Guidance on aquaculture and Natura 2000 : sustainable aquaculture activities in the context of the Natura 2000 Network.
Date: 2019-06-12
Institutions: Directorate-General for Environment
Subjects: aquaculture, conservation of fish stocks, conservation of resources, directive (EU), sustainable fisheries, user guide

Guidance on Aquaculture 
and Natura 2000

Sustainable aquaculture activities in the 
context of the Natura 2000 Network

Environment

Neither the European Commission nor any person acting on behalf of the Commission is responsible for the 
use that might be made of the following information.

Luxembourg: Publications Office of the European Union, 2018

© European Union, 2018 
Reuse is authorised provided the source is acknowledged. 
The reuse policy of European Commission documents is regulated by Decision 2011/833/EU (OJ L 330, 
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ISBN 978-92-79-99668-9 

doi:10.2779/34131 

KH-04-19-087-EN-N

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Guidance document on aquaculture activities in the context of the Natura 2000 Network 

3

TABLE OF CONTENTS 

TABLE OF CONTENTS ........................................................................... 3 

INTRODUCTION ..................................................................................... 5 

1.  AQUACULTURE IN THE EU............................................................ 7 
1.1  The aquaculture production in the EU................................................................... 7 
1.2    Aquaculture methods and systems practiced in the EU ....................................... 9 
1.2.1 Aquaculture in the sea and coastal areas ............................................................. 9 
1.2.2 Freshwater aquaculture....................................................................................... 13 
1.2.3 Integrated aquaculture......................................................................................... 14 

2. CONSERVATION OF BIODIVERSITY AND THE NATURA 2000 

NETWORK .....................................................................................15 
2.1    The EU Biodiversity Policy .................................................................................. 15 
2.2    The Habitats and Birds Directives ....................................................................... 15 
2.3  The Natura 2000 Network ................................................................................... 17 
2.4   Aquaculture activities in Natura 2000 sites ......................................................... 18 
2.5    Guidance on Natura 2000 ................................................................................... 19 
2.6    Other important relevant provisions .................................................................... 19 

3.   THE POTENTIAL IMPACTS OF AQUACULTURE ACTIVITIES ON 

NATURE AND WILDLIFE................................................................21 
3.1    The need for a case by case approach – relevant factors .................................. 21 
3.1.1 The site ................................................................................................................ 21 
3.1.2 The cultured species ........................................................................................... 22 
3.1.3 The culture method.............................................................................................. 22 
3.1.4 Sensitivity, resistance and resilience................................................................... 23 
3.1.5 Assimilative and carrying capacity ...................................................................... 23 
3.2   Main potential pressures and impacts from different aquaculture systems - 

possible mitigation and good management practices ......................................... 24 
3.2.1 Marine cage culture ............................................................................................. 25 
3.2.2 Shellfish rafts and longlines................................................................................. 27 
3.2.3 Intertidal shellfish culture ..................................................................................... 28 
3.2.4 Bottom shellfish culture ....................................................................................... 29 
3.2.5 Land based tank systems for marine species ..................................................... 30 
3.2.6 Land based ponds for marine species farming ................................................... 31 
3.2.7 Lagoon culture..................................................................................................... 32 
3.2.8 Freshwater fish aquaculture systems.................................................................. 33 
3.2.9 Summary overview of all potential pressures and impacts .................................33 
3.3    Examples of sustainable aquaculture in natural areas that contribute to 

biodiversit............................................................................................................. 34 

 
 
 
 
 
 
 
 
 
 
 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

4.   THE IMPORTANCE OF STRATEGIC PLANNING ............................37 
4.1  Spatial planning and strategic environmental assessment ................................. 37 
4.2 
Integrated Coastal Zone Management................................................................ 39 
4.3   Determining suitable locations for aquaculture developments ........................... 40 
4.4   Key information for spatial planning - identifying conflicts at a strategic level .... 40 
4.5   Examples of aquaculture planning and aquaculture activities in Natura 2000 

areas.................................................................................................................... 42 

5.    STEP-BY-STEP PROCEDURE FOR AQUACULTURE PLANS AND 

PROJECTS AFFECTING A NATURA 2000 SITE.............................45 
5.1  Article 6 of the Habitats Directive ........................................................................ 45 
5.2  When is the Article 6 procedure applicable?....................................................... 46 
5.3  A step-by-step procedure .................................................................................... 47 

STAGE 1. SCREENING ............................................................................................... 47 
5.4  When is an Appropriate Assessment (AA) needed?........................................... 47 
5.4.1 Gathering information about the plan or project and the Natura 2000 site(s)..... 47 
5.4.2 Determining if the plan or project "is likely to have a significant effect" .............. 50 
5.4.3 Assessing the risk of potential cumulative effects with other plans and projects 51 
5.4.4  Recording the screening decision ...................................................................... 51 

STAGE 2. CARRYING OUT THE APPROPRIATE ASSESSMENT............................ 54 
5.5  The purpose of the Appropriate Assessment...................................................... 54 
5.5.1 Determine the scope and focus of the assessment: setting the baseline and 

gathering further information ............................................................................... 54 
5.5.2 Assessing the impacts on the Natura 2000 site .................................................. 56 
5.5.3 Considering the cumulative effects ..................................................................... 63 
5.5.4 Identifying suitable mitigation measures ............................................................. 63 
5.5.5 Assessing whether there are no adverse effects on site integrity....................... 64 
5.5.6 Recording the results of the Appropriate Assessment........................................ 65 

STAGE 3. THE DEROGATION PROCEDURE UNDER ARTICLE 6.4 ....................... 70 
5.6.1 The absence of alternative solutions................................................................... 70 
5.6.2 Imperative reasons of overriding public interest (IROPI) .................................... 70 
5.6.3 The adoption of all necessary compensatory measures..................................... 68 

REFERENCES........................................................................................69 

ANNEXES..............................................................................................77 
Annex 1: EU Policy and legal framework, and initiatives to promote sustainable 
aquaculture .................................................................................................................   77 
1.   The EU Policy Framework for the aquaculture industry...................................... 77 
2.   Aquaculture trends and environmental factors influencing production in the EU 77 
3.   Relevant EU environmental legislation ............................................................... 78 
4.   Examples of Initiatives to promote sustainable aquaculture in the EU ............... 82 
Annex 2: information on Natura 2000 sites and habitats and species of European 
Interest in EU countries  .............................................................................................   85 

 
 
 
 
 
 
 
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INTRODUCTION 

Background  

Aquaculture  represents  a  growing  contributor  to  the  production  of  aquatic  food  worldwide. 
Most  fisheries  in  the  world  are  currently  near  or  above  sustainable  exploitation  limits.  In 
parallel,  global  consumption  of  fish  as  food  has  doubled  in  the  period  1973-2003  and  is 
expected  to  continue  to  rise  (EC  20071).  According  to  FAO,  globally,  aquaculture  accounted 
for  about  46%  of  the  world’s  fish  food  production  for  human  consumption  in  2008  and  it  is 
estimated  that  aquaculture  will  reach  more  than  50%  by  20122.  Currently,  about  70%  of  the 
fish consumed in the EU comes from outside the Union. 

In  the  EU,  aquaculture  production  is  an  important  economic  activity  in  many  coastal  and 
continental  regions  but  has  remained  stable  in  recent  years.  The  current  reform  of  the 
Common Fisheries Policy aims, inter alia, to develop the full potential of EU aquaculture in line 
with the Europe 2020 objectives: sustainability, food security, growth and employment.  

The challenges for the EU aquaculture sector are numerous; the limited access to space/water 
and  licensing  have  been  highlighted  in  particular.  A  better  implementation  of  relevant  EU 
legislation  by  Member  States  should  ensure  a  level-playing  field  among  economic  operators 
on  decisions  affecting  the  development  of  aquaculture.  In  view  of  this,  the  Commission  has 
committed itself to developing guidance documents to facilitate knowledge and implementation 
of  its  main  environmental  policy  instruments,  notably  a  guidance  document  on  aquaculture 
activities and Natura 2000. 

Natura 2000 is a network of sites designed to safeguard Europe’s rarest and most endangered 
species and habitat types in accordance with the EU Habitats and Birds Directives, which are 
the  cornerstones  of  the  Europe’s  biodiversity  policy.  There  is  no  automatic  exclusion  of  any 
economic activities in and around Natura 2000. Instead, human activities need to comply with 
the provisions outlined in Article 6 of the Habitats Directive to ensure that these activities are in 
line with the conservation objectives of Natura 2000 sites.  

In order to clarify applicable provisions the Commission has produced a number of guidance 
documents  on the management of  Natura 2000 sites (application of  Article 6 of the Habitats 
Directive) . Some Member States are also producing guidance for their aquaculture industries 
on  how  to  deal  with  this  issue.  However,  there  is  general  acceptance  about  the  need  to 
develop more specific EU guidance on the activities of aquaculture in relation to Natura 2000.  

Purpose of this Guidance document  

The  aim  of  this  document  is  to  offer  guidance  which  would  facilitate  the  knowledge  and 
implementation of EU legislation underpinning Natura 2000 in relation to aquaculture activities. 
The guidelines mainly focus on the implementation of the provisions of Art. 6(3) and 6(4) of the 
Habitats  Directive  (appropriate  assessment  of  plans  and  projects)  and  are  designed  to 
contribute to a better understanding of the conservation objectives of the sites, promoting best 
practices which illustrate how nature protection provisions can be compatible with sustainable 
aquaculture development.   

1  EC,  2007.  Opportunities  for  the  development  of  Community  aquaculture.  Consultation  Document. 
available at: http://ec.europa.eu/fisheries/partners/consultations/aquaculture/consultation100507_en.pdf 
2 FAO. The state of world aquaculture 2010. 

 
 
 
 
 
 
 
 
 
 
 
 
 
                                                 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

The  document  has  been  prepared  in  close  collaboration  with  representatives  of  the 
aquaculture sector, experts, public authorities and NGOs via a dedicated EC Working Group. 
It  is  aimed  at  providing  guidance  mainly  to  aquaculture  operators  and  public  authorities,  as 
well as to other stakeholders (e.g. site managers, NGOs, public) concerned.  

Limitations of the document 

This guidance document is intended to be bound by, and faithful to, the text of the Birds and 
Habitats Directives and to the wider principles underpinning EU policy on the environment and 
on  aquaculture.  Other  potentially  relevant  EU  environmental  legislation  (e.g.  the  Water 
Framework Directive, the Marine Strategy Framework Directive, the EIA and SEA Directives) 
are not discussed in detail.  

The document is not legislative in character, it does not make new rules but rather provides 
further  guidance  on  the  application  of  those  that  already  exist.  As  such,  it  reflects  only  the 
views of the Commission services and is not of a legally binding nature. It rests with the EU 
Court of Justice to provide definitive interpretation of a Directive. Wherever relevant, existing 
case law has been included when a clear position has already been taken by the Court. 

The  document  also  does  not  replace  the  Commission’s  existing  general  interpretative  and 
methodological  guidance  documents  on the  provisions  of  Article  6  of  the  Habitats  Directive3. 
Instead, it seeks to clarify specific aspects of these provisions and place them in the context of 
aquaculture  activity  in  particular.  The  present  guide  must  therefore  always  be  read  in 
conjunction with the existing general guidance and the two Directives4. 

Finally, the guidance recognises that the two nature Directives are enshrined by the principle 
of  subsidiarity  and  that  it  is  for  Member  States  to  determine  the  procedural  requirements 
deriving from the Directives. The good practice procedures described in this document are not 
prescriptive in their intent; rather they aim to offer useful advice, ideas and suggestions based 
on  extensive  discussions  with  aquaculture  industry  representatives,  NGOs  and  other 
stakeholders.  

3  “Managing  Natura  2000  sites.  The  provisions  of  Article  6  of  the  ‘Habitats’  Directive  92/43/EEC”.    
“Assessments of plans and projects significantly affecting Natura 2000 sites. Methodological guidance 
on the provisions of Article 6(3) and (4) of the Habitats Directive 92/43/EEC”.  “Guidance document on 
Article 6(4) of the ‘Habitats Directive’ 92/43/EEC”. 
http://ec.europa.eu/environment/nature/natura2000/management/guidance_en.htm 
4 The case-studies and examples mentioned in this document are included because of their illustrative 
value in terms of methodologies and approaches used, the Commission does not necessarily endorse 
all of their outcomes. 

 
 
 
 
 
 
 
 
                                                 
 
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7

1.   AQUACULTURE IN THE EU 

•  Aquaculture  should  be  understood  as  the  rearing  or  cultivation  of  aquatic  organisms  using 
techniques  designed  to  increase  the  production  of  the  organisms  in  question  beyond  the  natural 
capacity  of  the  environment.  The  organisms  remain  the  property  of  a  natural  or  legal  person 
throughout the rearing or cultivation stage, up to and including harvesting. 

•  Aquaculture can be characterised in a number of different ways, including the organism farmed, the 
culture  environment,  the  production  intensity  and  the  type  of  production  system  used.  An 
understanding  of  these  is  key  to  determining  the  interactions  of  aquaculture  operations  on  the 
environment. 

•  Aquaculture  in  the  EU  is  made  up  of  three  major  sub-sectors,  which  have  different  histories  and 
characteristics. These are shellfish farming (57% of total production in 2009), freshwater fish farming 
(18%)  and  sea  fish  farming  (25%)5.    Shellfish  aquaculture  produces  around  the  same  volume  as 
finfish aquaculture but only represents around 34 percent of the total value (Framian, 20096). 

1.1 

The aquaculture production in the EU 

Aquaculture  production  in  the  marine  environment  is  dominant  in  the  EU.  Freshwater 
aquaculture is however an important segment of European aquaculture, especially in Central 
and Eastern EU countries. 

Figure 1. Aquaculture production per product type (2009)  

Source: FAO  

5 http://ec.europa.eu/fisheries/cfp/aquaculture/facts/index_en.htm 
6 Source: Eurostat 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

The  EU  aquaculture  sector  is  essentially  dominated  by  small  and  medium-sized  enterprises. 
The  main  aquaculture  producers  in  the  EU  are  France,  Spain,  Italy,  UK  and  Greece. 
Enlargement  of  the  European  Union  has  added  importance  to  cyprinid  culture  in  the 
freshwaters of Central and Eastern Europe. Sustainable aquaculture provides opportunities to 
reduce the dependence on wild stocks, to meet increased consumer demand, and maintain or 
create new jobs and businesses.  

Figure 2: Aquaculture production by Member States (2009) 

The main products from Aquaculture in the EU are presented in the figure below. 

Figure 3: The top 10 species produced in aquaculture in the European Union (2009)  

Volume  in  tonnes  live  weight  and  percentage  of 
total 

Value  in  thousands  of  EUR  and  percentage  of 
total 

Source: Facts and figures on the CFP. 2012. Available at: 
http://ec.europa.eu/fisheries/documentation/publications/pcp_en.pdf 

 
 
 
     
 
 
 
 
 
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1.2  Aquaculture methods and systems practiced in the EU  

Aquaculture  can  be  characterised  in  a  number  of  different  ways,  including  the  organism 
farmed,  the  culture  environment,  the  production  intensity  and  the  type  of  production  system 
used. An understanding of these aspects is key to determining the interactions of aquaculture 
operations  with  the  environment.  The  main  aquaculture  systems  practiced  in  Europe,  in  sea 
water and fresh water, are summarily introduced in this section. 

As regards the production intensity, it is usually understood that in extensive aquaculture there 
is no external supply of feed and this type of culture depends entirely on natural processes for 
production and supply of feed. In semi-intensive aquaculture, some supplementary feed may 
be used in addition to natural capacity to increase the production of fish. In intensive culture 
systems there is a greater dependency on the use of external feeds. 

1.2.1  Aquaculture in the sea and coastal areas 

Aquaculture  activities  that  depend  on  sea  water  include  different  systems  of  shellfish  and 
finfish  farming,  which  are  briefly  introduced  below.  Hatchery  productions  for  these  types  of 
systems are also briefly mentioned. 

• 

 Shellfish farming 

Shellfish  farming  is  primarily  based  on  specimens  born  in  the  wild  and  on  nutriments 
provided by the environment. The majority of European shellfish are mussels farmed in Spain, 
Italy,  France  and  the  Netherlands.  Oyster  farming  is  also  an  important  activity  in  the  EU, 
especially in France. Other shellfish species farmed in quantity in the EU include clams, Italy 
being the main producer. 

Three main types of farming are practiced in the EU: shellfish rafts and longlines, intertidal and 
bottom shellfish culture (Huntington et al. 2006). 

-  Shellfish  rafts  and  longlines.  Mussel  and  other  shellfish  aquaculture  in  deeper  waters, 
through  the  use  of  suspended  ropes  and  longlines  from  floating  rafts,  has  developed  to 
take  advantage  of  spat  fall  locations  as  well  as  areas  of  good  water  quality  and  food 
availability.  This  form  of  aquaculture  has  become  a  particular  feature  of  the  Galician 
coastline  of  Spain,  as  well  as  south,  west  and  north  west  of  Ireland  and  some  Scottish 
lochs. 

- 

Inter-tidal shellfish culture is practiced extensively in the Western part of Europe and is one 
of the older, more traditional forms of aquaculture in the EU. It takes place within the inter-
tidal  area,  thus  benefiting  from  relatively  accessible  land-based  support  as  well  as  the 
dynamic physical environment of the land/water interface. 

-  Bottom shellfish culture is a form of shellfish culture where juvenile animals are placed or 
‘re-layed’ on a suitable substrate for on-growing. The substrate selected will depend upon 
the  shellfish  species  being  used  –  mussels  and  oysters  prefer  a  hard  or  firm  substrate 
whilst infaunal species such as clams prefer a softer substrate into which they can burrow. 
This form of aquaculture is often practised in shallow coastal or estuarine areas. 

As  regards  the  cultured species,  mussels  are  the main  species  produced in  the  EU-27,  with 
two  species:  the  blue  mussel  Mytilus  edulis  and  the  Mediterranean  mussel  Mytilus 
galloprovencialis.  Spain  is  by  far  the  greatest  producer  of  mussels  by  aquaculture,  greater 
than the combined total of other important mussel producing countries  such as Netherlands, 
France, Italy, Ireland and UK.  

 
 
 
 
 
 
 
 
 
 
 
 
 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

European  aquaculture  of  mussels  relies  on  collection  of  natural  seed  and  spat.  There  are 
three main methods of culturing mussels up to market size: bottom cultivation, bouchot culture 
and the suspended rope method. The large Spanish mussel farming industry is rope-grown in 
coastal  areas,  whilst  the  French  and  Netherlands  production  tends  to  be  on  the  bottom  or 
using bouchot poles. Italian mussel production tends to use longlines in lagoons.  

Some  countries  produce  shellfish  in  offshore  farms.  France,  for  example  has  commercial 
offshore mussel farming in 3 areas (the Mediterranean Sea, the Atlantic Coast and the North 
Sea), and Belgium has 4 mussel areas in the North Sea. A recent report of the ICES Working 
Group on Marine Shellfish Culture provides, among others, an overview of this type of shellfish 
culture in its member countries (ICES, 20117). 

In  relation  to  oysters,  two  species  are  cultured  in  Europe,  but  the  vast  majority  of  oysters 
farmed in the EU (over 95%) are the Pacific cupped oyster (Crassostrea gigas) rather than the 
native  European  flat  oyster  (Ostrea  edulis)  (Huntintong  et  al.  2010).  The  former  is  now  the 
most  widely  reared  oyster  worldwide,  and  Europe  is  the  world’s  fourth  producer  (118  132 
tonnes in  2009,  Eurostat  20118).  France  is Europe’s top  oyster  producer  (104  640 tonnes  in 
2009; Eurostat 2011).  

Four  main  methods  of  oyster  rearing  are  used  depending  on  environmental  characteristics 
(tidal  range,  water  depth,  etc.)  and  local  traditions  (EC  DG  MARE9):  Off-bottom  culture  (in 
mesh  bags  attached  to  trestles  on  the  intertidal  ground),  bottom  culture  (placed  directly  on 
inter  or  subtidal  ground),  deep-water  culture  (in  parks  at  depths  of  up  to  10  metres),  and 
suspended  culture  (on  ropes,  like  mussels,  making  it  possible  to  rear  them  offshore).  Since 
they are constantly submerged, they fatten more quickly. This method is suitable for rearing in 
waters without tides, or offshore. 

Other shellfish species cultured in Europe include clams, scallops and abalones. The two main 
species  of  clams  cultured  in  Europe  are  Ruditapes  decussatus  (Linnaeus,  1758;  also  called 
grooved  carpet shell) and  Ruditapes  philippinarum  (Adams  &  Reeve,  1850;  called  Japanese 
carpet shell or Manila clam). 

The  farming  of  clams  requires  seeds  which  are  obtained  through  natural  spawning  on 
production  sites  or  in  hatcheries.  The  spat  are  reared  with  different  methods  until  the  young 
clams  can  be  seeded  in  intertidal  zones  or  in  lagoons  to  be  harvested  later.  Growing 
techniques of clams are simple, consisting of regular maintenance of the substrate, avoiding 
algae, starfish and other predators, oxygenating the substrate, and maintaining an appropriate 
clam density and seeding juvenile clams.  

Different  techniques  can  be  used  for  harvesting,  by  hand  or  from  boats,  using  various 
collection  tools.  Mechanical  harvesting  can  be  carried  out  by  suction  or  elevator  dredges;  a 
tractor  equipped  with  a  lateral  conveyor  belt  can  dig  and  grade  clams  from  sandy  bottom 
areas (FAO, 201110). 

7 ICES. 2011. Report of the Working Group on Marine Shellfish Culture (WGMASC), 5–8 April 2011, La 
Trinité-sur-Mer, France. ICES CM 2011/SSGHIE:08. 92 pp. 
8 Eurostat, 2011. http://epp.eurostat.ec.europa.eu/portal/page/portal/fisheries/data/database# 
9 http://ec.europa.eu/fisheries/marine_species/farmed_fish_and_shellfish/oysters/index_en.htm 
10  FAO  2011.  Cultured  Aquatic  Species  Information  Programme.  Ruditapes  philippinarum.  Cultured 
Aquatic  Species  Information  Programme.  Text  by  Goulletquer,  P.  In:  FAO  Fisheries  and  Aquaculture 
Department 
2011]. 
2005. 
http://www.fao.org/fishery/culturedspecies/Ruditapes_philippinarum/en 

[online].  Rome.  Updated 

January 

[Cited 

June 

15 

1 

 
 
 
 
 
 
 
 
 
 
 
                                                 
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11

•  Shellfish hatcheries and mussel seed fisheries:  

Methods for culturing bivalves in a hatchery are well established for oysters and clams, while 
there  are  no  commercial  blue  mussel  hatcheries  or  nurseries  in  Europe,  although  controlled 
reproduction and subsequent spat and seed production is known to be technically feasible. A 
few hatcheries exist outside Europe (Blue Seed project11). 

A  number  of  successful  techniques  have  also  been  developed  for  scallop  hatcheries,  which 
provide  advantages  over  traditional  spat  collection  for  supplying  seed  to  aquaculture 
operations, most notably in selective breeding, as well as providing a regular supply of spat at 
a low price. 

Techniques for seed supply for mussel culture include collecting seed by natural settlement on 
ropes or other substrates, dredging wild seed beds and scraping mussel seed from rocks.  

•  Marine finfish farming 

Culture of finfish species in the sea can be divided according to the location of the fish farm, 
which can be placed on the coastal area, or offshore. 

Offshore aquaculture can be defined as taking place in the open sea with significant exposure 
to  wind  and  wave  action,  and  where  there  is  a  requirement  for  equipment  and  servicing 
vessels  to  survive  and  operate  in  severe  sea  conditions  from  time  to  time.  The  issue  of 
distance  from  the  coast  or  from  a  safe  harbour  or  shore  base  is  often,  but  not  always,  a 
factor.12 However, there is no common definition. For example Holmer (201013) provides some 
indication  of  the  parameters  that  may  be  useful  to  distinguish  three  types  of  location  of 
aquaculture (see Table 1).  

Table  1.  Definitions  of  coastal,  off-coast  and  offshore  farming  based  on  some  physical  and 
hydrodynamical settings (adapted from Holmer, 2010). 

Physical setting 

Exposure 

Coastal Farming 
< 500 m from shore 
< 10 m water depth 
Within sight of shore 
users 

Waves < 1m 
Lcal winds 
Local currents 
Strong tidal currents 
Sheltered 

Off-coast farming 
500 m to 3 km from shore 
10 to 50 m water depth 
Usually within sight 

Waves < 3 to 4 m 
Localised winds 
Localised currents 
Weak tidal currents 
Somewhat sheltered  

Offshore farming 
>3 km from shore 
>50 m water depth 
On continental shelf 
Not visible from shore 

(cid:190) 

Waves up to 5 m 
Ocean winds 
Ocean swell 
No tidal currents 
Exposed  

In the coastal area aquaculture systems can take place in coastal lagoons or in land-based 
ponds and tanks. Lagoon culture is a traditional coastal aquaculture system originated from 
the Mediterranean, which uses the coastal lagoons to capture migrating fish fry and grow them 
on for human consumption. Extensive fish culture has been a traditional activity in some salt-
marsh  areas  in  Europe,  where  farms  may  obtain  a  natural  fry  recruitment  by  an  adequate 
management of water in-flow with the tides.  

11 BLUE SEED Final Report. 2008. Available at: 
http://www.blueseedproject.com/client/files/BLUE_SEED_Final_Report.pdf 
12 Evaluation of the promotion of Offshore Aquaculture Through a Technology Platform 
(www.offshoreaqua.net) 
13 Holmer, M. 2010. Environmental issues of fish farming in offshore waters: perspectives, concerns and 
research needs. Aquacult Environ Interact Vol. 1: 57–70. 

 
 
 
 
 
 
 
 
 
 
 
 
 
                                                 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Methods  have  evolved  over  the  past  50  years,  leading  to  the  gradual  intensification  of 
production  as  artificial  feeding  and  water  management  technology  have  improved.  Large 
brackish areas are enclosed to prevent the fish returning to the sea and complex permanent 
capture systems, fish barriers, are developed consisting of barriers in the channels connecting 
with  the  sea  to  catch  the  adults.  Although  some  extensive  systems  depend  upon  natural  fry 
within the system, most now rely on the stocking of juveniles from external sources. 

Land-based  ponds  have  stemmed  from  an  intensification  of  lagoon  and  saltmarsh 
aquaculture where low-lying areas can benefit from the periodic inundation with spring tides. 
More  modern  pond  systems  have  been  built  above  the  spring  high  tide  mark  but  must  then 
rely upon pumped water. These systems tend to be shallow (e.g. 0.75 to 1.5 m pond depth), 
extensive and therefore fairly large in nature. Pond systems can be used for finfish (e.g., sea 
bass and sea bream, sole, sea-grown rainbow trout), but also for shrimp and shellfish.  

Earthen ponds are the main production system for seabass and seabream in Portugal and in 
Southern  Spain.  Different  farms  use  various  levels  of  intensification  and  pond  size,  but  in 
general  these  are  semi-intensive  systems  covering  large  areas,  ponds  ranging  from  one  to 
several  hectares.  Although  seabass  and  seabream  are  traditionally  the  target  species 
produced,  in  such  ponds  commonly  there  is  a  natural  stocking  with  wild  larvae  of  other  fish 
species, including the Senegalese sole (SEACASE project14) and, on an experimental scale, 
the North Sea sole (project Zeeuwse Tong, Netherlands). 

On land, aquaculture can also take place in tanks supplied with sea water. Land-based tank 
systems are an intensive solution to culturing high value fish. Most systems are closed and the 
growing facilities are contained within a site that is separated from the external environment by 
physical  filters  and  drains.  Many  such  farms  use  recirculation  systems  and  may  even  use 
artificial  seawater,  thus  reducing  the  inflow  and  discharge  of  water  to  and  from  the  farm. 
Progress in recirculation technology now offers new prospects for land-based aquaculture. Its 
use  is  being  investigated  for  different  species.  The  possibility  of  controlling  the  water 
parameters,  particularly  its  temperature,  frees  the  activity  from  climate  constraints.  The 
farming of turbot, sea bass and sea bream using this technique is thus expanding to the north 
of Europe. 

Other aquaculture systems practiced in the sea hold fish captive in a large pocket-shaped net 
anchored  to  the  bottom  and  maintained  on  the  surface  by  a  rectangular  or  circular  floating 
framework.  These  sea  cages  are  widely  used  for  rearing  finfish,  such  as  salmon,  sea  bass 
and sea bream, and to a lesser extent trout, in coastal and open waters. The openness of the 
system makes it vulnerable to external influences (i.e. pollution events or physical impact) as 
well as exposing the adjacent environment to the stock, and the fish farm effluents. 

In  the  EU,  hatchery  production  of  marine  finfish  species  is  dominated  by  the  commercial 
production of seabass and seabream in Greece. Other producing countries for these species 
include  Spain,  Portugal,  Italy  and  France.  Commercial  hatcheries  in  Europe  also  produce 
other aquaculture species as turbot, sole, etc. 

14 http://www.seacase.org/casestudies6.html   http://www.seacase.org/casestudies2.html 

 
 
 
 
 
 
 
 
                                                 
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13

1.2.2  Freshwater aquaculture 

Different freshwater fish production systems can be distinguished in the EU mainly based on 
the intensity of the activity, on the system used to manage water resources and on the species 
used.  There  may  be  however  some  overlaps  and  transitions  amongst  freshwater  fish 
production systems (Sustainaqua, 200915). 

Depending  on  the  system  used  to  manage  water  resources  as  in  marine  water,  one  may 
distinguish between pond fish farming, flow-through systems, recirculation systems, and cage 
cultures in freshwater lakes and rivers. One may also find mixed systems where two types are 
combined, one intensive and the other extensive and the water from the intensive  system  is 
taken and returned to the extensive system. 

Production of freshwater fish in ponds is often considered as the oldest fish farming activity in 
Europe, dating back to medieval times. Typical fish ponds are earthen enclosures in which the 
fish  live  in  a  natural-like  environment,  feeding  on  the  natural  food  growing  in  the  pond  itself 
from  sunlight  and  nutrients  available  in  the  pond  water.  Fish  pond  production  remains 
‘extensive’ or ‘semi-intensive’ (with supplementary feeding) in most countries.  

In  traditional  flow-through  aquaculture  systems,  water  passes  through  the  culture  system 
only once and is then discharged back to the aquatic environment. The flow of water through 
the  culture  system  supplies  oxygen  to  the  fish  and  carries  dissolved  and  suspended  wastes 
out of the system. Water is taken from the river, circulated through the farm and treated before 
being released  downstream.  All  water  in  the  farm  is  renewed  at  least  once  a  day.  The  most 
widely-practiced form of flow-through aquaculture in Europe is trout farming, which is spread 
throughout  Europe.  Rainbow  trout  (Oncorhynchus  mykiss)  largely  dominates  European  trout 
production (approximately 95% of the total production). The main producers in the EU are Italy 
and France, followed by Denmark, Germany and Spain. Most of the EU member states have 
trout farms near to rivers, and use concrete basins or ponds. Some lake cages are also in use.  

Recirculation  Aquaculture  Systems  (RAS)  are  land-based  systems  in  which  water  is  re-
used  after  mechanical,  chemical  and  biological  treatment.  These  systems  present  several 
advantages, such as: water saving, a rigorous control of water quality, high biosecurity levels 
and  an  easier  control  of  waste  production  as  compared  to  other  production  systems.  They 
have however high capital and high operational costs including high energy consumption. RAS 
represents  still  a  small  fraction  of  Europe’s  aquaculture  production  and  is  most  significant  in 
the  Netherlands  and  Denmark.  The  main  freshwater  species  produced  in  RAS  are  eel,  trout 
and catfish but other species are already being produced using this type of technology. 

Cage cultures in freshwater lakes and rivers also provide limited but important possibilities 
for freshwater aquaculture in certain water bodies. 

Table 2. Some important species farmed in freshwater aquaculture in the EU 

Common name 

Trout 
Carp 

Sturgeon 

Eel 

Latin name 
Oncorhynchus mykiss 
Cyprinus carpio 

Acipenser Baerii,  
A. gueldenstaedtii, A. naccarii 
Anguilla Anguilla 

Main EU producer countries 

Italy, France, Denmark, Spain, Germany 
Czech  Republic,  Poland,  Hungary,  Germany, 
Slovakia 
France Italy, Poland, Germany 

Netherlands, Denmark, Italy 

15 SustainAqua – Integrated approach for a sustainable and healthy freshwater aquaculture” (2009). 
SustainAqua handbook – A handbook for sustainable aquaculture. 

 
 
 
 
 
 
 
 
 
 
                                                 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

1.2.3 

Integrated aquaculture 

In  scientific  literature,  this  term  is  used  to  refer  to  different  forms  of  aquaculture,  which  may 
include  polyculture,  multi-trophic  aquaculture  and  the  integration  of  aquaculture  with  other 
activities,  such  as  agriculture,  etc.  At  the  aquatic  farm  level,  the  term  integration  can  be 
understood under two main concepts: 
•  rearing various species in the same production unit 
•  rearing a single species downstream from another (ICES, 200516). 

Integrated multi-trophic aquaculture (IMTA) includes organisms from different trophic levels of 
an ecosystem (e.g. fish, shellfish, algae), so that the byproducts of one become the inputs of 
another (Szeremeta et al., 201017).  

Such systems can be used to recycle waste nutrients from higher trophic-level species into the 
production  of  lower  trophic-level  crops  of  commercial  value  (Troell  et  al.,  2009).  IMTA  may 
reduce the environmental impacts directly through the uptake of dissolved nutrients by primary 
producers (e.g. macroalgae) and of particulate nutrients by suspension feeders (e.g. mussels), 
and  through  removing  the  nutrients  from  the  location  (Holmer  2010).  Bivalve  molluscs  filter 
algae  and  organic  particles  as  food  from  the  surrounding  water.  For  instance,  filter-feeding 
mussels  act  as  natural  nutrient-strippers  by  removing  phytoplankton  from  the  water.  If  the 
phytoplankton has grown using  N  and P originating from  cages or tank discharges, then the 
shellfish production removes some of the added nutrients.  

Molluscs  can  therefore have  a  positive  effect on  water quality  in  coastal  areas  and  are  well-
suited  to  polyculture  (co-production  with  other  organisms).  Some  countries  have  already 
launched some integrated aquaculture pilot projects18. 

16 ICES. 2005. Report of the Working Group on Environmental Interactions of Mariculture (WGEIM), 11–
15 April 2005, Ottawa, Canada. CM 2005/F:04. 112 pp. Available at: 
 http://www.ices.dk/products/CMdocs/2005/F/WGEIM05.pdf 
17  Szeremeta,  A.,  Winkler,  L.,  Blake,  F.,  Lembo,  P  (eds).  2010.  Organic  Aquaculture.  EU  Regulations 
(EC)  834/2007,  (EC)  889/2008,  (EC)  710/2009  -  Background,  Assessment,  Interpretation.  IFOAM  EU 
Group / CIHEAM - IAMB Bari. http://www.ifoam-eu.org/positions/publications/aquaculture/ 
18  For  example:  Spain,  where  the  National  Advisory  Board  for  Mariculture  (JACUMAR  in  Spanish) 
launched  a  project  called:  “Integrated  Aquaculture:  Pilot  experience  for  multi-trophic  aquaculture 
development”.  The  project  consists  of  developing  inland  and  offshore  pilot  experiences  of  integrated 
culture  systems,  in  order  to  indicate  whether  integrated  systems  improve  the  competitiveness  of  the 
undertakings,  bringing  them  economic  and  environmental  benefits  (18).  Successful  experiences  with 
clam 
(JACUMAR  2011). 
http://www.magrama.gob.es/app/jacumar/planes_nacionales/Ficha_planes.aspx?Id=es&IdPlan=101;   
 http://www.acuiculturaintegrada.com/proyecto/ 

culture  downstream  a 

farm  have  been 

carried  out 

fish 

 
 
 
 
 
 
                                                 
  
 
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15

2. CONSERVATION OF BIODIVERSITY AND THE 

NATURA 2000 NETWORK 

•  The Natura 2000 Network aims to protect habitats and species of European interest that are rare or 
threatened.  However  it  is  not  a  system  of  strict  nature  reserves  where  all  human  activities  are 
excluded. Its aim is to ensure that, within these Natura 2000 sites, human activities are undertaken 
in a way that still allows the site’s conservation objectives to be reached.. 

•  Within  Natura  2000  sites,  Member  States  must:  1)  take  appropriate  conservation  measures  which 
correspond to the ecological requirements of the protected habitat types and species present on the 
sites; and 2) avoid damaging activities that could significantly disturb these species or deteriorate the 
habitats of the protected species or habitat types. 

•  There are many interesting examples of win-win coexistence between aquaculture and Natura 2000 
sites.  In  many  of  those  sites  aquaculture  has  been  practiced  traditionally  and  is  considered 
compatible or has adapted its operation to the conservation needs of the sites. 

•  In addition to protecting core sites through the Natura 2000 network the two directives also require 
that  Member  States  establish  a  general  system  of  protection  for  all  naturally  occurring  wild  bird 
species in the EU and for species listed in Annex IV of the Habitats Directive. These provisions apply 
both inside and outside protected sites. 

2.1  The EU Biodiversity Policy   

The EU Biodiversity Strategy to 202019, published in May 2011, aims at reversing biodiversity 
loss and speeding up the EU's transition towards a resource efficient and green economy. It 
includes six mutually supportive and inter-dependent targets. The specific actions are set out 
in  the  Annex  to  the  Communication.  The  full  implementation  of  the  Habitats  and  Birds 
Directives  is  the  focus  of  Target  1.  In  relation  to  sustainable  use  of  fisheries  resources  the 
Strategy states, under its action 14b), that “the Commission and Member States will support 
the  implementation  of  the  Marine  Strategy  Framework  Directive,  including  through  providing 
financial incentives through the future financial instruments for fisheries and maritime policy for 
marine protected areas (including Natura 2000 areas and those established by international or 
regional agreements)”. 

2.2  The Habitats and Birds Directives  

The  Habitats  Directive  92/43/EEC,  together with  the  Birds  Directive  2009/147/EC20,  form  the 
cornerstones of the EU's nature conservation policy  They have two main purposes:  

• 

• 

to  protect  rare  and  endangered  species  across  their  entire  natural  range  within  the  EU 
through a series of species protection provisions; 

to conserve the core areas of a number of rare and endangered species and habitat types 
through the designation and management of sites under the Natura 2000 Network. 

19  COM(2011)  244  final..  Our  life  insurance,  our  natural  capital:  an  EU  biodiversity  strategy  to  2020. 
SEC (2011) 540 final. SEC (2011) 541 final. 
20 http://ec.europa.eu/environment/nature/legislation/index_en.htm 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

What does "favourable conservation status" mean in practice?  

The ultimate objective of the Habitats Directive is to ensure that the species and habitat types 
covered reach what is called a ‘favourable conservation status’ and that their long-term survival 
is deemed secure across their entire natural range within Europe.  

In the case of the species covered by the Directive (ref Article 1(i)) this means that: 
- 

populations  are  maintaining  themselves  over  the  long  term  and  are  no  longer  showing 
signs of continuing decline;  
their natural range is not being reduced; 
there  is,  and  will  probably  continue  to  be,  a  sufficiently  large  habitat  to  maintain  its 
populations on a long-term basis. 

- 
- 

In the case of a habitat type, a favourable conservation status (ref Article 1(e)) is achieved 
when: 
- 
- 

its natural range and the areas it covers within that range are stable or increasing; and  
the specific structure and function which are necessary for its long-term maintenance are 
present and are likely to continue to exist in the foreseeable future; 
the conservation status of typical species that live in these habitat types is favourable as well. 

- 

It  should  be  noted  that  the  two  Directives  do  not cover  every  species  of  plant  and  animal  in 
Europe (i.e., not all of the EU’s biodiversity). Instead, they focus on a sub-set of around 1500 
(out of ca 100 000 or more species present in Europe) - which are so rare or threatened that 
they  are  in  need  of  protection  to  prevent  their  extinction.  These  are  often  referred  to  as 
species of European interest or importance. These directives also protect around 230 "habitat 
types" (including marine and coastal habitats, freshwater habitats, wetlands, etc.), which are of 
European importance. 

In  2007  the  Member  States  reported  for  the  first  time  on  the  conservation  status  of  habitats 
and species covered by the Habitats Directive. On the basis of this, the Commission produced 
a  consolidated  report  on  the  conservation  status  of  each  species  and  habitat  type  a 
biogeographical and EU level. These reports provide useful contextual information21. 

Figure  4.  Assessment  of  conservation  status  of  some  groups  of  habitats  that  are  relevant  in 
relation  to  aquaculture  development  (the  number  in  brackets  refers  to  the  number  of  assessments 
carried out for each group) (from EC 200922). 

█   Favorable 

█   Unknown 

█   Unfavorable – inadequate 

█    Unfavorable - bad 

21 All reports are available at: http://biodiversity.eionet.europa.eu/article17 and  
http://ec.europa.eu/environment/nature/knowledge /rep_habitats/index_en.htm 
22  COM(2009)358  final.  Report  from  the  Commission  to  the  Council  and  the  European  Parliament  - 
Composite Report on the Conservation Status of Habitat Types and Species as required under Article 
17 of the Habitats Directive. Available at: 
http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=COM:2009:0358:FIN:EN:PDF 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                 
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17

2.3 The Natura 2000 Network 

At  the  heart  of  the  two  Nature  Directives 
lies the creation of a Natura 2000 Network 
of  sites  which  have  been  designated  for 
species  and  habitat  types  of  European 
importance 
respective 
annexes.  By May 2012, some 26,000 sites 
were 
the  Natura  2000 
Network23.  Together,  they  cover  around 
18%  of  the  land  area  in  the  EU-27  with 
significant additional marine areas24. 

included 

listed 

the 

in 

in 

conservation 

Each  site  will  contribute  to  this  process  by 
setting 
and 
implementing conservation measures, as required, to meet these objectives. These in turn will 
be  based  on  the  status  and  specific  ecological  requirements  of  the  protected  species  and 
habitats present within that particular site (see chapter 5 for details). 

objectives 

Figure 5: Distribution of Natura 2000 sites across EU-27. 

The Natura 2000 Network is not a system of strict nature reserves where all human activities 
are excluded. Instead, it supports the principle of sustainable development. Its aim is to ensure 
that, within these Natura 2000 sites, human activities are undertaken in a way that ensures the 
conservation objectives which have been set for the site (in function of the species and habitat 
types of European interest present), can still be reached.  

23 European Commission, http://ec.europa.eu/environment/nature/natura2000/barometer/index_en.htm 
24 There is sometimes considerable overlap between SPAs and SCIs so the figures are not cumulative 

 
 
 
 
 
 
 
 
 
                                                 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Article  6  lays  down  the  measures  that  must  be  taken  within  each  Natura  2000  site.  In 
particular Member States must:  

•  take appropriate conservation measures which correspond to the ecological requirements 

of the protected habitat types and species present on the sites (Article 6.1). 

•  avoid  damaging  activities  that  could  significantly  disturb  these  species  or  deteriorate  the 

habitats of the protected species or habitat types (Article 6.2). 

To help decide which conservation measures should be undertaken on individual Natura 2000 
sites,  the Habitats  Directive  encourages the  development  of  management  plans.  These  may 
be specifically designed for the site in question or integrated into other development plans. 

Whereas  Article  6(1)  and  (2)  of  the  Habitats  Directive  concern  the  day-to-day  management 
and  conservation  of  Natura  2000  sites,  Articles  6(3)  and  6(4)  lay  down  the  procedure  to  be 
followed  when  planning  new  developments  that  might  affect  a  Natura  2000  site25.  This 
stepwise procedure is examined in detail in Chapter 5. Each Natura 2000 site is unique and 
must be examined on an individual case by case basis, especially when it comes to carrying 
out Appropriate Assessments under Article 6 of the Habitat Directive. 

In addition to designating core sites under the Natura 2000 Network, Article 10 of the Habitats 
Directive  also  requires  Member  States  to  improve  the  ecological  coherence  of  the  network 
across the broader countryside by maintaining and, where appropriate, developing features of 
the landscape which are of major importance for wild fauna and flora, such as wildlife corridors 
or stepping stones, which can be used during migration and dispersal. 

2.4. Aquaculture activities in Natura 2000 sites 

Aquaculture  activities  are  carried  out  in  many  Natura  2000  sites.  From  a  first  analysis26  of 
existing  aquaculture  activities  in  the  network,  as  reported  by  Member  States  and  with  the 
information compiled from the Natura 2000 database, it is now known that over 5% of the sites 
reported to host aquaculture activities at the time of their designation, which means over 1200 
SPAs and SCIs27. In fact, many of these sites have been designated because this activity has 
maintained  suitable  habitats  (eg.  ponds)  for  species  of  EU  interest.  A  significant  number  of 
these sites  have  their  entire  surface  covered by  aquaculture  activities  and  include natural  or 
human-made ponds, lakes or lagoons.  

There are interesting examples of win-win coexistence between aquaculture and Natura 2000 
sites (see section 3.6). In many of those sites aquaculture has been practiced traditionally and 
is considered compatible or has adapted its operation to the conservation needs of the sites. 
Some  interesting  examples  are  found  in  Southern  Europe,  as  regards  coastal  aquaculture, 
and in Central Europe concerning freshwater aquaculture.  There are many well-known Natura 
2000 areas in Europe where aquaculture activities are currently taking place sustainably, such 
as  the  Wadden  Sea  in  the  Netherlands,  Arcachon  in  France,  the  Sado  Estuary  in  Portugal, 
Doñana in Spain, shellfish culture in England and Wales and several Lochs in Scotland. 

25 This applies to SCIs, SACs and SPAs and concerns not just plans or projects inside a Natura 2000 
sites but also those that are outside but could have a significant effect on the conservation of species 
and habitats within the site.  For instance a dam constructed upstream on a river that could alter or stop 
the regular flooding of an important wetland for birds within an SPA further downstream. 
26  This  analysis  was  made  using  the  Natura  2000  dataset  from  the  DG  ENV  of  the  European 
Commission (May 2011). This dataset contains 26124 Natura 2000 sites (SCIs and SPAs). 
27  The  Natura  2000  database  provides  information  about  the  sites  of  the  network  and  the  activities 
carried out in them, including aquaculture.: http://www.eea.europa.eu/data-and-maps/data/natura-2000 

 
 
 
 
 
 
 
 
 
 
                                                 
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2.5  Guidance on Natura 2000 

The European Commission has published several guidance documents on the establishment 
and  management  of  the  Natura  2000  network  that  are  also  relevant  for  the  development  of 
aquaculture  activities.  They  include  the  interpretation  of  the  provisions  of  Article  6  of  the 
Habitats Directive on the management of Natura 2000 sites, methodological guidance for the 
Assessment of plans and projects significantly affecting Natura 2000 sites28, guidelines for the 
establishment  of  the  Natura  2000  network  in  the  marine  environment29,  as  well  as  series  of 
good practice30. 

Other  relevant  guidance  is  also  available  at  national  level  on  management  of  Natura  2000 
sites  and  on  conservation  management  of  habitats  and  species  protected  by  the  Nature 
Directives31. A compilation of relevant information sources that may be useful for the purpose 
of this guidance document is provided in Annex 2. 

2.6  Other important relevant provisions 

In addition to the Natura 2000 network ,the two directives also provide for a general system of 
protection,  both  inside  and  outside  Natura  2000  sites,  for  all  naturally  occurring  wild  bird 
species in the EU (Birds Directive, Article 5) and for animal and plant species listed in Annex 
IV of the Habitats Directive (Article 1232 and Article 13) – see Annex 1.  

Furthermore, environmental objectives under the Water Framework Directive 2000/60/EC and 
the Marine Strategy Framework Directive 2008/56/EC need to be considered when planning or 
managing  aquaculture  activities.  Relevant  provisions  also  apply  both  inside  and  outside 
Natura 2000 sites and, like those for the EIA and SEA directives, are summarised in Annex 1. 

28 See: http://ec.europa.eu/environment/nature/natura2000/management/guidance_en.htm  
29 http://ec.europa.eu/environment/nature/natura2000/marine/index_en.htm 
30 http://ec.europa.eu/environment/nature/natura2000/management/best_practice_en.htm 
31  The  Joint  Nature  Conservation  Committee  website  for  instance,  provides  information  on  marine 
habitats  and  species,  as  well  as  on  SACs  and  SPAs  for  the  UK.  Also  the  Scottish  Natural  Heritage 
website  includes  an  interactive  map  identifying  the  Scottish  Natura  2000  site,  with  advice  on  SAC 
management also present. Another example is the Guidance on Natura 2000 and aquaculture that has 
been published in France (Référentiel pour la gestion dans les sites Natura 2000 en mer - Les cultures 
marines), which aim to help actors managing aquaculture activities in the marine sites.  
32 See Guidance document on the strict protection of animal species of Community interest under the 
Habitats Directive http://ec.europa.eu/environment/nature/conservation/species/guidance/index_en.htm 

 
 
 
 
 
 
                                                 
 
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21

3. THE POTENTIAL IMPACTS OF AQUACULTURE 

ACTIVITIES ON NATURE AND WILDLIFE 

•  The  effects  of  different  aquaculture  systems  depend  on  a  number  of  factors,  including  the 
hydrographic  conditions  of  the  farm’s  location,  the  type  of  cultured  organisms  and  the  production 
method, management practices, etc.. These factors must all be taken into account when assessing 
possible risks. 

•  Different aquaculture systems may exert different impacts and cause diverse effects on the natural 
environment,  which  may  include  habitat  loss  or  deterioration,  species  disturbance,  and  the 
displacement  of  species  as  well  as  changes  in  local  communities.  However,  some  aquaculture 
systems may have positive effects for the biodiversity of the site.  

•  The  sensitivity  and  resilience  of  ecosystems,  and  the  assimilative  capacity  of  the  environment  are 

key to determining the magnitude and significance of the impact. 

•  Siting is often the most important factor to consider in order to prevent and reduce potential impacts 
from  aquaculture  activities,  together  with  the  implementation  of  good  management  practices  and 
adequate mitigation measures, which are currently well known for the most significant pressures in 
the different aquaculture systems. 

3.1  The need for a case by case approach – relevant factors 

All types of farming interact with the environment, and aquaculture is no exception. Potential 
effects  of  different  aquaculture  systems  are  widely  described  in  the  scientific  and  technical 
literature. Those effects are highly  specific to the site and depend on the environmental and 
rearing  conditions.  Any  possible  risks  must  be  assessed  taking  into  account  all  the  relevant 
features and their specific condition as well as the conservation objectives of the relevant site. 
It  should  be  also  stressed  that  possible  negative  effects  may  be  mitigated  with  appropriate 
management, location etc.  

There  are  many  factors  that  influence  the  ultimate  impact  of  aquaculture.  Among  these,  the 
location  of  the  farm,  the  type  of  cultured  organisms  (fish,  crustaceans,  molluscs,  other 
invertebrates  and  seaweeds)  and  the  methods  used  (eg.  quantity  and  type  of  food,  stock 
density,  chemical  use)  determine  the  environmental  impact  of  the  different  kinds  of 
aquaculture activities. Moreover, the sensitivity or vulnerability of the environment to possible 
pressures  from  aquaculture  activities  is  also  a  key  factor.  All  these  factors  determine  the 
assimilative capacity of the environment to aquaculture activities.  

3.1.1  The site  

The  location  and  siting  of  aquaculture  is  probably  the  single  most  important  factor  in 
determining  its  environmental  impact.  The  ecological  characteristics,  e.g.,  biodiversity, 
ecosystem structure, dynamics and interrelationships of living communities may be distinct in 
different sites. Also the conservation objectives are specific to each Natura 2000 site.  

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Furthermore, environmental variables will determine, to a certain extent, the type and degree 
of  impact  from  aquaculture  pressures.  Hydrographic  and  topographic  site  characteristics  are 
very  important,  in  particular  for  sea-based  and  land-based  farms  relying  on  natural  water 
movements  (currents,  tides)  for  adequate  water  exchange  and  waste  dispersal.  Lifespan, 
possibilities  for  expansion  and  intensification,  and  the  ecological  effect  of  a  farm  are  often 
determined  by  the  physical  characteristics  of  the  selected  site.  The  level  and  extent  of 
ecological change may, therefore, vary from site to site.  

3.1.2  The cultured species  

Aquaculture  organisms  differ  significantly 
their  biological  and  eco-physiological 
characteristics.  Reproduction,  feeding  habits,  food  and  nutritional  requirements,  behaviour, 
growth capacities, water quality requirements, stress tolerance and susceptibility to parasites 
and disease characterize the suitability of a species to be cultured.  

in 

The very specific characteristics of the cultured organisms also determine the type, magnitude 
and  range  of  ecological  implications.  Biological  interactions  between cultured  organisms  and 
wild communities are also to be considered and may be restricted to the immediate vicinity of 
the site or affect wider areas.  

3.1.3  The culture method  

The choice of the culture method will, to some extent, depend on the selection of the species 
and  the  site.  Aquaculture  farms  can  operate  under  extensive,  semi-intensive  and  intensive 
conditions. 

For  certain  open  systems,  production  intensity  is  a  reasonable  indicator  of  potential  impact, 
not  withstanding  the  environmental  features  and  local  assimilative  capacity  (see  below).  In 
terms  of  European  aquaculture,  the  most  obvious  example  is  cage  culture,  where  a  site’s 
biomass  will  be  roughly  indicative  of  the  overall  potential  environmental  pressure  exerted  by 
the farm.  

Nevertheless the local conditions of the site and the management techniques can contribute to 
reducing or  eliminating  the  possible  impacts  of  this  kind  of  aquaculture  system.  However  for 
closed  systems,  the  intensity  of  production  is  not  necessarily  an  indicator  of  its  potential 
impact  on  the  environment  -  for  instance,  a  highly  intensive  farm  using  recirculation  may  be 
environmentally benign due to its isolation from the external environment. 

In  extensive  aquaculture,  mainly  shellfish  culture,  there  is  no  external  supply  of  feed  or 
medicine  and  this  type  of  culture  depends  entirely  on  natural  processes  for  production  and 
supply  of  feed.  It  is  carried  out  in  the  natural  environment  as  a  natural  component  of  the 
ecosystem.  Therefore  the  goods  and  services  of  shellfish  to  the  environment  (Ferreira  et  al, 
2011,  Coen  &  Shumway,  2011)  are  an  intrinsic  contribution  of  shellfish  culture  to  natural 
processes.  

This  concerns  filtration  and  nutrient  regeneration,  providing  food  for  higher  trophic  levels 
(birds)  and  habitat  for  (epi)benthic  species.  Although  in  this  report  the  focus  is  on  potential 
negative impacts of aquaculture on the conservation objectives of Natura 2000 areas, it should 
be  acknowledged  that  extensive  aquaculture  also  acts  as  an  instrument  in  nature 
management  and  conservation,  thereby  invoking  positive  effects  on  maintenance  goals 
(Smaal et al, 2010).    

 
 
 
 
 
 
 
 
 
 
 
 
 
 
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23

3.1.4  Sensitivity, resistance and resilience 

Some  types  of  ecosystems  are  more  sensitive  than  others  to  the  environmental  'pressures' 
resulting  from  aquaculture  (while  bearing  in  mind  that  the  latter  is  a  general  term  covering 
many  different  activities  which  may  have  different  effects  according  to  the  way  they  are 
managed).  The  word  sensitivity  in  relation  to  aquaculture  activities  may  be  described  as  the 
extent to which  aquaculture production will result in an 'impact' on the ecosystem in which the 
aquaculture takes place.  

It may depend on: 

• 

• 

the  different  kinds  of  environment  in  which  aquaculture  takes  place,  and  the  physical 
conditions; 

the  different  kinds  of  biological  community  that  are  found  in  environments  used  for 
aquaculture, and the 'resistance' of each type of community to aquacultural effects. 

Sensitivity is dependent on the intolerance of a species or habitat to damage from an external 
factor and the time taken for its subsequent recovery. A sensitive species or habitat is one that 
is  adversely  affected  by  an  external  factor  arising  from  human  activities  or  natural  events 
(killed/destroyed, 'high' intolerance) and is expected to recover over a very long period of time, 
i.e.  >10  or  up  to  25  years  ('low';  recoverability).  Intolerance  and  hence  sensitivity  must  be 
assessed relative to change in a specific factor (MarLIN, 2005). Environmental conditions that 
render  an  ecosystem  less  sensitive  include  greater  dispersion  at  the  farm  scale  and  faster 
exchange  at  the  water  body  scale.  Ecological  theory  suggests  that  well-balanced  biological 
communities  -  those  that  contain  a  variety  of  species  and  a  mixture  of  life  forms  -  are  more 
capable of resisting 'pressure' (Tett et al., 2007). 

Resistance  is  ‘the  ability  of  an  ecosystem  to  withstand  disturbance  without  undergoing  a 
phase shift or losing structure or function’ (Odum, 1989). Different species and habitats have 
different  degrees  of  resistance  to  pressures.  The  degree  to  which  a  particular  conservation 
unit  is  impacted  by  a  particular  pressure  varies  depending  on  the  conservation  unit  and  the 
pressure involved. (Crowe et al., 2011). 

Resilience is the capacity of the system to recover from change.  Marine ecosystems have an 
inherent resilience to damage and loss, which varies depending on natural conditions and the 
nature  and  level  of  pressures  impacting  on  them.  Relatively  exposed  areas  that  naturally 
experience  high  levels  of  physical  disturbance  may  recover  from  anthropogenic  physical 
disturbance more quickly than those in sheltered areas. (Crowe et al., 2011). 

3.1.5  Assimilative and carrying capacity33 

The assimilative capacity can be defined as the ability of the ecosystem in a water body to 
absorb anthropogenic inputs of substances without damaging the health of the ecosystem or 
its ability to provide goods and services.  

33  Further  information  about  determination  of  assimilative  and  carrying  capacity  can  be  found  in  the 
ECASA  toolbox  (http://www.ecasatoolbox.org.uk/the-toolbox/informative/key-ideas/  management-for-
sustainability). 
Recently,  a  model  for  the  estimation  of  the  aquaculture  carrying  and  waste  assimilating  capacities  of 
fjordic water bodies has been elaborated and tested testing in a typical Scottish fjord (Tett et al. 2011). It 
is  a  physical-biological  model,  intended  as  a  water  quality  management  support  tool  by  simulating 
pressure-impact relationships. 

 
 
 
 
 
 
 
 
 
 
                                                 
 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

The  carrying  capacity  in  aquaculture  is  defined  as  the  maximum  biomass  of  a  farmed 
species  that  can  be  supported  without  violating  the  maximum  acceptable  impacts  to  the 
farmed stock and its environment. Carrying capacity depends, inter alia, on the capacity of the 
ecosystem  to  re-supply  substances  such  as  oxygen,  consumed  by  all  farmed  animals,  or 
phytoplankton, consumed by filter-feeding bivalves (Tett et al., 2011).  

3.2  Main potential pressures and impacts from different aquaculture systems - possible 
mitigation and good management practices 

As  mentioned  above,  the  observed  impacts  of  aquaculture  on  a  given  site  are  generally  not 
directly transferable to another site, even under similar farming and environmental conditions 
since a number of parameters generate considerable variability in the observed effects. 

It  needs  to  be  stressed  that  by  properly  implementing  relevant  EU  and  national  legislation 
(including licensing and control) most of the potential pressures and impacts from aquaculture 
are  prevented  or  minimised.  In  addition,  the  aquaculture  operators  are  voluntarily  making 
significant  efforts  to  apply  good  management  practices  (e.g.  codes  of  conduct,  monitoring, 
certification).  In  addition,  organic  aquaculture  is  promoted  by  the  EU.  Some  relevant 
information in this regard is included in Annex 1. 

In the context of this guidance document, it is relevant to understand the potential effects on 
habitats  and  species  protected  under  the  Nature  Directives,  which  are  the  target  of 
conservation in Natura 2000 sites.  

The potential effects to be considered in this regard may be classified in two main categories: 

(cid:57)  Habitat loss or degradation and modification of the communities present on it. 
(cid:57)  Disturbance and displacement of species. 

Habitats  may  be  lost  or  degraded  owing  to  the  building  of  infrastructures,  installation  of 
facilities  and  use  of  equipment  and  tools  (e.g.  for  harvesting),  which  may  cause  a  direct 
physical impact on habitats and communities. Benthic habitats and communities may also be 
impacted  by  sedimentation  of  organic  wastes,  while  increased  turbidity  and  nutrient 
enrichment of water may alter the conditions on which some communities and pelagic species 
depend  and  cause  their  displacement  from  the  site.  The  effects  from  the  use  of  chemical 
products in some aquaculture activities must also be considered. 

Disturbance  to  species  and  their  displacement  from  the  site  can  arise  from  the  construction 
and the operation of aquaculture farms, for instance from noise and light during management 
activities or the need to control predation on farms. Other biological interactions between the 
farmed species and the species occurring in the site must be taken into account, in particular 
the possible effects of escapes, such as interbreeding or direct competition from alien species 
used in aquaculture. 

The  main  interactions  between  different  farming  systems  and  the  natural  environment  are 
briefly  described  below,  with  an  indication  of  the  possible  effects  on  habitats  and  species  of 
EU interest, and of the mitigation measures that can be applied to avoid or reduce the effects 
well as examples of measures applied to avoid the negative impacts. 

A  more  detailed  description  of  the  main  pressures  and  effects  that  can  arise  in  different 
aquaculture  systems  has  been  provided  in  previous  studies  financed  by  the  European 
Commission (Huntington et. al. 2006, 2010). 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
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25

3.2.1  Marine cage culture 

Cage  culture  can  lead  to  increased  sedimentation  of  particulate  organic  waste  beneath  the 
cages.  Mussel  and/or  polychaete  reefs,  seagrass  beds,  sand  &  mudflats,  maerl  beds  and 
seaweed  beds  may  be  potentially  affected  by  sedimentation  from  poorly  sited  cage  farms 
(Huntington et al. 20006, Crowe et al. 2011, Ragot 2009, Wilding and Hughes 2010). 

Seagrass beds directly beneath or in close proximity to fish cages can be adversely impacted 
by deposition of solid organic waste. Effects on Posidonia and Zostera beds are known (Ruiz 
et al. 2001, 2010, Diaz Almela et al. 2008, Apostolaki et al. 2007, Marba et al. 2006, Pergent-
Martini et al 2006, Cancemi et al. 2003, Crowe et al. 2011). The critical factor causing impacts 
appears  to  be  solid  waste  deposition  and  the  consequent  high  organic  loading  and 
deoxygenation of sediments (Wilding and Hughes 2010).  

The  accumulation  of  organic  material  on  the  substrate  increases  the  sediment  community’s 
oxygen  demand  and  can  have  effects  on  sediment  chemistry,  which  may  cause  changes  in 
species  diversity,  abundance  and  biomass  of  benthic  fauna  and  flora  (Wilding  &  Hughes, 
2010,  Holmer  et  al.  2007,  Maldonado  et  al.  2005,  Vezulli  et  al.  2008,  Tomasetti  et  al.  2009, 
Vita et al. 2004, Mirto el al 2009).  

Appropriate siting of the cages and farm management is particularly important in this kind of 
aquaculture system. Control and limitation of the stock density are used to reduce the possible 
impacts caused by particulate organic waste. The improvement of feed digestibility, as well as 
systems to reduce food waste can also mitigate these impacts. The use of extruded and high 
digestibility  feeds,  use  of  modern  automatic  feed  distribution  systems,  daily  control  of  the 
amount  of  feed  aimed  at  minimizing  the  feed  dispersion  and  waste  in  the  environment,  are 
some of the possible mitigation measures that are often applied to reduce this type of effects. 

Hydrodynamic  conditions  play  an  important  role  in  the  dispersion  of  organic  waste  and  the 
reduction of estimable effects (Cromey et al., 2002a; Modica et al., 2006; Sara et al., 2006). 

Computer  models  are  available  to  assist  in  predicting  the  extent  and  degree  of  organic 
deposition from aquaculture facilities and are used to identify potential impact from a farm. For 
instance, the DEPOMOD model predicts deposition and biological effects of waste solids from 
marine  cage  farms  to  the  seabed  based  on  the  site  bathymetry  and  hydrographic  regime 
combined  with  the  maximum  fish  tonnage  and  stocking  density  of  the  farm  (Cromey  et  al. 
2002b; Cromey et al. 2002c). The MERAMOD model  (Cromey, C., 2008) was developed from 
the  DEPOMOD  model  and  validated  for  sea  bass  and  bream  farms  in  the  Eastern 
Mediterranean. 

Fish cages release dissolved compounds directly into the surrounding water column, including 
ammonia, nitrate and phosphate together with dissolved organic carbon. Sources include fish 
excretory  products  and  dissolution  from  feed  pellets  or  faecal  particles.  The  effects  of  this 
input into the water column may be rather limited when there is rapid dispersal (Holmer 2010).  

Nutrient enrichment of the water column has been detected around sea bream and sea bass 
cages  in  the  Mediterranean  (Dalsgaard  &  Krause-Jensen,  2006,  La  Rosa  et  al.  2002). 
However, only limited impacts have been documented and this is generally considered one of 
the less severe impacts (Sara 2007). Machias et al. (2005) showed that the primary production 
increased  in  farm  surroundings  under  oligotrophic  conditions  in  the  Mediterranean  Sea, 
eventually stimulating productivity at higher trophic levels. 

Recent studies suggest that enrichment by salmon farm nutrients is generally little (Laurent et 
al.  2006)  and there  is  no evidence  of  eutrophication  or  algal  blooms  from  nutrient  release  in 
Scottish salmon farms (Smayda 2006). In view of the lack of evidence for harmful ecosystem 

 
 
 
 
 
 
 
 
 
 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

effects of nutrient release from  salmon farms,  it has been concluded that benthic  habitats of 
biodiversity  value  in  the  UK  are  unlikely  to  be  affected  by  this  form  of  discharge  (Wilding  & 
Hughes, 2010).  

By moving the farms further offshore to more exposed conditions, the dispersal of nutrients is 
expected to increase, minimizing the pressure on the environment (Wilding and Huges 2010, 
Pitta et al. 2009). 

Other potential risk impacts from marine cages that may be considered include those related 
to  chemical  use,  especially  over  sensitive  habitats  such  as  Zostera  and  Posidonia  beds 
(Ragot 2009, Huntington et al. 2006). Similarly, mud habitats, mussel beds and reefs have low 
tolerance  and  resistance  to  some  synthetic  compounds  used  in  aquaculture  (Crowe  et  al. 
2011, Huntington et al. 2006, Wilding and Hughes 2010).  

A reduced use of chemicals and other artificial substances in aquaculture has been promoted 
in recent years together with the development of alternative environment-friendly substances 
and  methods  of  treatment,  securing  favourable  conditions  for  fish.  Restrictions  to  the  use  of 
chemical  compounds  are  usually  applied  in  sensitive  areas.  Eco-friendly  antifouling  coatings 
and  products  can  be  used.  These  might  include  silicone-based  coatings,  polyurethanes  and 
enzymatic technologies (IUCN, 2007). Biological methods are being recently tested to control 
biofouling34. 

Risks  from  chemicals  can  be managed  through  the  application  of  appropriate  Environmental 
Quality  Standards  under  the  Water  Framework  Directive.  In  Scotland  environmental  quality 
objectives  (EQOs)  are  used  to  assess  the  impact  of  mariculture  and  to  control  discharges 
(OSPAR, 2009).  

Cages  may  attract  predators  (wild  fish,  piscivorous  birds,  aquatic  mammals),  which  may 
cause  damage  to the  netting.  (Holmer  2010).  In  Scotland,  the  common  seal (Phoca  vitulina) 
feeds  primarily  on  fish  and  can,  on  occasion  predate  on  salmon  farmed  in  pens.  To  protect 
their  stocks,  some  farms  use  good  husbandry  techniques,  the  acoustic  deterrent  (which 
should be in line with relevant international agreements) or anti predator nets. 

Physical  impacts  of  infrastructure  are  also  possible  since  cages  may  be  anchored  on  the 
seabed and risk to damage physically the seabed habitat. However, proper siting and design 
of  aquaculture  infrastructures,  avoiding  their  location  on  especially  sensitive  habitats  and 
considering the best technical solution for each type of area (e.g. adapting mooring structures 
to  the  conditions  of  the  seabed  substrate)  can  help  avoid  and  minimise  these  potential 
adverse effects. In Scotland, for instance, some mooring anchors and equipment required for 
securing  the  position  of  the  salmon  farm  pens  are  situated  in  deep  water  to  avoid  overlap 
between the farming activity and sensitive habitats (eg. reefs). 

Large enclosures could also have an effect on current circulation and light penetration. Risks 
can be managed, if necessary, by limiting the sizes of complexes and re-siting them regularly 
(Nash et al. 2005). 

Disturbance  impacts  from  management  activities  are  usually  fairly  low  and  transitory  when 
the cages are in deeper water, away from bird nesting of foraging areas. 

The  escape  of  fish35  from  cages  may  cause  undesirable  genetic  effects  in  wild  populations 
through interbreeding, and ecological effects through predation, competition and the possible 

34 See for instance the guidelines of the  CRAB project: 
http://www.crabproject.com/client/files/CRAB_Best_Practice_Guidelines.pdf 
35 The introduction of alien species for their use in aquaculture is regulated by Regulation 708/2007. 

 
 
 
 
 
 
 
 
 
 
                                                 
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27

transfer  of  diseases  to  wild  fish.  An  issue  of  particular  concern  is  that  of  interbreeding36  of 
Atlantic salmon as this may lead to loss of fitness in river-specific sub-populations (Naylor et 
al.  2005).  A  recent  EU  project  (Prevent  Escape37)  aims  to  elaborate  recommendations  and 
guidelines for aquaculture technologies and operational strategies that reduce escape events. 

As  mentioned  above,  benthic  impacts  can  be  minimised  by  siting  the  farm  in  highly  flushed 
areas and limiting the biomass and stocking density of the fish to avoid excessive waste. The 
approach  taken  by  farm  operators  in  order  to  minimise  adverse  effects  at  their  sites  now 
incorporates  selecting  sites  with  good  water  exchange  and  management  practices  that 
minimise food waste and chemical usage. The use of ‘high energy’ (i.e. resulting  in reduced 
ammonia-N loading) and ‘low pollution’ diets (i.e. high digestibility, low phosphorus), along with 
the  development  of  improved  feeding  management,  have  reduced  the  production  of  wastes. 
Routine removal of dead fish and fouling organisms is also usually applied. 

3.2.2  Shellfish rafts and longlines 

Mussel and other shellfish aquaculture in deeper waters, through the use of suspended ropes 
and longlines from floating rafts, has developed to take advantage of spat fall locations as well 
as areas of  good water quality and  food availability.  These systems  may lead to  increased 
levels  of  suspended  sediments  under  the  farms  resulting  from  the  deposition  of 
pseudofaeces, which in turn impact the benthos.  

The  deposition  of  faeces  and  pseudo-faeces  beneath  mussel  farms  may  lead  to  organic 
enrichment of sediments (Hargrave et al. 2008b) and cause changes in benthic communities 
(Danovaro  et  al.  2004,  Ysebaert  et  al.  2009).  The  effects  of  suspended  culture  depend  on 
local conditions and the scale under consideration. The impacts of suspended mussel culture 
on  benthic  infaunal  communities  are  typically  limited  in  magnitude  except  under  extreme 
conditions (poor flushing or exceedingly great stocking densities) ( McKindsey et al, 2011). 

Impacts of suspended rope culture are mainly limited to sedimentation effects on wild mussel 
reef  communities  and  other  sensitive  sublittoral  habitats  such  as  polychaete  reefs,  seagrass 
beds,  sandbanks,  maerl  beds  and  seaweed  beds  (Huntington  et  al.  2006).    Impacts  are 
considered to be lower under longlines than under rafts as the amount of pseudofaeces falling 
from  longlines  is  spread  over  a  larger  area  (OSPAR  2009).    An  overview  of  studies  on  the 
influence of mussel farms on benthic communities is provided in McKindsey at al. 2011. 

Suspended shellfish culture may also have an impact on the water column in both terms of 
dissolved  oxygen  levels  as  well  as  nutrients.  However,  the  location  of  this  type  of  system  in 
areas with good water exchange and thus good dispersion of nutrients usually reduces the risk 
for  such  effects.  In  fact,  the  regeneration  of  inorganic  nutrients  through  mineralization  of 
biodeposits,  either  in  the  water  column  or  on  the  bottom,  stimulates  nutrient  availability  for 
phytoplankton.  This  positive  feedback  by  filterfeeders  is  an  important  mechanism  in  shallow 
ecosystems,  that  eventually  stimulates  primary  production,  hence  bivalve  food  production 
(Smaal & Prins 1993; Dame,2012).  

Intensive shellfish farming strips primary production from the water column and, if a bay is too 
heavily farmed, the carrying capacity of the body of water in which the farms are located can 
be exceeded, resulting in adverse conditions for wild and cultured populations (WWF 2010b). 
As this would have a direct negative impact on the yield of the farmed shellfish, overgrazing 
would result in a reduction of the shellfish culture activities. 

36 A Research project funded by the European Commission has carried out an evaluation of genetic 
impact of aquaculture activities on native populations (GENIMPACT 2007).  
37 Prevent Escape: www.sintef.no/preventescape 

 
 
 
 
 
 
 
 
 
                                                 
 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

It has been estimated that mussel culture may extract around 10% of primary production from 
a given area (Figueiras et al. 2002) in the rías of Galicia. This may have beneficial results for 
oligotrophic communities such as sea grasses but might restrict food availability for other filter 
feeders such as polychaete worms and sand or mudflat communities (Huntington 2006).  

This  potential  to  remove  phytoplankton  can  also  be  used  as  a  solution  to  the  additional 
nutrient  loading  that  results  from  fish  cultivation.  By  integrating  fish  (fed)  aquaculture  with 
seaweed  and  shellfish  (extractive)  aquaculture,  the  wastes  of  one  resource  user  become  a 
resource (fertiliser or food) for the others (Scottish Executive 2002). There have been several 
studies  investigating  the  potential  benefits  of  cultivating  mussels  in  order  to  mitigate  nutrient 
input as part of an integrated multi-trophic aquaculture with farmed fish (Troell et al, 2009) 

Disturbance  to  sensitive  species  may  also  occur  but  the  maintenance  and  harvesting  of 
suspended grown bivalves has little direct impact (OSPAR 2009). Both longlines and rafts can 
increase  both  primary  and  secondary  production  by  providing  space  for  algae  and  fauna  to 
grow  on.  Such  systems  also  act  as  nursery  areas  for  fish  and  this  food  resource  can  also 
provide additional food resources for diving birds (OSPAR, 2009). 

Sedimentation of faeces and pseudofaeces can be estimated by simple models and compared 
with appropriate EQS in order to estimate a safe shellfish loading.  Some modelling tools are 
available to predict footprints of benthic loading around mussel farms (see reviews in Giles et 
al.  2009;  Weise  et  al.  2009).  The  degree  to  which  organic  matter  is  dispersed  initially  and 
redistributed  subsequently  is  positively  correlated  with  local  current  regimes  (Hartstein  and 
Stevens 2005; Giles et al. 2009). 

As  regard  the  removal  of  phytoplankton,  models  have  been  developed  to  determine  the 
optimum  stocking  density  at  which  shellfish  production  is  maximised  without  negatively 
impacting growth rates and minimising the impact on the environment (Kaiser and Beadman 
2002, Duarte et al. 2008). 

The  appropriate  location  of  shellfish  rafts  and  longlines  in  areas  with  good  water  exchange, 
and  the  adequate  dimensioning  of  the  farm  using  predictive  models  that  allow  estimating 
footprints of benthic loading can minimise the main possible effects of these systems. 

3.2.3  Intertidal shellfish culture 

Inter-tidal shellfish systems are generally fairly extensive, although they can be concentrated 
in  estuaries  and  may  have  an  impact  on  sensitive  habitats  or  on  important  bird  feeding  and 
fish nursery areas (Huntington et al. 2006). 

A potential impact is the smothering of nearby inter-tidal and sub-littoral habitats with faecal 
and pseudofaecal material, as well as other detritus generated by the culture process, which 
can affect reefs, sea grasses, sand flats and maerl beds (Huntington et al. 2006, Ragot 2009). 
In  highly  energetic  waters  faeces  and  pseudofaeces  may  be  spread  over  some  distance. 
Intertidal  systems  are  so  dynamic  that  normallysmothering  is  effectively  counteracted  by 
waves and currents. 

In order to gauge the significance of smothering effects due to shellfish cultivation, it is useful 
to: 

-  Identify  the  receiving  habitat  types,  understand their  response  to  smothering,  for example 
changes  to  infaunal  and  epifaunal  communities,  and  determine  the  affected  area,  which 
can thus be compared to the total area of these biotopes within the site where the mussel 
cultivation takes place (eg. the Natura 2000 site).  

 
 
 
 
 
 
 
 
 
 
 
 
Guidance document on aquaculture activities in the context of the Natura 2000 Network 

29

-  Evaluate the quantity of sediment that is displaced into the water column, and ascertain the 
level of sedimentation (sinking and deposition of suspended matter onto the seabed). The 
impacts of increased turbidity (resulting from deposition and dredging of cultivated mussels) 
could be assessed by comparison with background turbidity levels. 

There is also a potential risk when using alien organisms. However, the possible impact from 
the  introduction  of  alien  species  for  their  use  in  aquaculture  is  regulated  by  Regulation 
708/2007,  which  includes  a  permit  system  with  specific  procedures  and  risks  assessments. 
Furthermore,  the  use  of  alien  species  is  restricted  or  subjected  to  particular  conditions.    In 
North  Wales,  the  adoption  of  a  ‘Code  of  Good  Practice  for  Mussel  Seed  Movements’,  has 
been  put  in  place  to  avoid  the  accidental  introduction  of  non-native  species  through  the 
importation of mussel seed from other places.  

The  maintenance  required  by  inter-tidal  facilities  may  lead  to  disturbance,  including  from 
access roads, especially in important bird foraging and over-wintering areas (Huntington et al. 
2006). Some operational conditions regarding wildlife protection are usually applied in order to 
avoid any disturbance.  

3.2.4  Bottom shellfish culture 

This  form  of  aquaculture  is  often  practised  in  shallow  coastal  or  estuarine  areas  where 
habitats  of  conservation  interest  may  be  present,  such  as  sand  and  mud  flat  or  seagrass 
communities,  and  thus  there  may  be  conflicts  over  use  and  management  of  the  area 
(Huntington et al. 2006). 

The main potential pressures from bottom culture include some degree of sedimentation from 
both animal excretion and the dredging process used for harvesting, as well as some physical 
disturbance.  The  influence  of  bottom  cultures  on  the  sedimentary  environment  and  on  the 
macrobenthic community seems to be rather local (Ysebaert et al. 2009).  

Sublittoral  benthic  habitats  such  as  sand/mud  flats/banks  may  be  impacted  by  smothering 
from  sediments  generated  from  excretory  products  or  following  harvesting,  especially  if 
hydraulic  or  physical  dredges  are  used.  If  smothering  occurs  periodically  then  the  level  of 
recoverability is usually reasonable, especially if beds are scoured by currents (Huntington et 
al. 2006) 

The 
introduction  of  alien  species  may  represent  a  pressure  exerted  by  bottom 
culture38..There  may  be  also  a  risk  of  pathogen  transmission  from  cultured  to  wild 
populations, although high pathogen loads from bottom culture are unlikely (OSPAR 2009). 

Dredging for seed and the harvesting of on-bottom culture shellfish may have impacts on the 
seabed and benthic communities as well as on non-target commercial species, such as wild 
scallops and clams. 

In  some  countries  (eg.  United  Kingdom,  Ireland)  seed  mussels  are  dredged  once  a  layer  of 
mussel  mud  has  built  up  (mussel  mud  is  an  accumulation  layer  of  mussel  faeces  and 
pseudofaeces which can be 30 to 40cm thick and can detach from the underlying substratum 
and  become  unstable).  This  allows  the  collection  of  seed  mussels  with  a  relatively  small 
impact on the subsurface fauna. In addition, dredging activities are seasonal, which will allow 
a period of recovery for the seabed habitat and the benthos.  

38 As previously stated the possible impact from the introduction of alien species for their use in 
aquaculture is regulated by Regulation 708/2007. 

 
 
 
 
 
 
 
 
 
 
 
 
                                                 
30 

Guidance document on aquaculture activities in the context of the Natura 2000 Network  

In the Netherlands, the harvest of intertidal mussel seed beds is only permitted in autumn on 
unstable beds which are susceptible to being flushed away during winter storms (Maguire et 
al. 2007). However, in the Netherlands, if there is sufficient spat fall, a spring harvest may also 
take place.  

In 2009 a Dutch policy was developed for seed mussel collection systems, which consists of a 
floating  rope  for  seed  mussels  to  attach  themselves  to.  Since  2000,  experiments  have  been 
carried  out  to  test  in  how  far  these  systems  are  a  promising  alternative  to  bottom  seed 
fisheries, and an additional resource in case bottom recruitment might fail.  The mussel fishery 
sector,  government  and  nature  organisations  have  agreed  to  phase  out  traditional  methods 
and make room for the alternative collection systems. 

The  exploitation  of  mussel  seed  resources  may  be  of  particular  concern.  Currently  in  the 
Wadden Sea every year an inventory is made of shell fish stocks in the coastal zone to find 
out whether seed mussels are in sufficient supply to allow fishery to take place. The fishermen 
have organised themselves into a producer’s organisation (PO). The PO applies for a permit 
from  the  Ministry  of  Economic  Affairs,  Agriculture  and  Innovation.  The  application  is 
accompanied by an assessment, analysing the effects of the fishery against the conservation 
targets of the Natura 2000 site.  

For avoiding seabed disturbance the Government has initiated an open plan process together 
with  all  the  parties  concerned  (fishery  and  recreational  sectors,  nature  organisations, 
provincial  authorities)  to  draw  up  policy  for  the  years  2010-2013.  This  involved  selecting 
suitable locations for seed mussel collection systems.  

3.2.5  Land based tank systems for marine species 

Most of these systems are closed and the growing facilities are contained within a site that is 
separated  from  the  external  environment  by  physical  filters  and  drains.  Some  farms  use 
recirculation  systems  and  may  even  use  artificial  seawater,  thus  reducing  the  inflow  and 
discharge of water to and from the farm (Huntington et al. 2006). 

However,  some  effects  from  sedimentation,  biogeochemical  changes  and  chemical 
release can be noticed especially in the area near the culture site and at some distance form 
it. All benthic habitats sensitive to these pressures could be potentially affected (Huntington et 
al. 2006, Ragot 2009).  

To avoid this, in some farms (eg. in Italy) the outflow water, before being discharged into the 
communication canal between the lagoon and the sea, is microfiltered through a rotating filter 
and  is  settled  and  purified  through  a  circuit  of  settling  basins.  This  allows  the  absorption  of 
nourishing substances by the microalgae. An automatic grate cleaner at the exit of the water 
keeps  the  microalgae  in  the  purifying  basins.  Monitoring  of  the  algal  situation  in  the  coastal 
area  surrounding  some  tank  systems  is  also  carried  out  in  order  to  analyze  possible 
biogeochemical changes.  

There  may  be  some  impact  on  sublittoral  habitats  such  as  reefs  and  seagrass  beds  from 
increased  nutrients  and  biological  oxygen  demand.  However,  this  very  much  depends  upon 
the  level  of  wastewater  treatment  conducted  by  the  farm,  which  can  be  highly  efficient 
(Huntington et al. 2006, Ragot 2006, Aquaetreat 2007). 

Strict  controls  and  treatment  of  effluents  from  tanks  are  sometimes  carried  out.  This  might 
involve  aeration  of  effluents  to  increase  aerobic  breakdown  of  wastes  prior  to  discharge, 
thereby reducing biological oxygen  demand of  effluent. An  increased use of water  re-cycling 
would also  be useful to limit discharges. Control of leakage may also  be carried out through 

 
 
 
 
 
 
 
 
 
 
 
Guidance document on aquaculture activities in the context of the Natura 2000 Network 

31

pond/dyke  compaction  or  use  of  liners  to  avoid  seepage  and  nutrient  enrichment  of  nearby 
waters. 

Pressures  from infrastructure  could  impact  supralittoral habitats  such  as  saltmarshes,  sand 
dunes  and  shingle  if  the  farm  were  to  be  built  on  these  habitats.  In  practice  this  would  be 
highly unusual, as most land-based farms would be built upon firmer ground further inland and 
planned  to  avoid  any  conflicts  with  nature  conservation  interests.  As  such,  physical  habitat 
alteration can be minimized or mitigated.  

Most  intensive  land-based  farms  are  both  well  managed  to  reduce  the  eventual  use  of 
chemotherapeutant  or  pathogen  load  in  production  systems,  and  outputs  of  these  to  the 
external environment can be managed through filtration and water treatment (Huntington et al. 
2006, Ragot 2006).  

Disturbance from these farms is minimal, as many facilities are either indoors or confined to a 
small  area.  Predator  control  is  also  likely  to  be  minimal  and  mostly  passive  in  nature  i.e. 
netting and screening (Huntington et al. 2006, Ragot 2009). The introduction of alien species 
may also have an impact39. 

3.2.6  Land based ponds for marine species farming 

Pond systems often require considerable areas of land to support the ponds and their related 
infrastructure  (water  supply  and  effluent  canals).  The  construction  of  coastal  pond  farms, 
usually involving a ‘cut and fill’ approach, may have high potential impacts on these areas. If 
the ponds have been prepared from lagoon areas, there is the potential for altering the local 
hydrological  regime  and  thus  impacting  on  the  functionality  of  the  remaining  parts  of  the 
lagoon (Huntington et al. 2006).  

The impacts during operation of pond farms depend upon the species being cultured and the 
type  of  water  supply  regime  being  employed.  Whilst  some  species  require  flow-through 
systems,  others  may  require  only  the  occasional  topping  up  of  ponds  to  compensate  for 
seepage  and  evaporation  –  the  latter  then  have  a  short-term  pulse  of  detritus-laden  effluent 
during  harvest  draw-down.  There  is  the  potential  to  ameliorate  much  of  the  impact  of  both 
flow- through and pulse discharges using settlement ponds and biofiltration (Huntington et al. 
2006). 

Organic sediments can occur around the discharge area. To avoid organic sediments some 
commonly used measures in Italy are mechanical removal of algae on water surface, residual 
sediments  treatment  with  oxygen  and  water  movement  in  dedicated  ponds,  use  of  liquid 
oxygen  in  the  ponds  and  in  effluent  channels,  etc.  Pond  farms  frequently  fringe  the  edge  of 
lagoon areas (e.g. the Mesolonghi and Amvrakikos lagoons in Greece) and their discharges – 
both  individually  and  cumulatively  -  may  impact  seagrass  beds  as  well  as  other  sensitive 
habitats or the water body’s ecology. 

The  establishment  of  coastal  pond  farms  could  result  in  the  alteration  of  saltmarsh  areas, 
and supralittoral sand dunes and shingle could also be affected if the farm is located in areas 
where  those  habitats  are  present  (Huntington  et  al.  2006).    However,  suitable  siting  and 
management measures of pond farms can easily avoid impacting on these types of habitats. 

The control of predators may be a serious issue for pond farms. The use of nets for covering 
ponds against birds attack is, when feasible, a widely used measure in most of the farms. 

39 As previously stated the possible impact from the introduction of alien species for their use in 
aquaculture is regulated by Regulation 708/2007. 

 
 
 
 
 
 
 
 
 
 
 
                                                 
32 

Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Land-based farms are able to treat waste water streams before they are discharged into the 
environment. The use of ponds to settle suspended solids allows a large proportion of organic 
and  inorganic  materials  to  be  removed.  Dissolved  nutrients  can  also  be  removed  through 
filtration, with biological techniques such as reed bed systems and algal beds, as well as using 
bivalve-lined effluent canals (Huntington et al. 2006). 

3.2.7  Lagoon culture 

Extensive  lagoon  culture  has  in  general  low  pressures,  although  may  impact  on  the  local 
wildlife  and  bird  populations  through  a  combination  of  operational  disturbance  as  well  as 
targeted  predator  control.  Another  pressure  may  result  from  the  use  of  alien  or  locally-
absent species such as the Manila clam (Ruditapes philippinarum)40. 

The main habitats that may be impacted by lagoon farming are those typical of lagoon areas – 
sand and mud flats, seagrass beds and kelps and seaweeds. Other areas – polychaete and 
mussel reefs and maerl beds may also be potentially impacted if found within or adjacent to 
lagoonal areas.  

Sand  and  mudflats  might  be  subject  to  smothering  from  sediments  emanating  from  the 
farm, and by any change in the trophic status of the water body due to hypernutrification 
and  organic  deposition.  They  are  important  feeding  habitats  for  avian  waders  and  support 
considerable  invertebrate  infaunal  communities.  These  may  also  be  impacted  by  any 
significant  change  in  overall  productivity  resulting  from  the  introduction  and  husbandry  of 
monoculture or restricted polyculture.  

Sea  grass  communities  may  be  impacted  by  increased  water  turbidity,  either  due  to  some 
level  of  siltation  but  more  likely  from  harvesting  activities  that  involves  raking  or  hydraulic-
assisted extraction of clams. Seagrasses might also be subject to removal during harvesting 
and have low levels of recoverability from rhizome displacement. 

However,  as  mentioned  above  lagoon  culture  is  usually  an  extensive  system  with  low 
pressures,  which  under  good  practice  management  can  even  provide  suitable  habitats  and 
contribute to biodiversity conservation (see section 3.6). Ponds and lagoons may be designed 
to contain flood events and thus prevent release of effluents. 

Predator control is an issue in lagoon aquaculture. Nowadays, predator control is made more 
challenging, as many predators are protected by Member State and EU legislation, especially 
within designated sites of conservation interest41.  

For  extensive  lagoon  farms,  fisheries  lakes  and  those  farms  that  are  affected  by  migration 
routes,  this  issue  remains  a  very  severe  problem.  The  large  ponds  cannot  be  covered  by 
protective netting and face extensive losses every year. In many cases, the situation is further 
complicated by the existence of Natura 2000 sites in close proximity42.  

40 As previously stated the possible impact from the introduction of alien species for their use in 
aquaculture is regulated by Regulation 708/2007. 
41 Under Article 9 of the Birds Directive or Art. 16 of the Habitats Directive Member States can, by way 
of derogations, take measures to limit the impact of protected species. 
42  The  particular  case  of  the  Great  Cormorant  is  the  subject  of  research  projects  (e.g.  INTERCAFE: 
http://www.intercafeproject.net/index.html)  and  an  EU  platform  set  up 
(http://ec.europa.eu/ 
environment/nature/cormorants/home_en.htm) 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                 
Guidance document on aquaculture activities in the context of the Natura 2000 Network 

33

3.2.8  Freshwater fish aquaculture systems 

The  main  pressures  from  freshwater  aquaculture  may  be  sedimentation,  changes  in  bio-
chemistry and hazardous substances (Huntington et al. 2010). The relative impacts can be 
avoided or mitigated with different water treatment systems currently available43. 

Trout and carp are cultured in land-based pond and raceway systems. Sedimentation risk from 
land-based tanks and pond culture is moderate for rivers with low flow rates, but this can be 
minimised  with  settlement  ponds.  On  the  other  hand,  ponds  can  have  a  positive  role  eg.  by 
retaining the soil brought by the stream from the upper basin. 

There is also a possible risk of eutrophication through effluent discharge to rivers. As carp are 
omnivorous and mainly cultured in ponds, there is less likelihood of nutrient enrichment than 
with  raceway  and  tanks  systems  used  for  trout.    Currently  many  trout  farms  use  modern 
technologies  (low  production  intensity  index,  outflow  water  systems  like  settling  tanks, 
mechanical  aeration  systems  or  liquid  oxygen,  effluent  analysis,  etc.)  which  allow  them  to 
exploit water resources efficiently and to offset potential detrimental effects, eutrophization in 
particular, on the receiving water body. 

In  Atlantic  rivers  the  risk  of  reduced  oxygen  levels  from  nutrient  enrichment  increases  in  the 
summer months with higher temperatures and lower flows. The impact on flora and fauna can 
be  significant.  This  can  and  should  be  avoided  or  mitigated  with  seasonal  abstraction  limits. 
Continental rivers are typified by high volumes of water suggesting risk of nutrient enrichment 
is low, as is the risk from chemical use. 

Chemical  use  in  trout  culture  poses  moderate  risk  to  rivers.  For  trout  farming  within  river 
systems,  permits  are  generally  provided  based  on  dilution  being  sufficient  to  ensure 
downstream impacts are negligible. 

Aquaculture  in  ponds  is  dominated  by  extensive  carp  culture,  which  poses  low  or  negligible 
risk  to  water  quality  elements  other  than  the  potential  effect  on  hydromorphology  from  the 
construction of pond-lakes in flood plain areas. Most of the ponds have a very long history and 
therefore they have merged well with the landscape, where they play an important role in e.g. 
the ecological stability and increase the capacity of an area to receive flood waters and sustain 
water in the landscape.  

3.2.9 Summary overview of all potential pressures and impacts 

The table below illustrates the kind of issues to be considered when assessing different types 
of  aquaculture  systems.  It  is  only  intended  to  summarise  the  information  provided  in  the 
previous  sections  about  all  possible  effects.  It  must  be  stressed  that  these  potential 
impacts do not always appear or might not be relevant for the conservation objectives 
of a particular site.  

A case by  case approach is needed to identify the actual potential  impacts, which depend 
on the environmental and rearing conditions and on the mitigation measures and appropriate 
management  practices  that  must  be  applied  to  avoid  or  minimise  such  effects.  Furthermore, 
many of those issues are regulated under EU or national legislation. 

43 Water treatment of intensive aquaculture systems and new methods to reduce the farm effluents 
have been addressed in a project funded by the European Union under the Sixth Framework 
Programme (Sustainaqua, Varadi et al. 2009) 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                 
34 

Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Table 3. Checklist of issues to be considered in different aquaculture systems  

Lagoon 
culture 

Freshwater 
Fish 
ponds 

 Coastal and marine 
Cage 
culture 

Shellfish 
rafts and 
longlines 
X 
X 

Aquaculture system 

Intertidal 
shellfish 
culture 
X 

Bottom 
shelfish 
culture 
X 

Land 
based 
tanks 

Land 
based 
ponds  
X 
X 

X 

X 

X 
X 

Potential Impacts 
Sedimentation 
Biogeochemical 
change in water  
Chemical input 
Infrastructure impact 
Disturbance 
Predator control 
Interbreeding 
Pathogen 
transmisison 
Alien species 
(the introduction of alien species for their use in aquaculture is regulated by Regulation 708/2007) 

X 
X 
X 
X 
X 
X 

X 
X 
X 
X 
X 
X 

X 
X 
X 
X 
X 
X 

X 
X 
X 
X 

X 
X 
X 

X 
X 
X 

X 
X 
X 

X 
X 

X 
X 

X 
X 

X 
X 

X 

X 

X 

X 

X 

X 

X 

X 

X 

X 

X 

X 

X 

Flow- 
through 
system 
X 
X 

Recir-
culation 
system 

X 
X 
X 

Table 4. Example of a possible classification of key habitats and species sensitivity to guide risk 
assessment (from Huntington et al 2006) 

Pressure categories 

Habitats / species 

n
o

i
t

t

a
n
e
m
d
e
S

i

l

i

a
c
m
e
h
c
o
e
g
o
B

i

t

r
e
a
w
n

i

e
g
n
a
h
c

t

u
p
n

i

l

i

a
c
m
e
h
C

e
r
u

t
c
u
r
t
s
a
r
f
n

I

t
c
a
p
m

i

e
c
n
a
b
r
u

t
s
D

i

Reefs: mussel beds communities 
Reefs: polychaete worm communities 
Seagrass beds on sublitoral sediments 
Sandbanks, mudflats and sandflats 
Maerl beds 
Kelp and seaweed communities 
Saltmarsh communities 
Sand dune communities 
Shingle communities 
Cetaceans 
Pinnipeds  
Otters 
Fish 
Birds 

x 
x 
x 
x 
x 
x 
x 

x 

x 
x 
x 

x 
x 
x 
x 
x 
x 
x 

x 

x 
? 
x 
x 
? 
? 
x 
x 

x 
x 
x 
x 
x 

x 
x 
x 
x 
x 
x 
x 
x 
x 

x 

x 

x 

x 
x 
x 
x 
x 
x 
x 
x 

l

o
r
t

n
o
c

t

r
o
a
d
e
r

P

x 
x 

x 
x 
x 
x 
x 
x 

x 

i

s
e
c
e
p
s

n
e

i
l

A

x 
x 
x 
x 

i

g
n
d
e
e
r
b
r
e
n

t

I

n
e
g
o
h
a
P

t

i

i

n
o
s
s
m
s
n
a
r
t

x 
? 

? 

? 

x 

x 

x 

3.3  Examples of sustainable aquaculture in natural areas that contribute to biodiversity 

There are numerous examples of sustainable development of aquaculture activities that play 
an important role in environmental conservation and enhancement of biodiversity, retention of 
water  in  the  landscape  and  flood  protection.  Aquaculture  systems  can  be  compatible  with 
sensitive habitats and can provide environmental benefits and services. Aquaculture activities 
are carried out in many Natura 2000 sites and can be fully compatible with the preservation of 
the sites natural values.  

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Guidance document on aquaculture activities in the context of the Natura 2000 Network 

35

Providing suitable habitats for species of EU interest 

•  Fishponds, especially in Central and Eastern Europe, provide a very important habitat for 
large numbers of water birds. Very often such fishponds were created on the site of former 
natural  wetlands  and,  due  to  the  extensive  management,  have  evolved  into  semi-natural 
wetlands supporting high biodiversity. In this way inland aquaculture has replaced natural 
marshes in hosting a high diversity of aquatic plants and animals. At the moment many of 
these aquaculture facilities are within or close to Natura 2000 sites. In  countries  such as 
the  Czech  Republic,  Romania  and  Hungary,  sites  with  fishponds  make  up  a  quarter  or 
more of all special protection areas (SPAs) in the country (BirdLife, 2011). 

•  Extensive  fish  ponds  are  usually  surrounded  by  reed  belts  and  natural  vegetation,  thus 
providing  important  habitats  for  flora  and  fauna.  Many  pond fish farms  have  been  turned 
into  multifunctional  fish  farms,  where  various  other  services  are  provided  for  recreation, 
maintenance of biodiversity and improved water management (Varadi et al, 2009). 

•  Fish  farming  activity  has  also  preserved  ponds  and  wetlands  when  the  pressure  to  turn 
them  into  cultivated  areas  was  very  strong  (1970-1990).  Some  of  the  best  preserved 
freshwater  wetlands of the Region Friuli Venezia Giulia, survived the simplification  of the 
hydrographic  network  and  drainage  that  have  affected  the  Friuli  plain  during  the  last 
century  thanks  to  the  fish  farm  activity.  In  some  aquaculture  ponds  in  the  Veneto  Plain 
(Italy)  the  largest  wintering  colony  of  the  Cormorant  and  one  of  the  last  colonies  of 
Bombina variegata in the plain are found nearby the existing aquaculture areas. 

• 

In Belgium some aquaculture producers are involved in conservation projects aimed at the 
restoration  of open marsh landscape for Bittern and Little Bittern, and have implemented 
other measures like the maintenance of ponds free of fish to contribute to the conservation 
of tree frog. 

• 

In some farms in Lorraine, France, aquaculture systems allow the development of specific 
aquatic flora in highly natural ponds with shallow banks. 

•  Another example of positive effect of aquaculture activity is found in the Lombardia region, 
where a farm breeds autochthonous sturgeon (Acipenser naccarii), not only for the market, 
but also for restocking Po and Ticino rivers.  

Adopting best practices that contribute to biodiversity conservation  

•  Fish farms included in natural areas have often adopted a Code of Best Practice and apply 
suitable  measures  for  minimizing  any  potential  impacts.  They  also  contribute  to  the 
conservation of habitats and species that are present on the site.  

•  The Natural Park of La Brenne in France is made up of near 4000 ponds created by man 
from the High Middle Ages. Nowadays they play a key role in the preservation of flora and 
fauna,  especially  waterfowl  nesting  and  migratory  birds.  Aqua-environmental  measures 
"fish  ponds",  are  applied  in  the  park,  whose  main  objective  is  to  develop  aquaculture 
production methods contributing to the improvement of the environment and preservation 
of nature. Some of these measures aim to recreate or maintain favourable conditions for 
insects,  amphibians,  birds  and  fish  (creation  of  open  water  behind  the  reeds,  creation  of 
shallow, reed beds or planting nympheas, remove willows invading reed, etc.) to maintain 
vegetation  belts,  to  avoid  fertilization,  to  manage  alien  species  like  coypu,  muskrat  and 
crayfish (shooting, trapping, use of filters), etc. 

• 

In  some  fishponds  in  Slovakia,  a  common  practice  is  to  prevent  the  removal  of  aquatic 
vegetation, which has led to patches of Typha and Phragmites in a considerable part of the 
fishpond-system  farms.  These  serve  as  breeding  site  for  heron-like  birds  (Purple  Heron, 
Spoonbill,  Night  Heron),  for  the  Marsh  Harrier,  for  the  Bittern,  Little  Bittern,  Red-necked 
Grebe, Black-necked Grebe (now rare) and the Ferruginous Duck.  

 
 
 
 
36 

Guidance document on aquaculture activities in the context of the Natura 2000 Network  

• 

• 

In  Poland,  some  key  elements  of  good  practice  that  aim  to  make  compatible  farming 
activity  with  Natura  2000  conservation  objectives  are,  for  example,  the  maintenance  of 
important  breeding  places  for  birds  such  as  reeds,  islands  and  fragments  of  osiers, 
building of floating islands (platforms) for terns, use of the mown rushes left in the ponds 
as breeding space, construction of observation towers for birdwatchers, etc.  

In  Czech  Republic, 
the 
Nesyt  Fishpond  which  is 
part of the Natura 2000 site 
fishponds”  and 
“Lednice 
which  hosts  fish  farming 
activities,  has 
integrated 
summer  drainage  as  a 
management  measure  to 
create  suitable  environ-
for 
mental 
halophilous 
of 
exposed  pond  substrates 
and  for  some  threatened 
wetland  birds  (Sychra  & 
Danihelka, 201044). 

conditions 
plants 

Figure 6. Narrowleaf dock (Rumex maritimus) in the central part of 
Nesyt fishpond during its summer drainage 

•  Suitable  management  of  aquaculture  in  coastal  areas  has  proved  to  be  beneficial  to  the 
conservation  of  natural  areas  and  the  species  they  host,  e.g.  in  many  parts  of  Southern 
Europe.  In  Sado  Estuary  (Portugal)  aquaculture  is  mainly  based  on  the  use  of  ancient 
saltpans transformed for extensive and/or semi-intensive production in polyculture regime. 
Under this scope extensive and semi-intensive aquaculture activities are authorized under 
certain  conditions  of  sustainable  use  and  integrated  management  practices  that  aim  at 
protecting natural habitats for nature conservation and biodiversity.  

•  Similar  use  of  ancient  saltpans  for  aquaculture  is  made  in  the  Bahía  de  Cadiz  Natural 
Park,  Spain,  where  aquaculture  activities  are  included  in  the  Management  Plan  of  the 
protected area and are considered compatible with the preservation of the natural values 
of the site under certain conditions. 

Supporting the systems that provide environmental benefits and services 

•  Shellfish  culture  can  provide  ecosystem  services  through  the  removal  of  inorganic 
nutrients from eutrophied ecosystems (bioextraction). Mussels are cultured and harvested 
as  a  method  of  water  quality  management  in  areas  with  diffuse  nutrient  inputs,  e.g.  in 
Sweden (Lundalv, 2011). Shellfish and seaweed can also be cultured in combination with 
fish  farming,  in  integrated  multitrophic  aquaculture  (IMTA),  where  shellfish  and  seaweed 
are harvested to compensate for nutrient enrichment through the metabolism of fish feed. 
This is under development in Norway and the Mediterranean.  

•  The  abandonment  of  traditional  fish  farms  can  lead  to  their  drying  up,  encroachment  by 
scrub  and  trees  or  replacement  with  other  land  use;  all  of  which  leads  to  the  decline  of 
biodiversity.  It  is  therefore  advisable  that  fishponds  that  provide  important  habitats  are 
adequately  managed  and  supported  so  that  their  natural  values  and  the  ecosystems 
services they provided are conserved and possibly enhanced.  

44 Sychra, J. and Danihelka, J. 2010. The summer drainage of Nesyt Fishpond in 2007: a successful 
conservation measure or ecological catastrophe?, pp 10-11, In: European Pond Conservation Network, 
Newsletter No. 3, Spring 2010. Available at:  
http://campus.hesge.ch/epcn/pdf_files/newsletters/EPCN_Newsletter_3.pdf 

 
 
 
 
                                                 
Guidance document on aquaculture activities in the context of the Natura 2000 Network 

37

4. THE IMPORTANCE OF STRATEGIC PLANNING 

•  The  development  and  application  of  spatial  planning,  including  maritime  spatial  planning  (MSP), 
together with integrated coastal zone management (ICZM) can facilitate the allocation of appropriate 
sites - with the correct water quality - for aquaculture activities. 

•  Most of the potential environmental impacts of aquaculture can be managed and minimized through 
the appropriate siting and management of farms. Site selection is a critical factor for determining the 
environmental pressures originating from an aquaculture activity and for ensuring the acceptability of 
aquaculture systems in sensitive sites. 

•  Key information is needed for spatial planning to allow the identification of conflicts between different 
interests at a strategic level. In particular, information about all Natura 2000 sites in the areas where 
aquaculture  activities  are  planned  will  be  crucial.  Sensitivity  maps  can  be  prepared  taking  into 
account the type of aquaculture activities that are planned, the type of ecosystems and habitats and 
the hydrodynamic conditions in those areas.  

•  Operational measurements of the capacity of the environment to accommodate aquaculture without 
unacceptable  impacts  should  be  taken  into  account  for  aquaculture  farm  site  selection  and  site 
management. Areas with evidence of limited assimilative capacity should be avoided. 

4.1  Spatial planning and strategic environmental assessment 

The  challenges  that  emerge  from  the  growing  competing  uses  of  freshwaters-  and  sea  (e.g. 
maritime  transport,  fishing,  aquaculture,  leisure  activities,  energy  production,  etc.)  must  be 
addressed,  while  the  needs  of  local  populations  and  the  protection  and  conservation  of  the 
environment have to be fulfilled. 

Spatial planning, including maritime spatial planning, is a public process which allows different 
demands  of  the  sectoral  policies  to  be  examined  in  an  integrated  way  across  a  broad 
geographical  area  so  that  a  more  coherent  regional  development  strategy  can  be  drawn  up 
that maximises win-wins and minimises conflicts wherever possible.  

It  also  provides  for  a  more  balanced  development  framework  because  it  enables  social, 
economic  and  environmental  concerns  to  be  taken  into  account  very  early  in  the  planning 
process.  In  addition,  it  may  encourage  different  economic  sectors,  interest  groups  and  the 
general  public  to  become  engaged  through  public  consultation,  thereby  ensuring  greater 
transparency in the decision making process. 

Spatial planning is a particularly useful tool for examining how to support economic and social 
development  whilst  at  the  same  time  avoiding  or  reducing,  wherever  possible,  potentially 
negative impacts on the natural environment, and preserving the integrity of Natura 2000 sites. 
The fact that this happens at early stage in the planning process is important as the scope for 
examining alternative approaches and scenarios is usually much greater at this level. Strategic 
spatial planning leads to a more predictable and stable planning framework for all concerned. 
This should, in turn, help reduce the risk of unforeseen difficulties and delays at later stages, 
for instance at the level of individual projects.  

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
38 

Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Some Member States have signalled their intention to update their inventory of potential sites 
for  aquaculture.  Furthermore,  many  Member  States  have  already  introduced  a  regime  for 
maritime spatial planning at national level or are in the process of doing so. In this context, a 
level playing field at national level should be ensured for aquaculture activities alongside with 
other sectors and policies. Spatial planning has a key role to play in providing guidance and 
reliable  data  for  the  location  of  economic  activities,  giving  certainty  to  investors,  avoiding 
conflicts and finding synergies between activities and environments. The role and function of 
aquaculture should be identified in this context. 

The European Commission is promoting maritime spatial planning as a stable and transparent 
way  to  improve  the  competitiveness  of  the  EU  maritime  economy  and  to  ensure  effective 
cross-border planning on trans-national issues. In 2008, the European Commission published 
a maritime spatial planning roadmap45. This roadmap was followed up by a progress report in 
2010 which, inter alia, concluded that further work on marine spatial planning (MSP) would be 
needed at EU level46. 

Test projects on Maritime Spatial Planning: MASPNOSE and Plan Bothnia 

The Commission has co-financed two test projects on MSP in the Baltic Sea (BOTHNIA) and in the 
North East Atlantic, including the North Sea and the Channel area (MASPNOSE). Each project 
involves bodies from different Member States and aims to gain practical experiences in applying 
MSP in a cross-border area. These projects run for 18 months and were concluded in May 2012. A 
call for proposals for further test projects in other European sea basins will be launched during the 
course of 2012.  

Further information about these tests projects can be found at:  
 http://ec.europa.eu/maritimeaffairs/spatial_planning_en.html 

The development and application of maritime spatial planning together with integrated coastal 
zone management (ICZM) (cf. 4.2) can facilitate the allocation of appropriate sites - with the 
correct  water  quality  -  for  aquaculture  applications.  In  addition,  these  planning  tools  could 
facilitate anticipating risks from, for instance, climate change effects, floods or coastal erosion 
that may affect aquaculture sites. 

The  Commission  is  preparing  a  new  proposal  to  develop  integrated  processes  for  maritime 
planning  and  coastal  management  which  would  help  in  achieving  the  above-mentioned 
objectives  for  nature  protection.  In  the  context  of  strategic  planning,  spatial  plans  or 
aquaculture  plans  and  programmes,  will  need  to  be  subject  to  a  Strategic  Environmental 
Assessment under the SEA Directive if they fulfil relevant conditions under that Directive. 

Where such plans and programmes are likely to significantly affect one or more Natura 2000 
sites, an Appropriate Assessment in accordance with article 6.3 of the Habitats Directive will 
also  be  required47.  These  assessments  provide  a  mechanism  for  examining  the  extent  and 
degree of potential negative effects on the environment and for exploring viable alternatives. 
For more details about the Appropriate Assessment of Plans and Programmes see chapter 5. 

45 http://ec.europa.eu/maritimeaffairs/spatial_planning_en.html 
46 COM(2010) 771. Maritime spatial planning in the EU - Achievements and future development. 
47  The  need  for  such  assessment  should  also  take  into  account  the  potential  for  aquaculture  to 
adversely affect the integrity of Natura 2000 sites even where there is no spatial overlap between the 
Natura 2000 area and the aquaculture site (e.g. water quality downstream). 

 
 
 
 
 
 
 
 
 
 
                                                 
Guidance document on aquaculture activities in the context of the Natura 2000 Network 

39

European Research and maritime spatial planning  

The European Commission finances, within the 7th Framework Programme, several projects 
related to the management of coastal areas and maritime spatial planning in order to increase 
the knowledge base necessary to support sustainable management and the related decision 
making processes.  

The most relevant projects are: 
•  MESMA – Monitoring and evaluation of spatially managed areas 
•  COEXIST – Integration in coastal waters: a roadmap to sustainable integration of 

aquaculture and fisheries 

•  SECOA – Solutions for environmental contrasts in coastal areas  
•  COCONET – Network of marine protected areas and assessment of the wind energy 

potential in the Mediterranean and Black Sea 

Further information can be found on the Research and Innovation website: 
http://ec.europa.eu/research/index.cfm    

4.2 

Integrated Coastal Zone Management 

Integrated  coastal  zone  management  (ICZM)  is  a  dynamic  process  which  promotes  the 
sustainable management of coastal zones and seeks to balance the environmental, social and 
economic  dimensions  of  sustainable  development  within  the  limits  set  by  the  area’s  natural 
characteristics  and  carrying  capacity.  The  objective  of  ICZM  is  to  properly  take  into 
consideration  all  policies,  sectors  and,  as  far  as  possible,  individual  interests,  involving  all 
coastal  stakeholders  in  a  participatory  way.  Aspects  like  ecosystem  conservation  and 
economic  development  are  also  taken  into  account.  ICZM  can  facilitate  aquaculture  site 
selection and sustainable management together with Maritime Spatial Planning. 

Following a EU Recommendation in 200248, Member States have used ICZM to regulate the 
spatial  deployment  of  economic  activities  and  set  up  spatial  planning  systems  for  Europe's 
coastal waters. The Recommendation identifies aquaculture among the sectors and areas to 
be addressed in the future National ICZM strategies. Building on the experiences gained with 
this  Recommendation,  the  European  Commission  is  preparing  a  new  joint  initiative  on 
integrated processes for maritime planning and coastal management (see also 4.1).  

Examples of ICZM in Europe  

All around Europe, there are many efforts being made to implement ICZM and many lessons could 
be taken from others' experiences if they were more easily accessible. The website OURCOAST 
seeks to bring to light these experiences, the knowledge and the tools that have been developed, 
why and how they have been put into practice. The data base can be searched according to: 
- Geographical selection 
- Themes (Adaptation to risk, Sustainable use of resources, Sustainable economic growth) 
-  Key  approaches  (Integration,  Participation,  Knowledge-based,  Ecosystem  based  approach, 
socio-economic and technical) 

The following examples for aquaculture activities can be highlighted: 
- Co-ordinated Local Aquaculture Management Systems for selected Irish water bodies (CLAMS) –  
-  Integrated  management  of  mussel  fishery  and  aquaculture  under  changing  baselines  due  to 
regime shifts in Denmark. 

Source: http://ec.europa.eu/ourcoast/index.cfm?menuID=3 

48  Recommendation  2002/413/EC  of  the  European  Parliament  and  of  the  Council  of  30  May  2002 
concerning the implementation of Integrated Coastal Zone Management in Europe. 

 
 
 
 
 
 
 
 
                                                 
40 

Guidance document on aquaculture activities in the context of the Natura 2000 Network  

4.3 Determining suitable locations for aquaculture developments 

It is widely acknowledged that most of the potential environmental impacts of aquaculture can 
be managed, minimised or enhanced through an understanding of the processes involved and 
the appropriate siting and management of farms.  

Site selection is a critical factor for determining the environmental pressures originating from 
an  aquaculture  activity  and  in  ensuring  the  acceptability  of  aquaculture  systems  in  sensitive 
sites.  This  includes  the  position  of  the  site  relative  to  the  feature  of  conservation  interest, 
whether the facility is concentrated in one position or dispersed around a number of sites and 
whether  the  facility  is  exposed  to  risk  from  natural  elements  (e.g.  strong  prevailing  winds, 
wave  action,  etc)  or  conflict  with  other  coastal  users  (e.g.  navigation,  fishing  activities, 
recreational users) (Huntington et al., 2006). 

In  order  to  develop  a  sustainable  aquaculture  plan  or  project  and  to  minimise  the  potential 
negative impacts and even strengthen the positive ones, aquaculture planners need to be fully 
aware of the environmental context. Aquaculture planning and site selection should be based 
on  the  best  legal,  environmental,  technical  and  socio-economic  knowledge  to  enhance  the 
viability of the process.  

Operational  measurements  of  the  capacity  of  the  environment  to  accommodate  aquaculture 
without unacceptable impacts should be taken into account for aquaculture farm site selection 
and site management. Areas with evidence of limited carrying or assimilative capacity should 
be avoided (IUCN 2009, Scottish Parliament, 200249) when determining suitable locations. 

Seed mussel collection systems in Natura 2000 sites in Netherlands 

In  2009  a  policy  was  developed  for  seed  mussel  collection  systems  in  Netherlands.  The  mussel 
fishery sector, government and nature organisations have agreed to phase out traditional methods 
and make room for the alternative collection systems.  The Government has initiated an open plan 
process together with all parties concerned (fishery and recreational sectors, nature organisations, 
provincial authorities) to draw up policy for 2010-2013. This involved selecting suitable locations for 
seed  mussel  collection  systems.  Some  890  hectares  in  Natura  2000-sites  Waddenzee, 
Oosterschelde  and  Voordelta  were  designated  as  potential  locations.  Apart  from  nature,  other 
interests relating to recreation, safety and archaeology were also weighed in the selection process.  

The  Government  carried  out  an  appropriate  assessment  of  the  potential  locations.  The 
assessments  were  based  on  a  worst-case  scenario.  The  ecological  effects  of  the  seed  mussel 
collection systems on the seabed, birds and seals were studied.  

mosselzaadinvanginstallaties 

Sources:  
Beleid 
publicaties/brochures/2010/01/04/beleid-mosselzaadinvanginstallaties-mzi-s-2010-t-m-2013.html  
Rapport  C089/09:  Passende  Beoordeling  voor  mosselzaadinvang 
http://english.minlnv.nl/portal/page?_pageid=116,1640321&_dad=portal&_schema=PORTAL&p_file_id=43669  

http://www.rijksoverheid.nl/documenten-en-

in  Nederlandse  kustwateren 

2013. 

(MZI) 

2010 

t/m 

4.4 Key information for spatial planning - identifying conflicts at a strategic level 

A key to good spatial planning is sound geographical knowledge. Much of the planning is done 
with  the  help  of  maps  which  makes  it  possible  to  overlay  different  interests,  activities, 
resources, etc. on base maps that show the area’s natural geography and existing land uses. 
From these overlays, decisions can be made about zoning certain areas for particular types of 
development.  

relevant 

49  The 
found 
http://www.scottish.parliament.uk/business/committees/historic/x-transport/reports-02/trr02-05-vol01-02.htm#2 
(beginning just above paragraph 19). 

the  Scottish  Parliament's 

section 

report 

can 

be 

of 

at 

 
 
 
 
 
 
 
 
 
                                                 
Guidance document on aquaculture activities in the context of the Natura 2000 Network 

41

A  first  step  to  identify  possible  conflicts  with  Natura  2000  would  require  overlying  maps 
showing  the  location  and  boundaries  of  Natura  2000  sites  within  a  particular  geographical 
region  with  the  potential  aquaculture  sites  identified.  By  this  means,  it  should  be  possible  to 
quickly identify areas where there may be a higher risk for conflict. The Natura 2000 viewer is 
available online and may be is used for detailed site specific overviews (see box). 

The Natura 2000 viewer – immediate online access to Natura 2000 maps 

The European Commission, with the assistance of the European Environment Agency (EEA), has 
developed a new on-line facility called the ‘Natura 2000 viewer’ which enables the user to locate 
and explore Natura 2000 sites anywhere in the EU at the press of a button. 
See: http://natura2000.eea.europa.eu/) 

Various different search options are available: 
•  browse in a particular area to see which, if any, Natura 2000 are present – for instance along a 
coastal zone. By typing in the location: eg nearest village, the map will automatically zoom into 
that area and highlight all the Natura 2000 sites present there. 
locate a specific Natura 2000 site for which the name or site code is already known   

• 
•  search for a particular species or habitat type protected under the Habitats Directive and see 

which sites have been designated for it  

•  search according to different backgrounds: a street map, a satellite map, a Corine Land Cover 

map or a biogeographical map.  

For each Natura 2000 identified on the map a standard data sheet is available which identifies the 
species and habitat types for which it was designated, estimated population sizes and conservation 
status, and the importance of that site for the species. These Standard Data Forms are the forms 
that have been officially submitted to the Commission as part of the designation process and need 
to be cross referenced with the annexes of the Directives   

Example  of  map  from  Natura  2000  viewer  for  the  Atantic  coast  in  France.  In  Red  the  SPA  site 
designated  under  the  Birds  Directive,  in  blue  the  SCI  site  designated  under  the  Habitats  Directive 
(sometimes they overlap)  

 
 
 
 
 
 
 
 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Detailed  investigation  of  potential  conflict  areas  should  also  consider  the  sensitivity  of  the 
ecosystems and habitats that are present in the respective Natura 2000 sites where (or close 
to  which)  aquaculture  activities  are  planned,  as  well  as  the  hydrodynamic  conditions  in  the 
concerned  area,  as  these  have  a  significant  influence  on  the  transport  of  sediments  and 
waste.  

Sensitivity maps can be prepared taking into account the type of aquaculture activities that are 
planned  and  their  predictable  pressures,  the  type  of  ecosystems  and  habitats  and  the 
hydrodynamic conditions in those areas. 

The  new  Commission  initiative  on  maritime  spatial  planning  and  coastal  zone  management 
(cf.  4.1)  is  inter  alia  intended  to  contribute  to  the  integration  of  these  different  information 
needs  leading  to  the  preparation  of  such  multi-user  maps.  The  experiences  gained  with  the 
Natura 2000 areas will be helpful to this end.  

4.5 Examples of aquaculture planning and aquaculture activities in Natura 2000 areas 

Some administrations provide support for a good planning of aquaculture activities, especially 
in  areas  where  this  kind  of  activity  has  a  traditional  importance  for  the  local  economy.  A 
relevant  example  can  be  found  in  Scotland  where  aquaculture  is  guided  by  the  Scottish 
Government, with planning of individual developments governed by Local Authorities.  

Scotland: planning for aquaculture 

The Scottish Government aims to promote a policy that supports the sustainable economic growth 
of  aquaculture.  The  need  for  high  standards  of  environmental  protection  is  recognised  at  every 
stage of fish farm planning, operation and regulation 

Spatial  planning  for  aquaculture  in  Scotland  dates  back  to  the  late  1980s,  when  Fish  Farming 
Framework Plans where first produced to fill a perceived gap in planning guidance for the industry 
at  local  level.  This  approach  has  since  been  adopted  by  other  local  authorities  and  refined  over 
time. Currently the Local Authority is the competent authority in relation to fish farm developments. 
All new or modifying fin-fish developments (over 0.1 ha) are subject to EIA. 

The  Local  Authority  is  also  required  to  take  into  account  the  direct  and  cumulative  effects  of  the 
proposed development on the environment. This may include the carrying capacity (designated on 
the  basis  of  predictive  modelling  to  estimate  nutrient  enhancement  and  benthic  impact  in  sea 
lochs),  visual  impact  and  the  effects  on  the  landscape  (landscape  guidance  is  produced  by 
Scottish Natural Heritage), effects on the marine historic environment and the sea or loch bed, and 
fish disease risk. 

Any  new  development  (or  modification,  depending  on  what  that  modification  involves)  must  also 
obtain a licence either from the Scottish Environment Protection Agency or from Marine Scotland in 
relation  to  discharges  from  fish  farm  sites,  or  wellboats.  In  addition,  a  voluntary  Code  of  Good 
Practice  has  been  developed  by  fish  farming  stakeholders  addressing  a  range  of  issues  outwith 
planning control, including: cage and equipment design, bio-security, management and operational 
practices. 

In  instances  where  a  development  is  likely  to  have  a  significant  effect  on  a  Special  Areas  of 
Conservation,  an  Appropriate  Assessment  is  undertaken  to  address  the  potential  impact  on  the 
conservation feature prior to any planning decision being taken by the competent authority. Loch 
Sunart is an example of an aquaculture framework plan that incorporates a marine SAC50. 

50 More information available at: http://www.highland.gov.uk/NR/rdonlyres/9676B889-D077-4B70-8706-
0AF9EBAE3720/0/loch_sunart_september_2004.pdf 

 
 
 
 
 
 
 
 
 
 
 
                                                 
Guidance document on aquaculture activities in the context of the Natura 2000 Network 

43

Recently,  there  have  been  attempts  to  develop  more  integrated  plans,  covering  aquaculture 
alongside other activities, and extending into the marine environment. Detailed plans like those for 
Sound  of  Mull  and  Loch  Fyne  have  attempted  to  highlight  areas  for  potential  expansion  of 
aquaculture developments, based on constraints mapping. This has proved more difficult in plans 
covering larger areas (like that for Shetland).  

Examples of these more integrated plans are: 
•  Sound  of  Mull  marine  planning  pilot:  General  policies  on  aquaculture,  Locational  policies  for 

aquaculture  

•  Loch Fyne ICZM plan  
•  Shetland marine planning pilot  

A National Marine Plan will govern more detailed planning at the regional level and bring greater 
clarify  to  decision  making  in  the  marine  environment.  In  addition,  Local  Authority  development 
plans will provide advice on areas that are suitable for aquaculture development and areas where 
such development may be constrained. 

The  Southwest  Finland  and  Satakunta  aquaculture  site  selection  plan  is  an  example  of 
regional planning. The selection plan was prepared in a wide regional expert working group, 
with  delegates  from  the  aquaculture  industry,  environmental  and  fishery  administration, 
regional planning organisations and research. 

Finnish aquaculture site selection plan 

The purpose of the national aquaculture site selection plan is to direct new fish farms to water 
areas, which are suitable from the environmental, fish farmers´ and other coastal users’ point 
of  view.  The  Southwest  Finland  and  Satakunta  working  group  used  GIS  spatial  planning  tool  to 
identify suitable water areas for aquaculture production. At the coast, unsuitable water areas were 
excluded  with  buffers  concerning  the  depth  of  sea,  summer  cottages,  water  ways,  nature 
protection areas etc. 

 
 
 
 
 
 
 
 
44 

Guidance document on aquaculture activities in the context of the Natura 2000 Network  

In the preliminary site selection plan fish farms were not directed in national parks. Moreover, the 
working  group  suggested  that  new  fish  farms  should  not  be  without  complete  investigations 
established  in  Natura  2000  areas  with  underwater  reefs  (SCI  sites/Habitat  Directive),  if  depth  is 
lower  than  20  meters.  In  addition,  a  500  meter  wide  safety  zone  during  the  nesting  time  was 
modeled around the bird Islands in Natura 2000 areas (SPA sites/Bird Directive).  

With  these  wide  safety  zones  it  is  unlikely  that  fish  farms  have  a  significant  effect  to  the  nature 
values  protected  with  Natura  2000  sites.  However,  the  need  for  an  Appropriate  Assessment  is 
evaluated  in  connection  with  production  license  application.    Fish  farmers  can  apply  production 
licenses  in  the  water  areas,  which  are  not  identified  in  the  aquaculture  site  selection  plan.  If  this 
kind  of  site  is  inside  NATURA  area,  exhaustive  assessments  are  needed  to  support  the 
application. 

 
 
 
 
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45

5.  STEP-BY-STEP PROCEDURE FOR AQUACULTURE 
PLANS AND PROJECTS AFFECTING A NATURA 
2000 SITE 

•  The Habitats Directive (article 6) sets out a series of safeguards that must be applied to plans and 
projects  that  are  likely  to  have  a  significant  effect  on  a  Natura  2000  site.  The  first  step  is  to 
determine whether a plan or project may have a significant effect upon a Natura 2000 site. In such 
case, it should undergo an Appropriate Assesment (AA). 

•  The  purpose  of  the  AA  is  to  assess  the  implications  of  the  plan  or  project  in  respect  of  the  site’s 
conservation objectives, individually or in combination with other plans or projects. The conclusions 
should  enable  the  competent  authorities  to  ascertain  whether  or  not  the  plan  or  project  would 
adversely affect the integrity of the site concerned. 

•  The  appropriate  assessment  must  consider  all  the  potential  pressures  and  impacts  on  the  sites’ 
conservation  interests.  The  Appropriate  Assessment  must  focus  on  the  species  and  habitats  that 
have justified the site’s designation as a Natura 2000 site and all the elements that are essential to 
the functioning and the structure of that site. 

•  AAs should be made on a case by case basis, with a degree of expertise available at each stage of 
the  assessment.  The  appraisal  of  effects  should  be  based  on  the  best  scientific  knowledge 
available, expert judgement and on-site surveys, as required. 

• 

 The outcome of the AA is legally binding. If it cannot be ascertained that there will be no adverse 
effects on the integrity of the Natura 2000 sites, even after the introduction of mitigation measures 
or  conditions  in  the  development  permit,  then  the  plan  or  project  cannot  be  approved  unless  the 
derogation procedure under Article 6 (4) is invoked. 

5.1  Article 6 of the Habitats Directive  

Article  6  of  the  Habitats  Directive  sets  out  provisions  which  govern  the  conservation  and 
management of Natura 2000 sites and determines the relationship between conservation and 
land-use. Paragraph (1) requires the establishment of the necessary conservation measures, 
and  is  focused  on  positive  and  proactive  interventions.  Paragraph  (2)  requires  that  within 
Natura 2000 sites habitat deterioration and significant species disturbance is avoided.  

Paragraphs  (3)  and  (4)  on  the  other  hand  set  out  a  series  of  procedural  and  substantive 
safeguards that must be applied to plans and projects that are likely to have a significant effect 
on a Natura 2000 site. This procedure is designed to:  

•  Fully assess the impacts of plans or projects that are likely to have a significant negative 

effect on a Natura 2000 site by means of an Appropriate Assessment;  

•  Ascertain through the Appropriate Assessment, whether the impact will adversely affect 
the  integrity  of  the  site  and,  if  this  is  the  case,  whether  the  plan  of  project  can  still  be 
approved if certain mitigation measures or planning conditions have been introduced that 
remove or minimise the adverse effects on the site to a non-significant level;   

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
46 

Guidance document on aquaculture activities in the context of the Natura 2000 Network  

•  Provide a mechanism for approving, in exceptional circumstances, plans or projects that 
have  an  adverse  effect  on  a  Natura  2000  site  even  after  the  introduction  of  mitigation 
measures,  if  these  plans  or  projects  are  considered  to  be  necessary  for  imperative 
reasons of overriding public interest but where no suitable alternative solutions exist (cf 
Art 6.4)   

ARTICLE 6 (3) and (4) of the HABITATS DIRECTIVE 

•  6(3).   Any plan  or project not  directly connected with or  necessary to the  management of the site 
but likely to have a significant effect thereon, either individually or in combination with other plans or 
projects,  shall  be  subject  to  appropriate  assessment  of  its  implications  for  the  site  in  view  of  the 
site's conservation objectives. In the light of the conclusions of the assessment of the implications 
for  the  site  and  subject  to  the  provisions  of  paragraph  4,  the  competent  national  authorities  shall 
agree to the plan or project only after having ascertained that it will not adversely affect the integrity 
of the site concerned and, if appropriate, after having obtained the opinion of the general public. 

•  6(4).  If,  in  spite  of  a  negative  assessment  of  the  implications  for  the  site  and  in  the  absence  of 
alternative  solutions,  a  plan  or  project  must  nevertheless  be  carried  out  for  imperative  reasons  of 
overriding  public  interest,  including  those  of  a  social  or  economic  nature,  the  Member  State  shall 
take all compensatory measures necessary to ensure that the overall coherence of Natura 2000 is 
protected. It shall inform the Commission of the compensatory measures adopted.  Where the site 
concerned  hosts  a  priority  natural  habitat  type  and/or  a  priority  species,  the  only  considerations 
which  may  be  raised  are  those  relating  to  human  health  or  public  safety,  to  beneficial 
consequences  of  primary  importance  for  the  environment  or,  further  to  an  opinion  from  the 
Commission, to other imperative reasons of overriding public interest. 

5.2  When is the Article 6 procedure applicable?  

The assessment and authorisation procedure under Article 6(3) and (4) applies to any activity 
(or changes to an existing activity) which: 
a)  Is not directly connected with or necessary to the management of a Natura 2000 site; 
b)  Is likely to have a significant effect thereon, either individually or in combination with other 

plans or projects, in view of the site's conservation objectives. 

It covers:  
•  Plans or projects affecting sites classified under the Birds Directive and sites designated or 
proposed to be designated under the Habitats Directive (both are part of the Natura 2000 
network.)51 

•  Plans  that  serve  as  a  framework  for  development  consents  and  individual  projects.  This 
ensures that the potential impacts on Natura 2000 sites are taken into account at both the 
strategic planning level and at the level of each individual project52. 

•  Plans  or  projects  inside  and  outside  the  Natura  2000  site  if  they  are  likely  to  have  a 
significant effect on the Natura 2000 site (e.g.  a project  located upstream a Natura 2000 

51  For  Potential  SPAs  (IBA),  Article  6(3)-(4)  is  not  applicable  but  Article  4(4)  of  the  BD  is  applicable. 
Areas which have not been classified as SPAs but should have been so classified continue to fall under 
the  regime  governed  by  the  first  sentence  of  Article  4(4)  of  the  Birds  Directive  [Basses  Corbières,  C-
374/98]. For potential pSCIs:  MSs are required to take protective measures that are appropriate, from 
the point of view of the Directive’s conservation objective, for the purpose of safeguarding the relevant 
ecological interest which those sites have at national level [Dragaggi, C-117/03; Bund Naturschutz, C-
244/05].   
52 Case C-6/04: 20 October 2005. 

 
 
 
 
 
 
 
 
                                                 
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47

site  may  still  have  a  significant  effect  on  the  species  and  habitats  downstream  in  that 
Natura 2000 site and vice versa)53. 

•  Aquaculture  activities  that  were  authorised  before  the  designation  of  the  site  as  Natura 
2000 must, to the extent that they constitute a project and are likely to have a significant 
effect  on  the  site  concerned,  undergo  an  assessment  of  their  implications  for  that  site 
where  they  are  continued  after  designation  of  the  site54.  This  also  applies  to  authorised 
aquaculture developments where new aspects are introduced or management is changed 
(e.g. intensification). 

5.3  A step-by-step procedure 

The  procedure  laid  out  in  Article  6(3)  and  6(4)  should  be  carried  out  in  stages.  Every  stage 
determines whether a further step in the process is required. For instance if, after the first step, 
it is concluded that there will be no significant effects on the Natura 2000 site, then the plan or 
project can be approved without the need for further assessment.  

The  following  flow  chart  (Figure  7)  demonstrates  how  the  stages  are  applied  and  how 
decisions  are  reached  on  the  authorisation  or  rejection  of  a  plan  or  project.  Subsequent 
sections in this chapter examine each of the stages to be undertaken as part of the process 
under Article 6.3.  

It  is  clear  from  the  above  that  this  decision-making  process  is  underpinned  by  the 
precautionary  principle.  The  emphasis  should  be  on  objectively  demonstrating,  with  reliable 
supporting  evidence,  that  there  will  be  no  adverse  effects  on  the  integrity  of  Natura  2000 
sites55.  For  this  reason,  the  lack  of  scientific  data  or  information  on  the  potential  risk  or 
significance of impacts cannot be a reason to proceed with the plan or project. 

5.4  When is an Appropriate Assessment (AA) needed? 

STAGE 1. SCREENING 

The first step is designed to determine whether or not an AA is needed. If it can be determined 
with certainty that the plan or project is not likely to have a significant effect, either individually 
or in combination with other plans or projects, then the plan or project can be approved without 
further assessment. 

5.4.1  Gathering information about the plan or project and the Natura 2000 site(s) 

The screening exercise is usually carried out by the authority responsible for the adoption of 
the plans or the approval of development applications and/or the nature authorities. Most often 
they will  seek  the  assistance  of, and  base their  evaluation  on, the  information received  from 
the  developers,  environmental  authorities  or  contracted  experts.  The  collaboration  of  nature 
conservation  authorities  is  crucial,  as  they  can  provide  all  the  relevant  information  on  the 
Natura 2000 sites that should be taken into account at this stage. 

53 Case C-98/03  paragraph  32:  "…In its definition  of  measures  to  be subject to an  assessment of the 
implications, the Directive does  not distinguish between measures taken outside  or inside a  protected 
site." 
54 See Judgement of the ECJ on case C-226/08 (Papenburg). “Ongoing maintenance works which were 
authorized under national law before the expiry of the time-limit for transposing the Habitats Directive, 
must, to the extent that they constitute a project and are likely to have a significant effect on the site 
concerned, undergo an assessment of their implications for that site where they are continued after 
inclusion of the site in the list of SCIs pursuant to the third subparagraph of Article 4(2) of that directive”. 
55 See Waddensea ECJ ruling C-127/02  

 
 
 
 
 
 
 
 
 
 
 
 
                                                 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Figure 7.  Flow chart of Article 6(3)-(4) procedure 

 
 
 
Guidance document on aquaculture activities in the context of the Natura 2000 Network 

49

To  carry  out  the  screening  exercise,  sufficient  information  should  be  gathered  both  on  the 
aquaculture plan or project and on the Natura 2000 site(s) that might be affected. In the case 
of  the  plan  or  project,  this  information  should  include  data  on  the  location  of  the  farm  and 
associated infrastructures in relation to the Natura 2000 site(s), as well as details on the timing 
and  duration  of  all  the  planned  activities  during  each  stage  of  the  project’s  cycle,  i.e. 
construction, operation, maintenance, etc. 

Information must also be gathered on the species and habitat types for which the sites have 
been  designated  and  on  the  overall  conservation  objectives  of  the  site  (see  further  details 
under 5.5). Part of this information can be found in the Natura 2000 Standard Data Forms or 
in the site designation or management plans where available. 

Natura 2000 Standard Data Form 

The Standard Data Form which is available for each Natura 2000 site contains information on the EU 
protected species and habitat types for which the site has been designated (often referred to as ‘target 
features’) and provides a broad assessment of the condition of each species or habitat type on that site 
(scored  from  A  to  D).  It  provides  information  about  surface  area,  representativity  and  conservation 
status of the habitats present in the site, as well  as the global assessment of the value of the site for 
conservation of the natural habitat types concerned. For the species present in the site, information is 
provided on their populations, status (resident, breeding, wintering, migratory) and on the site value for 
the species in question. 

Conservation measures and management plans  

For special areas of conservation, Member States shall establish the necessary conservation measures 
involving, if need be, appropriate management plans specifically designed for the sites or integrated into 
other  development  plans,  and  appropriate  statutory,  administrative  or  contractual  measures  which 
correspond  to  the  ecological  requirements  of  the  natural  habitat  types  in  Annex  I  and  the  species  in 
Annex II present on the sites. 

When available, Natura 2000 management plans can provide information about the sites’ conservation 
objectives, the location and status of the species and habitats occurring in the site, their threats and the 
conservation  measures  required  to  improve  their  conservation  status,  which  can  be  useful  for  the 
screening stage and for the appropriate assessment.  

It  is  worth  recalling  that  the  initial  screening  undertaken  here  is  not  the  same  as  a  full-scale 
Appropriate Assessment – it only requires sufficient information to be able to decide if there is 
likely to be a significant effect or not. 

It  is  strongly  recommended  that  information  on  the  Natura  2000  site  is  gathered  prior  to  the 
design  of  a  plan  of  project  (i.e.  even  before  screening  stage)  so  that  possible  sensitivities 
regarding  nature  and  wildlife  can  be  identified  and  taken  into  consideration  during  the 
preparation  of  a  development  proposal.  This  could,  for  instance,  influence  the  choice  of 
location  for  the  farm  as  well  as  its  actual  design  so  that  only  the  most  appropriate  sites  are 
taken forward.  

It is also very useful, at an early pre-screening stage, for developers to hold initial discussions 
with  their  planning  authority  and  with  the  statutory  nature  conservation  authorities  to  learn 
more about the potential environmental constraints the project might face and how these might 
be best avoided. This could also help to identify any potential issues to watch out for or any 
gaps in scientific knowledge that might need further investigation before the plan or project is 
approved.  

Experience  has  shown  that  good  research  and  consultation  right  from  the  start  before  work 
begins  on  the  development  proposal  helps  to  avoid  unnecessary  time  and  expense  on 
unsuitable sites later on. 

 
 
 
 
 
 
 
 
 
 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Key activities at the stage of screening: 

• 
• 
• 

Identify the geographical scope of the plan or project, and its main characteristics 
Identify all Natura 2000 sites that might be affected by the plan or project. 
Identify  the  qualifying  interests  of  the  Natura  2000  sites  concerned  (i.e.  the  habitats  and 
species for which the sites are designated) and the sites’ conservation objectives.  
• 
Identify which of those species and habitats could be affected by the planned activities  
•  Analyse  other  plans  or  projects  which  could,  in-combination  with  the  planned  activities, 

give rise to a likely significant effect on Natura 2000 sites. 

•  Analyse all possible interactions between the plan or project activities, either individually or 
in  combination  with  other  plans  or  projects,  and  the  qualifying  interests,  the  ecological 
functions and processes that support them. 

•  Determine whether significant impacts are likely to occur, justify the conclusion and record 

the final decision of the screening stage. 

5.4.2  Determining if the plan or project "is likely to have a significant effect" 

An Appropriate Assessment will only be required for those plans or projects that are ‘….likely 
to have a significant effect ...’. The first step is therefore to identify which of the species and 
habitats  for  which  the  Natura  2000  has  been  designated  (the  qualifying  interests)  could  be 
significantly affected by the planned activities. 

All  the  potential  pressures  from  the  planned  aquaculture  activities,  either  through  direct 
overlap  (e.g.  sedimentation  on  seabed  areas)  or  induced  at  a  larger  scale  (e.g.  nutrient 
enrichment),  that  might  have  significant  effects  on  the  conservation  objectives  of  the  Natura 
2000 site should be identified and the sensitivity and vulnerability of the relevant species and 
habitats to those pressures should be considered to assess the risk of significant effects. 

The  emphasis  is  on  a  ‘likelihood’  of  significant  effects  –  not  certitude.  This  shows  the 
precautionary nature of this initial test. The biodiversity elements liable to be affected (habitats, 
species,  ecological  processes)  should  be  determined,  taking  into  account  their  sensitivity  in 
relation to the planned activities. Where the preliminary evaluation indicates that there may be 
grounds for concern, or where there is a doubt whether the effects are likely to be significant 
or not, an Appropriate Assessment must be carried out to ensure that these potential effects 
can  be  studied  in  full.  The  lack  of  information  or  data  cannot  be  used  as  a  reason  for  not 
carrying out an Appropriate Assessment56. 

The  significance  of  the  effects  is  linked  to  the  site’s  conservation  objectives  and  will 
depend  on  the  degree  of  the  impact  and  the  sensitivity  or  vulnerability  of  habitats  and 
species to the potential pressures and impacts from the aquaculture activities. The degree to 
which a particular area is impacted by a particular pressure varies depending on the species 
and  habitats  present  in  the  area  and  on  the  pressure  involved.  Effects  must  also  be 
considered  for  other  species  and  habitats  that  may  be  important  (e.g.  as  a  food  source,  for 
breeding or refuge, etc.) for the species and habitats for which the site has been designated, 
which can be included in the conservation objectives for that reason. In assessing the potential 
effects of a plan or project, their significance must be established in the light, inter alia, of the 
characteristics  and  specific  environmental  conditions  of  the  site  concerned  by  that  plan  or 
project57. 

The analysis of sensitivity of marine habitats has been the focus of recent projects and studies 
that are relevant to this guidance document. The Marine Life Information Network (MarLIN), an 

56 ECJ ruling C-127/02 Waddensea, paragraph 43 et. seqq.:  
57 Case C-127/02, paras 46-48 

 
 
 
 
 
 
  
 
 
                                                 
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51

initiative  of  the  Marine  Biological  Association  of  the  United  Kingdom,  has  undertaken  an 
assessment  of  sensitivity  to  different  impacts  for  habitats  around  the  coasts  of  Britain  and 
Ireland58. 

A  recent  study  in  Ireland  has  carried  out  an  assessment  of  potential  impacts  of  pressures 
associated with human activities on sea bed habitats (Crowe et al 2011)59. The study involved 
a  systematic  review  of  the  literature  and  consultation  with  appropriate  experts  and  analysed 
the  resistance  of  sea  bed  habitats  to  potential  impacts  of  different  pressures  on  extent  and 
quality, as well as the likely time to recovery (resilience).  

In  relation  to  species  and  habitats’  potential  sensitivity  to  impacts  of  aquaculture,  some 
countries  (e.g.  France  and  United  Kingdom)  have  published  guidelines  to  help  identify  the 
potential negative effects derived from fish farming activities on some habitats and species of 
the  Habitats  and  Birds  Directives.  Some  other  national  initiatives  provide  useful  tools  and 
information  to  support  marine  species  and  habitat  conservation,  sustainable  management, 
protection and planning. Relevant information sources are included in Annex 2. 

5.4.3 Assessing the risk of potential cumulative effects with other plans and projects 

The  screening  process  applies  to  plans  or  projects  either  individually  or  in  combination  with 
other  plans  or  projects.  It  may  be  that  one  aquaculture  project  alone  might  not  have  a 
significant  effect  but,  if  taken  in  combination  with  other  plans  or  projects  (other fish farms  or 
other developments) within the area, the cumulative effects may turn out to be significant. It is 
necessary  at  the  stage  of  screening  to  identify  other  plans  or  project  which  might  have 
combined effects on the site with the project under assessment.  

The  geographical  scale  over  which  these  cumulative  effects  need  to  be  considered  will 
depend on the exact circumstances and scale of the plan or project being studied but should 
cover  a  sufficiently  large  area  to  capture  any  cumulative  effects.  The  relevant  nature 
conservation authorities will be able to help identify the possible plans or projects that need to 
be considered as part of the in-combination test. 

5.4.4  Recording the screening decision  

As screening is a legal requirement, the reasons for the final decision is to whether or not to 
carry out an Appropriate Assessment should be recorded and sufficient information should be 
given to justify the conclusion.  

If  the  conclusion  of  screening  is  that  no  significant  effects  on  Natura  2000  sites  are  likely  to 
occur, there is no need to proceed further. Where it is concluded that the planned activities are 
likely to cause significant effects on the site, the screening stage can also be useful to identify 
the issues to be considered in detail in the Appropriate Assessment.  

58  MarLIN  2005.  Marine  life  protection.  Marine  Life  Information  Network:  Biology  and  Sensitivity  Key 
Information Sub-programme [on-line]. Plymouth: Marine Biological  Association of the United Kingdom. 
Available at: http://www.marlin.ac.uk 
59 A framework for managing sea bed habitats in near shore Special Areas of Conservation. 
Tasman P. Crowe, Jayne E. Fitch, Chris L. J. Frid & Paul J. Somerfield. Report for the Department of 
the Environment, Heritage and Local Government, Ireland. April 2011 

 
 
 
 
 
 
 
 
 
 
 
 
                                                 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network 

EXAMPLE OF TEST OF LIKELY SIGNIFICANT EFFECT (‘SIGNIFICANCE TEST’) 

Mussel seed cultivation in the Wash and North Norfolk Coast European Marine Site (SAC), England 
The assessment of impacts of mussel cultivation activities considered issues at the on-growing and harvesting stages of mussel cultivation, but not the seed collection stage – which is subject 
of another consent procedure. The Test of Likely Significant (TLS) Impact was prepared by the consenting authority and submitted to the nature conservation authority (Natural England). The 
TLS concluded that the leasing of plots for shellfish cultivation was not necessary for conservation management purposes, and that the leases were likely to have a significant effect on the 
site. The specific issues were: changes in nutrient levels (through the presence of a large additional biomass of mussels compared with the natural level), and the smothering of natural 
biotopes by covering with cultivated mussel beds or disturbed and re-settled sediments. Table below provides a summary of some of the potentially affected features, the relevant conservation 
objectives for those features, and the potential impact mechanisms for effects resulting from the mussel cultivation activities. It shows the issues to be considered in detail in the appropriate 
assessment, based on Natural England’s scoping advice for this review. 
Conservation 
features or 
sub- features 

Significant: to be considered in full appropriate 
assessment 

Relevant conservation objectives  
(outlines) 

Potential impact 
mechanisms from 
mussel cultivation 
activities 
Physical loss by  
smothering. 

Intertidal 
mudflats and 
sandflats 

Physical damage by 
abrasion 

Biological 
disturbance through 
selective introduction 
of species 

Subtidal 
sandbanks 

Physical loss by  
smothering. 

Physical damage by 
abrasion 

Biological 
disturbance through 
selective introduction 

Biotope composition of littoral sediment – maintain the variety of 
biotopes in each sub-feature (mud, muddy sand, sand & gravel), allowing 
for natural succession / known cyclical change. 
Sediment character (sediment type) – maintain distribution of mud, 
muddy sand, sand & gravel, allowing for natural succession / known 
cyclical change. 
Extent of characteristics biotopes 
Distribution of biotopes – maintain distribution of biotopes in each sub-
feature (mud, muddy sand, sand & gravel), allowing for natural 
succession / known cyclical change  
Species: composition of characteristic biotopes. 

Extent – no change in extent of sublittoral sediment habitat  
Distribution – maintain the pattern of distribution of predominant 
habitats throughout the feature (within “Large shallow inlets and bays” 
feature) 

Yes, the intertidal area potentially lost through smothering 
because of shellfish cultivation is not significant compared 
with the total extent of intertidal area in the Site, but the 
proportion of individual biotopes affected needs to be 
considered.  
No, no potential for significant damage through abrasion 
since mussel dredge scoops mussel from surface of 
pseudofaeces but does not abrade intertidal substratum. 
No: Mytilus edulis occurs naturally within this sub-feature.  
Presence of mussels increases epifaunal diversity compared 
with original substratum, though cultivated mussel beds less 
divers than natural beds (cultivation leases not granted in 
natural mussel or cockle bed areas). 
Yes, the intertidal area potentially lost through smothering 
because of shellfish cultivation is not likely to be significant 
compared with the total extent of subtidal sandbanks in the 
Site, but this needs further evaluation in the full assessment.  
No, no potential for significant damage through abrasion 
since mussel dredge scoops mussel from surface of 
pseudofaeces but does not abrade intertidal substratum. 
Cultivated mussel lays primarily in intertidal areas with only 
very small spill-over into adjacent shallow subtidal areas. 
No: Mytilus edulis occurs naturally within this sub-feature.  
Presence of mussels increases epifaunal diversity compared 
with original substratum, though cultivated mussel beds less 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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53

of species 

Large shallow 
inlets and bays 

Changes in nutrient 
and/or organic 
enrichment 

Common seal 
(Harbour seal) 

Physical loss  
through  
smothering 
Disturbance through 
noise or visual 
presence 

Sabellaria 
spimulosa reef 

Physical loss  
through  
smothering 

Physical damage by 
abrasion 

Disturbance through 
noise or visual  
presence 

Biological 
disturbance through 
selective extraction / 
introduction of 
species 

SPA species 
 Non-breeding 
birds, non-
breeding Annex 
I birds, non-
breeding 
assemblage of  
> 20,000 
waterfowl 

divers than natural beds (cultivation leases not granted in 
natural sublittoral mussel bed areas). 
Yes: There is potential for significant changes in nutrient 
levels through the presence of large additional biomass of 
filter-feeding and faeces/pseudo-faeces-producing mussels 
compared with natural levels. Potential competition for food 
with natural cockle and mussel populations. Extent and 
impacts of changes require further evaluation in full 
assessment 
Smothering – Yes, the intertidal area potentially lost through 
smothering because of shellfish cultivation is not significant 
compared with the total extent of intertidal area in the Site, 
but the proportion of seal haulout sites affected needs to be 
considered. 

Disturbance – No: the unobtrusive nature of lay activities, 
habituation by Common seals to human activity, and location 
of mussel lays away from identified haulout sites means that 
lay activities are not likely to cause significant disturbance to 
this feature 
Yes, possibly mussels lays are not granted in or adjacent to 
areas where Sabellaria spimulosa occurs. However, the 
potential for smothering Sabellaria spimulosa reef within the 
Site as a result of disturbance and re-settlement of sediment 
resulting from shellfish cultivation needs further evaluation in 
the full assessment. 
No, mussel lays are not permitted in or adjacent to areas 
where Sabellaria spimulosa reef occurs. 
No – the Tofts, Roger, Thief and Hull Sands are bird-rich core 
areas but there is no evidence that either relaying or dredging 
mussels, or lay inspection on foot, have a significant 
disturbance effect on SPA species. 
No: Mytilus edulis occurs naturally within the Site. Presence 
of cultivated mussels provides additional food supply to 
mussel-predating SPA-species and to birds feeding on 
associated epifauna. This Review does not consider origin of 
seed mussel (since that aspect is not regulated by the WFO). 

Water quality – target values should default to appropriate national or 
international standards where appropriate. If sufficient local data are 
available to establish the baseline condition, site-specific targets can be 
set. 

Extent (distribution of moulting harbour seals within the site) – a stable 
or increasing area of usage within the site 

Population – a stable or increasing number of harbour seals throughout 
the site 

Extent – no change in extent of Sabellaria spimulosareef allowing for 
natural succession / known cyclical change 

Habitat extent – no decrease in extent from established baseline, subject 
to natural change. 

Population size (non-breeding birds, non-breeding Annex I birds, non-
breading assemblage of  > 20.000 waterfowl) – populations must not 
decline by 50% or more from recorded baselines 

 
 
 
 
 
 
 
 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

STAGE 2. CARRYING OUT THE APPROPRIATE ASSESSMENT 

5.5  The purpose of the Appropriate Assessment 

The purpose of the Appropriate Assessment (AA) is to assess the implications of the plan or 
project in respect of the site’s conservation objectives, taking into account any cumulative 
effects which result from the combination of that project with other plans and projects. The AA 
must precede the approval decision and enable the competent authority to ascertain whether 
the plan or project would not adversely affect the integrity of the site. 

It is the responsibility of the competent authority to ensure  that the AA  is carried out. In that 
context the developer may be required to provide all necessary information to the competent 
authority  in  order  to  enable  the  latter  to  take  a  fully  informed  decision.  In  so  doing  the 
competent authority may also collect relevant information from other sources as well. 

The  term ‘appropriate’  essentially  means that  the assessment needs to  serve the aim of the 
Habitats  and  Birds  Directives  –  i.e.  that  of  conserving  the  species  and  habitat  types  of 
European  importance  covered  by  the  two  Directives  in  the  context  of  the  conservation 
objective of the Natura 2000 sites, and that the assessment has to be a reasoned decision – 
i.e. to disclose the reasoned basis for the subsequent decision.  

In this respect, it is important to recall that, in contrast to the EIA or SEA, the outcome of the 
Appropriate Assessment is legally binding for the competent authority and conditions its final 
decision. Thus, if it cannot be ascertained that there will be no adverse effects on the integrity 
of  the  Natura  2000  site,  even  after  the  introduction  of  mitigation  measures,  then  the  plan  or 
project cannot be approved, unless the conditions of Article 6(4) are met. This applies also in 
the case of doubt over the impacts. 

Steps for an Appropriate Assessment of aquaculture plans and projects 

5.5.1    Determine  the  scope  and  focus  of  the  assessment:  setting  the  baseline  and 
gathering further information  

The  focus  of  the  Appropriate  Assessment  should  be  on  the  possible  effects  of  the  plan  or 
project on the habitat types and the species for which the Natura 2000 site is designated. This 
should also include any indirect effects on these species and/or habitat types, for instance on 
their  supporting  ecosystems  and  natural  processes.  Scoping  will  ensure  that  the  AA  is  well 
focused and provides clear terms of reference for evaluating the potentially negative effects of 
the aquaculture project on the conservation objective of the Natura 2000 site(s). Its aim is to 
identify  more  precisely  what  impacts  the  AA  should  cover  and  to  ensure  that  all  necessary 
information is gathered to enable these impacts to be assessed correctly.  

The  terms  of  impact  analysis  should  be  agreed  with  the  authorities  in  order  to  improve  the 
cost-efficiency  of  the  evaluation  procedure  and  simplify  the  process.  At  this  stage  it  is  also 
useful to define the study area; some modelling tools are available to predict the areas where 
effects from s possible aquaculture pressures (e.g. sedimentation, nutrient enrichment) can be 
noticed, taking into account the local conditions (eg. currents, depth, etc.). 

This  stage  builds  on  the  information  already gathered under the  screening  exercise  but,  this 
time, any gaps in knowledge should also be filled in as far as possible so that the assessment 
can  be  made  on  sound  scientific  grounds.  Sound  baseline  data  is  of  vital  importance  as 
the  AA  has  to  be  able  to  ascertain  with  certainty  that  the  proposal  will  not  affect  the 
integrity of the site concerned.  

 
 
 
 
 
 
 
 
 
 
 
 
 
 
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55

Information needed for the AA and who is expected to provide the information 

The information about the plan or project should contain details of all elements that are relevant 
for the assessment, including the following: 
- 
-  Maps with precise location of all the aquaculture activities and associated works (in relation to 

Information on all the activities involved in the aquaculture development  

the Natura 2000 site(s) in the given area); 

-  Details  about  the  implementation,  duration  and  timing  of  all  the  aquaculture  activities 

(construction, operation and maintenance, harvesting, etc.) 

-  Details about mitigation measures to be applied in relation to the potential impacts. 
This information is usually expected to be provided by developers. 

The information about the Natura 2000 site should contain relevant details on the following:  
-  The  conservation  objectives  of  the  site  and  the  conservation  measures  set,  including 

management plans etc;  

-  On  each species and habitat type for  which the site is  designated and suitable maps of their 

location within the site over time (eg over an annual lifecycle);  
-  Evaluation of extent and quality of habitats and species in the site. 
-  Data  on  the  usage  of  the  site  for  activities  such  as  foraging,  breeding,  resting,  staging  or 

hibernating, by relevant species;   

-  Data on the representativity and conservation status of habitats and species in the site and in 
general (including, inter alia, data on population size, degree of isolation; ecotype, genetic pool; 
age class structure, etc.);  

-  Data on ecological structure and functioning of the site and its overall conservation state; 
-  The role of the site within the biogeographical region and the Natura 2000 network; 
-  Any other aspects of the site or its wildlife that is likely to have an influence on its conservation 

state and objectives (eg current management activities, other developments..) 

This  information  should  be  provided  by  the  competent  authorities  for  Natura  2000,  which  are 
responsible  for  setting  conservation  objectives  and  conservation  measures  for  the  Natura  2000 
sites. 

Details of any other plans or projects in the area whether planned or already on-going. 
The  authorities  responsible  for  giving  the  consent  and  the  competent  nature  conservation 
authorities  should  identify  the  possible  plans  or  projects  that  need  to  be  considered  to  assess 
possible cumulative effects; information could also be gathered by the operator wherever possible. 

In  some  cases,  further  baseline  ecological  and  survey  field  work  may  be  necessary  to 
supplement  existing  data.  Detailed  surveys  and  fieldwork  should  focus  on  those  qualifying 
interests that are sensitive to the project actions.  

Sensitivity  should  be  analysed  taking  into  account  the  possible  interactions  between  the 
project  activities  (nature,  extent,  methods,  potential  pressures  and  effects,  etc.)  and  the 
habitats  and  species  concerned  (location,  ecological  requirements,  vital  areas,  behaviour, 
etc.).  Such  survey  work  should  be  based  on  agreed  scoping  with  relevant  competent  public 
authorities,  appropriate  nature  conservation  public  bodies,  aquaculture  sector,  NGOs, 
scientists and the public. 

Information gathering is necessarily an iterative process. If the first identification and analysis 
of  effects  reveals  that  there  are  important  gaps  in  knowledge,  then  further  surveys  and 
monitoring work will need to be undertaken in order to complete the picture. This will ensure 
there is a sufficient basis of scientific knowledge to be able to make a reasoned decision. 

Detailed  surveys  may  also  help  design  the  proposed  activities  in  a  way  that  prevents  any 
possible adverse effects on the sites’ qualifying features (see example below). 

 
 
 
 
 
 
 
 
 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Fish farms in Loch Sunart, Scotland 

In  2005  Marine  Harvest  Scotland  carried  out  a  major  restructuring  of  its  operations  within  Loch 
Sunart  SAC;  9  salmon  and  halibut  farms  were  consolidated  into  3  larger  salmon  farms  with  the 
remaining  leases  surrendered  or  made  dormant.  The  consolidation  resulted  in  smaller  farms  in 
shallower  water  being  surrendered  in  favour  of  deeper  sites  (greater  than  30m  of  water). 
Appropriate  assessments  were  carried  out  on  the  whole  of  Loch  Sunart  during  the  consolidation 
project.  The  Annex  I  habitats  present  as  a  qualifying  feature  include  reefs  which  are  present  in 
Loch Sunart. The Annex II species that are a primary reason for selection of this site includes the 
otter (Lutra lutra). 

Video surveys of the seabed were completed prior to finalising these development proposals. The 
aim  of  these  baseline  studies  was  to  determine  whether  any  qualifying  features  were  present  in 
areas  of  potential  impact.  The  development  proposals  were  then  adapted  accordingly  to  prevent 
significant impacts to the integrity of the SAC. 

Advice and guidance was taken from Scottish Natural Heritage as to the most appropriate method 
of positioning moorings avoid impact on qualifying features (reefs. Drop down cameras were used 
during installation to prevent mooring equipment from being installed upon qualifying reef species. 

Source:  Marine  Harvest  (Scotland)  Ltd.,  Scottish  Salmon  Producers’  Organisation,  Joint  Nature 
Conservation Committee. 

5.5.2 Assessing the impacts on the Natura 2000 site 

The  Appropriate  Assessment  should  address  the  potential  effects  on  the  conservation 
objective of the Natura 2000 site from all the aspects of the plan or project, and cover all the 
stages  of  the  aquaculture  project,  for  instance:  site  preparation,  building  or  installation  of 
infrastructure and facilities, operation and maintenance activities, decommissioning, etc.  

It  will  be  useful  to  describe  the  precise  location,  timing,  frequency  and  duration  of  all  the 
activities involved in the aquaculture development. This is necessary to analyse the potential 
pressures and impacts which may occur at different times of the year or of the day. Details of 
potential  ecological  effects  of  each  activity  on  the  site,  their  sources  and  the  mechanism  by 
which the impact may occur should also be provided. 

 
 
 
 
 
 
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57

Table  5.  Example  of  seasonal,  daily  and  tidal  profile  of  activities  associated  with  mussel 
production in a shellfish farm in the Atlantic Region60 

Activity 

SEED MUSSEL FISHERY: Dredging of 
seed mussel in the fishery area 
NURSERY: Placement of seed in the 
nursery and husbandry of seed 
ONGROWING:  Dredging of transplanted 
seed mussel from intertidal to subtidal 
ongrowing areas 
HARVESTING:  
Dredging of mussels from the sub-tidial 
channel for harvest and sale 
Disturbance (related to mussel production, 
other fishing and aquaculture and 
recreation) 

e
d
i
t

w
o
L

e
d
i
t
h
g
H

i

y
a
D

t
h
g
N

i

X  X 

J 

F  M A  M J 

J  A  S  O  N  D 

L  H 

X  X  X 

L 

L 

L 

L 

L 

H 

L 

L 

L 

X  X 

H  H  H 

X  X 

  H 

L 

L 

L  H  H  H 

X  X  X 

L 

L 

L 

L 

L 

L 

L 

L 

L 

L 

L 

L 

X= Activity, H= high levels of activity, L= Low levels of activity 

Table 6. Example of potential impacts of mussel cultivation –lay activities– on SPA interests61 

60  Adapted from: Appropriate Assessment of the impact of mussel fishing and mussel, oyster and clam 
aquaculture on Castlemaine Harbour SAC and SPA, Marine Institute, Ireland. 2011). 
61 Source: Mussel Cultivation in The Wash. Assessment. Additional Information. ESFJC. 2008 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Chapter  3  gives  an  overview  of  the  kind  of  effects  that  may  be  associated  with  aquaculture 
systems  and  identifies  the  species  or  habitat  types  that  have  proven  to  be  particularly 
vulnerable to this form of development. The effects of each project will be unique and must be 
evaluated on a case-by-case basis.  

The  impacts  of  the  plan  or  project  should  be  measured  against  the  site’s  conservation 
objectives.  For  instance  if  the  objective  is  to  ensure  that  the  population  of  a  bird  species 
reaches  a  certain  population  within  10  years  and  conservation  measures  are  foreseen  to 
ensure  this  happens,  will  the  plan  or  project  prevent  this  conservation  objective  from  being 
realised?    If  no  specific  conservation  objectives  have  been  set  then  it  can  be  taken  that  the 
conservation objective is to prevent further deterioration of the site and its target features from 
the time it was included in the Natura 2000 network (Article 6(2) of the Habitats Directive). 

Conservation objectives 

The conservation objectives for a Natura 2000 site are determined at member state level. The 
SDF provides information regarding the qualifying interests of a Natura 2000 site and, in the 
absence of more detailed definition of conservation objectives for a Natura 2000 site, they can 
be  considered  as  such.  Some  countries  have  developed  more  detailed  conservation 
objectives for their Natura 2000 sites either at a strategic level across a suite of sites, or at an 
individual site level. Some sites may also have management plans or management objectives 
that provide clear indications about the conservation objectives to be attained. 

Examples of site-specific conservation objectives developed for Annex I habitats may include, 
for instance, keeping certain habitat area stable or increasing; for species occurring in the site, 
conservation  objectives  can  set  e.g.  population  numbers  to  be  maintained,  long  term 
population trend stable or increasing or distribution area to be preserved. Adequate baseline 
information is needed to set site-specific conservation objectives. 

The site’s qualifying interest and conservation objectives should have been already identified 
in the screening stage. At this stage however more detailed information may be needed to be 
able to properly conduct the assessment.  

In  this  regard,  it  may  be  useful  to  consider  the  parameters  that  are  used  to  assess  the 
conservation  status  of  habitats  and  species  of  EU  interest.  As  regards  habitats,  these 
parameters include the range, the area covered by the habitat type within its range, as well as 
specific  structures  and  functions  (including  typical  species)62.  These  parameters  can  also  be 
useful both for setting conservation objectives (at the site level) and for the assessment of the 
effects  of  aquaculture  activities  on  habitats  and  species  for  which  the  site  has  been 
designated.  

The assessment should analyse any possible change or deterioration of the extent and quality 
of  habitats  and  species  present  in  the  site,  based  on  the  potential  effects  identified  for  the 
different  project  activities  and  on  the  location,  status  and  sensitivity  of  those  habitats  and 
species. 

62 A first assessment of the conservation status of the species and habitats protected under the Habitats 
Directive was published in 2009. This provides useful information on the conservation status of each of 
the species and habitats listed in the Habitats Directive per country and biogeographical region. 

 
 
 
 
 
 
 
 
 
 
                                                 
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59

Example of conservation objectives considered in the Appropriate Assessment 

AA of aquaculture developments in Castelmaine Harbour SAC and SPA (Ireland) 

A  full  appropriate  assessment  process  was  conducted  for  multiple  aquaculture  and  supporting 
projects  in  Castlemaine  Harbour  SAC  and  SPA.  The  site-specific  conservation  objectives  set  by 
the nature conservation authorities (National Parks and Wildlife Service, NPWS) for the site were 
considered in the AA: 

-  To  maintain  the  favourable  conservation  condition  of  the  following  species:  sea  lamprey,  river 
lamprey,  salmon,  otter,  petalwort,  red  throated  diver,  cormorant,  light  bellied  brent  geese, 
wigeon,  mallard,  pintail,  scaup,  common  scoter,  oystercatcher,  ringed  plover,  sanderling,  bar 
tailed godwit, redshank, greenshank, turnstore and chough.   

- To maintain the favourable conservation condition of the following habitats: estuaries, mudflat and 
sandflats  not  covered  by  seawater  at  low  tide,  annual  vegetation  of  driftlines,  perennial 
vegetation  of  stony  banks,  salicornia  and  other  annuals  colonising  mud  and  sand,  Atlantic  salt 
meadows,  Mediterranean  salt  meadows,  embryonic  shifting  dunes,  shifting  dunes  along  the 
shoreline  with  Ammophila  arenaria,  fixed  coastal  dunes  with  herbaceous  vegetation  (grey 
dunes), dunes with Salix repens ssp. argentea (Salix arenariae) and humid dune slacks.  

-  To  restore  the  favourable  conservation  condition  of  alluvial  forests  with  Alnus  glutinosa  and 

Fraxinus excelsior. 

An example of specific conservation objectives and targets for a marine habitat included in Annex I 
of the Habitats Directive to facilitate the appropriate assessment process is presented below. 

Objective: to maintain the favourable conservation condition of Mudflats and sandflats not covered 
by seawater at low tide in Castlemaine Harbour, which is defined by the following list of attributes 
and targets. 
   -  Target 1: The permanent habitat area is stable or increasing, subject to natural processes 
   -  Target  2:  The  extent  of  the  Zostera  dominated  community  is  conserved,  subject  to  natural 

processes. 

   - Target 3 The following community types should be conserved in a natural condition: Intertidal 
muddy  fine  sand  community  complex;  Fine  to  muddy  fine  sand  with  polychaetes  community 
complex; Intertidal sand with Nephys cirrosa. 

 
 
 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Once  all  the  necessary  baseline  data  has  been  gathered,  the  assessment  of  the  potential 
impacts can begin. As described above this should be done in light of: 
-  best scientific knowledge in the field (ECJ Ruling on case C-127/02)  
- 
-  ecological characteristics and conservation condition of the site and its target features. 

site conservation objectives; 

The  appraisal  of  effects  must  be  based  on  objective  and,  if  possible,  quantifiable  criteria.  A 
common  means  for  that  is  through  the  use  of  key  indicators,  such  as  habitat  loss  or 
degradation, species population affected, key ecological functions altered, etc. Some possible 
attributes to be considered in the assessment are presented in the following table. 

Table  7  Some  examples  of  attributes  considered  in  the  assessment  of  potential  effects,  in 
relation to possible conservation objectives at the site 

Attributes 
Habitat area  

Habitat 
structure and 
function 

Species 
abundance 
and 
distribution, 
population 
structure, etc. 

Conservation objectives 
The area occupied by the target habitats 
should be stable or increasing (overall 
target areas can be set). 

Assessment of effects 
Possible reduction of habitat areas 
(estimated surface and percentage of 
total area in the site).  

The communities of target habitats 
should be stable in distribution and 
composition. 
Habitat functions and the ecological 
parameters on which the habitat 
persistence depends are maintained. 
Species populations are stable or 
increase (target numbers can be set). 
Population trends are improving.  
Species distribution, including vital areas 
and connectivity, is maintained or 
improved (e.g. through habitat 
improvement and re-colonisation of 
improved areas). Population structure is 
conserved. 

Possible losses in distribution area, 
deterioration in species composition, 
disturbance of typical species, etc. 
Loss or degradation of functions (e.g. 
as feeding, refuge or breeding areas) 

Species disturbance and displacement 
from areas that it would otherwise 
occupy. Changes in the numbers or 
distribution areas used by the target 
species. 
Loss or degradation of critical habitats 
and vital areas (surface affected and 
percentage of total area in the site). 
Effects on critical stages in the species-
life cycle. 

Example of parameters that may be considered in the appraisal of effects on habitats/species of 
Community interest that have justified the site designation  

-  Total  amount  of  affected  habitat  and  percentage  in  relation  to  the  estimated  total  habitat  surface 

within the Natura 2000 site. 

-  Estimated number of affected individuals and proportion of the species population occurring in the 

site. 

-  Estimated habitats and species population trends in the affected area and on the site. 
-  Rarity and overall trends of affected habitats and species; 
-  Existence of a habitat or species restoration programme which may be affected by the project. 
-  Reversibility of the effect or potential recovery of damaged elements from existing sources inside or 

outside the site. 

-  Distribution  of  concerned  habitats  or  species  distribution  within  the  Natura  2000  site  (continuous, 

scattered, dispersed, etc.) 
Effects on the overall ecological functioning of the Natura 2000 site. 

- 

Predicting the likely impacts of an aquaculture project/plan can be difficult as one should have 
a  good  understanding  of  ecological  processes  of  the  environment  and  conservation 
requirements of particular species or habitat types likely to be affected. Cooperation between 
operators and authorities is crucial in the appropriate assessment. It is strongly recommended 
that the competent authorities secure the necessary expert advice and support in carrying out 
the field surveys and impact assessment.  

 
 
 
 
 
 
 
 
 
 
 
 
 
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61

The  assessment  should  apply  the  best  available  techniques  and  methods  to  estimate  the 
extent and magnitude of the effects. A number of models are currently available, for instance, 
to simulate and predict the effects of nutrient enrichment from fish farms over marine areas.  

Commonly used methods for predicting impacts: 

Some of the techniques commonly used are listed below: 

-  Direct  measurements,  for  example  of  areas  of  habitat  lost  or  affected,  proportionate  losses  from 

species populations, habitats and communities.   

- 

Flow  charts,  networks  and  systems  diagrams  to  identify  chains  of  impacts  resulting  from  direct 
impacts;  indirect  impacts  are  termed  secondary,  tertiary,  etc.  impacts  in  line  with  how  they  are 
caused.  Systems  diagrams  are  more  flexible  than  networks  in  illustrating  interrelationships  and 
process pathways.  

-  Quantitative  predictive  models  to  provide  mathematically  derived  predictions  based  on  data  and 
assumptions  about  the  force  and  direction  of  impacts.  As  regards  aquaculture  projects,  predictive 
modelling  often  plays  an  important  role  as  some  impacts  often  depend  on  hydrological  conditions 
that may influence for instance sedimentation processes that may affect the underwater biota. 

-  Population level studies are potentially beneficial for determining population level effects of impacts 

to bird or bat or marine mammal species, for instance. 

-  Geographical  information  systems  (GIS)  used  to  produce  models  of  spatial  relationships,  such  as 
constraint overlays, or to map sensitive areas and locations of habitat loss. GIS are a combination 
of  computerised  cartography,  storing  map  data,  and  a  database-management  system  storing 
attributes  such  as  land  use  or  slope.  GIS  enable  the  variables  stored  to  be  displayed,  combined, 
and analysed speedily.  

- 

Information from previous similar projects may be useful, especially if quantitative predictions were 
made and have been monitored in operation.  

-  Expert opinion and judgment derived from previous experience and consultations on similar projects 

-  Description  and  correlation:  physical  factors  (eg  water  regime,  current,  substrate)  may  be  directly 
related to distribution and abundance of species. If future physical conditions can be predicted then 
it  may  be  possible  to  predict  future  developments  of  habitats  and  populations  or  responses  of 
species and habitats on this basis.  

-  Carrying  out  assimilative  and  capacity  analyses  involves  identifying  the  threshold  of  stress  below 
which  populations  and  ecosystem  functions  can  be  sustained.  It  involves  the  identification  of 
potentially  limiting  factors,  and  mathematical  equations  are  developed  to  describe  the  capacity  of 
the resource or system in terms of the threshold imposed by each limiting factor.  

- 
Adapted 
from:  "Assessment  of  plans  and  projects  significantly  affecting  Natura  2000  sites. 
Methodological  guidance  on  the  provisions  of  Article  6(3)  and  (4)  of  the  Habitats  Directive  92/43/EEC"; 
http://ec.europa.eu/environment/nature/natura2000/management/docs/art6/natura_2000_assess_en.pdf.  

Impacts  should  be  predicted  as  precisely  as  possible,  and  the  basis  of  these  predictions 
should be made clear (this means also including some explanation of the degree of certainty 
in the prediction of effects). Wherever possible, predictions should be presented in such a way 
as to make them verifiable. 

For each effect identified, the significance of the impact will depend on a number of relevant 
parameters  such  as:  the  magnitude  of  the  impact,  the  extent,  the  duration,  the  intensity,  the 
timing, the probability, etc. 

 
 
 
 
 
 
 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Example: Methods for the assessment of effects.   

Appropriate  Assessment  of  mussel  fishing  and  mussel,  oyster  and  clam  aquaculture  on 
Castlemaine Harbour SAC  

The significance of the possible effects of the proposed activities on habitats is determined on the basis 
of Conservation Objective guidance prepared by the nature conservation authority (National Parks and 
Wildlife Service, NPWS), considering: 

1.  The degree to which the activity will disturb the qualifying interest. By disturb it is meant a change 
in  the  characterising  species,  as  listed  in  the  Conservation  Objective  guidance  for  constituent 
habitats. 

2.  The persistence of the disturbance in relation to the resilience of the habitat. 
3.  The  area  of  habitats  or  proportion  of  populations  disturbed.  A  percentage  is  set  above  which  an 

effect shall be considered significant. 

An example for two of the project activities is shown below: 

FCS: Favourable Conservation status (as measured by the parameters) indicated 

 
 
 
 
 
 
 
 
 
 
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63

5.5.3  Considering the cumulative effects 

Cumulative  effects  may  arise  when  several  aquaculture  projects  are  present  within  a  given 
area, or as the result of the combined impacts of aquaculture and other types of activity (e.g. 
fishing, recreation, etc.); this points to the benefits of strategic planning (see Chapter 4). 

In  many  coastal  areas  multiple  human  activities  overlap  and  the  combined  effects  of  more 
than  one  activity  can  lead  to  a  greater  or  lesser  impact  than  each  acting  individually  (an 
interactive  effect).  When  decision  making  occurs  it  is  important  to  consider  the  potential 
additive  or  interactive  (synergistic  or  antagonistic)  effects  of  pressures  and  the  subsequent 
impacts they may cause.  

For example, seafloor disturbance aside, an area with active fin fish aquaculture may benefit, 
ecologically,  from  the  introduction  of  algal  or  shell  fish  aquaculture  because  these  species 
effectively consume excess nutrients derived from fin fish aquaculture (an antagonistic effect). 
On  the  other  hand,  adding  sewage  effluent  to  a  bay  with  fin  fish  aquaculture  may  cause 
deleterious effects greater than those expected from each pressure individually (a synergistic 
effect) (Crowe et al 2011).  

The  geographical  scale  over  which  these  cumulative  effects  need  to  be  considered  will 
depend on the exact circumstances and scale of the plan or project being studied, on the site 
conditions  (e.g.  currents,  etc.)  and  on  the  potential  for  far  field  effects  from  the  project 
activities. However, it should cover a sufficiently large area to capture any cumulative effects 
that  may  arise  with  the  plan  or  project  under  assessment.  Again,  the  competent  nature 
conservation authorities will be able to help identify the possible plans or projects that need to 
be considered as part of the in-combination test.  

The  cumulative  impact  assessment  should  focus  on  the  receptor  as  opposed  to  the 
environmental effect, and looks at the capacity of the receptor to adapt to additional change. 
The  cumulative  impact  assessment  may  consider  issues  that  have  been  scoped  out  of  the 
impact assessment because they are not considered to be significant individually, but may be 
significant when considered in combination with others (Scottish Government, 200763). 

Different  methods  have  been  developed  to  help  assess  the  potential  for  cumulative 
environmental  effects  of  activities.  An  example  of  this  type  of  tools  is  a  model  developed  by 
Sutherland  et  al.  (200764)  for  the  evaluation  of  marine  sites.  To  estimate  cumulative  effects, 
the  model  utilizes  site  specific  spatial  datasets  representing  natural  resources  abundance, 
habitat  inventory,  values  from  commercial  and  recreational  activities,  and  influence  plumes 
from sources of effluents present at the site.   

These  datasets  are  processed  as  thematic  layers  in  a  GIS  describing  the  marine  site. 
Experiments  determined  that  the  model  works  well  in  estimating  the  cumulative  effects  of 
interacting component layers associated with various marine sites. 

5.5.4  Identifying suitable mitigation measures 

Mitigation  measures  are  aimed  at  minimising  or  even  cancelling  the  negative  impact  of  a 
project. As such, they should be directly linked to the likely negative effects which have been 
identified  during  the  assessment  described  above.  Avoidance  or  reduction  of  impacts  at 
source should be the preferred options (EC 2000). 

63Scottish Government, 2007. Environmental Impact Assessment - Practical Guidelines Toolkit for Marine Fish 
Farming. Prepared by RPS, Epsilon Resource Management Limited.  
64 Sutherland, M., Y. Zhao, D. Lane, and W. Michalowski. 2007. Estimating Cumulative Effects using Spatial Data: 
An aquaculture case study.  In Geomatica, Vol. 61, No. 1, pp. 349-353. 

 
 
 
 
 
 
 
 
 
 
                                                 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Mitigation measures are an integral part of the specifications of a plan or project and should be 
considered  during  the  AA.  In  practice  this  creates  an  iterative  process:  projects  which  may 
seem  unsuitable  at  first  can  thus  be  improved  with  the  introduction  of  adequate  mitigation 
measures to ensure that adverse effects on the integrity of the Natura 2000 site are prevented. 

The identification and description of mitigation measures should contain: 
-  details of each of the measures proposed and an explanation of how it will avoid or reduce 

the adverse impacts which have been identified; 

-  evidence of how they will be implemented and by whom; 
-  a timetable for implementation relative to the plan or project (some may need to be put in 

place before the development can proceed); 

-  details of how the measure will be monitored and how the results will be fed back into the 

day-to-day operation of the aquaculture project. 

Mitigation  measures  in  the  aquaculture  context  should  be  understood  as  technically  feasible 
solutions  that  are  the  least  damaging  for  habitats,  for  species  and  for  the  integrity  of  the 
Natura  2000  site,  especially  if  alternative  locations  are  not  feasible.  Mitigation  measures 
should be focused on ensuring that the sites’ conservation objectives can continue to be met 
and  on  retaining  those  elements  on  which  the  integrity  of  the  site  depends.  Examples  of 
potential measures for avoiding or minimising impacts from aquaculture operations have been 
included  in  Chapter  3  in  relation  to  the  main  potential  impacts  described  from  different 
aquaculture systems. 

5.5.5  Assessing whether there are no adverse effects on site integrity 

Once  the  potential  effects  of  the  project  have  been  assessed  as  accurately  as  possible,  the 
Appropriate  Assessment  can  move  onto  the  next  stage  which  is  to  determine  whether  the 
impacts  will  adversely  affect  the  integrity  of  the  Natura  2000  site,  either  alone  or  in 
combination with other plans or projects.  

This means determining whether the plan or project will adversely affect: 
- 
- 
- 

the coherence of the site’s ecological structure and function, across its entire area,  
the habitats, complex of habitats and/or  
the populations of species for which the site is designated.  

Integrity of the site 

Biological  integrity  can  be  defined  as  all  those  factors  that  contribute  to  the  maintenance  of  the 
ecosystem,  including  structural  and  functional  assets.  In  the  framework  of  the  Habitats  Directive,  the 
“integrity”’ of the site is linked to the conservation objectives for which the site was designated as part of 
the  Natura  2000  Network  (EC  2007b).  It  has  been  usually  defined  as  “the  coherence  of  the  site’s 
ecological structure and function, across its whole area, that enables it to sustain the habitat, complex of 
habitats  and/or  populations  of  species  for  which  the  site  is  classified”  (EC  2000b).  As  regards  the 
meaning of ‘integrity’, this can be considered as a quality or condition of being whole or complete. In a 
dynamic  ecological  context,  it  can  also  be  considered  as  having  the  sense  of  resilience  and  ability  to 
evolve in ways that are favourable to conservation. (EC 2000b). 

A site can be described as having a high degree of integrity where the inherent potential for meeting site 
conservation  objectives  is  realised,  the  capacity  of  self-repair  and  self-renewal  under  dynamic 
conditions  is  maintained,  and  a  minimum  of  external  management  is  required.  When  looking  at  the 
“integrity  of  the  site”,  it  is  therefore  important  to  take  into  account  a  range  of  factors,  including  the 
possibility of effects manifesting themselves in the short, medium and long-term (EC 2000b).  

Authorisation  of  a  plan  or  project  granted  in  accordance  with  Article  6(3)  of  the  Habitats  Directive 
necessarily assumes that it is considered not likely to adversely affect the integrity of the site concerned 
and, consequently, not likely to give rise to deterioration or significant disturbances within the meaning 
of Article 6(2) (ECJ ruling on case C-127/02 para. 36). 

 
 
 
 
 
 
 
 
 
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65

The assessment of effects on site integrity should focus on identifying whether the project: 
•  causes changes to significant ecological functions necessary for the target features; 
•  significantly  reduces  the  area  of  occurrence  of  habitat  types  or  viability  of  species 

• 
• 
• 

populations in the given site which are target features; 
reduces the site diversity; 
leads to the site fragmentation; 
leads to a loss or reduction of the key site characteristics (e.g. tree cover, regular annual 
floodings) which the status of the target feature depends on; 

•  disturbs or deteriorates critical species habitats such as roosting, feeding or breeding sites 

of species for which the site was designated; 
•  disturbs meeting the site conservation objectives. 

It  is  important  to  bear  in  mind  that  the  focus  of  the  assessment  should  be  on  objectively 
demonstrating, with supporting evidence, that there will be no adverse effects on the integrity 
of the Natura 2000 site, in light of its conservation objectives65. Thus, the competent authority, 
in  order  to  authorise  a  plan  or  project,  has  to  be  sure  that  no  reasonable  scientific  doubt 
remains as to the absence of such effect (ECJ ruling C-127/02, Waddensea). 

To sum up, there are two possible conclusions that can be drawn from this assessment: 
- there is no adverse effect and the project or plan can be approved as it stands; 
- there will be adverse effects or adverse effects cannot be ruled out. 

The  latter  does  not  necessarily  mean  that  the  plan  or  project  is  automatically  refused.  The 
competent  authority  could  ask  the  developer  to  redesign  or  relocate  the  farm  or  introduce 
mitigation  measures  that  would  avoid  or  eliminate  the  predicted  adverse  effects.  This  would 
then normally imply a second evaluation round in the Appropriate Assessment to ensure that 
the mitigation measures/safeguards are indeed sufficient. 

5.5.6  Recording the results of the Appropriate Assessment 

Whatever  the  results  of  the  AA,  they  should  be  clearly  recorded.  In  this  respect,  the 
Appropriate  Assessment  report  should  be  sufficiently  detailed  to  demonstrate  how  the  final 
decision  was  reached,  and  on  what  scientific  grounds  the  decision  was  made.  This  is 
confirmed  by  an  ECJ  ruling:  The  appropriate  assessment  should  contain  complete,  precise 
and definitive conclusions capable of removing all reasonable scientific doubt as to the effects 
of the works proposed on the site concerned (Commission/Italy, C-304/05).  

The Appropriate Assessment report should: 

•  describe the project or plan in sufficient detail for members of the public to understand its 

size, scale and objectives; 

identify the adverse effects of the project or plan on the Natura 2000 site; 

•  describe the baseline conditions and conservation objectives of the Natura 2000 site; 
• 
•  explain how those effects will be avoided through mitigation; 
•  set out a timescale and identify the mechanisms through which the mitigation measures 

will be secured, implemented and monitored. 

The Appropriate assessment can also set relevant conditions for the project implementation to 
ensure that potential effects are avoided. 

65  A plan or project with significant adverse effects cannot be accepted on the grounds that the conservation status 
of  the  habitat  types  and  species  it  hosts  will  anyway  remain  favourable  within  the  Member  State  or  the  EU  as  a 
whole.  

 
 
 
 
 
 
 
                                                 
 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Outline for an Appropriate Assessment Report  

Example: AA of mussel aquaculture on a SAC and SPA 

•  Details of the proposed operations/activities 
o  Mussels seed fishery and ongrowing 
o 

Intertidal/seafloor aquaculture  

•  Activities with potential in combination effects  

•  Potential disturbance effects 

•  Conservation objectives and interests at the site  

o  Qualifying interests and conservation objectives in the SAC  
o  Qualifying interests and conservation objectives in the SPA 

•  Ecological effects 

o  Details of potential ecological effects of each proposed activity, on the SAC 

and SPA conservation objectives, their sources and the mechanism by which 
the impact may occur. 

•  Appropriate Assessment Screening 

•  Appropriate Assessment: Special Area of Conservation 

o  Methods for Appropriate Assessment 
o  Assessment of sub-tidal fishing for seed mussel 
o  Assessment of relaying of seed mussel on the inter-tidal sand flat 
o  Assessment of dredging of half-grown mussel from the inter-tidal area  
o  Assessment of relaying and dredging of mussels in the sub-tidal area 
o  Assessment of predator control, winkle picking, discharges 
o  Assessment of the effects of shellfish production and in combination effects on 

the Conservation Objectives for Otter, Salmon and Lamprey 

•  Appropriate Assessment: Special Protection Area 

o  Assessment of the effects of fisheries and aquaculture production on 

waterbirds 

(cid:131)  The status of bird populations of special conservation interest in the 

SPA 

(cid:131)  Assessment of mussel seed fishery 
(cid:131)  Assessment of the effects of intertidal mussel relay in the fishery 
area:effects of mussel cover on habitat suitability for waterbirds  
(cid:131)  Assessment of intertidal relay of mussels in the mussel order area: 

effects of human disturbance 

(cid:131)  Assessment of sub-tidal relaying of mussels 
(cid:131)  Assessment of potential for cumulative impacts: the combination of 

aquaculture activities 

(cid:131)  Assessment of potential for cumulative impacts: recreation in 

association with aquaculture 

•  Appropriate Assessment Conclusion Statement  

o  SAC Features  
o  SPA Features  

•  Scope for additional monitoring and mitigation  

•  Annexes: detailed technical information in support of the conclusions in the 

assessment. 

 
 
 
 
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67

STAGE 3. THE DEROGATION PROCEDURE UNDER ARTICLE 6.4 

5.6  The scheme of Article 6.4 

The requirements of Article 6(4) of the Habitats Directive establish a set of conditions, which 
must be met for the competent authority to authorise, by way of derogation, a plan or project in 
case  the  AA  cannot  show  that  the  integrity  of  the  Natura  2000  site  concerned  will  not  be 
adversely  affected  by  it.  Being  an  exception  to  Article  6(3),  the  fulfilment  of  the  conditions 
under  which  it  may  be  applied  is  subject  to  strict  interpretation  and  will  only  be  passed  in 
exceptional circumstances. 

These conditions relate to the absence of alternatives, the presence of imperative reasons of 
overriding public interest (IROPI) and the adoption of all necessary compensatory measures. 

The  European  Commission  has  published  a  Guidance  Document  on  Article  6(4)  of  the 
Habitats  Directive  (EC  2007b)  which  provides  clarification  of  the  concepts  of  alternative 
solutions,  imperative  reasons  of  overriding  pubic  interest,  compensatory  measures,  overall 
coherence and the opinion of the Commission required in some cases66. 

5.6.1 The absence of alternative solutions 

The search for alternatives can be quite broad and should be linked to the public objectives of 
the  plan  or  project.  It  could  involve  alternative  locations,  different  scales  or  designs  of 
development,  or  alternative  processes.  If  the  intention  is  to  develop  or  increase  aquaculture 
production, the question is then: can this be achieved in a less damaging way, for instance, by 
selecting a more appropriate site elsewhere or by resizing or scaling down the plan or project.  

In  practice,  alternative  solutions  should  normally  already  have  been  identified  within  the 
framework of  the  initial  assessment  under  Article  6(3).  They are  part of  the iterative process 
seeking to improve the siting and design of a plan or project at the earliest stages.  

In conformity with the principle of subsidiarity, it rests with the competent national authorities to 
assess the relative impact of other alternatives on the site concerned or any other Natura 2000 
site that might be affected.  The alternative solutions chosen should also in principle undergo 
the same screening exercise as the original plan or project and could be subject to a new AA. 

The competent authorities have also to analyse and demonstrate first the need of the plan or 
project  concerned.  Thus,  the  zero  option  should  also  be  considered  at  this  stage  –  i.e.  the 
option of not carrying out the project. 

5.6.2 Imperative reasons of overriding public interest (IROPI) 

In  absence  of  an  alternative  solution  IROPI  may  be  considered.  The  concept  of  imperative 
reason of overriding public interest is not defined in the Directive. However, it is clear from the 
wording  of  Article  6(4)  that  only  public  interests,  irrespective  of  whether  they  are  promoted 
either  by  public  or  private  bodies,  can  be  balanced  against  the  conservation  aims  of  the 
Directive.  Thus,  projects  developed  by  private  bodies  can  only  be  considered  to  meet  this 
condition of Article 6(4) where such public interests are served and demonstrated (EC 2007b).  

66 http://ec.europa.eu/environment/nature/natura2000/management/guidance_en.htm 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Such  public  interests  may  include  human  health,  public  safety,  beneficial  consequences  of 
primary importance for the environment, and other interests of a social (e.g. employment) or 
economic nature. 

To  fulfil  the  requirements  of  Article  6(4)  of  the  Habitats  Directive,  the  competent  national 
authorities  have  to  make  their  approval  of  the  plans  and  projects  in  question  subject  to  the 
condition  that  the  balance  of  interests  between  the  conservation  objectives  of  the  Natura 
site(s)  affected  by  those  initiatives  and  the  above-mentioned  imperative  reasons  weighs  in 
favour of the latter.  

It  should  be  noted  that  the  conditions  of  overriding  public  interest  are  even  stricter  when  it 
comes to the realisation of a plan or project likely to adversely affect the integrity of a Natura 
2000  site  that  hosts  qualifying  priority  habitats  and/or  species,  where  those  habitats  and/or 
species are affected. These can only be justified if the imperative reasons of overriding public 
interest concern: 

-  human health and public safety or 
-  overriding beneficial consequences for the environment, or, 
-  for other imperative reasons if, before granting approval to the plan or project, the opinion 

of the Commission has been given (EC 2007b). 

5.6.3 The adoption of all necessary compensatory measures 

Compensatory measures, as described in Article 6(4) of the Habitats Directive, constitute the 
"last  resort"  and  are  used  only  when  the  decision  has  been  taken  to  proceed  with  a  plan  or 
project that could have an adverse effect on the integrity of the Natura 2000 site because no 
alternatives exist and the project has been judged to be of overriding public interest under the 
conditions described above.   

The compensatory measures constitute measures specific to the unavoidable adverse effects 
of a project or plan. They aim to ensure that the overall coherence of Natura 2000 is protected, 
and should provide compensation corresponding directly to the negative effects on the species 
or habitat concerned.  

It  is  considered  good  practice  to  take  compensatory  measures  as  close  as  possible  to  the 
affected area in order to maximise chances of protecting the overall coherence of the Natura 
2000  network.  As  a  general  principle,  the  compensatory  measures  should  be  in  place  and 
working before the work on the plan or project has begun. This is to help buffer the damaging 
effects of the project on the species and habitats by offering them suitable alternative locations 
in the compensation area.  

The  information  on  the  compensatory  measures  should  be  submitted  to  the  Commission 
before  they  are  implemented  and  indeed  before  the  realisation  of  the  plan  or  project 
concerned (EC 2007b).  

 
 
 
 
 
 
 
 
 
 
 
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69

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ANNEX  1.  EU  POLICY  AND  LEGAL  FRAMEWORK,  AND  INITIATIVES  TO 
PROMOTE SUSTAINABLE AQUACULTURE 

1. The EU Policy Framework for the aquaculture industry  

Under  the  Common  Fisheries  Policy  the  main  instruments  addressed  to  aquaculture  are  the 
European  Fisheries  Fund  (Council  Regulation  (EC)  No  1168/2006)  and  the  Common 
organisation  of  the  markets  in  fishery  and  aquaculture  products  (Council  Regulation  (EC) 
No.104/2000). Many of the factors and drivers shaping aquaculture have a strong dimension 
of  subsidiarity  and  are  shaped  by  the  priorities  and  decisions  taken  at  national  and  regional 
level. 

The European Fisheries Fund (EFF) adopted in 200667 sets the framework to contribute to the 
sustainable growth of aquaculture in Europe until 2013. Under its Axis 2, in particular, aqua-
environmental  measures  may  support  the  use  of  aquaculture  production  methods  helping  to 
protect and improve the environment and to conserve nature.  

The on-going process of reform of the Common Fisheries Policy aims to promote sustainable 
aquaculture through national strategic guidelines and the creation of an Advisory  Council for 
Aquaculture  for  stakeholder  consultation  and  advice.  EU  "horizontal"  legislation,  such  as 
environmental  protection  requirements,  public  health  protection  rules  for  fisheries  products, 
animal health law is applicable to aquaculture industry and its products as appropriate.  

2. Aquaculture trends and environmental factors influencing production in the EU 

Globally, aquaculture remains a growing and important production sector – with annual growth 
rate  of  8.3  %  worldwide  between  1970  and  2008  (5.3%  between  2006  –  2008).  The 
aquaculture production reached 68.3 million tonnes in terms of volume and US$105.4 billion in 
terms  of  value  in  2008.  Globally,  aquaculture  accounted  for  45.7%  of  the  world's  fish  food 
production for human consumption in 2008 (up to 42.6% in 2006). 

The total aquaculture production in the EU was close to 1.3 million tonnes, worth some €3.2 
billion  in  2009.  The  EU  overall  aquaculture  unfortunately  does  not  follow  the  global  trend  of 
growth and is rather stagnating. 

Evolution of EU aquaculture production 
(total tonnage) 

T otal EU-27
production

Crustaceans
and molluscs

Freshwater
fish

Marine fish

)
t
h
g
i
e
w
e
v
i
l
(
s
e
n
n
o
t

1.750.000

1.500.000

1.250.000

1.000.000

750.000

500.000

250.000

0

5
9
9
1

7
9
9
1

9
9
9
1

1
0
0
2

3
0
0
2

5
0
0
2

7
0
0
2

9
0
0
2

67 Council Regulation (EC) No 1198/2006 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

The  absolute  majority  of  the  EU  production  is  destined  for  the  EU  market.  Exports  of  EU 
aquaculture  products  remain  very  limited  (about  122.000  tonnes  “live  weight  equivalent”  in 
2009).  The  aquaculture  products  imported  to  the  EU  play  an  important  role  (about  2  million 
tonnes  “live  weight  equivalent”,  worth  app.  €  4.6  billion  in  2009)  –  they  represent  22%  of 
volume and 32% of value of the total seafood imports. 

The EU is committed to a high level of environmental protection and a number of provisions 
exist to ensure that the development of aquaculture is sustainable from an environmental point 
of view. It also needs to be stressed that aquaculture requires water of the highest quality to 
guarantee  health  of  aquatic  animals  and  safe  and  high  quality  products.  Environmental 
aspects of aquaculture are confirmed to be very important issues for this sector. 

In  terms  of  nature  conservation,  the  implementation  of  Natura  2000  is  often  perceived  as  a 
major  limiting  factor  for  development  of  aquaculture  and  access  to  space  in  some  Member 
States.  The  development  of  interpretation  or  guidance  documents  on  EU  environmental 
legislation,  of  common  estimators  of  "carrying  capacity",  of  scientific  evaluations  and  impact 
assessment guidelines on the basis of common predictive models, are often quoted as ways 
forward.  Increased  consultation  and  discussion  among  stakeholders  and  authorities  (rather 
than imposed measures) are also called for. 

The  increasing  competition  for  space  and  water  represents  a  major  challenge  for  further 
development  of  freshwater  fish  farming  and  aquaculture  production  sites  in  coastal  areas. 
Public acceptance of aquaculture development in an area is usually inversely proportional to 
the  population  density  and  the  tourist  attractiveness  of  the  area.  Extensive  aquaculture  in 
inland ponds and wetlands or in coastal lagoons also faces increased competition with other 
economic  developments  (agriculture,  industry,  tourism…)68.  Spatial  planning,  including 
Integrated Coastal Zone Management, is considered a useful tool for the allocation of suitable 
sites for the development of aquaculture activities. 

3. Relevant EU environmental legislation 

Under  the  EU  environmental  law,  the  Water  Framework  Directive  and  the  Marine  Strategy 
Framework  Directive  provide  a  framework  for  the  definition  and  preservation  of  fresh  and 
marine  waters  in  the  EU.  Other  EU  Directives  relevant  to  the  environmental  aspects  of 
aquaculture  are:  Directive  67/548/EEC  on  dangerous  substances,  Directive  2006/113/EC 
known as “Shellfish Directive”69 and Directives affecting the marketing of veterinary medicinal 
products. Of relevance  is also the  Regulation on "alien species"70 which aims to assess and 
minimise the possible impact of the introduction of alien species for its use in aquaculture by 
establishing a permit system at Member State level. Resolutions and Communications related 
to  ICZM71  are  also  relevant  for  aquaculture  sector.  Furthermore,  the  EU  Directives  on 
Environmental Impact Assessment (EIA) and Strategic Environmental Assessment (SEA) may 
also apply. The Birds and Habitats Directives are addressed in the main document focusing on 
site management provisions; however their species-related provisions may also be relevant. 

Summary information on some of these provisions is provided below. 

68  Opportunities  for  the  development  of  Community  aquaculture.  Consultation  document.  European 
Commission, 2007. Available at: http://ec.europa.eu/fisheries/partners/consultations/aquaculture/index_en.htm 
69  This  directive  will  be  replaced  in  2013  by  the  EC  Water  Framework  Directive  (WFD).  This  must 
provide at least the same level of protection to shellfish waters as the Shellfish Waters Directive. 
70  Council  Regulation  (EC)  No  708/2007  of  11  June  2007  concerning  use  of  alien  and  locally  absent 
species in aquaculture. 
71 Available at:http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:C:2009:295E:0001:0004:EN:PDF 

 
 
 
 
 
 
 
 
 
 
                                                 
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79

3.1 The Water Framework Directive (WFD) 

The WFD (2000/60/EC), which applies to inland water and coastal water up to 1 nautical mile 
from coastal State baselines, aims to protect and enhance all surface waters and groundwater 
so that they reach a good ecological and chemical status by 2015. It establishes a framework 
to prevent further deterioration of aquatic ecosystems and introduces the consideration of the 
biological community, as well as the natural structure and functions of the aquatic ecosystem, 
as a quality element in the assessment of surface water status. 

There  are  strong  links  between  the  WFD  and  the  Habitats  and  Birds  Directives,  they  have 
broadly similar ambitions in terms of aiming to prevent further deterioration and enhance the 
ecological condition of aquatic ecosystems but have different legal requirements and important 
differences too. If the Natura 2000 measures require stricter ecological conditions in terms of 
water quality than those required for achieving Good Ecological Potential under the WFD then 
the stricter measures must be applied (in accordance with Art 4.2 of the WFD) and vice versa  

3.2 The Marine Strategy Framework Directive (MSFD)  

The MSFD (2008/56/EC) applies to marine waters which  include the coastal waters  covered 
by  the  WFD  (in  those  particular  aspects  not  addressed  by  the  WFD)  but  extends  to  those 
waters  which  are  still  under  sovereignty  of  the  Member  States  (mainly  EEZ).  Some  of  the 
MSFD objectives are similar to the WFD but it goes beyond in many areas such as descriptors 
on  biodiversity  or  marine  litter  and  noise.    Although  the  lesser  concentration  of  aquaculture 
activities  in  marine  areas  beyond  1  nautical  mile  makes  this  instrument  less  relevant  at 
present, the expected development of offshore aquaculture means this could be more relevant 
for aquaculture in the future. (Huntington et al. 2010). 

The Directive requires Member States to develop, on a regional basis, marine strategies that 
must  contain  a  detailed  assessment  of  the  state  of  the  environment,  a  definition  of  good 
environmental  status  at  regional  level  and  the  establishment  of  environmental  targets  and 
monitoring  programmes  with  the  overall  objective  of  maintaining  or  achieving  good 
environmental status in the marine environment by 2020 at the latest. Requirements under the 
MSFD  apply  to  all  aquaculture  activities  in  marine  waters,  whether  located  within  or  outside 
Natura 2000 areas. In all cases the stricter obligations apply. 

Aquaculture is one of the pressures to be addressed in the initial assessments performed by 
Member  States  and  due  in  October  2012.  On  this  basis,  good  environmental  status  criteria 
and  environmental  targets  are  set  by  Member  States.  Member  States  must  also  identify 
marine protected areas other than those designated as Natura 2000 sites (cf. Article 13.4 and 
13.5).  

3.3  Species protection provisions under the Birds and Habitats directives 

In addition to protecting core sites through the Natura 2000 network the two Nature directives 
also  require  that  Member  States  establish  a  general  system  of  protection  for  all  naturally 
occurring  wild  bird  species  in  the  EU  and  for  species  listed  in  Annex  IV  of  the  Habitats 
Directive These provisions apply both inside and outside protected sites. The exact terms are 
laid  down  in  article  5  of  the  Birds  Directive  and  Article  12  (for  animals)  and  Article  13  (for 
plants) of the Habitats Directive72. 

72 See Guidance document on the strict protection of animal species of Community interest under the 
Habitats Directive http://ec.europa.eu/environment/nature/conservation/species/guidance/index_en.htm 

 
 
 
 
 
 
 
 
 
 
                                                 
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Guidance document on aquaculture activities in the context of the Natura 2000 Network  

Article 5 of Birds Directive 

Articles 12 and 13 of Habitats Directive 

Member  States  should  take  the  requisite 
measures  to  establish  a  general  system  of 
protection for all wild bird species throughout 
their natural range within the EU. 

they  should  prohibit 

the 

In  particular 
following: 
- 

deliberate  killing  or  capture  by  any 
method; 
deliberate  destruction  of,  or  damage  to, 
their  nests  and  eggs  or  removal  of  their 
nests; 
taking their eggs in the wild and keeping 
of eggs; 
deliberate  disturbance  of  these  birds 
particularly during the period of breeding 
and rearing, in so far as this would have 
a significant negative effect on the birds; 
keeping  the  birds  in  captivity  and  their 
sale. 

- 

- 

- 

- 

the 

take 

Member  States  should 
requisite 
measures  to  protect  the  species  listed  in  Annex 
IV  throughout  its natural range  within Europe. In 
the  case  of  protected  animals  this  means 
prohibiting the: 
- 
- 

deliberate killing or capture by any method; 
deliberate  disturbance,  particularly  during 
breeding, rearing, hibernation and migration; 
deliberate destruction or taking of eggs in the 
wild; 
deterioration  or  destruction  of  breeding  sites 
or resting places; 
the keeping, sale and transport of specimens 
the from the wild. 

- 

- 

- 

In  the  case  of  protected  plants  this  means 
prohibiting the: 
deliberate 
cutting, 
- 
uprooting or destruction of such plants in the 
wild; 
keeping,  transport  of  sale  of  such  species 
taken from the wild. 

collecting, 

picking, 

- 

3.4 The SEA and EIA Directives 

The  purpose  of  the  Directive  on  Strategic  Environmental  Assessment  (SEA  Directive 
2001/42/EC)  is  to  ensure  that  the  environmental  consequences  of  certain  plans  and 
programmes  are  identified,  assessed  and  taken  into  account  during  their  preparation  and 
before their adoption. 

for  agriculture, 

A  Strategic  Environmental  Assessment  is  mandatory  for  a  variety  of  plans  and  programmes 
(i.e.  prepared 
transport,  waste 
management, water management, telecommunications, tourism, town and country planning or 
land use) which set the framework for future development consent of projects listed in the ‘EIA 
Directive’. An SEA should also be carried out on any plans or programmes, which, in view of 
the likely significant effect on sites, have been determined to require an assessment pursuant 
to Article 6 or 7 of the Habitats Directive. 

fisheries,  energy, 

industry, 

forestry, 

Ultimately, the SEA aims to encourage a more integrated and efficient approach to territorial 
planning  where  environment,  including  biodiversity  considerations,  are  taken  into  account 
much earlier on in the planning process and at a much more strategic level. This usually leads 
to  fewer  conflicts  further  down  the  line  at  the  level  of  individual  projects.  It  also  allows  for  a 
more  appropriate  siting  of  future  developments  away  from  areas  of  potential  conflict  with 
nature conservation73. 

While  the  SEA  process  operates  at  the  level  of  plans  and  programmes,  the  Directive  on 
Environmental  Impact  Assessment  (85/337/EEC,  amended  in  200974operates  at  the  level  of 
individual  public  and  private  projects.  Thus,  development  consent  for  projects75  which  are 

73 To be noted that the Aarhus Convention requires public consultation on plans relating to the 
environment even without an SEA 
74 Consolidates version available at: 
http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=CONSLEG: 1985L0337:20090625:EN:PDF 
75  The  EIA  Directive  defines  ‘project’  as  the  execution  of  construction  works  or  of  other  installations, 
schemes, or interventions in the natural surroundings and landscape. 

 
 
 
 
 
 
                                                 
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81

likely  to  have  significant  effects  on  the  environment  should  be  granted  only  after  an 
assessment of its likely environmental effects has been carried out. 

The EIA Directive distinguishes between projects requiring a mandatory EIA (so-called Annex 
I projects) and those where Member State authorities  must determine, in a procedure called 
“screening”,  if  projects  are  likely  to  have  significant  effects,  taking  into  account  criteria  in 
Annex III of the Directive (so-called Annex II projects). Intensive fish farming is included under 
Annex II. In accordance with article 4.2 of the EIA directive, for projects listed in Annex II, the 
Member States shall determine through: (a) a case-by-case examination, or (b) thresholds or 
criteria set by the Member State, whether the project shall be made subject to an assessment. 
Member States shall ensure that the determination made by the competent authorities under 
paragraph 2 is made available to the public.  

The  relationship  between  SEA,  EIA  and  the  Appropriate  Assessments  under  the  Habitats 
Directive 

There  are  many  similarities  between  the  procedures  for  SEA  and  EIA,  and  the  Appropriate 
Assessments carried out for plans or projects affecting Natura 2000 sites under the Habitats 
Directive.  But  this  does  not  mean  they  are  one  and  the  same,  there  are  some  important 
distinctions  too.  Therefore,  an  SEA  and  EIA  cannot  replace,  or  be  a  substitute  for,  an 
Appropriate Assessment as neither procedure overrides the other. 

They may of course run alongside each other or the Appropriate Assessment may form part of 
the  EIA/SEA  assessment  but,  in  such  cases,  the  Appropriate  Assessment  should  be  clearly 
distinguishable  and  identifiable  in  the  SEA’s  Environmental  Report  or  in  the  EIA’s 
Environmental documentation, or should be reported on separately so that its findings can be 
differentiated from those of the general EIA or SEA76. 

One  of  the  key  distinctions  between  SEAs/EIAs  and  Habitats  Directive’s  Appropriate 
Assessments  is  that  they  measure  different  aspects  of  the  natural  environment  and  have 
different  criteria  for  determining  ‘significance’.  Another  is  the  scope  of  the  Directives: 
SEAs/EIAs apply in the case of all plans and projects that fall within their scope irrespective of 
where  they  are  proposed  to  be  located  in  the  EU  territory.  The  Appropriate  Assessment,  on 
the  other  hand,  is  only  applicable  to  those  plans  and  projects  that  could  have  an  adverse 
effect on a Natura 2000 site. 

There  is  also  an  important  distinction  as  regards  the  outcome  of  the  assessment.  The 
assessments under the SEA and EIA lay down procedural requirements and do not establish 
obligatory environmental standards. The assessment under the Habitats Directive on the other 
lays down obligations of substance. In other words, if the Appropriate Assessment determines 
that  the  plan  or  project  will  adversely  affect  the  integrity  of  a  Natura  2000  site,  the  authority 
cannot  agree  to  the  plan  or  project  as  it  stands  unless,  in  exceptional  cases,  they  invoke 
special procedures for projects deemed to be of overriding public interest.  

This contrasts with the SEAs/ EIAs which are designed to make the planning authorities fully 
aware  of  the  environmental  implications  of  the  proposed  plan  or  project  so  that  these  are 
taken into account in their final decision.  

76 See EC guidance document: “Assessments of plans and projects significantly affecting Natura 2000 
sites.  Methodological  guidance  on  the  provisions  of  Article  6(3)  and  (4)  of  the  Habitats  Directive 
92/43/EEC”.   

 
 
 
 
 
 
 
 
 
 
                                                 
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Examples of Initiatives to promote sustainable aquaculture in the EU  

 
 
 
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83

In  addition  to  the  above-mentioned  EU  policy  and  legal  framework,  many  organisations  and 
Member  States  have  undertaken  action  to  boost  sustainable  aquaculture  development. 
Various  initiatives  on  a  national,  European  and  also  global  level  develop  and  permanently 
update codes of conduct, sustainability indicator and certification systems, in order to achieve 
a common and accepted understanding of sustainability in aquaculture among all stakeholders 
and how to achieve these goals in practice.  

Organic  fish  farming  has  been  introduced  in  several  European  countries  since  the  1990s 
according  to  specific  national  codes  of  practice.  In  order  to  harmonise  national  rules  and 
private schemes and give a minimum standards for organic aquaculture at EU level, rules on 
organic  aquaculture  animal  and  seaweed  production  were  laid  down  under  EU  organic 
legislation77. The new Regulation applies as from 1 July 2010.   

the  Sustainable  Development  of  Mediterranean  Aquaculture. 

Some examples are the FAO Technical Guidelines for Aquaculture development78, the Guide 
for 
Interaction  between 
Aquaculture and the Environment developed by the  World Conservation Union (IUCN)79, the 
Guide for sustainable aquaculture on trout farming (UICN, 2011)80, and the Code of Conduct 
for European Aquaculture (FEAP), which are used ues  

Another relevant example is the ICES Code of Practice on the Introductions and Transfers of 
Marine  Organisms  (2003)81,  which  sets  out  recommended  procedures  and  practices  to 
diminish the risks of detrimental effects from the intentional introduction and transfer of marine 
(including brackish water) organisms.  

In  addition,  the  EU  is  a  member  of  the  North  Atlantic  Salmon  Conservation  Organization 
(NASCO). Particularly relevant to the aquaculture sector is the Resolution by the Parties to the 
Convention  for  the  Conservation  of  Salmon  in  the  North  Atlantic  Ocean  to  Minimise Impacts 
from Aquaculture, Introductions and Transfers, and Transgenic on Wild Salmon Stocks (2003). 

The  EU  is  also  a  party  to  the  1992  OSPAR  Convention  for  the  Protection  of  the  Marine 
Environment of the North-East Atlantic, which has direct implications for marine aquaculture, 
for  example,  through  Recommendation  94/6  on  Best  Environmental  Practice  (BEP)  for  the 
Reduction of Inputs of Potentially Toxic Chemicals from Aquaculture. 

There  are  also  national  initiatives  that  aim  at  promoting  sustainable  aquaculture  production, 
through  relevant  guidance  (eg.  France,  Denmark,  UK,  etc.)  or  accreditation  schemes  (eg. 
Ireland, etc.). 

77 Commission Regulation (EC) No 710/2009 
78 FAO Technical Guidelines for Responsible Fisheries. No. 5: Aquaculture development. 
79 Guide published in 2007, developed in collaboration with the Spanish Ministry of Agriculture, Fisheries and Food 
and the European Federation of Aquaculture Producers (FEAP). 
80 UICN (2011). Guide pour le développement durable de l’aquaculture : Réflexions et recommandations pour la 
pisciculture de truites. Gland, Suisse et Paris, France : UICN. 
81 Available from: http://www.ices.dk/reports/general/2003/Codemarineintroductions2003.pdf 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                 
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4.1 Examples of EU funded projects to promote sustainable aquaculture 

Some  EU  funded  projects  aim  at  promoting  methods  for  the  sustainable  aquaculture 
development.  Among  these,  the  SEACASE  project  is  worthy  of  note82.  The  final  goal  of  this 
project  was  to  develop  effective  tools  for  sustainability  of  extensive  and  semi-intensive 
aquaculture  production  in  Southern  Europe,  while  minimizing  its  environmental  impacts  and 
improving the quality and public image of its products. They had also analyzed and developed 
environmentally friendly farming protocols as well as certification possibilities to be proposed 
for voluntary use by the industry. 

Another  project  aimed  to  develop  an  Ecosystem  Approach  for  sustainable  aquaculture 
(ECASA)83. A key deliverable of this project is a virtual toolbox to help owners and operators of 
fin-fish  and  shell-fish  farms  in  selecting  farm  sites  and  operating  farms,  so  as  to  minimize 
environmental impact and ensure the sustainability of sites and water bodies for aquaculture. 

The  EU  project  CONSENSUS  (2005-2008)84,  a  "Multi-stakeholder  involvement  towards 
protocols  for  sustainable  aquaculture  in  Europe",  developed  a  set  of  sustainability  indicators 
as  a  starting  point  for  a  certification  system  for  sustainable  aquaculture  and  for  a 
benchmarking process that is based on low environmental impact, high competitiveness and 
ethical  responsibility  with  regard  to  biodiversity  and  animal  welfare.  All  major  organisations 
and associations within aquaculture production were involved.  

The  EU  project  SustainAqua85  aimed  to  make the  European  freshwater  aquaculture  industry 
more  sustainable  by  improving  production  methods,  research  potential  market  applications 
and  increase  product  quality,  SustainAqua  undertook  five  different  case  studies  in  Europe 
representative of the most relevant freshwater aquaculture systems and fish species. Various 
practical  techniques  were  tested,  on  how  to  strengthen  the  diverse  aquaculture  farms  in 
Europe  in  a  sustainable  way,  from  extensive  and  semi-intensive  pond  systems,  which 
predominate  in  Central  and  Eastern  Europe,  to  intensive  recirculation  aquaculture  systems 
(RAS) as they are practiced in North-Western Europe. The main findings are described in the 
Handbook for Sustainable Aquaculture, which is a main product of the project. 

The  EATIP  –  European  Aquaculture  Technology  & 
Innovation  Platform  website 
(http://www.eatip.eu)  contains  summaries  (Technical  Leaflets)  of  EU-funded  aquaculture 
research  projects  made  in  the  5,  6  and  7  Framework  Research  Programmes.  These 
documents  were  prepared  within  the  scope  of  the  Profet  Policy  and  Aquainnova  projects. 
Many projects address the environmental impacts and sustainability issues of aquaculture. 

82  SEACASE  will  undertake  case  studies  of  extensive  and  semi-intensive  aquaculture  production  systems  in 
Portugal, Spain, France, Italy and Greece to develop good-practice guides and quality certification standards. See 
also: http://www.seacase.org/ 
83 ECASA project: http://www.ecasa.org.uk/index.htm 
84 CONSENSUS project, available from: http://www.euraquaculture.info/ 
85  Integrated  approach  for  a  sustainable  and  healthy  freshwater  aquaculture:  a  handbook  for 
sustainable aquaculture. Project N°: COLL-CT-2006-030384, 6th Framework Programme. 

 
 
 
 
 
 
 
 
                                                 
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85

ANNEX  2.  Information  on  Natura  2000  sites  and  habitats  and  species  of 
European interest in EU countries 

Some national sources (web sites) provide useful information to support species  and habitat 
conservation,  sustainable  management,  protection  and  planning.  These  tools  can  also  be 
useful to determine the sensitivity of habitats and species to different pressures, including from 
aquaculture activities, as they provide information about ecological requirements, threats and 
other relevant issues. Some relevant sources are included below. 

AUSTRIA 

Indikatoren  und  Schwellenwerten  zur  Beurteilung  des 
Entwicklung  von  Kriterien, 
Erhaltungszustandes  der  Natura  2000-Schutzgüter  (Development  of  criteria,  indicators  and 
threshold  values  to  the  judgement  of  the  condition  of  the  Natura  2000  protection  goods).  In 
German 
http://www.umweltbundesamt.at/umweltschutz/naturschutz/natura_2000/gez/ 

Lower Austria: Natura 2000 - Der niederösterreichische Weg (regional government website on 
Natura 2000 in n Lower Austria). In German. 
http://www.noe.gv.at/Umwelt/Naturschutz/Natura-2000.html 

Tyrol: Website with general information on N2000 in the Tyrol region (in German). 
http://www.tirol.gv.at/themen/umwelt/naturschutz/natura2000-tirol/ 

BELGIUM 

Natura  2000  habitats:  doelen  en  staat  van 
instandhouding.  Versie  1.0  (ontwerp). 
Onderzoeksverslag.  (Natura  2000  habitats:  conservation  objectives  and  conservation  status. 
In Dutch) http://www.inbo.be/docupload/2426.pdf 

Flanders:  Information  about  Natura  2000  plans  in  Flanders  (in  Dutch),  including  the 
conservation  objectives  for  the  sites,  parameters  for  the  favourable  conservation  status  in 
terms of habitats surface, and “measures and instruments”. 
http://www.natuurenbos.be/nl-BE/Thema/Natuur/Natuurrichtplannen.aspx 

BULGARIA 

Maps and information on Natura 2000 sites in Bulgaria: 
http://www.natura2000bg.org/natura/bg/index1.php 

CZECH REPUBLIC 

Zásady  managementu  stanovišť  druhu  v  evropsky  významných  lokalitách  (Principles  of 
management of the habitat of species at sites of European importance). In Czech 
http://www.mzp.cz/cz/zasady_managementu_stanovist 

Provides recommendations for the conservation of selected habitats of species of wild fauna 
and  flora  of  European  importance  (103  taxa:  63  animal  and  40  plant  species),  which  are 
primarily  intended  for  the  preparation  of  management  plans  for  Natura  2000  sites.  Includes 
information on the biology and ecology of each species and main threats, factors and activities 
that may negatively affect the the species population of in sites of European importance. 

Website with information on Natura 2000 sites in the country. In Czech. www.natura2000.cz. 
See also: http://drusop.nature.cz 

 
 
 
 
 
 
 
 
 
 
 
 
 
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DENMARK 

Natura 2000 plans: 
http://www.naturstyrelsen.dk/Naturbeskyttelse/Natura2000/Natura_2000_planer 
Technical  and  scientific  background  documents  are  also  available  from  the  National 
Environmental Research Institute at: www.dmu.dk. 

GERMANY 

Information about Natura 2000 sites (management, interactive map, etc.), and the habitats and 
species of European interest (conservation status monitoring, etc.) in Germany: 
http://www.bfn.de/0316_natura2000.html 

Habitat Mare web site. The Federal Agency for Nature Conservation provides in this website 
extensive  information  on  current  research  findings  and  background  information  on  marine 
nature  conservation,  in  particular  the  Natura  2000  -  SPAs  in  the  German  North  and  Baltic 
Seas: .http://www.bfn.de/habitatmare/de/ 

Managementmaßnahmen  in  Küstenlebensräumen  und  Ästuarien  der  Nord-  und  Ostsee 
(NaBiV 91, 2010). Management measures in coastal habitats and estuaries of the Baltic and 
North Seas (NaBiV 91, 2010). Publication. BfN. 

Baden-Württemberg  http://www.lubw.baden-wuerttemberg.de/servlet/is/44492/ 
http://www.uvm.baden-wuerttemberg.de/servlet/is/66368/ 

Bayern: http://www.lfu.bayern.de/natur/natura_2000/index.htm 
http://www.stmug.bayern.de/umwelt/naturschutz/natura2000/index.htm 
http://www.forst.bayern.de/funktionen-des-waldes/biologische-
vielfalt/schutzgebiete/natura2000/index.php 

Berlin: 
http://www.stadtentwicklung.berlin.de/natur_gruen/naturschutz/natura2000/de/management/in
dex.shtml 

Brandenburg: http://www.mugv.brandenburg.de/cms/detail.php/bb1.c.221574.de 
http://www.naturschutzfonds.de/unsere-arbeit-fuer-die-natur/natura-2000-
managementplanung.html 

Hesse: www.natureg.de , still in preparation/progress; at the moment: 
http://natureg.hessen.de/natureg/index.html#  provides information used for Natura 2000 
management (Artensteckbriefe, Artenhilfskonzepte – in German); additional information will be 
uploaded soon, such as management plans, special information on species/habitats 
occurrence in the Natura 2000 sites, guidance documents, expert reports, etc 

Mecklenburg-Vorpommern: http://www.regierung-
mv.de/cms2/Regierungsportal_prod/Regierungsportal/de/lm/Themen/Naturschutz_und_Lands
chaftspflege/NATURA_2000/Managementplanung/index.jsp 

North-Rhine-Westfalia: http://88.198.49.242/mako/install/ 

Rheinland-Pfalz:  http://www.naturschutz.rlp.de ; http://www.natura2000.rlp.de 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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87

Sachsen: Management planning: http://www.umwelt.sachsen.de/umwelt/natur/21184.htm 
Short versions of plans: http://www.umwelt.sachsen.de/umwelt/natur/18744.htm#19114 
Mapping and valuation codes etc.: http://www.umwelt.sachsen.de/umwelt/natur/18723.htm 

Sachsen-Anhalt: Information on ongoing planning as well as final plans available (website of 
the Landesamt für Umweltschutz): http://www.sachsen-anhalt.de/index.php?id=35704 

Schleswig-Holstein: www.natura2000.schleswig-holstein.de 
Provides information on Natura 2000, including conservation objectives, conservation-oriented 
water maintenance, etc. In German 

Thuringia: Artengruppen (Groups of species) In German 
http://www.tlug-
jena.de/de/tlug/umweltthemen/natur_und_landschaft/artenschutz/artengruppen/ 
Provides  factsheets  on  species  of  different  groups  (Mammals,  bats,  amphibians,  reptiles, 
crustaceans, molluscs, dragon-flies, beetles, butterflies, flower plants, ferns, lichens, birds) 

ESTONIA 

http://www.envir.ee/1684 

SPAIN 

Information  about  Natura  2000:  http://www.magrama.gob.es/es/biodiversidad/temas/red-
natura-2000/ 

Bases  ecológicas  preliminares  para  la  conservación  de  los  tipos  de  hábitat  de  interés 
comunitario  en  España  (Ecological  bases  for  conservation  of  habitat  types  of  Community 
interest in Spain). Information about ecological requirements, conservation Management, etc. 
for 
in  Spain. 
types 
http://www.jolube.es/Habitat_Espana/indice.htm 

of  European 

present 

interest 

habitat 

that 

are 

all 

Directrices  para la redacción de planes o instrumentos de  gestión de las Zonas de Especial 
Protección  para  las  Aves  (ZEPA).  Guidelines  for  the  preparation  of  Management  plans  for 
SPAs.  Includes  information  about  conservation  measures  for  all  bird  species  included  in 
Annex I of the Birds Directive which are present in Spain, their main treats and activities which 
may be in conflict with their conservation, disturbance from human activities, etc. 
http://www.seo.org/programa_seccion_ficha.cfm?idPrograma=24&idArticulo=3331 

FRANCE 

Cahiers  d’habitats:  factsheets  with  an  updated  synthesis  of  the  scientific  knowledge  and 
conservation  management  measures  for  all  habitats  and  species  present  in  France  (incl. 
activities that may affect the habitats, etc.). 
http://natura2000.environnement.gouv.fr/habitats/cahiers.html 

Référentiel  pour  la  gestion  dans  les  sites  Natura  2000  en  mer  -  Les  cultures  marines 
Guidance  on  Natura  2000  and  aquaculture  in  France  Agence  des  aires  marines  protégées. 
2009. 
http://www.aires-
marines.fr/images/stories/donnees/RTE/TOME1_Referentiel_CULTURES_MARINES_01_201
0_BD.pdf 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
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Les habitats et les espèces Natura 2000 en mer. Référentiel pour la gestion des activités de 
pêche professionnelle, cultures marines, sports et loisirs en mer dans les sites Natura 2000 en 
mer. Agence des aires marines protégées. 2009. Provides information on conservation status 
and threats for all habitat types protected under Natura 200 and on the possible pressures on 
them from fisheries, aquaculture and leisure activities in the sea. 
http://ecorem.fr/files/_TOME_2_Les_HABITATS_et_les_ESPECES_Natura_2000_en_mer_V2
_comp.pdf 

HUNGARY 

Information about Natura2000 sites: 
http://www.naturaterv.hu/ 

IRELAND 

Information about all Natura2000 sites (Conservation objectives, etc.): 
http://www.npws.ie/protectedsites/conservationmanagementplanning/ 

ITALY 

Abruzzo:  
http://www.regione.abruzzo.it/xAmbiente/index.asp?modello=menuAreeProBio&servizio=xList
&stileDiv=mono&template=default&msv=areeProt 

Regione Marche: 
http://www.ambiente.regione.marche.it/Ambiente/Natura/ReteNatura2000.aspx 

Piedmont: http://www.regione.piemonte.it/parchi/retenatura2000/ 
http://www.regione.piemonte.it/sit/argomenti/parchi/retenatura2000.htm 
http://gis.csi.it/parchi/datialfa_2k.htm 

Sardinia: http://www.sardegnaambiente.it/foreste/foreste_parchi/areeprotette/retenatura.html 

Sicilia:  http://www.artasicilia.eu/web/natura2000/index.html 

Trentino: http://www.areeprotette.provincia.tn.it/natura2000/index.html 

NETHERLANDS 

http://www.natura2000.nl/pages/homepage.aspx 

LITHUANIA 

A resolution adopted in 2004 informs about restricted and permitted activities for each habitat 
type of European interest. In Lithuanian 
http://www3.lrs.lt/pls/inter3/dokpaieska.showdoc_l?p_id=274764&p_query=&p_tr2= 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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POLAND 

Information about Natura 2000, habitats and species. 
http://natura2000.gdos.gov.pl/natura2000/#1 

PORTUGAL 

Plano  sectorial  da  rede  Natura  2000.  Sectoral  Plan  of  the  Natura  2000  network.  Provides 
information  about  all  Natura  2000  sites,  habitats  and  species  of  European  interest  that  are 
present in Portugal. 
http://www.icn.pt/psrn2000/fichas_sitios.htm 
http://www.icn.pt/psrn2000/fichas_valores_naturais.htm 

SLOVAKIA 

Information about natura 2000: www.sopsr.sk/natura/,  
www.enviro.gov.sk, and www.daphne.sk. 

SLOVENIA 

Information about Natura 2000: http://www.natura2000.gov.si/ 

SWEDEN 

Information  about Natura  2000, species  and  habitats,  management  plans  for  Natura  2000  in 
Sweden, available via SEPA's web-site:  
http://www.naturvardsverket.se/sv/Start/Naturvard/Skydd-av-natur/Natura-2000/ 

UNITED KINGDOM 

Joint Nature Conservation Committee (JNCC) - SAC Interest Features 
http://www.jncc.gov.uk/ProtectedSites/SACselection/SAC_habitats.asp 

UK Biodiversity Action Plan – Habitats: http://www.ukbap.org.uk/habitats.aspx 

JNCC  Assessment  of  the  conservation  status  of  each  habitat  on  Annex  I  of  the  Directive: 
http://www.jncc.gov.uk/page-4064 

Marine Protected Areas: http://jncc.defra.gov.uk/page-4524 

Marine Life Information Network: Biology and Sensitivity Key Information Sub-programme [on-
line].  Marine  Biological  Association 
at: 
of 
http://www.marlin.ac.uk 

the  United  Kingdom.  Available 

Scotland: 
designations/sac/sac-location/ 

http://www.snh.gov.uk/protecting-scotlands-nature/protected-areas/international-

England: http://www.naturalengland.org/ourwork/conservation/designatedareas/default.aspx 

Northern Ireland: http://www.doeni.gov.uk/niea/protected_areas_home 

Wales: http://www.ccw.gov.uk/Splash.aspx 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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