for the management of the Natura 2000 site?

The European Commission supports a broad interpretation of No

the terms ‘plan’ and ‘project’ in the implementation of Article No

Screening
Is the plan or project likely to have
6(3). A project can involve construction works, installations and significant effect on the Natura 2000 site?
other interventions in the natural environment including regular Yes
activities aimed at utilising natural resources. The term ’plan’
includes land-use or spatial plans and sectoral plans (e. g. for

Appropriate assessment
transport, energy, water management).
Implicit in the Habitats Directive is the application of the
precautionary principle, i.e. that absence of scientific evidence
on the significant negative effect of an action cannot be used
Is it ascertained that [having applied the necessary
mitigation measures and consulted the public] the plan or
project will not have significant effect [with other plans Yes
or projects] on the integrity of the Natura 2000 site in
view of its conservation objectives?

as justification for approval of this action. The emphasis of the

assessment should thus be on objectively demonstrating, with No
supporting evidence, that:
• either there will be no likely significant effects on a Natura 2000 Yes Are there alternative solutions to achieve the goals
site (stage one: screening); of the plan or project?
• or there will be no adverse effects on the integrity of a Natura No
2000 site (stage two: appropriate assessment);
• or there is an absence of alternatives to the plan/project, there No Are there imperative reasons of overriding public
interest, including socio-economic ones?
are imperative reasons of overriding public interest to carry out
the plan/project and compensation measures, which maintain or Yes
enhance the overall coherence of Natura 2000, are put in place Does the site concerned host priority
(stage three: derogation procedure). habitats or species?

Yes No
Are there human health or safety
Article 6(4 )

considerations or beneficial
consequences of primary importance for
the environment?
No Yes

Authorisation Authorisation Authorisation Authorisation

cannot be can be granted can be granted can be granted
granted provided the provided the
compensation compensation
measures are measures are
Flow chart of the Article 6(3) and (4) procedure in relation to the implemented and implemented
stages of the guidance. the Commission and the
opinion is Commission is
Source: Managing Natura 2000 sites. The provisions of Article 6 obtained informed
Outcome

of the Habitats Directive 92/43/EEC (2019/C 33/01). European

Commission, 2019.

5
Methodology

Article 6(3) and (4) define a step-wise procedure, which follows significant effect on Natura 2000 site(s), either individually or
three main stages. in combination with other plans or projects, the plan or project
needs to be subject to an appropriate assessment.
Stage one: screening. The first part of the procedure consists
of a pre-assessment stage (‘screening’) to determine whether Differences between the screening and the appropriate
the plan or project is directly connected with or necessary to assessment:
the management of the Natura 2000 site and whether, either
Screening Appropriate Assessment
alone or in combination with other projects or plans, it is likely
to have a significant effect on the site. If the screening concludes Ascertains whether significant Assesses the likely effects on
negative effects on a Natura the Natura 2000 site in view of
that significant effects on the site are likely, an appropriate
2000 site are likely as a result of its conservation objectives and
assessment has to be carried out. implementing the plan or project assesses whether adverse effects on
in view of the site’s conservation the integrity of the site will or might
The screening may differ for plans and projects, depending on objectives. occur.
the scale of the developments concerned and the likely effects. It If the occurrence of significant The plan or project can be
can be carried out in four steps: effects cannot be excluded with authorised only if adverse effects on
• determining whether the plan or project is directly connected certainty, the plan or project the integrity of the Natura 2000 site
with or necessary to the management of a Natura 2000 site; has to undergo an appropriate can be excluded.
assessment.
• identifying the relevant elements of the plan or project and
Typically based on existing Requires a detailed examination,
their likely impacts;
data, available knowledge and often field surveys, expert advice,
• identifying which (if any) Natura 2000 sites may be affected, experience, and expert opinion. and an expert assessment of the
considering the potential effects of the plan or project alone or in specific case.
combination with other plans or projects; Mitigation measures cannot be Assesses mitigation measures to
• assessing whether likely significant effects on the Natura 2000 considered. eliminate or reduce adverse effects.
site can be ruled out, in view of the site’s conservation objectives.

Determining whether a plan or project is likely to have a

significant effect will have practical and legal consequences.
Plans and projects not likely to have significant effects can be
processed without going through the subsequent steps of Article
6(3). Member States will need to justify and record the reasons
for reaching such a screening conclusion.

The possibility of there being a significant effect on the site will

generate the need for an appropriate assessment (stage two).
This conclusion may be reached without an in-depth screening
and be based on a simple consideration of the type, size or scale
of the plan/project, or the characteristics of the Natura 2000 site.

In case of doubt, i. e. if it cannot be excluded, on the basis

of objective information, that a plan or project can have a

6
Stage two: the appropriate assessment. This assessment
must determine whether the plan or project, either alone or
in combination with other plans or projects, will affect the
integrity of the Natura 2000 site, considering possible mitigation
measures. If it will or might affect the integrity of the site, it
cannot be authorised. The appropriate assessment applies both
to plans and projects. It can be coordinated with or integrated
in other environmental assessments, namely the environmental
impact assessment (EIA) for projects and the strategic
environmental assessment (SEA) for plans and programmes. It
must be noted, however, that there are important differences
in the interpretation of some of the terminology used in the
relevant Directives and the extent to which the assessments
affect the overall decision-making process. The conclusion of the
appropriate assessment must therefore be presented clearly and
separately from those of the EIA or SEA.
An appropriate assessment involves the following steps:
Gathering information on the project and on the Natura 2000
sites concerned
The information needed to complete the appropriate assessment
includes all relevant data on the Natura 2000 sites likely to be
affected by a plan or project under consideration.
Assessing the implications of the plan or project in view of the
site’s conservation objectives
The assessment should be done for all of the designating
features (species, habitat types) that are significantly present
on the site (habitats and species with A, B or C, but not D,
site assessment in the Standard Data Form for the site) in
view of their conservation objectives. The lack of site-specific
conservation objectives or the establishment of conservation
objectives, which are not in line with the required standard,
as specified in the Commission note on “Setting conservation
objectives of Natura 2000 sites” (EC, 2012), jeopardises
compliance with the requirements of Article 6(3).

Key information sources

Information on the site(s), such as Natura 2000 standard

data forms, site-specific conservation objectives (set out in
the special areas of conservation (SAC) designation acts or
in the special protection area (SPA) classification acts, or in
the site management plan, or in a separate act).

National reports on conservation status of habitat and

species and main threats and pressures to them.

Current and historical maps. Survey material. Information

from nature conservation agencies and other relevant
organisations and experts.

Project or plan documents (blueprints, maps, etc.).

Environmental impact assessments’ statements,

appropriate assessment reports and other documentary
evidence from similar plans or projects assessed in the past.

7
The assessments should take account of the impact of the entire
plan or project in question, with all the activities it comprises in
the different phases (preparation, construction, operation and,
where relevant, decommissioning). Each element of the plan
or project should be examined and its potential effects should
be considered in relation to each relevant species or habitat
type in view of their conservation objectives. The importance or
significance of the impacts must be assessed and quantified for
each relevant habitat and species, using appropriate indicators,
e.g.: area of habitat loss or deterioration (ha and % of total area
in the sites); changes in a species’ demographic parameters (e.g.
breeding success).
Cumulative impacts with other plans or projects must be
also considered in the assessment. These can result from the
successive, incremental, and/or combined effects of a plan/
project when added to other existing or planned developments.
Other plans and projects that might have effects on the same
species and habitats should be considered.
Determining whether the plan or project can have adverse
effects on the integrity of the site
The ‘integrity of a site’ relates to the site’s conservation objectives,
its key natural features, ecological structure and function. It also
Examples of conservation objectives
Otter (Lutra lutra). Maintain the current population
(XX individuals). Maintain the extent and continuity of
freshwater (river) habitat (xx km); maintain couching sites
and holts (number provided) and fish biomass available
(Xx kg) with no significant decline.
Dry heaths (4030). Maintain the extent (xx ha) and
distribution of the habitat within the site (map provided).
Maintain the abundance of the typical species (list
provided). Maintain a low cover of scattered native trees
and scrub (<10% cover). At least 1% but not more than
10% cover of the area of the habitat consist of bare
ground. Maintain nitrogen deposition below critical load
values defined for the site (e.g. 10-20 kgN/ha/yr).
8
concerns the main ecological processes and factors that sustain
the long-term presence of the species and habitats in a Natura
2000 site. When a permanent loss of a part of a habitat or a
species population for which the site is designated, or a long-
lasting deterioration of the site’s ecological structure, function
and processes are expected from the implementation of a plan or
project, it can be concluded that it will cause an adverse effect on
the integrity of the site.
From the information gathered and the predictions made about
the changes that are likely to result from the construction,
operation or decommissioning stages of the plan or project, it
should be possible to complete the checklist of the box below:
Assess the effects on the integrity of the site: a checklist
Does the plan or project have the potential to:
• hamper or cause delays in progress towards achieving
the site’s conservation objectives?
• reduce the area, or quality, of protected habitat types or
habitats of protected species present on the site?
• reduce the population of the protected species
significantly present on the site?
• result in disturbance that could affect the population size
or density or the balance between species?
• cause the displacement of protected species significantly
present on the site and thus reduce the distribution area
of those species in the site?
• result in a fragmentation of Annex I habitats or habitats
of species?
• result in a loss or reduction of key features, natural
processes or resources that are essential for the
maintenance or restoration of relevant habitats and
species in the site (e. g. tree cover, tidal exposure, annual
flooding, prey, food resources)?
• disrupt the factors that help maintain the favourable
conditions of the site or that are needed to restore these to
a favourable condition within the site?
• interfere with the balance, distribution and density of
species that are the indicators of the favourable conditions
of the site?
Considering mitigation measures
Mitigation measures may be proposed by the plan or project
developer and/or required by the competent authorities in
order to remove, pre-empt or reduce the impacts identified in
the appropriate assessment to a level where they will no longer
affect the site. The description of mitigation measures could
include the following aspects:
• list each measure to be introduced in relation to each adverse
effect identified;
• explain how the measures will avoid/reduce the adverse effects
on the integrity of the site;
• provide evidence of how they will be implemented and by
whom;
• provide evidence of their effectiveness (e. g. based on scientific
evidence/expert rationale);
• provide a timescale, relative to the project or plan, when they
will be implemented;
• explain the proposed monitoring scheme, including how any
possible unexpected impacts will be addressed.
Conclusions of the appropriate assessment
The assessment carried out under Article 6(3) of the Habitats
Directive must contain complete, precise and definitive findings
and conclusions on the effects of the plan/project proposed on
the Natura 2000 site concerned. The competent authorities can
only approve the plan or project after having ascertained that it
will not adversely affect the integrity of the site.
Where the appropriate assessment cannot exclude adverse
effects on the integrity of the site, even after applying mitigation
measures, it should identify residual adverse effects. This will be
important in case the plan or project is intended to be subject to
the derogation procedure according to Article 6(4).
Stage three: derogations under Article 6(4). If, despite a
negative assessment, it is necessary go ahead with a plan or
project, Article 6(4) allows for derogations from Article 6(3) under
certain conditions. Plans or projects may only be approved by the
competent authorities if the following three key requirements of
Article 6(4) are met and documented:
• no other feasible alternative exists that would not adversely
affect the integrity of the site(s);
• there are imperative reasons of overriding public interest,
including those of a social or economic nature;
• all compensatory measures necessary to ensure that the overall
coherence of the Natura 2000 network is protected are taken.
The steps for the implementation of the Article 6(4) provisions are
the following:
Identification and comparative assessment of alternative
solutions
The alternatives considered should include different feasible
options to implement the activities proposed in the plan or
project, with the aim to avoid the impacts on the Natura 2000
site integrity. The alternatives may consist of different:
• ways to achieve the objectives of the proposed development;
• locations that may be available for the development having
regard to protected habitats and species, for example, by
defining different land transportation corridors in master plans
for roads and motorways or different housing development
zones;
• scale and size of the development;
• design solutions for the development;
• techniques, methods of construction or operational methods
for the implementation of the development;
• timetable of the various activities and tasks at each of
the implementation stages, including during construction,
operation, maintenance and, if applicable, decommissioning or
reconditioning.
The comparative assessment of the alternatives should examine
their effects on the site concerned based on comparable scientific
criteria. It should thereby consider the habitats and species for
which the site is designated, the site’s integrity and its importance
in the overall coherence of the Natura 2000 network.
9
Determine the existence of imperative reasons of overriding
public interest that justify the implementation of the plan or
project
In the absence of alternative solutions with reduced adverse
effect on the integrity of the Natura 2000 site(s) concerned,
the competent authorities must examine whether imperative
reasons of overriding public interest exist which would require
the implementation of the plan or project.
It is reasonable to consider that the ‘imperative reasons of
overriding public interest, including those of social and economic
nature’ refer to situations where plans or projects envisaged
prove to be indispensable:
• within the framework of actions or policies aiming to
protect fundamental values for the citizens’ life (health, safety,
environment);
• within the framework of fundamental policies for the State and
the society;
• within the framework of carrying out activities of an economic
or social nature, fulfilling specific obligations of public service.
10
The competent national authorities have to make their approval
of the plan or project subject to the condition that the balance of
interests between the conservation objectives of the site affected
and the above-mentioned imperative reasons weighs in favour of
the latter.
All compensatory measures necessary to ensure the protection
of the overall coherence of Natura 2000 are taken
Compensation should refer to the Natura 2000 site’s conservation
objectives and to the habitats and species negatively affected in
comparable proportions in terms of quality, quantity, functions
and status. At the same time, the role played by the site
concerned in relation to the bio-geographical distribution must
be properly considered.
In principle, the result of compensation measures has to be
achieved at the time when the damage occurs on the site
concerned. Under certain circumstances where this cannot be
fully achieved, overcompensation would be required for the
interim losses.
Strategic planning and appropriate assessment of plans

An effective way to avoid potential conflicts with Natura 2000
sites and EU protected species is to consider new plans/projects
at a strategic planning level. This can be done for instance
through a regional or national development plan for sectoral
activities (e. g. in the energy sector, transport, extractive activities,
aquaculture, etc.) or through land-use or other spatial plans.
Strategic planning can:
• promote a transparent planning process and iterative
dialogue with the relevant actors
• consider information about environmental concerns at
an early planning stage
• help to avoid or reduce site-specific conflicts at a later
stage
• provide a suitable framework to consider cumulative
effects of various plans or projects
• contribute to cost effectiveness in the long run
• contribute to an improved public image of the projects
At the level of plans, significant adverse effects may be uncertain
or not possible to determine with enough confidence for some
elements or components of the plan. This would require such
elements to be further considered and duly assessed at the
project level. National strategies often involve the definition of
key planned investments like new reservoirs, routes, etc. Although
these can have an impact on some Natura 2000 sites, their exact
location, construction and/or operation details are not defined yet
at the national, strategic level. In such cases the assessment should
conclude that is not possible to exclude adverse effects with
certainty, e. g. because the plan components are lacking details,
with the consequence that the concerned components/elements
must be obligatorily subject to appropriate assessment at the
project level.
It may be appropriate to foresee the follow up and re-assessment
of the expected effects and risks throughout the plan lifetime
to ensure that the predictions and estimates are realistic and to
identify any possible new effects not considered due to lack of
information or to new elements or changes introduced in the plan.

Through sensitivity mapping, strategic planning can help to

identify suitable or unsuitable sites for plans/projects, such as
sensitive birds and bats areas that may be unsuitable to wind
energy developments, potential conflict areas for industrial
activities, etc.

Article 6(3) of the Habitats Directive applies to strategic planning

and sectoral/spatial plans or programs. The appropriate
assessment of plans or programs should follow the same
procedure as the assessment of projects. However, the level of
detail of the plan or program itself will determine the possible
extent of the assessment, which should nevertheless attempt
to assess the impacts as precisely as possible. Every assessment
should attempt to identify sensitive or vulnerable areas or other
potential risks or conflicts that need to be considered at later
stages in the planning process.

11
Links with EIA, SEA, WFD
Several pieces of EU legislation contain provisions on
environmental assessment procedures. Besides the Habitats
Directive, this is in particular the case of the Environmental
Impact Assessment (EIA) Directive, the Strategic Environmental
Assessment (SEA) Directive and the Water Framework Directive
(WFD), Article 4(7).
The integration and coordination of environmental assessment
procedures set under various pieces of EU legislation provides
an essential contribution to the improved efficiency of
administrative processes.
The EIA Directive includes provisions for streamlining the
assessment procedures related to environmental issues required
under various EU directives, including the Habitats Directive,
the SEA Directive and the Water Framework Directive. It requires
specifically that Member States should put in place coordinated
and/ or joint procedures fulfilling the requirements of these
Directives, where appropriate and taking into account their
specific organisational characteristics (Article 2(3) of the EIA
Directive).
A number of important procedural similarities but also
distinctions exist however between the EIA/SEA and appropriate
assessment procedures, which means that a SEA or an EIA
cannot replace an appropriate assessment as neither
procedure overrides the other. In all cases it is essential that
the appropriate assessment remains clearly distinguishable and
identifiable in the impact assessment report, or is reported on
separately so that its findings can be differentiated from those of
the general EIA or SEA.
The appropriate assessment is focused on the conservation
and protection of Natura 2000 sites and requires more rigorous
tests. Its results are binding and determine whether the plan or
project can be adopted or not. The competent authorities can
agree to the plan or project only after having ascertained that
it will not adversely affect the integrity of the site, whereas the
results of the EIA or SEA only have to be taken into account in
12
the development consent procedure. At the same time the EIA
and SEA Directives provide important procedural benefits to the
appropriate assessment when run jointly or in coordination (e. g.
scoping, consultations, transboundary impacts, monitoring).
The WFD has also specific provisions to assess the effects of new
developments on water bodies. According to Article 4(7) of the
WFD, exemptions can be approved by the authorities for new
modifications and sustainable human development activities
that result in the deterioration of the status of the water body
or that prevent the achievement of good status under certain
conditions. When applying such exemptions, Member States
must ensure consistency with the implementation of other
Community environmental legislation. If the development
potentially affects both a WFD objective and a Natura 2000 site
then both the Article 4(7) procedure under the WFD and the
Natura 2000 assessment procedure under Article 6(3) of the
Habitats Directive must be undertaken (ideally in a coordinated
or integrated manner).
Each assessment has a different legal focus: one will assess if
the project is likely to compromise the primary objectives of
the WFD, the other will assess whether it will adversely affect
the integrity of a Natura 2000 site. However, this does not
prevent certain aspects of the assessment being coordinated,
e. g. through surveys and consultations, leading to significant
cost and time savings. In all cases the distinct focus of the
various tests under each Directive needs to be fulfilled. If the
conditions of one Directive are met but not of the other, then
the authorities may not authorise the project and it should be
examined whether amendments can be made so that it satisfies
the requirements of all relevant directives.
For further reading

This publication represents a summary of the EC Guidance

Document “Assessment of plans and projects in relation with
Natura 2000 sites -Methodological Guidance document on the
provisions of Article 6(3) and (4) of the Habitats Directive 92/43/
EEC”

The Habitats Directive: https://eur-lex.europa.eu/legal-content/EN/

TXT/?uri=CELEX:31992L0043

The Birds Directive: https://eur-lex.europa.eu/legal-content/EN/

TXT/?uri=CELEX:32009L0147

Environmental Impact Assessment Directive (EIA)

https://eur-lex.europa.eu/legal-content/EN/
TXT/?uri=CELEX:32014L0052

Directive 2001/42/EC on the assessment of the effects of certain

plans and programmes on the environment (SEA Directive):
https://eur-lex.europa.eu/legal-content/EN/
TXT/?uri=CELEX:32001L0042

Commission notice “Managing Natura 2000 sites. The provisions

of Article 6 of the Habitats Directive 92/43/EEC”(2019/C 33/01):
https://eur-lex.europa.eu/legal-content/EN/
TXT/?qid=1555085968125&uri=CELEX:52019XC0125(07)

PHOTO CREDITS
cover: Rétimajor fish ponds / Fent Győző
page 3: Power line / Pxhere
page 4: Salmon aquaculture in Norway / Brataffe
page 7: Limestone quarry / Ria Garcia
page 10: Wetland / Pxhere
page 13: Wind turbines / Pxhere

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