Updated Conservation Advice is now available for Scanner Pockmark SAC under the Conservation Advice tab below.

The public consultation on a proposed boundary amendment for this site closed on November 17th 2017.  Further information on the consultation is available here. JNCC are currently reviewing comments and a post-consultation report will be available in due course.

Scanner Pockmark MPA


Status: Special Area of Conservation (SAC)


Scanner Pockmark is a seafloor depression containing submarine structures made by leaking gases approximately 185km off the north-east coast of Scotland near the centre of the Witch Ground Basin.


Click to link to the interactive map

The Scanner pockmark complex in the south of the site is a large seabed depression of approximately 320,000m2 containing two deep areas about 17m below the surrounding sea floor. Carbonate blocks known as ‘Submarine structures made by leaking gases’ form when methane is released from the seabed and reacts with the surrounding seawater and have been recorded in the base of these pockmarks. The pockmark sediment provides habitat for the phosphorescent sea pen Pennatula phosphorea, slender sea pen Virgularia mirabilis and tube anemone Cerianthus lloydii. The carbonate structures in the base of the pockmark support animals usually associated with rocky reef, such as squat lobsters Munida sp., anemones and fish. Chemosynthetic organisms are also present feeding off the bubbling methane with the gutless nematode Astomonema southwardorum, thought to occur only at the Scanner pockmark complex. The northern section of the site contains the Scotia pockmark complex with two deep sections and active methane seeps. These large pockmarks reach a depth of approximately 15m below the surrounding sea floor.


More detailed site information can be found on the Summary tab.

Map displaying MPA boundary and

associated protected feature data.

Visit the JNCC MPA Mapper to further

view and explore data for this MPA.


Legislation: EU Habitats Directive 1992 transposed into UK law by the Conservation of Offshore Marine Habitats and Species Regulations 2017.


Protected features

Features Feature Type
1180 Submarine structures made by leaking gases Annex I Habitat*

* For the latest Annex I habitat resource figures, please see the link to the latest Habitats Directive Article 17 reporting in the Assessment tab.


The acquisition of new data may result in updates to our knowledge on feature presence and extent within this site. The most up to date information is reflected on the map on this page and in JNCC’s MPA mapper and the evidence underpinning this can be viewed in the Evidence tab.

Site timeline

The diagram below is a summary of the key milestones involved in the selection and designation of Scanner Pockmark SAC. More detail can be found within the Relevant Documentation.

Scanner Pockmark Timeline

Revelant Documentation

The documents referred to below and any other historical documents relating to Scanner Pockmark were produced during the selection and designation process and therefore may be out of date. This Site Information Centre is the most up to date source of information for this MPA, and will reflect any additional information gathered since these documents were produced. Information about the SAC site selection process is available on the JNCC SAC pages.





Last updated: October 2017


Information for this site summary was adapted from the SAC Selection Assessment and incorporates any further information gathered since this document was produced.


Site overview

The site contains 61 pockmarks of varying sizes. Four of these are unusually large and occur in two pockmark complexes: Scanner pockmark complex in the south of the site and the Scotia pockmark complex in the north.


The Scanner pockmark complex comprises of two large pockmarks with a combined area of approximately 320,000m2  and depths of up to 16.7m below the surrounding sea floor. These pockmarks have a considerably greater volume than more typical pockmarks in the vicinity of the site. The pockmarks were created by the expulsion of shallow methane gas and have been maintained by active gas seepage. At the base of the pockmarks, blocks of ‘methane derived authigenic carbonate’ (MDAC) have been recorded. These carbonate rocks, formed by the precipitation of calcium carbonate and cementation of the surrounding sediment, have been identified as ‘Submarine structures made by leaking gases’ - a listed habitat under Annex I of the EC Habitats Directive. The location and extent of carbonate blocks has not been precisely mapped. However, the latest survey data from 2012 pointed to areas of high acoustic reflectance within the pockmarks, suggesting the presence of a hard substrate. These require further investigation to examine whether they represent MDAC, shell hash or variations in sediment particle size.


There is some evidence of chemosynthetic bacteria in the Scanner pockmark which grow by oxidising sulphur and may support some of the site’s other notable fauna. The most important species in the pockmark from a conservation perspective is the gutless nematode Astomonema southwardorum, which may derive some of its nutrition from chemosynthetic bacteria. The Scanner pockmark is the only known locality for this species found to date. Other important species associated with the gas seepage in the pockmark are the bivalves Thyasira sarsi and Lucinoma borealis. The structures and pockmark depression attract fish species such as hagfish Myxine glutinosa, four-bearded rockling Rhinonemus cimbrius, haddock Melanogrammus aeglefinus and Norway redfish Sebastes viviparus on top of the carbonates and wolf fish Anarhichas lupus in cavities underneath. Conspicuous invertebrates at the site include Anthozoans such as phosporescent sea pen Pennatula phosphorea, slender sea pen Virgularia mirabilis and tube anemone Cerianthus lloydii in pockmark sediment and deeplet sea anemone Bolocera tuediae, Dahlia anemone Urticina felina and plumose anemone Metridium senile on the carbonate structures.


The Scotia pockmark complex is composed of two deeper sections with active methane seeps. The Northern Scotia pockmark is approximately 76,000m2 in size with a depth of 12m below the level of the surrounding seabed. The Southern Scotia pockmark is at least 72,400m2 with a depth of 14.5m. Numerous surveys since the 1990s have found evidence for the active seepage of methane in this complex, but the presence of carbonate blocks has not been confirmed. The latest survey data suggest that small patches of harder substrate do occur within the Scotia pockmarks, but whether these represent MDAC requires further confirmation.


Scanner Pockmark is one of three sites identified for protection of Annex I Submarine structures made by leaking gases in the UK. Braemar Pockmarks SAC also contains this feature and is found 80km north-east of Scanner Pockmark. While both sites are characterised by the presence of carbonate structures, Scanner Pockmark has a slightly less diverse biological community and less varied morphology. As there are few cases of this Annex I habitat in the UK, both sites make important contributions to the sufficiency of the UK MPA network for this feature. Further detail on the evidence for this SAC can be found on the Evidence tab.


Site location:  Coordinates for this SAC can be found in the Natura 2000 Standard Data Form listed in the Relevant Documentation.

Site area:  3.35 km2

Site depth range:  Depth at the site ranges from 150m below sea level down to 165m below sea level at the base of the pockmark.

Charting Progress 2 Biogeographic Region: Northern North Sea.


Site boundary description
The boundary for Scanner Pockmark is a simple polygon enclosing the minimum area necessary to ensure protection of the Annex I habitat. Coordinate points have been positioned as close to the edge of the interest feature as possible. As bottom trawling is a significant threat to the interest feature, the proposed boundary includes a margin to ensure its protection.




Last updated: October 2017

Click to link to the interactive map


The full overview of the data used to support site identification along with information on confidence in feature presence and extent is available in the Scanner Pockmark SAC Selection Assessment. All data that can be made publicly available are displayed on the JNCC Interactive MPA Map. Some of the data for this SAC has been collected through JNCC funded or collaborative surveys and some through other means. These data provide direct evidence confirming the presence of the protected features within the site.


Survey and data gathering

Map displaying the MPA and relevant underpinning data

Data analysis reports

  • Offshore seabed survey of Braemar Pockmarks and Scanner Pockmark (2017) - This report presents the findings from the analyses of the data gathered during the seabed survey of the Braemar Pockmarks and Scanner Pockmark in 2012 (cruise CEND19x/12). The report describes the presence, location and extent of the pockmark features, along with detail relating to the presence and location of any associated seafloor carbonate structures where they are observed to occur. 
  • Geological investigation of pockmarks in the Scanner Pockmark SCI area (2015) - JNCC commissioned the British Geological Survey to compare 2012 survey data and earlier geological data to assess changes in pockmark morphology and condition. The study confirmed the presence of 61 pockmarks within the site, four of which measured over 72,000 m2 with a depth of greater than 12 metres compared to the surrounding seabed. Comparison of acoustic data between 2001 and 2012 surveys revealed that some pockmarks are becoming filled in with sediment, believed to be the result of collapsing pockmark sidewalls. Strong acoustic reflections shown in multibeam backscatter data suggest that the muddy sea floor is punctuated with patches of harder substrate in nearly half of the pockmarks. These require further investigation (such as through visual observation or seabed sampling) to determine whether they are examples of carbonate blocks, shell fragments or a change in sediment particle size.
  • Seabed fluid flow: the impact on geology, biology and the marine environment (2007) - A review of survey data and associated studies by Judd and Hovland (2007) indicates that the volume of the Scanner and Scotia pockmarks is approximately 1 million m3 and they are deep enough to cut through surrounding sediments, revealing stiffer clay beneath. These pockmarks are larger and deeper than those found nearby. The largest carbonate block observed in Scanner pockmark measured 2 x 1 metre and was 20-50 centimetres thick.
  • A review of pockmarks in the UK part of the North Sea (2001) - Dando (2001) reviewed data from a 1989 survey in which grab samples were taken to characterise the sediment, including chemical and gas composition, and 1990 and 1991 surveys in which a manned submersible was deployed to study infauna, taking 18 box-core sediment samples. These surveys found that the macro-infauna of Scanner pockmark was similar to that of the surrounding area, with the exception of the bivalve Thyasira sarsi which was confined to sulphur-rich sediments. The micro-infauna was dominated by the gutless nematode while anthozoans were the most conspicuous epifauna, found at higher densities in the pockmark than in surrounding areas.
  • Pockmarks in the UK Sector of the North Sea (2001) - Preliminary analysis by Judd (2001) of acoustic records including sidescan, backscatter and bathymetry taken during a 2001 survey of petroleum block 15/25. Gas seeps and carbonate blocks were identified in this area of the North Sea.
  • Pockmark formation and activity in UK block 15/25, North Sea (1994) - Seismic data from surveys in 1983, 1989, 1990 and 1991 found evidence of gas plumes on the seabed and gas accumulations at shallow depths beneath the seabed. The study by Judd et al. (1994) estimates that the Scanner pockmark was formed 13,000 years ago. 
  • Ecology of a North Sea pockmark with an active methane seep (1991) - Analysis of grab samples collected on two 1989 surveys by Dando et al. (1991) found that the pockmark fauna was characterised by the gutless nematode and the bivalve Thyasira sarsi, which was confirmed to be feeding on chemosynthetic bacteria. The chemical composition of samples suggested sediment displacement had taken place – a feature of typical feature of methane seeps.
  • Characteristics of two natural gas seepages in the North Sea (1985) - Hovland and Sommerville (1985) describe the discovery of the Scanner pockmark from acoustic and seismic records taken during a routine environmental survey by the petroleum industry in 1983. Acoustic data indicated the presence of an active seep in the form of gas bubbles, low density liquid or suspended sediments.


Additional relevant literature
Further supporting scientific literature consulted during the identification of this site can be found in the Selection Assessment. Please be aware that although these sources contain information which is of interest in relation to this MPA, they do not necessarily represent the views of JNCC.

  • Judd, A.G. and Hovland, M. (2007). Seabed fluid flow: the impact on geology, biology and the marine environment. Cambridge: Cambridge University Press.
  • Holmes, R. and Stoker, S.J. (2005). Investigation of the origin of shallow gas in Outer Moray Firth open blocks 15/20c and 15/25d. Report to the Department of Trade and Industry No. GC04/22. - A review of data from British Geological Society regional surveys and commercial data showing that gas is seeping from the seabed in the Scanner and Scotia pockmarks and that these are unusually large pockmarks compared to others in the surrounding area. Methane derived authigenic carbonate is documented in both.
  • Dando, P.R. (2001). A review of pockmarks in the UK part of the North Sea, with particular respect to their biology. Technical report produced for Strategic Environmental Assessment – SEA2. Department of Trade and Industry Technical Report No. TR_001.
  • Judd, A.G. (2001). Pockmarks in the UK Sector of the North Sea. Technical report produced for Strategic Environmental Assessment – SEA2. Department of Trade and Industry Report No. TR_002.
  • Judd, A., Long, D. and Sankey, M. (1994). Pockmark formation and activity, UK block 15/25, North Sea. Bulletin of the Geological Society of Denmark, 41: 34-49.
  • Dando, P.R., Austen, M.C., Burke, R.J., Kendall, M.A., Kennicutt, M.C., Judd, A.G., Moore, D.C., O' Hara, S.C.M., Schmaljohann, R. and Southward, A.J. (1991). Ecology of a North Sea Pockmark with an active methane seep. Marine Ecology Progress Series, 70: 49-63.
  • Hovland, D.M. and Sommerville, J.H. (1985). Characteristics of two natural gas seepages in the North Sea. Marine and Petroleum Geology, 2 (4): 319-326.


Knowledge gaps
If you are aware of any additional information not referred to in any of the Relevant Documentation, please contact JNCC.


Conservation Advice


Last updated: February 2018


Updated formal conservation advice is now available for this MPA.  Further information on the approach used to develop this advice is available on the Conservation Advice webpage along with a Glossary of Terms used in JNCC conservation advice and a short video explaining how to use the conservation advice packages. 


You must refer to this advice if you:

  • undertake a Habitats Regulation Assessment (HRA) for a plan or project that could impact the site;
  • provide information for a HRA;
  •  respond to specific measures to support delivery of the conservation objectives for the site; and 
  • consider the need to put new or additional management measures in place.


You may also find it useful to refer to this advice if you:

  • Carry out any other activity that could impact the site.


We will engage with stakeholders to identify any lessons which JNCC can learn from customers who have used the advice, with a view to continuing to ensure it is fit-for-purpose.

The following table provides an overview of the components of the conservation advice, and provides hyperlinks to each of the products for this MPA. These elements together form JNCC’s formal conservation advice for this site and should be read in conjunction with each other. This updated advice replaces the previous Regulation 18 package for the site. This advice reflects the most up-to-date evidence held by JNCC (correct as of February 2018). A zipped folder enabling these documents to be downloaded together is available at the bottom of this page.


Document  Overview
Background Information Explains the purpose of the advice and when it must be referred to.

Conservation Objectives


Supplementary Advice on the Conservation Objectives (SACO)

The conservation objectives set out the broad ecological aims for the site. JNCC provide supplementary advice in the SACO which is essential reading to support interpretation of these conservation objectives. It provides further detail and site-specific information for each feature within the site including which of the attributes need to be conserved and which ones recovered.

You can use these documents to assess the impacts of your planned activity on the important attributes of the site.

Conservation Advice Statements

These statements provide a summary of the Supplementary Advice on the Conservation Objectives (SACO).

  • Site condition presents our up to date understanding of the condition of features within the site;
  • Conservation benefits which the site can provide, these help you understand what is important about the site and why it needs protecting; and
  • Conservation measures which JNCC consider are needed to support achievement of the conservation objectives. These provide clarity around measures needed to support restoration or maintenance of the feature(s) within the site.
Advice on Operations

Provides information on the activities capable of affecting site integrity and therefore achievement of the site’s conservation objectives.

This is a starting point for determining potential management requirements. It does not take into account the intensity, frequency or cumulative impacts from activities taking place. It is simply to advise you of the possible adverse impacts that your activity can have on a MPA’s features.

Use the advice on operations to determine those pressures your activity causes that could harm the habitat and/or species features of the site.




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Activities and Management


Last updated: October 2017


Management status: Progressing towards being well managed


Progress is ongoing with the recommendation of fisheries management proposals to the European Commission and ongoing site condition monitoring work will be required in order to conclude with confidence as to the degree to which the site is moving towards or achieving its conservation objectives.


This site forms part of the UKs contribution to the OSPAR commissions network of MPAs, Europe’s Natura 2000 network and the Emerald network established under the Bern Convention. As the UK is a signatory to the OSPAR commission, JNCC are committed to ensuring that the OSPAR MPA network is ‘well-managed’ by 2020.


JNCC consider ‘well-managed’ to mean the timely progress of an MPA around the ‘MPA management cycle’. This involves:

1)    The documentation of appropriate management information - conservation objectives, advice on activities capable of affecting the protected features of a site, and spatial information on the presence and extent of the protected features of a site.

2)    The implementation of management measures - management actions considered necessary to achieve the conservation objectives of a site.

3)    Site condition monitoring programmes – collecting the information necessary to determine progress towards a sites conservation objectives.

4)    Assessment of progress towards conservation objectives – using available information to infer whether or not a site is moving towards, or has achieved, its conservation objectives.


The sub-sections that follow provide an account of the progress of Scanner Pockmark SAC around each of the four stages in the MPA management cycle.


The documentation of appropriate management information

  • The conservation objectives and advice on activities capable of affecting the conservation status of the protected feature of this site are available under the conservation advice tab.
  • JNCC are in the process of improving our MPA conservation advice packages. Further information is available on our conservation advice pages.
  • Spatial information on the presence and extent of the protected feature of this MPA is available via JNCC's MPA mapper.
  • JNCC are in the process of developing downloadable MPA data packages where appropriate permissions to share datasets are in place.


The implementation of management measures

This section details progress towards the implementation of management measures for activities considered capable of affecting the conservation status of the protected feature of the site. The protected feature of the site is considered sensitive to pressures associated with fishing and ‘licensable’ activities.



  • Mobile demersal trawling by UK vessels is the predominant activity in Scanner Pockmark SAC. There is little evidence of activity from non-UK fishing interests.
  • The site falls outside the UK’s 12 nautical mile limit and is to be exclusively managed under the EU Common Fisheries Policy (CFP). In accordance with Article 18 of the revised CFP, requests for management will be developed jointly between the UK Government and any Member States with a direct management interest in the area affected.
  • Marine Scotland are the lead authority regarding the implementation of, and compliance with, any measures to managing fishing activity. Further information on progress is available via Marine Scotland’s web pages.


Licensable activities

  • Two abandoned, explorative oil wells occur within the site. The south-east corner of the MPA overlaps with the Blenheim oil field (production ceased).  
  • Any activities or future proposals would have to comply with Article 6(3) of the EU Habitats Directive 1992, which is transposed into UK law by the Conservation of Offshore Marine Habitats and Species Regulations 2017.
  • Our conservation advice supports the consents process by setting out the conservation objectives for the protected feature of this MPA and advice on activities that may result in pressures to which the protected feature is considered sensitive.
  • Further information on JNCC's role in the provision of advice for licensed activities in the UK offshore area is available on JNCC's offshore industries advice webpage



  • There is low density of commercial shipping in this area and due to its offshore location, vessel anchorage is unlikely.
  • Under international law (UNCLOS, Article 17), ships have a right of innocent passage at sea, including in areas designated as MPAs. The pressures associated with shipping activity within Scanner Pockmark SAC are not considered likely to impact the protected feature of the site.


Site condition monitoring

A baseline condition survey was undertaken in 2012 which was also used to gather evidence to support the development of fisheries management measures. Further information is provided in the Evidence tab and Monitoring tab.


Assessment of progress towards conservation objectives

No long-term condition monitoring data is available to determine whether the MPA is moving towards or has reached its conservation objectives. The site has a ‘restore’ conservation objective based on the findings of a vulnerability assessment which suggests the site is unlikely to be moving towards its conservation objectives.  Further information will be provided under the Assessment tab.




Last updated: October 2017


JNCC is currently leading on the development of a strategy for biodiversity monitoring across all UK waters, to include MPA monitoring. For MPAs, data and evidence collected from monitoring activities will aim to:

  • Enable assessment of condition of the features within sites;
  • Enable assessment of the degree to which management measures are effective in achieving the conservation objectives for the protected features;
  • Support the identification of priorities for future protection and/or management; and,
  • Enable Government to fulfil its national and international assessment and reporting commitments in relation to MPAs and help identify where further action may be required.


Information on monitoring of this MPA will be provided when it becomes available.



Last updated: October 2017


Assessments of the condition of designated features in offshore MPAs are required to report against our legal obligations. Ideally these assessments should be based on observed data, and then measured against targets for predefined indicators. However, for MPAs in offshore waters we do not always have the appropriate information to be able to do so. This is particularly true for seabed habitats, which are the main type of feature designated for protection in offshore MPAs. 


To address these challenges, JNCC has been an active partner in the development of new approaches and tools for the assessment of habitats and species for a variety of national and international status reports. They include the second cycle of the Conservation Status Assessment reports under the EU Habitats Directive, Charting Progress 2 and the OSPAR Quality Status Report. JNCC continues to develop and pilot tools for the assessment of marine habitats and species in offshore waters to improve the quality and transparency of our offshore MPA assessments, and contribute to the monitoring of marine biodiversity in UK waters. These tools cover methods for producing interim assessments of site features and their responses to pressures, as well as developing more robust indicators for determining condition of the features.


Every six years, Member States are required under Article 17 of the EU Habitats Directive to report on the Conservation Status of Annex I habitats and Annex II species on the Habitats Directive.  The assessments should consider the habitat or species both within the Natura 2000 network and in the wider sea.  The latest report was submitted by the UK in 2013 and provided a second assessment of the conservation status of relevant habitats and species within UK marine waters during 2007-2012. . The next report is for the period 2013-2018 and is due in 2019; information on the condition of features within SACs will make a contribution to this report. The assessments of features within MPAs will also feed into six yearly reports on the state of the marine environment under the Marine Strategy Framework Directive, which aims to achieve Good Environmental Status by 2020.


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