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Fish farm manual

Water Column Monitoring

Please note: the manual is currently being updated and links have been supplied for revised documents only. If you require a copy of a document that is not available below please email

This manual has been produced to provide SEPA staff with detailed guidance on the legislation, policy and procedures which should be considered when regulating Scotland’s marine cage fish farming industry. Although primarily an internal procedures manual, we have made it available online to help ensure that we work within a clear and understandable regulatory framework. We will update the manual as we develop policies and practice (in consultation with interested parties).

ID Title Version   Date        


 1.3 May 2005
 2 Pre-Application Consultations  1.3 May 2005
 3 Receipt of Applications  1.2 May 2005
 4 Assessment of Applications  1.3 May 2005
 5 Setting licence Limits  1.3 May 2005
 6 Process for Granting or Refusing a Consent  1.4 May 2005
 7 Monitoring  1.5 Aug 2006
 8 Data Management and Use of Information  1.3 May 2005
 9 Review of Consents  1.2 May 2005
 10 References  1.0 Nov 1998
 11 Glossary of Terms  1.2 May 2005
 A Standards  1.3 May 2006
 B Quality Systems and Reporting  (27k)  4.0 Oct 2009
 C SEPA's Conservation Duties  1.0 Nov 1998 
 D Environmental Assessment Procedures  1.0 Apr 2000 
 E Water Column Monitoring  1.1 Apr 2000 
 F Seabed Monitoring  (338k)  2.0 Sep 2008 
 G Models for Assessing the use of Medicines in Bath Treatments  (237k)  2.2 Oct 2008 
 H Methods and Modelling In-Feed Anti Parasitics  (2.08mb)  2.3 May 2005
 I Guidance on drafting a Marine Cage Fish Farm Licence (177k)  5 Sep 2016
 III Definition of Best Environmental Practice: Legislative Background  1.1 Dec 2005
 IV Guidance on Cage Fish Farm and Shore Base Inspections  3.1 Sep 2005
  Supplement 1 - Pre Inspection Checklist  2.2 Sep 2005
  Supplement 2 - Inspection Report Form  2.2 Sep 2005
 V Guidance on Consenting of Medicines and Other Chemical Therapeutics including ATC Trials at MCFF  1.0 Jun 2003
 VI Guidance on Appreciable Effect  1.0 Jun 2003
 VII Dealing with a COPA Application for Consent from a Marine Cage Fish Farm  1.0 Sep 1998
 VIII Hydrographic Data Requirements for Applications to Discharge from Marine Cage Fish Farms  (463k)  2.7 Oct 2008
 IX Consent Application Form and Guidance on its Completion  (41k)  1.1 May 2005
 X Guidance Note on the Ensiling of Fish and Fish Offal  (42k)  2.1 Sep 2007
 XI Guidance on the use of emamectin benzoate at Marine Cage Fish Farms  1.0 Mar 2004

Framework for the application of SEPA’s interim position on the use of emamectin benzoate in fin fish farms

 1.0 October 2017
 XII Guidance note on the completion of the Monitoring Protocol Specification (MPS) Data Templates  (72k)  2.0 May 2007
  Supplement 1 - Amendments to MPS Data Templates  (33k)  2.0 Jun 2007
 XIII Guidance note on the licensing of discharges of Panacur (fenbendazole) at marine cage fish farms  (79k)  1.0 May 2007
XIV Guidance note on the licensing of discharges of AMX (deltamethrin) at marine cage fish farms  (86k)  1.0 Jun 2008
  Supplement 1 - Guidance on dealing with technical variations to add AMX (deltamethrin) to licences for marine cage fish farms  (76k)  1.0 Jun 2008
 XV Marine Cage Fish Farm CAR Licence Review  (302k)  1.0 Apr 2011
  SEPA Policies    
 17 Cage Fish Farms: Sea Lice Treatment Chemicals Risk Assessment of Azamethiphos  (77k)  2.0 Nov 1998
 40 Policy On Regulation And Expansion Of Caged Fish Farming Of Salmon In Scotland  (105k)  1.0 Sep 2000
  Monitoring Protocol Specification (350k)  1.0 July 2017
  Permitted Substances Working Plan  (66k)  2.0 Apr 2011

Freshwater Cage Fish Farm Template  (207k)

 2.0 Apr 2011
  Freshwater Tank Fish Farm Template  (50k)  1.0 Sep 2003
  Marine Cage Fish Farm Template  (432k)  7.0 Sep 2016
  Benthic – Standard  (62k)  2.0 Sep 2008
  Benthic – Extended  (68k)  2.0 Sep 2008
  Benthic - Site Specific  (66k)  2.0 Sep 2008
  Visual Monitoring Specification  (35k)  2.0 Sep 2008
  Baseline Visual – Standard  (187k)  1.0 Sep 2008
  Baseline Visual – Site Specific  (55k)   1.0 Sep 2008
  Calicide Table 1 and Record Sheet (67k)  1.0 Jul 2003

Baseline Benthic – Standard  (53k)

 2.0 Sep 2008
  Baseline Benthic - Extended  (58k)  2.0 Sep 2008
  Standard Baseline Survey Data Returns Template  (390k)  3.0 Oct 2009
  Extended Baseline Survey Data Returns Template  (478k)  3.0 Oct 2009
  Standard Monitoring Survey Data Returns Template  (460k)  3.0 Oct 2009
  Extended Monitoring Survey Data Returns Template  (572k)  4.0 Oct 2009
  Site Specific Monitoring Survey Data Returns Template (513k)  3.0 Oct 2009
  Visual Monitoring Survey Data Returns Template  (91k)  3.0 Oct 2009