Regulation of fish and shellfish farm deposits: consultation analysis

Consideration of key points raised

Proposal to identify SEPA as the responsible authority for fish and shellfish farm discharges between 3 to 12 nautical miles

Benefits of the proposal

A number of respondents recognised the benefits that consistency in the inshore zone (0 – 12 nautical miles) would bring, including to reduce duplication, and the expertise which SEPA holds. Respondents that agreed included organisations that are either involved in either regulating aquaculture activities or providing advice to lead regulators through established consenting processes. Most recognised the potential for increased complexity should different arrangements exist from 3 – 12 nautical miles, compared to the framework for consenting between 0-3 nautical miles. For example, under this scenario SEPA would remain a statutory consultee to planning, but MD-LOT would lead for discharges, while having to also rely on SEPA’s advice as consultee to marine licencing processes. SEPA themselves highlighted that acting solely as a consultee to the marine licence process, would not enable them to recover costs under their current charging schemes.

A number of respondents agreed with the position that unifying the regulation of fish farm discharges across the 0-12 NM area would avoid regulator inefficiencies, which would arise from both SEPA and MD-LOT being responsible for the same regulatory function but in different geographic areas. On this point, it is the Scottish Government’s view that in determining which authority is best placed to regulate this activity, the issue of regulatory experience within a given geographic area is not the primary consideration, but rather which has the relevant experience and resource in regards to the assessment and regulation of a particular activity, in this case fish farm environmental discharges. It is also the case that conditions found beyond 3 nautical miles may also be found in areas within 3 nautical miles. SEPA themselves have stated that they already determine applications for farms in a range of different locations, including exposed locations, under its current remit of regulating up to 3 nautical miles.

Regulator resourcing

A number of respondents, both those who agreed and those who disagreed with the proposal, included comments that suggested SEPA would need to be appropriately resourced to ensure effective monitoring and enforcement of environmental discharges for fish farms beyond 3 nautical miles. While some respondents simply stated that SEPA must be adequately resourced to effectively carry out the function, others suggested SEPA would require a significant increase in resourcing to regulate the activity.

We agree that the regulator should be appropriately resourced and deliver effective environmental protection. In considering how fish farm environmental discharge activity between 3-12 nautical miles could be most effectively regulated, advice was sought from both MD-LOT and SEPA on their ability to carry out this function based on existing resource and expertise, and through any constraints in regulating the activity arising from the nature of the legislation under which both bodies operate.

Advice from MD-LOT was that at present it did not have the relevant expertise in place to directly carry out assessment and licensing of fish farm discharge activity. MD-LOT also advised that until sufficient expertise was in place it would need to rely on SEPA as a consultee to support the assessment and determination of any application. This would in effect require SEPA to carry out an assessment as it would if it were acting as regulator, and SEPA has indicated it would be unable to do so without a cost recovery mechanism. This raises the challenge of how to facilitate cost recovery for SEPA to enable them to carry out application assessment on behalf of MD-LOT, as there is currently not a clear mechanism to do this. Additionally, as SEPA would also remain a statutory consultee to planning, their ability to effectively engage with both processes may be weakened. Also, as noted in the partial BRIA, there would be a need to amend existing marine licence regulations as it is considered that existing marine licensing charging rules do not suitably cover subsistence requirements or ongoing monitoring which would be needed for efficient ongoing regulation of fish farm discharges.

In its formal response to the consultation, SEPA has agreed that it should be designated as the responsible authority for regulating environmental discharges from fish farms located between 3 -12 nautical miles. On resourcing SEPA stated that, “the proposed expansion in geographic remit will increase the sea area within which SEPA has an obligation to carry out the assessment, licensing, and regulation of marine pen fish farming. SEPA will apply its existing expertise in assessment, licensing and regulation of fish farm environmental discharges to allow SEPA to regulate this activity between 0-12 nautical miles. The impact upon SEPA’s resources is dependent upon the volume and complexity of applications within this new geographic area. At this stage, the scope and impact of this is not yet known. We are mindful of implications on how we monitor, audit and regulate and are in active discussions with Marine Directorate to explore how we can optimise our relative strengths and capabilities.” It was also noted that “to build capacity to take up this duty SEPA anticipate that any additional resourcing will be for the preparation work.” SEPA also highlighted that, “alternative approaches, such as acting solely as a consultee to the marine licence process, would not enable us to recover costs under our current charging schemes.”

It is considered that SEPA would be best placed to carry out this function in respect to resource capacity as SEPA already has staff in place with experience of assessing and regulating marine fish farms. It is also anticipated that in the short to medium term a small number of proposals for development between 3 – 12 nautical miles are likely to come forward. While some increase in resourcing may be required in future depending upon the volume and complexity of applications, impacts on SEPA’s resourcing in the short term is likely to be limited, noting SEPA’s statements that any initial additional resourcing will be for preparation work. It is also considered that SEPA’s existing charging mechanisms, which allow for cost recovery through application fees and subsistence charging, are suitably adaptable to allow for cost recovery to be achieved in relation to licensing and regulation of fish farming activity between 3-12 nautical miles.

In contrast it is considered that MD-LOT would need to increase resource to ensure appropriate expertise is in place to undertake assessment of the activity. This may be considered as a duplicated effort in resourcing appropriate expertise across the public sector, as relevant expertise already sits within SEPA. As noted above, until appropriate resource is in place MD-LOT would require SEPA to provide extensive advice to aid in assessing and determining applications, raising challenges in enabling SEPA to achieve cost recovery for this work. Marine Licence charging mechanisms are also less adaptable than those used by SEPA, leading to challenges in seeking cost recovery for monitoring activity.

Manner of regulation and existing regulator expertise

A number of respondents requested that further detail was required on how the regulation would be carried out. There was also a range of views on the level of environmental regulation that should be applied to fish farming.

Some respondents indicated that stricter environmental regulations should be included with full cost recovery and transparency of environmental monitoring data. The Scottish fish farming sector stated its view that SEPA’s existing method of assessing fish farm discharge activity would not be appropriate for farms beyond 3 nautical miles, noting the differences in environmental conditions between “inshore” and “offshore” locations, and SEPA’s existing assessment methodology not being suitable to model impacts in more exposed locations. It was also stated that MD-LOT would be best placed to regulate beyond 3 nautical miles due to its experience in licensing other activities in this area, including marine dredge and dumping.

In terms of likely methods of assessment, as noted above MD-LOT has advised that until resources were in place, it would need to rely on SEPA as a consultee to support the assessment and determination of any application for fish farm discharges. In regard to MD-LOT’s existing expertise in licensing other forms of marine activity, including marine dredging, MD-LOT has advised that it follows a more simple process of assessment against established action levels for determining such applications. Assessment of the effects of aquaculture discharges would require specific technical knowledge and expertise, beyond what MD-LOT currently requires for assessing dredging and deposit licence applications.

In its response to the consultation, SEPA has stated that it proposes to apply the existing regulatory framework for Marine Pen Fish Farming, adapting where necessary and noting that EASR is designed to be flexible, with SEPA’s frameworks focusing on the environmental outcome allowing them to assess novel or offshore infrastructure and setting appropriate conditions to control any potential impacts. It was also highlighted that SEPA already determines applications for farms in a range of different locations, including exposed locations, under its current remit of regulating up to 3 nautical miles.

It is therefore considered that SEPA is best placed to carry out assessment, licensing and on-going regulation of fish farm environmental discharge activity between 3-12 nautical miles. We agree that there should be no one size fits all approach and that environmental assessment may need to adapt. The adaptable nature of the regulations under which SEPA operate, will allow assessment processes to be varied as required to ensure fish farming development is permitted while ensuring farms operate within environmental limits. SEPA has also noted it would be happy to discuss assessment methods further with industry representatives and interested third parties.

Duplication in aquaculture consenting

A majority of respondents, including SEPA, Local Authorities, Nature Scot, Crown Estate Scotland and Fisheries Management Scotland, agreed with the proposals, noting that they would create a consistent approach to aquaculture consenting within the 0-12 nautical mile region. The Scottish salmon farming sector stated that extending the existing regulatory framework out to 12 nautical miles would maintain existing structural duplication in the fish farm consenting process, and that consenting arrangements from 3-12 nautical miles provided a potential opportunity to pilot an alternative consenting framework. Scottish producers propose MD-LOT should remain lead regulator for fish farm environmental discharges from 3 – 12 nautical miles, instead of SEPA. One of the key potential benefits raised is streamlined environmental assessment activity.

The Scottish Government has been working to consolidate SEPA as the independent environmental regulator of fish farms, including transfer of wellboat discharges from MD-LOT to SEPA in November 2020, and by appointing SEPA as lead regulator to manage the risk that sea lice from fish farms impact upon wild fish in October 2021. While it is possible for Scottish Ministers to remain lead regulator for discharges from 3 – 12 nautical miles, divergence of controls in the inshore zone is expected to result in a number of challenges (discussed in this consultation response), while identifying SEPA as lead also provides scope to explore streamlined environmental assessment activity.

To ensure consenting processes are efficient and effective, Scottish Ministers are continuing working to address the recommendations of the 2022 independent review of aquaculture regulation. Businesses are a key partner alongside regulators and other public bodies in taking forward work to streamline these consenting activities, with a Consenting Task Group working to identify, pilot and review new measures to achieve an improved, multilateral consenting process framework.

Pilots of a new, coordinated, pre-application process are ongoing in Shetland and Highland local authority areas. We have seen benefits in the aligned pre-application approach and intend to improve that process and to broaden out testing to additional local authority areas for the benefit for all. Work is also underway to align the formal application process and review Environmental Impact Assessment and Habitat Regulators Appraisal processes to seek opportunities to reduce regulatory duplication. A consistent framework for aquaculture consenting in Scotland’s inshore zone provides the opportunity for the adoption of processes developed by the Consenting Task Group Scotland-wide, which is transparent to all stakeholders.

Views have also been sought through this consultation on proposals to clarify the intent of the existing marine licence exemption on deposit of farm equipment, to enable businesses to consider its application as a means to reduce regulatory duplication further.

Impact on businesses

Scottish salmon farming businesses stated that SEPA’s approach to assessing applications would be too precautionary and therefore limit development and impact business growth. It also stated that existing operators would be negatively impacted by SEPA requiring to resource development of a new framework to assess development between 3-12 nautical miles, noting interest to date is from other businesses that currently operate outside of the Scottish and UK economic area.

Based on the advice received from SEPA, it is considered that SEPA’s frameworks, which are adaptable, will allow for sustainable levels of farm biomass to be permitted, ensuring the environment is protected while allowing for increased levels of production where conditions allow. As noted above in the section on regulator resourcing, the levels of additional resource required by SEPA is likely to be limited, noting SEPA’s statements that any additional initial resourcing will be for preparation work. It is also considered that SEPA’s existing charging mechanisms, which allow for cost recovery through application fees and subsistence charging, are also suitably adaptable to ensure that any fees are appropriate to the scale of development and regulatory requirements.

While it is noted that there is a suggested lack of interest from existing operators in Scotland to develop operations beyond 3 nautical miles at present, it is expected that clarifying consenting processes between 3-12 nautical miles will encourage developers to consider opportunities in this emerging sector in future. The Scottish Government is committed to supporting a diverse and innovative sector, and also recognises the value that inward investment brings to Scotland’s economy, both in terms of the direct benefits that accrue from job creation, but also the wider economic benefits through stimulating supply chain activity associated with an individual project. By clarifying consenting processes for aquaculture between 3-12 nautical miles we hope to signal to businesses at home and abroad that Scotland is open to innovative aquaculture development, including those which have the potential to support fish health and welfare and reduce environmental interactions.

Applicability of proposals within existing legislation

Scottish salmon farm business respondents raised the issue of how the proposals related to existing legislation, in particular the Water Framework Directive and The Marine (Scotland) Act 2010. A number of respondents also queried how SEPA’s role would align with other regulators between 0-12 nautical miles.

As noted in the consultation, SEPA would be identified as the regulator for fish farming environmental discharges between 3-12 nautical miles, via amendments to the Environmental Authorisations (Scotland) Regulations 2018 (“EASR”). EASR is the regulatory mechanism by which SEPA’s Integrated Authorisation Framework operates. EASR was enacted using powers under the Regulatory Reform (Scotland) Act 2014 and those powers would also be used for this amendment. The framework under EASR aims to integrate, as far as possible, the authorisation, procedural and enforcement arrangements relating to water, waste management, radioactive substances and pollution prevention and control. SEPA would take on responsibility for fish farm environmental discharge activity between 3-12 nautical miles by including this as a regulated water activity within EASR. This would not fall within the scope of the water framework directive, but amendments to EASR would ensure such activity is licensed to ensure any impacts to the environment between 3-12 nautical miles are appropriately controlled. As is referenced in schedule 10 of EASR, requirements from section 15(1) of the Marine (Scotland) Act 2010 to take authorisation and enforcement decisions in accordance in accordance with relevant marine plans would apply to SEPA granting permits under EASR.

The proposed amendments would result in regulatory responsibilities for fish and shellfish farming across Scotland’s inshore region (0-12 nautical miles) being consistent as detailed in the table below:

Amendments to the Marine Licence Exempted Activities Order to extend the existing exemption on requirements for marine licensing of deposit of “substance” from fish farms from 3 nautical miles to 12 nautical miles.

Benefits of the proposal

The majority of respondents agreed that the proposal would reduce regulatory duplication and streamline the consenting process. The Scottish Government is committed to removing regulatory duplication in consenting processes where it exists. Extending the existing exemption on marine licence requirements for the deposit of substance from fish farms, will recognise SEPA’s role as regulator for this activity and reduce regulatory burden for businesses.

Loss of regulatory oversight and transparency

Some of the respondents noted concerns of fish farms moving further offshore and potentially into more sensitive areas. One respondent who disagreed with the proposal noted that the Marine Licence is an important checkpoint for considering location and impacts of the development and that removing the Marine Licence would reduce transparency for anyone to comment on the project.

The Scottish Government is committed to ensuring that the fish farming sector is both efficiently and effectively regulated and that local communities and wider stakeholders have the opportunity to comment on development proposals. The intention of the amendments described in the proposal are to ensure the same activity is not regulated twice by different bodies. The proposed extension of the exemption on substances, recognises SEPA as the regulator for assessing and licensing fish farm discharge activity, as is the case currently for fish farms located out to 3 nautical miles. Individuals and organisations, are able to comment on SEPA licence applications and further detail on this can be found on SEPA’s website. Formal representations on proposed developments are also able to be made through the planning process.

Amendment to the Marine Licence Exempted Activities Order to clarify the scope of the existing exemption for the deposit of fish and shellfish farm equipment.

Benefits of the proposal

The vast majority of respondents agreed with the proposal, noting that improving the wording of the exemption to confirm that it applies to all equipment used in the course of fish and shellfish farming, will make its application clear to businesses and support streamlining of the consenting process.

Clarifying the application of the exemption may provide confidence to businesses to use the exemption where relevant conditions are met. When applied, as well as reducing regulatory burden, the exemption would also mean no fees would need to be paid for a marine licence which may be of significant benefit to smaller businesses, particularly shellfish farmers.

Clarification on scope of the exemption

A number of respondents provided suggestions and recommendations as to how the scope of the exemption could be clarified further, including to updates to the corresponding guidance on use of the exemption. Some responses also highlighted some issues which may continue to limit use of the exemption by businesses, such as whether insurers would be content with the exemptions use.

The amendments to the Exempted Activities Order will replace the current description of equipment subject to the exemption from “deposit of any trestle, raft, cage, pole, rope or line in the course of the propagation or cultivation of fish” to “deposit of any equipment in the course of the propagation or cultivation of fish”. In addition, a new condition on the use of the exemption will be included which will require that any equipment to which an exemption is to be applied must have planning permission in place. This will ensure that the deposit of all forms of equipment in the marine environment used in relation to fish and shellfish farming, including indirectly, will require either planning permission or a marine licence. As both planning and marine licence application processes are subject to Environmental Impact Assessment and Habitats Regulations Appraisals, where an application falls within the scope of those regulations, it will be the case that placement of fish and shellfish farm equipment will always be appropriately assessed.

Ensuring navigational risk of fish farms are addressed

A number of respondents highlighted concerns that updated wording of the exemption, may lead to fish farms not being appropriately assessed or licensed on the basis of navigational risk.

The assessment of navigational risk is a key aspect of aquaculture consenting, and the Scottish Government is clear that navigational safety must be considered fully before a farm is able to operate.

The deposit of fish and shellfish farm equipment may be considered as an activity where there is duplication of regulation due to overlap between matters considered in relation to applications for marine licences and planning permission in respect of equipment being deposited in the sea for the purposes of fish and shellfish farming.

In practice we find that both planning authorities and Marine Directorate Licensing Operations Team consult with navigation authorities and include duplicated conditions in the planning consent and marine licence, based on navigation authorities’ advice.

The proposed amendments to the existing amendments are intended to identify that all equipment used directly in the course of the propagation or cultivation of fish and shellfish, may apply the exemption where the relevant conditions for the deposit of the equipment are met. The existing condition that the exemption will not apply if the deposit “causes or likely to cause obstruction or danger to navigation” will remain. A developer seeking to use the exemption must satisfy themselves that the condition has been met. Current guidance advises that advice is sought from navigation bodies and any mitigation they advise is included in the development. Improved engagement with navigation bodies is being implemented through the Consenting Task Groups pre-application pilot programme. As part of the aligned pre-application process for fish fam consenting, key consultees, including navigation bodies, are engaged with at the early stages of the development process, allowing developers to receive early advice on potential constraints and recommended mitigation measures for fish farm proposals. Work is on-going to further improve the aligned pre-application process and broaden out the process to relevant local authority areas across Scotland.

Impact Assessments

The Scottish Government is required to consider the impacts of proposed policies, plans or strategic decisions in relation to equalities, various societal groups and sectors, data protection and the environment, under a range of legislation and commitments. Impact assessment and impact assessment screening documents were published alongside the consultation paper. A number of respondents provided comments in relation to these impact assessments.

These included a range of views in relation to the partial Businesses and Regulatory Impact Assessment (BRIA) and the partial Island Communities Impact Assessment (ICIA). Both these impact assessments were published in a partially completed form to allow comments provided in the consultation to be incorporated into final versions of these impact assessments. These responses will be included and considered in the final versions of these impact assessments which will be published on the Scottish Government Website

In regard to the Strategic Environmental Assessment (SEA), one respondent agreed with the findings of the SEA but noted that SEPA would need to be well resourced for it to be implemented. Having consulted with NatureScot, Scottish Environment Protection Agency and Historic Environment Scotland, as required by the Environmental Assessment (Scotland) Act 2005, Scottish Ministers determined that a full SEA was not required.

One respondent sought clarity as to why there was requirement for an impact assessment in respect of Child Rights' and Wellbeing. A Child Rights and Wellbeing Impact Assessment (CRWIA) is a process which is used to identify, research, analyse and record the anticipated impact of legislation and strategic decisions. These requirements are set out in the UNCRC (Incorporation) (Scotland) Act 2024 (UNCRC Act).

Further points raised

Transparency

A number of the respondents referenced the need for further transparency in the process, including suggestions for a single platform for environmental monitoring data which is publicly available.

On 21 August 2025 SEPA launched an updated version of the Scotland’s Aquaculture Website. The update will ensure that the website has secure infrastructure and that it is more intuitive and accessible for users. As well as a more user-friendly design and improved access to interactive maps and datasets, the refreshed site makes aquaculture data generated from regulators and the sector more accessible and meaningful, reflecting an ongoing commitment to transparency and environmental protection.

SEPA has secured funding from the Scottish Government Public Sector Reform

Invest to Save Fund to undertake scoping work for the design and delivery of a digital platform to support efficient, effective and transparent marine fish farm regulation, including the roll out of streamlined and integrated consenting and modernised access to comprehensive multi-agency information about aquaculture in Scotland. This project will particularly focus on the touch points between regulators and the publication of the outputs of the consenting process.

Building on SEPA’s recent website upgrade and with Scotland’s Aquaculture Website partners, we will continue to identify updates to the website content that improves signposting and explanations in relation to a number of aquaculture datasets, enhancing useability and transparency. We will prioritise improvements on the range of publicly available farmed fish mortality datasets.

Cumulative impacts

A number of the respondents sought further detail on how assessment of cumulative impacts across 0-12 nautical miles would be managed, including consideration of the potential for future overlap between fish farm applications and other marine developments.

The Scottish Government is committed to working with stakeholders to develop a new national marine plan for Scotland which will deliver an updated planning framework to address the increased competition for marine space, whilst balancing the need for protection and enhancement of the marine environment, and sustainable development of existing and emerging sectors. We will explore, through the development of National Marine Plan 2, how to bring the range of management measures and spatial constraints data for salmon farming into one place beyond the expected adoption of the plan in 2027, in addition to continued progress of our Regional Marine Plan programme.

Development of SEPA’s assessment protocols

The Scottish Salmon Farming Industry Modelling Working Group offered to collaborate with SEPA to address the industry’s concerns that the existing risk assessment protocol used by SEPA to assess fish farm environmental discharges protocol is inappropriate for exposed environments, including those within 3 nautical miles.

SEPA has stated it would be happy to discuss modelling methods further with industry representatives and interested third parties, noting the regulatory framework is adaptive, allowing processes to be updated in response to the best available science and evidence.