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Aquaculture is the growing of finfish and shellfish. In Scotland, this primarily involves the farming of:

  • salmon and rainbow trout held in sea pens;
  • salmon and trout in freshwater pens and;
  • shellfish (oysters and mussels) on rafts and lines in the sea.

As one of a number of organisations regulating finfish aquaculture, SEPA's job is to protect the marine environment for the people of Scotland. We do this by ensuring that the aquaculture industry meets environmental standards.

A high quality environment and abundant freshwater resources are vital to Scotland’s aquaculture sector. SEPA regulates discharges from finfish farms by issuing permits that limit the levels of pollutants that they discharge to the water environment. Where farms use fresh water SEPA issues permits to control the amount of water that can be abstracted. SEPA does not regulate shellfish growing. 

Our powers to deliver these functions are defined under the Water Environment (Controlled Activities) (Scotland) Regulations 2011 (CAR).

Regulatory framework for marine pen fish farms

SEPA, as one of a number of organisations regulating finfish aquaculture, will maintain a high quality environment by setting permit conditions which limit the impacts associated with fish farms and then by ensuring that operators comply with these conditions.

As part of our determination, SEPA will consider risks to the water environment (including potential impacts to marine species and habitats) and the interests of other users of the water environment resulting from an aspect of the proposed farm development that we regulate.

What SEPA regulates

  • Discharges of organic matter, medicine residues and other chemicals and interactions between sea lice from farmed fish on wild salmon.

What others regulate

  • Fish Health Inspectorate - Fish escapes and farmed fish health
  • Animal and Plant Health Agency and the relevant local authority - Fish welfare and disposal of farmed fish mortalities
  • Marine Directorate Licensing - Moorings and navigation
  • Relevant local authority – Lead for visual amenity, noise
  • Health & Safety Executive and the relevant local authority - Workforce safety

SEPA introduced a new Regulatory Framework in 2019 and has continued to develop this framework to include managing the interactions of sea lice from farmed fish with wild salmon populations.

Finfish aquaculture sector plan

SEPA is changing today, creating a world-class environment protection agency fit for the challenges of tomorrow. By moving away from the traditional site by site regulation to grounding our regulation and activities across whole sectors, we will shape our interactions with every sector and the businesses in them.

The finfish aquaculture sector plan was the focus of a Scotland-wide, seven week consultation in November 2018. This provided an invaluable opportunity to speak with local communities, discuss the key issues which matter most to them and hear directly from a diverse range of interests, including NGOs, marine and freshwater fishery groups and representatives of the industry. A summary from this consultation is available by clicking here.

The sector plan is ambitious in its aspirations for an industry where in the future:

  • The Scottish finfish aquaculture sector recognises that protecting the environment is fundamental to its success and is foremost in all its plans and operations.
  • The sector is a world-leading innovator of ways to minimise the environmental footprint of food production and supply.
  • The sector has a strong and positive relationship with neighbouring users of the environment and the communities in which it operates.  It is valued nationally for its contribution to achieving global food security.

A key focus of the sector plan is to ensure that all operators in the sector will reach and maintain full compliance with Scotland’s environmental protection laws, while working to help as many operators as possible to move beyond compliance.