Regulation of Designated Shellfish Waters

The European Community Shellfish Waters Directive 2006/113/EC (the Directive) was adopted to protect and, where necessary, improve the quality of waters where shellfish grow and to contribute to the high quality of directly edible shellfish products. It supersedes the original Shellfish Waters Directive 79/923/EEC.

The Directive concerns the quality of shellfish growing waters. Along with other Member States, the UK has designated those coastal and brackish waters needing protection or improvement in order to support shellfish (bivalve and gastropod molluscs) life and growth and to contribute to the high quality of directly edible shellfish products. In Scotland, the Scottish Environment Protection Agency (SEPA) is the competent authority charged with the task of delivering the water quality standards laid down in the Directive.

The Directive prescribes the minimum quality criteria which must be met by shellfish waters, and guideline values which Member States must endeavour to observe. Details of these standards as applied in Scotland are given in Annex 1 on the shellfish waters introductory web page. The Directive also specifies the minimum sampling frequency and the reference methods of analysis which must be used. If the set environmental standards are not met, the Directive requires measures to be taken to ensure compliance within six years of waters being designated.

The Surface Waters (Shellfish) (Classification) (Scotland) Regulations 19971 transpose the Directive into Scottish law. The Regulations establish classification and sampling criteria and confer a duty on SEPA to investigate and adopt appropriate measures where monitoring results indicate that the waters do not meet the minimum quality standards specified in the Directive. An accompanying Direction instructs SEPA to endeavour to achieve guideline values as specified in a Schedule to the Direction.

The first shellfish growing waters in Scotland were formally identified in 1981. By 1998, 22 waters had been officially designated by Direction, with a further 11 designated in 2000. In 2002 an additional set of 75 waters were designated, followed by another 5 in 2005. Together with some de-designation and amalgamation of existing sites, the total number of designations by the end of 2005 stood at 108. In 2006 all of these sites were re-designated en bloc by means of a new Direction, and all previous Directions dating back to 1998 were revoked. In November 2008 a further 7 designations were made by Direction, including extensions to 3 existing designations. A further review in the summer of 2009 resulted in over 30 waters being de-designated, and the number of designations at this point stood at 78. The most recent review and Direction issued in May 2012 resulted in 9 new designations, 4 extensions to existing sites, and 7 sites being de-designated, bringing to 80 the number of currently designated sites. The next review of designations is scheduled for the summer of 2013, the principal aim of this review being to improve the degree of overlap between shellfish waters and harvesting areas as identified by the Food Standards Agency.

SEPA maintains a Pollution Reduction Plan (PRP) for each of the designated sites (with the exception of the 9 sites newly designated in 2012 for which plans are still to be drafted). Each PRP provides background information on the site, reports the results of annual compliance monitoring, identifies point source discharges and potential risks of diffuse pollution and highlights required improvement actions. The overall aim of the PRP is to ensure that each site complies with the minimum mandatory standards in the Directive within six years of designation, and to ensure that progress is made towards observing guideline values. Information up to the end of 2010 can be found in the latest versions of the PRPs (plans for the sites de-designated in 2009 and 2012 are also available, but will not be updated).

Monitoring in 2011 indicated that all of the designated sites met the minimum environmental quality standards. Most of the sites (71) also observed the stricter guideline values for physical and chemical parameters. However, exceedances of the bacteriological guideline value were recorded at some 29 sites. The Directive specifies a guideline value for faecal coliforms (FC) of not more than 300 FC per 100ml of shellfish flesh and intervalvular fluid. No clear relationship has been established between FC levels in shellfish tissue and the microbiological quality of the surrounding waters, excepting those waters which are polluted2.

In the absence of guidance on deriving a water quality objective that would achieve the guideline value set by the Directive, SEPA adopts a precautionary approach, as detailed in SEPA Regulatory Method WAT-RM-133, whereby dischargers of sewage effluent must demonstrate design to achieve no more than 100 FC/100 ml and 100 Faecal Streptococci (FS)/100 ml in the receiving water (equivalent to the guideline values in the EC Bathing Waters Directive). These limits, however, only apply to harvesting areas as designated by the Food Standards Agency (FSA) under the terms of the Shellfish Hygiene Directive (see below for more information on this). SEPA effectively treats shellfish growing waters as impact zones to protect the FSA harvesting areas that lie within them. Water quality cannot therefore be guaranteed outside the FSA designated harvesting areas.

Because of the significant number of sites failing to observe the guideline value for FC, the PRPs strongly emphasise measures being taken to reduce those sources of coliform bacteria which are controllable. SEPA recognises that FC levels in waters and shellfish flesh are influenced by complex factors and inter-relationships such as rainfall and diffuse pollution from agriculture, as well as by direct and indirect sewage discharges. The two former are thought to be highly involved in the failures of the guideline value, and a recent study on Loch Etive in Argyll has provided some useful information on sources of bacteria4. Further information on SEPA's role in controlling diffuse sources of pollution can be found below in the section on the Water Framework Directive.

The PRPs frequently refer to Scottish Water's sewerage and sewage treatment assets, particularly where these require upgrading. The capital investment needed to improve these assets is now identified and approved through a formal investment planning exercise for the water industry in Scotland. This Quality and Standards (Q&S) process is run by the Scottish Government, in collaboration with Scottish Water, SEPA, Scottish Natural Heritage, the Water Industry Commissioner and other stakeholders.

The current Scottish Water investment programme, Q&SIII, covers a double period, with the first period running from 1 April 2006 to 31 March 2010 and the second running from 1 April 2010 to 31 March 2014. The Q&SIII planning process, which must address all current and future regulatory requirements on Scottish Water, has presented various investment options for consideration by Scottish Ministers. A minimum level of improvement has been specified as part of this process to ensure some movement towards guideline values specified by the Shellfish Waters Directive. A prioritised list of all investment needs has been developed by taking account of the level of risk posed by Scottish Water assets. This has predominantly been achieved by looking at the scale and proximity of discharges to shellfish waters currently failing the guideline value for FCs on a regular basis. This should ensure that the most significant risks are addressed first.

Monitoring at designated sites has so far produced limited data on the specific impact of human sewage. If subsequent data indicate that a site requires urgent improvement to the sewage treatment, there is a mechanism within Q&S for substitution. Under substitution, planned investment can be diverted away from one site in order to finance infrastructure investment at another, if it is agreed that the second site has become a higher priority for improvement.

Where agricultural or urban diffuse inputs are suspected of being the dominant sources of FC contamination, SEPA will look to devise and implement site-specific plans to ensure such inputs are minimised (see below for more information on this).

Other relevant legislation  

  • EC Shellfish Hygiene Directive

    Compliance with the Shellfish Waters Directive in itself will not ensure the protection of public health. This is the objective of the Shellfish Hygiene Directive 1991/492/EEC, as transposed into the Food Safety (Fishery Products and Live Shellfish) (Hygiene) Regulations 1998.

    In Scotland, the Shellfish Hygiene Directive and relevant Regulations are the responsibility of the Food Standards Agency (FSA). This includes responsibility for the designation of harvesting areas, setting standards and reporting the classification of harvesting areas according to the presence of faecal indicator organisms. The degree of shellfish contamination determines the degree of depuration (purification) required before the produce may be commercially marketed.

    SEPA has established direct liaison with the FSA to discuss issues of common interest, develop relevant research and exchange information. Results and information supplied by the FSA are taken into consideration in the PRP production process. In 2006 new regulations relating to the Hygiene Directive came into effect. These regulations provide SEPA with the opportunity to have greater involvement in the designation of new shellfish areas. This will help to ensure that new harvesting areas are located where the necessary water quality can reasonably be achieved without compromising existing and future social or economic activities.

    SEPA has also reached an agreement with the FSA to share data, and from 2007 onwards FSA data has been used at many sites to determine whether or not the guideline value for FC is being observed.

  • EC Water Framework Directive

    The Water Framework Directive (WFD) (2000/60/EC) seeks to improve or maintain the ecological and physico-chemical quality of all waterbodies – rivers, lochs, groundwater, transitional waters (estuaries) and coastal waters. When fully operational, the WFD will achieve the level of protection afforded by a number of existing directives, including the Shellfish Waters Directive, which is scheduled to be repealed in 2013. These objectives will be achieved through the operation of River Basin Management Plans (RBMPs), which incorporate the improvement actions specified within the Shellfish Water PRPs presented on the accompanying web pages. The first River Basin Management Plan runs from 2009 – 2015.

    In order to meet the requirements of the WFD, the Water Environment (Diffuse Pollution) (Scotland) Regulations were introduced in April 2008. These regulations are referred to as the Diffuse Pollution General Binding Rules (DP GBRs).  The seven DP GBRs focus solely on rural land use activities, and all rural land users have a responsibility to ensure that they are followed. In particular, DP GBRs 18 and 19 (covering the storage and application of fertilisers and the keeping of livestock) are aimed at minimising the input of bacteriological and nutrient inputs to watercourses, which in turn should result in reduced inputs to designated shellfish waters.

    A new programme of rural diffuse pollution work started in March 2010, to help deliver the objectives outlined in the recently published RBMPs for the Scotland and Solway-Tweed river basin districts.

    As part of this work, diffuse pollution priority catchments have been identified by SEPA as catchments where significant numbers of waterbodies are failing to meet environmental standards. Fourteen priority catchments, containing some of Scotland's most important waters (for conservation, drinking water, bathing and aquaculture), have been selected using a risk based approach for action in the first RBMP cycle. Only two of these catchments contain designated shellfish waters, but it is envisaged that many more catchments containing shellfish waters will be prioritised for action during the second and third RBMP cycles, which run from 2015-2021 and 2021-2027 respectively. In the meantime, work will be carried out to identify the main sources of bacteriological contamination in those shellfish waters that are failing to meet the guideline value for faecal coliforms on a regular basis.

    Further information on priority catchments and DP GBRs can be found on our DP priority catchment webpage.


  1. Statutory Instrument 1997 No. 2470 (S. 162). Surface Waters (Shellfish) (Classification) (Scotland) Regulations 1997.
  2. Investigation of the relationship between indicator bacteria in mussel flesh and intervalvular fluid and surrounding waters. Phase 3 SR97(07) F., Milne, D.P., Higgins, J.E. and Brodie, I.J. (1998). Scotland and Northern Ireland Forum for Environmental Research.
  3. Regulatory Method (WAT-RM-13) Microbiological Discharges.
  4. SARF013 / SAMS Report No. 256, Risk Factors in Shellfish Harvesting Areas, Scottish Aquaculture Research Forum, 2008.