FREE CHAPTER from ‘A Practical Guide to Habitats Law in Planning and Permitting in England’ by Brendon Moorhouse


A ‘habitat’ can be defined as the natural home or environment of an animal, plant or other organism. It follows from that definition, that almost any planning or permitting decision is capable of having some effect on the home and environment of organisms that rely on them directly or indirectly.

By way of overview, the treaties and laws relating to ‘habitat protection’ in fact are often aimed at the protection of specific species while others are directed towards protecting specific habitat types. Some regulation is aimed at protecting the environment from polluting material.

A key part of wildlife and habitat protection is the Habitats Directive that, as implemented in the UK, draws on a number of threads of environmental protection legislation and treaties that have developed over the years in what could be perceived as an ad hoc manner. Many of these threads remain ‘in force’ and are administered and regulated by different bodies. The intention of the following paragraphs is to provide a concise context to the current legal framework and the current system of ‘habitat protection’ that is now underpinned by species and ‘National Site Network’ protections as well as the environmental assessment provisions commonly encountered in planning applications.

The following sections of this overview chapter of the guide will summarise important treaties and legislation. These including the Berne Convention on the Conservation of European Wildlife and Natural Habitats, the ‘Birds Directive’, the ‘Habitats Directive,’ the Ramsar Convention on Wetlands of International Importance, Marine Habitat Provisions as well as Environmental Impact Assessment provisions. Together, these form the main regulation applicable to habitat protection.

The Berne Convention

Many Habitats Directive principles, and therefore the concepts that underpin the Conservation of Habitats and Species Regulations 2017 (SI 2017/1012) (‘the Habitats Regulations’), derive from the Berne Convention on the Conservation of European Wildlife and Natural Habitats (1979). The Berne Convention aims to protect the natural heritage of Europe and some African countries[1]. It was ratified by both members of the Council of Europe and also non-members.

The treaty not only prescribed certain acts against protected species, but also required Contracting Parties to implement the necessary legislative measures to ensure the conservation of the habitats of the protected flora and fauna.

From a UK perspective, the treaty was signed in September 1979, ratified in May 1982 and came into force the following September. It was implemented through the adoption of Natural Nature Reserves[2] and Sites of Special Scientific Interest[3]. Both of these types of designated areas are overseen by Natural England.

Article 1 of the Berne Convention sets out three objectives:

  • to conserve wild flora and fauna and their natural habitats
  • to promote cooperation between states
  • to give particular attention to endangered and vulnerable species including endangered and vulnerable migratory species

The Chapters, Articles and Appendixes of the Berne Convention that followed made provision that Contracting Parties should take measures for the protection of designated habitats[4] and designated species[5]. Appendix I lists ‘strictly protected flora’ and Appendix II lists ‘strictly protected fauna’. Appendix III lists ‘protected fauna species’ that hold a lesser degree of protection. Habitat protection under the Berne Convention was further strengthened by, amongst others, Resolution No 1 (1989) of the Standing Committee of the Berne Convention that placed obligations on signatory states to take ‘necessary measures’ to protect habitats and by Resolution No 5 (1998) that set up a ‘Network of Areas of Special Conservation Interest (Emerald Network).’

Within the EU structure, the ‘Emerald Network’ of sites was replicated by the ‘Natura 2000’ Birds and Habitat Directive sites (explained further below) and the necessary protection afforded by those Directives.

On leaving the EU, the UK through the agency of the Joint Nature Conservation Committee (JNCC) ensured all Natura 2000 sites’ information was registered as part of the Emerald Network in order to meet the UK’s continuing obligations under the Berne Convention.

At a higher level, the Standing Committee of the Bern Convention or its Bureau are able to receive and consider complaints about failure by a nation state to properly implement the protections of the Convention.[6]

The Birds Directive

The Birds Directive was the first environmental legislation implemented by the then European Economic Community in April 1979. Upon formation of the European Union and amendment it became Council Directive 79/409/EEC.

The cornerstone of the Birds Directive was the creation of Special Protection Areas (SPAs). Designated SPAs are aimed at protecting wild birds from urban sprawl, intrusive transport networks, intensive agriculture, and other environmental harm, for example, the use of pesticides that diminish food supplies.

The Birds Directive makes provision for the protection of all species of naturally occurring birds in the wild state within the European territory and protects birds, their eggs and habitats.[7] The legal obligation is on Member States to ‘take the requisite measures to preserve, maintain or re-establish a sufficient diversity and area of habitats.’ That legal obligation extends to the requirement to create ‘protected areas,’ the upkeep and management in accordance with the ecological needs of habitats inside and outside the protected zones, and the creation of and re-establishment of destroyed biotopes. A biotope is synonymous with a habitat, being the assemblage of plants and animals necessary to maintain the organism, in this case the bird(s), subject to protection.[8]

Of approximately 500 species of Birds naturally occurring within Europe, 194 species were identified as being particularly threatened and were listed within Annex 1 of the Birds Directive. Member States, pursuant to Article 4 of the Birds Directive, are required to monitor trends and variations to population levels for background evaluations, and to classify special protection areas in the most suitable territories for the conservation of these Annex 1-listed species.

Article 4 requires Member States to take similar protective measures for regularly occurring migratory species not listed in Annex 1, and to pay particular attention to the protection of wetlands and wetlands of international importance.[9] Article 4 also sets a legal requirement on Member States to avoid the pollution or deterioration of habitats.

By way of overview, the Birds Directive also makes provision for Member States to implement protection for 82 Annex 2 species of birds that can be hunted. Annex 2 limits the periods when hunting is permissible and restricts activities that directly threaten birds in general, save for 26 species listed in Annex 3. Annex 4 sets out provisions for sustainable management of birds including outlawing non-selective and largescale killing of birds especially by methods shown in Annex 4.[10]

Protections afforded to Annex 1 birds under the Birds Directive are largely, although not completely, synonymous to those for other species listed under the Habitats Directive.

The Habitats Directive

The Habitats Directive was the then European Economic Communities’ (EEC) response to the Berne Convention. Council Directive 92/43/EEC on the ‘Conservation of natural habitats and of wild fauna and flora’ was adopted by the European Community in 1992. The Habitats Directive was retained upon the formation of the European Union in 1993. These provisions largely remain in force as ‘retained law’ following the UK’s departure from the EU.

The purpose of the Habitats Directive is the conservation of a wide range of animal and plant species, and the protection of characteristic habitat types that are protected in their own right. There are six Annex’s within the Directive. Of those, Annex I and Annex II are regularly referred to in relation to habitat and wildlife protection.

Annex I of the Habitats Directive lists 233 European natural habitat types, including 71 ‘priority habitats’ – those habitat types in danger of disappearance and whose natural range mainly fell within the territory of European Union countries. These habitat ranges include coastal habitats, for example, Atlantic and Continental salt marsh and salt meadows; coastal and inland dunes; freshwater habitats; temperate heath and scrub; certain grassland formations; bogs and fens; rocky habitats and forests.[11]

Annex II of the Habitats Directive lists approximately 900 animal and plant species of community interest whose conservation requires designation of Special Areas of Conservation (SAC). The types of species include invertebrates, for example freshwater pearl mussels; fish, for example the Atlantic salmon; amphibians such as the great crested newt; mammals, examples of which include certain bat species, otters, harbour porpoise and grey seals; and lower and higher plant species including petalwort and floating water-plantain.

Within England and Wales, the principal legislation implementing the Habitats Directive is the Conservation of Habitats and Species Regulations 2017 (SI 2017/1012). (‘the Habitats Regulations’).

Ramsar Convention

The Convention on Wetlands of International Importance especially as Waterfowl Habitat (the ‘Ramsar Convention’) was created in 1971 in the Iranian city bearing the Convention name.

The objectives of the Ramsar Convention were stipulated and described as being constituted of ‘three pillars.’ These are to work towards the wise use of all Contracting Party wetlands, to designate suitable wetlands for the list of Wetlands of International Importance (the ‘Ramsar List’) and to ensure their effective management and to co-operate internationally on transboundary wetlands.

The UK ratified the Ramsar Convention and designated its first site in 1976. The designation of Ramsar Sites is formalised within England through their designation as having SSSI status and therefore protection under the Wildlife and Countryside Act 1981.

Of greater significance for wider habitat protection in relation to Ramsar Sites is the Ministerial Statement of Mr Michael Meacher on 13th November 2000[12]:

  1. Local planning authorities are expected to extend the scope of their appropriate assessments when carrying out Regulation 50 reviews on Natura 2000[13] sites to consider the effects on coincident or overlapping Ramsar sites. Where the planning authority reaches the conclusion that there would be no adverse effect on the integrity of the Natura 2000 site from allowing the consent to proceed, but there would be an adverse effect on integrity on the Ramsar site, it should consider whether to issue a modification or revocation order using powers available under Section 97 of the Town and Country Planning Act 1990. In cases where the authority considers modification or revocation is warranted, the Government will consider reimbursing local authorities where the costs were high, where the action taken was no more than necessary to remove the risk to the site, and less costly alternatives have been fully explored.

  2. Local planning authorities are expected to adopt a similar approach where listed Ramsar sites are not within the Natura 2000 network, by carrying out an appropriate assessment analogous to that required by Regulation 50 and by issuing modification or revocation orders under Section 97 of the Town and Country Planning Act 1990, at the earliest opportunity following the listing of a Ramsar site. Where the integrity of a Ramsar site would be adversely affected by the full implementation of an extant consent and modification or revocation of the consent is warranted, the Government will again consider reimbursing local authorities where the costs were high, where the action taken was no more than necessary to remove the risk to the site, and less costly alternatives have been fully explored.
  3. The Government expect competent authorities, other than planning authorities, to use whatever review powers are available within the regimes they administer to address any potential adverse effects on the integrity of listed Ramsar sites from extant consents by adopting a general approach analogous to that advocated for planning authorities in paragraphs 24 & 25 above.

Ramsar sites are, in practice, protected to the same extent as sites designated under the Habitats and Birds Directive This is both in a planning context as well as in other decisions such as permitting decisions that are likely to have a significant effect on the site.

The JNCC maintains information for all UK Ramsar sites.

Marine Protection Areas

The term Marine Protected Areas includes marine areas designated for protection under a variety of different mechanisms. These include SACs, SPAs and SSSIs with a marine component, Ramsar sites and also Marine Conservation Zones (MCZs).

Marine protected areas include areas within UK territorial waters (up to 12 nautical miles,) and offshore areas within the exclusive economic zone (up to 200 nautical miles.)

Marine Conservation Zones are created by DEFRA pursuant to Section 116 of the Marine and Coastal Access Act 2009, listing the features that are to be protected and also setting the conservation objective(s) of the MCZ. The designations are made for the purpose of conserving marine flora or fauna, marine habitats, or for types of habitats and/or features of geological or geomorphological interest.[14]

There is a general duty placed upon public authorities that have any function, the exercise of which is capable of affecting other than insignificantly, the protected features of an MCZ or any ecological or geomorphological process on which the conservation of any protected feature of an MCZ is wholly or in part dependent. The obligation placed upon public authorities is to exercise their functions so as to best further the conservation objectives, or where it is not possible to further those objectives, to exercise their functions in a manner that least hinders the achievement of those objectives.[15] There are duties of notification to the Marine Management Organisation (MMO)[16] by a public authority where a relevant event takes place. A relevant event includes any act in relation to the public authority exercising its functions, which the authority believes to be an offence and which the authority considers will or may significantly hinder the achievement of the conservation objectives of the MCZ.

The Marine and Coastal Act 2009 also introduced the concept of ‘Marine Plans’ that are created by the MMO with a view to setting priorities and the direction of future development, informing sustainable use of marine resources, and assisting in determining where any new development is most appropriate within the plan area.

A central domestic regulation in relation to offshore marine habitats protection is the Conservation of Offshore Marine Habitats and Species Regulations 2017 (SI 2017/1013) (‘Offshore Marine Habitats Regulations’) that applies to areas beyond the 12 nautical mile limit. The Habitats Regulations (SI 2017/2012) are applicable to the inshore area up to 12 nautical miles.

Sites of Special Scientific Interest

In England, Natural England have responsibility for the designation and management of Sites of Special Scientific Interest (‘SSSIs’).[17] Sites are designated because they contain features of special interest, by reason of their flora, fauna, geology, and physiographical features.[18] There are over 4,000 such sites in England. A feature of SSSIs is that they only cover land above the mean low water mark, or estuarial waters, and so SSSIs have limited interaction with many marine works.

Once a site has been notified by Natural England it attracts protection of the features, even while the formal confirmation process is concluded.

Once notified, Natural England have a duty to achieve ‘favourable condition’ status for SSSIs, meaning that the habitats and features of the site are in a healthy state and are being conserved by appropriate management. The notification process sets out operations which the owner or occupier of a site is required to seek written permission from Natural England before they can carry out. Such permission may be granted with conditions and be for a time-limited period.[19] Operations may also be carried out in accordance with the terms of an agreement made under Section 7 of the Natural Environment and Rural Communities Act 2006 with a person having an interest in the land, or in accordance with a management scheme for the site.

In planning terms, the effect of the designation of an area as a SSSI provides restrictions on permitted development. It is also a material consideration within the planning process. The Current version of the National Planning Policy Framework provides[20]:

Development on land within or outside a Site of Special Scientific Interest, and which is likely to have an adverse effect on it (either individually or in combination with other developments), should not normally be permitted. The only exception is where the benefits of the development in the location proposed clearly outweigh both its likely impact on the features of the site that make it of special scientific interest, and any broader impacts on the national network of Sites of Special Scientific Interest;

Criminal liability can attach to certain breaches of the requirements to protect SSSIs.

Retained Law – European Union Withdrawal

The European Union has had a central role in defining UK and English Habitats protection regulation. On the 31st December 2020 at 11pm, the United Kingdom left the European Union. Since then, the European Union (Withdrawal) Act 2018 governs the role which legislation and case-law derived from EU legal instruments continues to have in the UK.

Section 2 of the European Union (Withdrawal) Act 2018 retains EU-derived domestic legislation ‘as it has effect in domestic law immediately before IP completion day, continues to have effect in domestic law on and after IP completion day.’[21] Sections 3 and 4 respectively dealt with savings of directly applicable EU law and the saving of rights, powers, liabilities, obligations, restrictions, remedies and procedures.

The applicability of the Habitats Regulations was specifically considered in the case of Harris and Harris v Environment Agency and Natural England [2022] EWHC 2264 (Admin) with Johnson J, in summary, finding that: (i) the Habitats Regulations, passed under Section 2(2) of the European Communities Act 1972 is EU-derived domestic legislation and continues to have effect in domestic law pursuant to Section 2(1) of the European Union (Withdrawal) Act 2018, (ii) that the Habitats Directive is not ‘direct EU legislation’ and does not form part of domestic law, (iii) obligations that were recognised and available in domestic law continue and are recognised and available in domestic law (iv) the precautionary principle is a retained general principle if EU law pursuant to Section 6(7) of the European Union (Withdrawal) Act 2018.

In relation to the status of previously decided European Court (CJEU) decisions, the Court of Appeal has confirmed that such decisions are still binding. While the Supreme Court and Court of Appeal[22] has the power to depart from CJEU case law, it can only do so on the same basis that the Supreme Court can depart from its own precedent. Such power must be ‘exercised with great caution.’[23]

Environmental Impact Assessment

Separate to the Habitats Directive, the EEC created an Environmental Impact Assessment Directive[24] that came into force in 1985. It has been updated four times and the main law is now within Directive 2011/92/EU as amended by Directive 2014/52/EU.

In England these were implemented by the Town and Country Planning (Environmental Impact Assessment) Regulations 2017 (SI 2017/571) (the ‘EIA Regulations’), which remain in force post Brexit and apply to certain planning applications and regulated marine activities. There are corresponding Welsh regulations.[25]

An Environmental Impact Assessment (EIA) is required to be submitted for certain specified types of development listed in Schedule 1 of the EIA Regulations.

Schedule 2 of the EIA Regulations identifies categories of development in what are described as ‘sensitive areas,’ for example SSSIs, national parks or Habitats Regulation Sites, or where the development exceeds the criteria listed in the schedule. Should a potential development fall within such a site or fulfil the criteria, the planning authority or Secretary of State is required to screen the application using selection criteria set out in Schedule 3 of the EIA Regulations to determine whether the development is likely to have a significant effect on the environment. In screening such an application particular regard has to be paid to factors that include the use of natural resources, in particular land, soil, water and biodiversity,’ ‘pollution and nuisances’ and ‘the risk to human health (for example, due to water contamination or air pollution).’[26]

There are separate Environmental Impact Assessment regulatory provisions relevant to planning applications made for, amongst others, harbours, highways and transport[27] (that amends primary legislation, such as the Harbours Act 1964, the Highways Act 1980) and certain agricultural applications.[28] For marine works the Marine Works (Environmental Impact Assessment) Regulations 2007[29] are applicable and The Infrastructure Planning (Environmental Impact Assessment) Regulations 2017[30] are applicable to nationally significant infrastructure projects.

Strategic Environmental Assessment

The Environmental Assessment of Plans and Programmes Regulations 2004[31] (as amended) was implemented in the UK to give effect to EU Directive 2001/42/EC, known as the ‘SEA Directive,’ and applies to plans and programmes adopted by an authority at a national, regional or local level or that are prepared by an authority for adoption through legislative procedure by Parliament or Government.

In summary, the assessments are intended to provide a high-level environmental consideration to plans or programmes that can include both planning development, for example local or marine plans, but are also applicable to many other sectors including agriculture, forestry, fisheries, energy, industry, transport, waste management, telecommunications and tourism where the plan or programme is likely to have significant environmental effects.

Summary / Concluding the Introduction

The various provisions set out above are an overview of the main safeguard provisions in relation to the protection of habitats in England, and also in many cases a history of how they arose. The following chapters include a detailed examination of the central features of said provisions.


[1]   African signatories include Burkina Faso, Morocco, Tunisia, and Senegal

[2]   Prior to this the National Parks and Access to the Countryside Act 1949 made provision for National Parks, managed by a National Parks Commission, a role now occupied by Natural England in England and Natural Resources Wales in Wales.

[3]   Introduced by Section 28 of the Wildlife and Countryside Act 1981.

[4]   Chapter 2 – particular attention was to be given to habitats containing protected species or important for migratory birds.

[5]   Chapter 3 and Appendixes.

[6]   For example, T-PVS/Files (2014) 38, a series of complaints brought against France, Ireland and the UK in relation to alleged failure to protect the Eurasian Badger. In the UK’s case the complaint, in relation to the ‘badger cull’, was rejected. More recently Azerbaijan has brought a complaint against Armenia for biodiversity and environmental destruction consequent on the war between both states.

[7]   Article 1.

[8]   Article 3

[9]   There is an overlap with the Ramsar Convention obligations afforded by these requirements.

[10]  These provisions were implemented in Great Britain by the Wildlife and Countryside Act 1981. Of historical interest, the structure and approach adopted in the Protection of Birds Act 1954 was largely followed and replicated by the EEC in the Birds Directive.

[11]  The EU prepared various Interpretation Manuals, for example, ‘Interpretation Manual of European Union Habitats – EUR28’ published in April 2013, to assist in identifying suitable habitats and specific areas to protect.

[12]  Hansard 13th November 2000: Columns: 491W and 492W.

[13]  An ecological network of protected areas including SPAs and SACs designated under the Birds and Habitats Directives. This is now called the ‘National Site Network’ within the UK.

[14]  Section 117 Marine and Coastal Access Act 2009.

[15]  Section 125 Marine and Coastal Access Act 2009.

[16]  In Wales and Scotland the notification requirements are to the respective Ministers.

[17]  In Wales, Natural Resources Wales, have responsibility. In Scotland it is Scottish Natural Heritage.

[18]  Section 28 Wildlife and Countryside Act 1981.

[19]  Section 28E Wildlife and Countryside Act 1981.

[20]  Para 180(b) NPPF 2021.

[21]  ‘IP Completion day’ means 31st December 2021 at 11.00 p.m. (Section 39 of the European Union (Withdrawal Agreement) Act 2020.)

[22]  Section 6(4) European Union (Withdrawal) Act 2018.

[23]  Kanaka Durga Chelluri v Air India Ltd [2021] EWCA Civ 1953, following Tunein inc v Warner Music and Sony Music Entertainment [2021] EWCA Civ 441.

[24]  Environmental Impact Assessment Directive (85/337/EEC)

[25]  SI 2017/567.

[26]  Town and Country Planning (Environmental Impact Assessment) Regulations 2017 (SI 2017/571) Schedule 3(1).

[27]  Environmental Impact Assessment (Miscellaneous Amendments Relating to Harbours, Highways and Transport) Regulations 2017 (SI 2017/2010)

[28]  Environmental Impact Assessment (Agriculture)(England)(No2) Regulations 2006 (SI 2006/2522) as amended.

[29]  SI 2007/1518

[30]  SI 2017/572

[31]  SI 2004/1633