Publication - Progress report

Conservation (Natural Habitats, &c.) Regulations 1994 (as amended) - Regulation 3ZA: implementation report 2019 to 2024

Published: 30 January 2026
Directorate: Environment and Forestry Directorate
Topic: Environment and climate change
ISBN: 9781806436545

Overview of the implementation of measures taken in Scotland to meet the provisions of the Birds and and Habitats Directives, and to achieve the objectives of those Directives between 2019 and 2024.

Supporting documents

2. General information sources on the implementation of the Habitats Regulations

2.1 General information

Scottish Government – Wildlife Habitats
NatureScot

i. Habitats Directive and Regulations;

ii. Protected Areas and Species

Conservation and Management Advice Documents are published on the JNCC and NatureScot webpages.

2.2 European site research and survey

This is not an exhaustive list, but it illustrates the research and survey work that has been undertaken and is on-going and provides links to where the information and data are available.

Commissioned Research and Survey

NatureScot publishes commissioned or research reports on its website. Additional reports and surveys may be published elsewhere. See References for links to research and survey reports.

NatureScot publishes survey data on its spatial data hub. Recent surveys include:

Cairngorms National Park Grassland Mapping Project 2020-2022
Mountain woodland relict sites and restoration sites
Raised bog sites
Riparian woodland

As well as survey specific data sets, Open Data also includes GeMS (Geodatabase of Marine features in Scotland) which is a collation of marine habitats and species data from relevant marine research and survey.

The Habitat Map of Scotland (HabMoS) is a composite dataset comprising different layers of detailed habitat data. All the data has been given a common Habitat Coding from EUNIS, the European Nature Information System as well as an Annex I code from the Habitats Directive, where appropriate. More information on habitat data and the Habitat Map of Scotland is available on the NatureScot website.

Aerial photography Interpretation (API – a form of Earth Observation) can give us information about Annex I habitats. NatureScot developed a methodology for mapping Annex I upland habitats using stereo colour near-infrared aerial imagery interpretation (Scobie 2018). The methodology has been used to help map Raised Bog in Scotland, data which has been used for Reporting in 2025.

The Scottish Government Environment, natural resources and agriculture – strategic research programme is a portfolio that “seeks to improve our understanding of Scotland’s environment, communities, its people and the rural economy”.

Peatland ACTION

Peatland ACTION undertakes a variety of monitoring activities in support of the partnership’s monitoring priorities. Vegetation surveys were undertaken on 13 sites in 2015 to create a baseline, and repeated in 2021.

Six of these sites fall within boundaries of a SAC:

Airds Moss
Carsegowan Moss
Flanders Mosses
Inverpolly (Drumrunie)
Moine Mhor
Muir of Dinnet (Black Moss)

The remaining seven sites fall within Annex I habitats (D1 raised and blanket bogs). To date a single Peatland ACTION Restoration Monitoring Network (RMN) site falls within a European site, the Caithness and Sutherland Peatlands. The network continues to grow, and further sites within SAC boundaries maybe added in the future. A further 16 RMN sites fall within Annex I habitats (D1 raised and blanket bogs).

Peatland ACTION operates a network of hydrological monitoring equipment across Scotland with the data published online, in the Peatland Action Hydrological Monitoring Data Explorer. Twelve of the hydrological monitoring sites are within SAC boundaries. Several sites have now been decommissioned whilst others continue to operate, gathering long-term post-restoration hydrological trends:

Ben Lawers
Blawhorn Moss
Cairngorms (Abernethy)
Carrifran
Coalburn Moss
Flanders Mosses
Longbridgemuir
Moffat Hills (Carrifran)
Moine Mhor
Muir of Dinnet (Black Moss)
Red Moss of Netherley
Threepwood Moss

There are 35 hydrological monitoring sites in total; in addition to those 11 within a European site boundary, there are 20 hydrological monitoring sites that lie within Annex I habitats (D1 raised and blanket bogs).

The RSPB has been supported for many years by Peatland ACTION to carry out monitoring of the restoration work at the Forsinard Reserve (Caithness and Sutherland Peatlands); the vegetation and hydrological monitoring data is available online.

Peatland ACTION projects undertake peat depth and condition surveys in support of applications for funding, to date over 190,000 peat depth measurements have been undertaken from across Scotland and published online. In the region of 24,000 points fall within an SAC boundary.

Peatland ACTION has supported the development of landscape monitoring techniques that use Sentinel_-1 InSAR data to record and interpret surface motion as a proxy for an aspect of peatland condition; work reported to 2025 included a total of ~680,000 ha of peatland. The data covers the period 2015–2023, and is available to download from the InSAR Peatland Condition Class and Condition Change.

Collaborative research on marram grass in the Outer Hebrides

Historic Environment Scotland and NatureScot have undertaken the first two phases of work to better understand the impacts of marram harvesting on dune resilience, recognising its cultural importance in the Outer Hebrides and the need to safeguard both the dunes and the availability of traditional thatching materials. The research to date has focused on gaining a better understanding of cutting practices, improving mapping of dune habitat and the acquisition of baseline surveys, as well as undertaking research trials to investigate the effects of cutting frequency on marram recovery.

Research and SAC/MPA monitoring documents for marine habitats

Scotland’s Marine Assessment 2020 provides a precis of current research and survey undertaken for marine habitats in the intertidal and continental shelf, highlighting case-studies where valuable insight has been gained for specific habitats in some areas. It notes that significant knowledge gaps remain and makes recommendations on how these may be addressed.

The Scottish MPA Monitoring Strategy developed by Marine Directorate, NatureScot and JNCC outlines an agreed approach to survey and monitoring marine habitats that will gather sufficient information to assess the condition of protected features, determine the effectiveness of management measures, and meet national and international reporting obligations. The strategy provides a framework for prioritising monitoring efforts, standardising methodologies, and promoting collaboration among government bodies, academia, industry, and citizen science programs. A Scottish imp Monitoring Programme to implement the Strategy and details proposals for seabed and intertidal habitats monitoring 2026-2038 is in preparation.

Monitoring and research for the period covered by the present report has concentrated on:

Establishing baseline conditions for MPAs to support the effective management of fishing activity.
Examining time series data for sensitive habitats at priority MPAs.
Investigating pressure/state relationships within MPAs.
Adding to our understanding of the distribution and abundance of habitats of high conservation importance in Scottish inshore waters.

Examples of research recently published include:

NatureScot Research Report 1372 evaluates change in selected protected features since the introduction of management measures.

NatureScot Research Report 1213 explores methodologies which might assist in more systems-based nature conservation work.

NatureScot Research Report 1156 presents the results of monitoring of Loch Creran’s protected biogenic habitats.

NatureScot Research Report 1275 evaluates long-term monitoring approaches for maerl beds and makes recommendations on innovative approaches.

(See References – Research and SAC/MPA monitoring documents for Marine Habitats for full list and links.)

Collaborative Research and SAC/MPA monitoring documents for marine mammals

NatureScot works closely in collaboration with many citizen science monitoring programmes and research institutes to deliver monitoring and research work that feed into the evidence base for assessments. These include:

The Hebridean Whale and Dolphin Trust (HWDT)
Whale and Dolphin Conservation (WDC)
The Sea Mammal Research Unit (SMRU)
The University of Aberdeen
Scottish Association for Marine Science (SAMS)

Monitoring and research work for the period covered by the present report has focused on gaining a better understanding of marine mammal distribution patterns (seasonality), abundance trends, habitat use and quality/availability of available prey resources. This has been through a combination of dedicated surveys, collation/processing, statistical analysis and interrogation of existing long-term datasets, and the development of analytical methods and testing new technologies. Examples of recent commissioned research reports are below (See References – Research and SAC/MPA documents for Marine mammals for full list and links):

NatureScot Research Report 1364 presents results from boat-based surveys undertaken in the Hebrides by the Hebridean Whale and Dolphin Trust as part of their long-term cetacean monitoring and research programme.

NatureScot Research Report 1360 presents results from dedicated boat-based bottlenose dolphin photo-ID surveys in the Moray Firth SAC and Firth of Tay, with an updated population estimate for the SAC and Coastal East Scotland Management Unit.

NatureScot Research Report 1369 presents preliminary results from 14 years of dedicated boat-based Risso’s dolphin photo-ID surveys undertaken by WDC in the North Minch and North-east Lewis MPA, as a phase 1 review to a more comprehensive phase 2 statistical analysis and catalogue creation for the west coast of Scotland currently underway.

NatureScot Research Report 1379 presents a suite of proposed ecosystem health metrics that can be used for assessments of habitat quality and anthropogenic impacts/pressures on cetacean populations and protected sites.

Survey and reporting partnership data for birds reporting

The present Implementation Report draws on surveys which were funded or organised, inter alia, by the following organisations (and their predecessor bodies):

British Trust for Ornithology (BTO);
Game and Wildlife Conservation Trust;
Joint Nature Conservation Committee;
Rare Breeding Birds Panel;
Royal Society for the Protection of Birds;
Scottish Ornithologists’ Club (SOC);
Scottish Raptor Study Group;
Shetland Oil Terminal Environmental Advisory Group;
Wildfowl and Wetlands Trust.

We thank especially BTO, BWI and SOC for the use of data and information from the Britain and Ireland Bird Atlas 2007-2011 and The State of the UK’s Birds 2020 (Burns et al. 2020).

Contribution of Citizen Science

The assessments would not have been possible without the massive voluntary efforts of many tens of thousands of volunteers who have given their time (and resources) to participate in citizen science.

Data from recording schemes and the NBN Atlas provided much of the information needed to complete the reports, and citizen science contributes significantly to monitoring species, including Annex I species in Scotland.

Monitoring of Protected Areas

Features on protected areas are monitored by NatureScot’s Site Condition Monitoring programme. The purpose of Site Condition Monitoring is to determine the condition of the natural features within each site, to work out whether a natural feature is likely to maintain itself in the medium to longer term under the current conditions. These include the management regime in place, and wider environmental or other influences. The condition of individual features on a site can be found by searching for a protected area on NatureScot’s SiteLink website.

The data is also available to view using the Protected Nature Sites interactive tool on the Scotland’s Environment website.

2.3 Information on the network of European Sites

European sites represent the very best of Scotland’s nature and are internationally important for threatened habitats and species. These sites are ambitious in their aim, requiring more than just the avoidance of species extinctions and habitats loss. Instead, the objective is for all species and habitats covered to contribute towards their favourable conservation status (FCS). More information on European sites is available on the NatureScot website.
SiteLink provides easy access to data and information on Protected Areas across Scotland ranging from sites of local natural heritage to designations of national and international importance, including European sites.
Additional information on European marine sites is also available on the NatureScot website.

2.4 Monitoring schemes

Information on protected area monitoring in Scotland is available on the NatureScot website;
National Biodiversity Network mobilises a wealth of (mainly location-related) species records across the UK.
The Scottish MPA monitoring strategy is available on the Scottish Government website.
Further information on marine monitoring is available on the NatureScot website.

Terrestrial monitoring schemes

Marine mammal and habitat monitoring schemes

Joint Cetacean Data Programme;
MarClim programme;
Scottish Marine Animal Stranding Scheme;
Small Cetacean Abundance in the European Atlantic and North Seas (SCANS) (SCANS IV);
Special Committee on Seals (SCOS);
Hebridean Whale and Dolphin Trust Monitoring Programme and Whale Track;
Whale and Dolphin Conservation ShoreWatch Monitoring Programme;
Scottish Passive Acoustic Network (SPAN) (and predecessor programmes ECOMMAS/COMPASS prior to 2022);
UK Bycatch Monitoring Programme, which is now part of the Marine Wildlife Bycatch Mitigation Initiative (BMI);

Monitoring schemes for birds

Avian Influenza monitoring;
Breeding Bird Survey (common breeding birds); (BBS also includes Mountain hare)
Constant Effort Sites Scheme (productivity assessment);
Goose and Swan Monitoring Programme (non-breeding geese and swans);
National Beached Bird Survey (monitoring seabird mortality);
National Game Bag Census (bag records from shooting estates) (NGBC also includes Mountain hare);
Nest Record Scheme (productivity assessment);
Predatory Bird Monitoring Scheme (monitoring of pesticide and other pollution residues);
Rare Breeding Birds Panel;
Ringing Scheme (movements and survival);
Scottish Raptor Monitoring Scheme (birds of prey in Scotland);
Seabird census programmes;
Seabird Monitoring Programme (breeding seabird numbers, productivity and survival);
Waterways Breeding Bird Survey (common breeding birds of waterway habitats);
Wetland Bird Survey (non-breeding waterbirds);
British Trust for Ornithology also produce a non-avian taxa dataset.

2.5 Protection of species

Information on legal protection for species in Scotland is available on the NatureScot website;
Information on protected species in Scotland is available on the NatureScot website;
Information regarding the protection of marine species in the UK is available on the JNCC website.
Information regarding the protection of bird species (Articles 5-8), which includes international conventions and agreements, conservation listing, priority species, protected areas, surveillance and monitoring, indicators, reporting, and advice is available on the JNCC website.
Wildlife management and wildlife crime.

2.6 Research and advice (including research and work required as a basis for the protection, management and sustainable use – birds only)

Research relevant to the reporting period that has contributed to the assessments is provided in the References, with links to published reports and articles. There is also research on the management of certain bird species.

2.7 Impact of measures

A summary of the impact of the measures taken in Scotland to meet the provisions of the Birds and Habitats Directives, and to achieve the objectives of those Directives during the period 2019-2024 is provided. The full assessments are available on the NatureScot website (terrestrial habitats and species and marine habitats) and on the JNCC website (marine mammals and birds).

Conservation Status Overall Assessment by Reporting Group - Table — Figure 3. Conservation Status Overall Assessment by Reporting Group

The chart in Figure 3 reflects data of varying age (1962-2024) and collected for a range of use cases. Action to address the causes of the decline in these species and habitats was an important part of the development of the Scottish Biodiversity Strategy and associated Delivery Plan, published in 2024. This is the framework through which partners can work to improve nature and nature’s contributions to people and improve the impact of measures portrayed in the chart .

2.8 Transposition of the Directive (legal texts) and translation after EU Exit

For Scotland the Habitats and Birds Directives are transposed through a combination of the Conservation (Natural Habitats, &c.) Regulations 1994 And the Wildlife & Countryside Act 1981. The Conservation of Habitats and Species Regulations 2017 apply in relation to reserved matters see:

The Habitats Regulations have been amended as a result of leaving the EU so that European sites are both protected, and continue to operate as they have done since their original designation. The changes to the Regulations also mean that the requirements of the Directives continue to be relevant to the management of European sites.

Part 2 of the Nature Conservation (Scotland) Act 2004 provides for the notification, management and protection of Sites of Special Scientific Interest (SSSI). This designation underpins the majority of terrestrial SACs and SPAs, and the associated provisions work in conjunction with the legislation listed above.

Through the Natural Environment (Scotland) Bill, Scotland is developing statutory nature recovery targets which aim to improve the management and effectiveness of existing protected areas. The Scottish Biodiversity Strategy to 2045 also includes commitments to increase the extent and connectivity of protected areas as well improve condition.

Contact

Email: biodiversity@gov.scot

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