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New Commission guidance has been released to clarify issues around fishing activity in protected Natura 2000 sites. There are no new recommendations, the purpose of the document is to provide guidance to EU Member States on how to apply the Habitats Directive (Article 6) and Birds Directive (Article 4) to marine fishing activities. It aims to ensure fishing complies with conservation obligations in Natura 2000 marine sites. This document is not legally binding, although it explains the legally binding aspects of other regulations. Only 4% of Marine Protected Areas (MPAs) in the EU currently have all required conservation measures in place and effectively implemented. Below we look more in depth at the Articles, explaining some of the key terms (conservation objectives/measures, appropriate assessments, site deterioration) as well as highlighting key points made by the Commission and some issues around Ireland’s implementation of these EU laws.
In Ireland there appears to be regular confusion over whose jurisdiction it is to monitor protected areas in our waters. The Department of Housing has responsibility over the designation of Natura 2000 sites and the National Parks and Wildlife Service has responsibility to manage SACs (Special Areas of Conservation) and SPAs (Special Protection Areas). However, when it comes to regulating fishing activities in protected areas the NPWS has no responsibility here. The Department of Agriculture, Food and the Marine can issue Fisheries Natura Declarations (FNDs) to manage fishing activities in protected sites, however there are currently around 5 active FNDs in the whole of Ireland. It is also the Sea Fisheries Protection Agency’s job to ensure compliance with fishing regulations. Due to responsibility being split across departments and different bodies, confusion can arise and it can be difficult to get the correct information. Who is ensuring protected areas are effectively protected? Who is monitoring fishing activities in regards to the conservation objectives of protected sites? Natura sites at sea do not appear on nautical maps, so it’s extremely difficult for fishing vessels to even know when they are entering a protected area.
These are the sections of the Birds and Habitats Directive that the new Commission document gives guidance on.
Article 6(1) requires that Member States establish the necessary conservation measures.
Article 6(2) lays down the obligation to avoid habitat deterioration and significant disturbance of species.
Articles 6(3) and (4) contain specific rules which apply when plans and projects are proposed that are likely to have a significant effect on a Natura 2000 site. (N.B. fishing activities in Ireland are not considered plans or projects but an activity).
Article 4 of the Birds Directive contains similar rules to Article 6(1) of the Habitats Directive, and Article 7 of the Habitats Directive makes the rules in its Article 6(2), (3) and (4) applicable to SPAs under the Birds Directive.
The guidance first looks at applying these articles to fishing activities. It then looks at applying these articles in the context of the Common Fisheries Policy (one of the EU’s main pieces of legislation on fishing) and measures that can be adopted at a national level as well as measures under the Technical Measures Regulation. Finally, it looks at measures which can be adopted at an EU level and measures outside of the CFP which are still applicable to fishing vessels.
Commercial and recreational fishing activities can have a negative impact on habitats and species which are protected in Natura 2000 sites. The first step is to identify fishing activities that are likely to pose a risk of deterioration for the habitat types and species listed under the habitats directive. There are 9 marine habitat types, 16 marine species and 60 bird species listed under these laws. Member States should take appropriate steps to avoid the deterioration of habitats and significant disturbances to the species. Secondly, Member States should consider measures which go beyond preventing deterioration and actually result in achieving the conservation objectives for that site.
Conservation objectives define the site specific goals for maintaining or restoring the habitat and the conservation measures are the actions taken to achieve these goals. Appropriate assessments then assess any implications of plans or projects in terms of the site’s conservation objectives.
Site specific conservation objectives must be set based on the ecological requirements of the habitats and species and should define the desired condition using specific attributes and targets. Using historical data before industrial fishing occurred is useful here.
Establishing these objectives is an important step to ensure the correct conservation measures are then applied. The ecological requirements of habitats and species include both abiotic (non living components such as water quality, salinity, temperature, underwater noise etc) and biotic (living components such as predator/prey interactions etc) factors. These factors vary between species and even vary within a species depending on where it is in its life cycle and where it is found. Ecological requirements should be looked at on a case by case basis and this is the responsibility of each Member State.
Conservation measures not only need to be adopted they also above all, need to be implemented. In regards to fishing, conservation measures can include regulating catches or fishing effort or the application of technical measures such as, closures, gear adaptations, minimum sizes for species and the use of alternative gear. Wider regulation of fishing activities may have an impact on compliance with article 6(1) and these measures must be checked against the conservation objectives of a specific site. To ensure good practice, Member States should consult and involve stakeholders in defining these conservation measures and this requires timely and effective involvement and participation in the development and implementation of conservation measures. Socio economic impacts and benefits also need to be taken into account. To mitigate against any potential short term negative impacts, Member States can make use of financial supports and incentives such as the European Maritime, Fisheries and Aquaculture Fund (EMFAF) and the LIFE programme. However, the EU’s 2028 – 2034 Multiannual Financial Framework has allocated a minimum of 2 billion euros for fisheries. This is a drastic reduction compared to the 6 billion in the previous budget. In the next proposed Multiannual Financial Framework it states that the EU LIFE budget will no longer be standalone and will be absorbed between the European Competitiveness Fund and the EU Facility. The LIFE programme was the only dedicated funding for the environment and climate and so this proposal is extremely worrying.
Regular and effective monitoring of the condition of habitats and species must also be undertaken to check how the measures are working and to ensure the compliance and enforcement of them. In regards to fishing this includes, surveillance of activities in the site in accordance with the Control Regulation (another piece of fisheries legislation which requires CCTV on certain vessels and up to date log book reporting. Some of these measures will not be in place until 2026).
What is Ireland currently doing?
Ireland was taken to the EU Court of Justice over its failure to adopt site specific conservation objectives and measures across its protected sites on land and sea. There is no available timeline online as to when site specific conservation measures will be in place. Currently, they are ensuring that there are site specific conservation objectives in place for each site and measures will come after that. There are very few measures in place for marine SACs and SPAs aside from a list of Activities Requiring Consent from the Minister. There is evidence that some FNDs overlap with Natura sites and provide some form of management, however monitoring is lacking. Some FNDs prohibit high impact fishing (be it in very small areas) but others are less restrictive and only contain seasonal measures or the requirement of GPS.
What is an Appropriate Assessment (AA)?
If fishing activities are deemed to have an impact on the site and are not connected to the management of the site, they must be assessed by an appropriate assessment. It applies to activities that do not require authorisation but are likely to have a significant impact on a site including, recurring activities, intensification of an activity, modification of plans or projects and activities outside of the site likely to have an impact within the site. There is no restriction relating to the size of a project or activity. The law also states that there can be no general exemption of certain activities. As an example, sometimes fishing permits are issued or renewed by a Member State allowing specific fishing activities during a specified period in a given area or for a given fishery under specific conditions. If such fishing activities are likely to have a significant impact on Natura 2000 sites, those permits should be subject to an appropriate assessment
The focus of an appropriate assessment (AA) should be on the impact an activity could have on habitats or species listed under the Habitats and Birds Directives. In order to comply with the law, AAs need to –
Potential impact of fishing activities must be assessed against the conservation objectives of the site. If there is not enough data to do this, then the precautionary principle should be applied until enough data are collected. Fishing activities within and outside the site may fall within the scope and be likely to cause deterioration of the site. Recreational and commercial activities are included regardless of permits, licences or lack thereof and whether any potential impact is intentional or unintentional. Data should also be collected on the biological, environmental, economic and social impacts of fishing and used to compile conflict matrices for each site. These matrices should describe whether each type of fishing gear poses a risk of impacting or causing deterioration of the site. Habitats should be broken down into the smallest scale possible (examples level 4 and 5 of EUNIS classification system) and the same may be necessary for fishing gear.
Figure 1. Methodology protocol for assessing the impact of fisheries on marine Natura 2000 sites taken from Commission Guidance
What has Ireland done so far?
The Marine Institute put together several documents over 10 years ago looking at the risks of fishing in Marine Natura sites. However, since then site specific plans for measures addressing these issues haven’t materialised for the majority of marine sites. In these documents it states that a risk assessment will be undertaken and for each site the following outputs will be produced
There does not appear to be any marine protected site that has all nine of these outputs analysed and only a handful of areas which have a few of the outputs looked at. In the Commission court case against Ireland it stated that Ireland had not yet carried out AAs for all fishing activities across its protected sites. Some AAs or risk assessments do exist in some sites but they are geared more towards aquaculture and are only partial for some fishing activities. Boats are issued with licences but are not tied to a particular SAC or SPA and so most fishing activities do not undergo AAs or risk assessments. However, EU guidance has made it clear that should not be the case. More information on Article 6(3) below showcases this.
Deterioration and Significant Disturbance
The ecological characteristics are not allowed to go below their reference level at the time of designation and if they improve, the higher level is the new reference. For habitats this could mean the area covered by the habitat is reduced or the structure or functions are reduced. Species significant disturbance is when an activity contributes to the long term decline of a population or a decline in its range or available habitat for the species. The deterioration and significant disturbance should be assessed in a dynamic way taking into account the evolution of the condition of the habitats and species. Preventative measures should be put in place in the site to prevent deterioration and this includes areas where fishing occurred before designation. When destructive fishing is removed from an area, the area will begin recovering immediately although this may not be immediately noticeable and Member States must ensure no damaging activities are allowed to occur again. The Habitats and Birds Directives are the main tools in achieving favourable conservation status of the environment and so it is against the law to allow habitats and species in protected sites to remain in ‘not good’ condition. Voluntary agreements such as a code of practice are likely to be insufficient and the EU Court found that a failure to adopt legally binding protective measures against activities causing deterioration is a breach of the Habitats Directive.
This article is applicable to any fishing activity in Natura 2000 sites for which specific permits are issued or renewed or that do not require authorisation but are likely to have a significant effect on a site. ‘In the context of fishing, there are likely to be circumstances where there is insufficient scientific knowledge regarding the likely effects, for example in relation to new fishing methods, changing intensity of existing fishing activities, existing fishing gear which is used in novel ways, or in the case of less well-studied interactions. Under such circumstances, the CJEU has ruled that, in the event of doubt as to the absence of significant effects, an appropriate assessment in view of the site’s conservation objectives must be carried out, and that determination of effects must be based on the precautionary principle’
Figure – Commission guidance outlining when Article 6(3) applies
In combination effects also need to be accounted for as cumulative impacts from numerous projects or plans will all affect whether a site will deteriorate or not. Assessment of in combination effects also need to take on activities happening at different times (summer/winter fisheries), in different areas (sandbanks and adjacent reefs) or separated across the water column (sea bed and mid water trawling).
Fisheries are also transboundary by nature. The Espoo Convention which is implemented in the EU through Environmental Impact Assessments and Strategic Environmental Assessments Directives requires that transboundary effects must be taken into account and therefore under article 6(3) of the Habitats Directive must also be considered in AAs. Fishing in the waters of one Member State may have impacts in a Natura site of another Member State or a fishing fleet from one Member State may fish in the Natura site of another Member State
National authorities ‘cannot authorise interventions where there is a risk of lasting harm to the ecological characteristics of sites which host priority habitats types’. Furthermore, ‘the lasting and irreparable loss of the whole or part of a priority natural habitat type whose conservation was the objective that justified the designation of the site … will adversely affect the integrity of that site.’ The precautionary principle should be applied for the purposes of that appraisal. The logic of such an interpretation would also apply to non-priority habitat types and to habitats of species. An example of fishing activity affecting site integrity would be demersal towed gear (bottom trawling) reducing the structural integrity of soft sediment habitats and lead to changes in the typical species found there.
This Article allows for exemptions if a plan or project must be carried out for imperative reasons of overriding public interest despite a negative assessment on its implications for the integrity of the site. When the site contains priority habitats/species the only exception to be considered must relate to human health or public safety, beneficial consequences of primary importance for the environment or another reason of overriding public interest if confirmed by the Commission. Three key requirements must be met to allow the activity to continue.
For fishing it must be shown that the species being targeted cannot be caught elsewhere, it cannot be caught with other fishing gear and that a different species cannot replace this as a food provision.
Measures for compliance with the Habitats Directive in regards to fishing activities must be adopted according to the rules and procedures of the CFP. In some cases, Member States are empowered to adopt national measures affecting fisheries. These measures must be non discriminatory and at least as stringent as measures under EU law. Article 11 of the CFP provides the framework for these measures to ensure compliance with the Habitats Directive. However, these measures must not affect other EU vessels. If other Member States will be affected, this must go through a process called Joint Recommendations and the EU is involved.
Article 20 of the CFP is a very under utilised article, where member states can put in measures to conserve and manage fish populations or improve the status of marine ecosystems within 12 nautical miles of its baselines. If these measures will affect other Member States fishing vessels they can only be adopted after consulting the Commission, the relevant Member States and Advisory Councils.
‘Article 13 of the CFP Regulation empowers Member States to adopt emergency measures, under certain conditions, on the basis of evidence of a serious threat to the conservation of marine biological resources or to the marine ecosystem that requires immediate action. For example, in January 2024, the French authorities adopted an ‘emergency measure’ under Article 13(1) of the CFP Regulation. The measure aimed at protecting small cetaceans by establishing a one-month ban on fishing with certain fishing gear in the French waters of the Bay of Biscay for all Member States’.
Has Ireland established any emergency measures?
Reports from the Marine Institute have shown that tangle nets have significant bycatch including critically endangered shark and ray species as well as seal species protected under the Habitats Directive. A shellfish stocks and fisheries review report from 2024 states, ‘Critically endangered species cannot sustain by-catch mortality caused by the tangle net fishery. Measures should be introduced to eliminate the by-catch of critically endangered species and to significantly reduce the by-catch of protected species.’ Emergency measures can last up to 3 months but it is clear, more significant measures are needed. The critically endangered Angel shark has been recorded as bycatch in these reports and under the EU Nature Restoration Law, it is legally required to ensure this species (and the habitats it relies upon) are protected and restored. Flapper skate has also been recorded as bycatch in tangle nets. This species is also critically endangered and ‘depleted populations of skate cannot sustain significant fishing mortality at local level (given high site fidelity) or over wider geographic areas given life history and in particular high age at maturity.’ There is information available for these critically endangered species and certain types of fishing that affect them and so more measures (including emergency measures) need to be undertaken to effectively protect them.
Joint Recommendations and the Nature Restoration Law
The Joint Recommendation process is widely known as being lengthy and not extremely clear to Member States. This document doesn’t focus on the process but does refer to it and links it to the new EU Nature Restoration Law. Member States have until August 2026 to submit their National Restoration Plans and Ireland has already begun the stakeholder engagement process with the public and with experts and industry through the Leader’s Forums and the Independent Advisory Committee. However, when it comes to the marine side of the plan, information is currently scarce and we were left feeling disheartened after the Marine Leader’s Forum as no concrete measures for how to restore marine habitats and species were being discussed.
While the recent EU guidance document has not given extra recommendations to effectively protect marine sites against methods of fishing that could affect the integrity of a protected area, it does highlight key aspects of different laws which need to be adhered to. It’s clear Ireland is lacking in many measures and this Commission document will be a quick and useful way for stakeholders to highlight the legal requirements that need to be met. There is a lack of information in regards to inshore fishing and this is something that needs to be rectified. The Marine Institutes documents detailing the risk assessment process around fisheries should also be adhered to. The Irish Government are letting down fishing communities and also not adhering to legal requirements around ensuring the protection of vital habitats and species. In order to improve the condition of habitats and species under the Nature Directives the Government must provide greater support to fishing communities around additional administrative burdens. Ensuring a fairer share of quota across all fishing vessels will also help to diversify fishing and lower the pressure on certain species which can have negative impacts on protected habitats and species. There are damaging fishing activities happening in (and out off) protected sites which will need to change and this will also require extra support from the Government to allow a sustainable transition away from them. Clear, consistent conversations with fishing communities ahead of assessments should be a top priority and this process should be built upon as we move forward with designating MPAs through upcoming national MPA legislation.
Grace Carr
Marine Advocacy Officer
Marine Institute reports – Effects of fisheries on qualifying interests , Risk assessment for fisheries, Catch and bycatch in tangle net fishery, Shellfish stock and fisheries review