Aquaculture
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 Environmental Authorisations (Scotland) Regulations.
What we regulate
Our aim is to maintain a high-quality environment and reduce the risks of proposed marine pen fish farm developments to marine species, habitats, and other water users. We achieve this by setting permit conditions which limit the impacts associated with fish farms and then by ensuring that operators comply with these conditions. We are responsible for regulating:
- Discharges of organic matter
- Medicine residues and other chemicals
- Interactions between sea lice from farmed fish on wild salmon
We are one of a number of organisations responsible for regulating finfish aquaculture:
- 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
- Health & Safety Executive and the relevant local authority - Workforce safety
- Relevant local authority - Lead for visual amenity, noise
Regulatory framework
We are implementing a revised regulatory framework that will strengthen the protection of the marine environment for the people of Scotland. Our regulation of permits will follow four key components:
- Pre-application work
- Application and issue of permits
- Compliance, and
- Enforcement
These all sit within the context of the finfish aquaculture sector plan, company plans and our joint working with other regulators.
Preparing your application
Before you apply for a permit you need to collect the information that SEPA requires to support a permit application. You should talk to SEPA about this work so that you can be sure that you collect the right information and that it is of the correct standard. Find out more information about the pre-application process.
When you have collected the information that we require to make an application you can submit your application for a permit. Find out more information about the permit application process.
Using standards to protect the environment
We protect the environment by preventing impacts from regulated activities from exceeding defined standards. These standards may define the concentrations of chemicals or the condition of biological communities. Many of these standards are set by Scottish Government in Directions. Where there are no standards set in Directions we will use the best available science. Further information on the standards that we use to protect the environment are explained on the environmental standards page.
Control of medicines and chemicals
One of the challenges faced by the industry is to maintain the health of the fish by protecting them from disease and parasites. To do this they use a range of management techniques which include the use of medicines and chemicals as prescribed by a vet. These medicines and chemicals can be very toxic to marine life and their use must be closely controlled. Further information on how we manage the use of chemicals is explained on the medicines and chemicals page.
Sea lice regulatory framework
SEPA is the lead regulator responsible for managing sea lice and wild salmon interactions and for managing sea lice and sea trout interactions. Read an overview of the Sea Lice Regulatory Framework for more about the approach. All applications for new or expanding marine fish farms will be considered under our sea lice regulatory framework. SEPA is seeking to bring all existing fish farms into regulation under the sea lice regulatory framework. View FAQs on Sea Lice Regulatory Framework implementation.
Our Sea lice regulatory conditions position statement, published in September 2025, was made in response to interest by fish farm developers in:
- The use of semi-enclosed and fully enclosed fish pen systems
- Establishing farms using more conventional open-net pen designs in locations distant from the coast
Contact us
Have a question about your applications? Contact us for more help and guidance.