Regulatory framework

Regulatory framework

SEPA, as one of a number of organisations regulating finfish aquaculture, is implementing a revised regulatory framework that will strengthen the protection of the marine environment for the people of Scotland.

We 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.

Protection of the Marine Environment, Discharges from Marine Pen Fish Farms: A Strengthened Regulatory Framework sets out the new framework for regulating discharges from fish farms.

SEPA’s regulation of permits has the following 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.

SEPA Sector Plans Image Revision

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. Details of the pre-application process.

Application process

When you have collected the information that we require to make an application you can submit your application for a permit. Details of the permit application process.

Transitional arrangements

Our new approach to regulating the marine pen fish farm industry came into force on 1 June 2019. The new framework introduces substantial changes to the pre-application process and the information required to support the application. We recognise that companies will have been developing applications over the previous 12 months so, to accommodate this, there will be a transitional period up to the end of 2019 during which we will allow some applications to continue with pre-existing information requirements. We will assess these applications and come back to operators if we consider that further work is necessary. The basis upon which these decisions will be made are explained on the Transitional Arrangements page.

SEPA will review existing permits to transfer them to the new regulatory regime. The plans for how we will undertake this work are being developed and details of the transition arrangements will be available soon.

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 has to be closely controlled. Further information on how we manage the use of chemicals is explained on the Medicines & Chemicals page.

Overview of the regulatory framework

The framework follows months of work by colleagues across SEPA, a 2017 consultation and two Scottish Parliamentary committees. Our proposals for the regulatory framework were shared alongside the consultation on the sector plan. It described our intention to protect marine life and the interests of people who use the resources provided by the marine environment (e.g. fishing, shellfish farming). We have reviewed our proposals on the basis of the feedback we received. An explanation of how the regulatory framework will operate is explained in the Overview of Regulatory Regime page. The framework is also set out in Protection of the Marine Environment, Discharges from Marine Pen Fish Farms: A Strengthened Regulatory Framework.


The regulatory framework is intended to provide a clear and transparent approach to regulation and we will continue to engage with our stakeholders on the implementation of the framework. 

The way we share information should also be clear and transparent and we welcome your comments on how we have presented the information on this website. You can contact us by using our online contact form