Wild salmon protection zones will be introduced in the Hebrides and west coast of Scotland from February, the Scottish Environment Protection Agency (Sepa) has said.

The fish are under threat due to a range of pressures, including habitat barriers, invasive species, and commercial aquaculture, and their numbers have declined in rivers across Scotland.

Rising sea temperatures and dry rivers in the summer may also be contributing to the decline, affecting salmon migration and spawning, and making them more susceptible to diseases and parasites.

Stocks have reduced across the North Atlantic from eight to 10 million in the 1970s to an estimated three million today.

In October 2021, Scottish ministers made Sepa responsible for managing the particular risk to wild salmon and sea trout posed by sea lice, which are linked to the £1 billion aquafarm industry.

Sepa has since developed and consulted on a sea lice framework, a regulatory approach to protect young salmon from the parasite which will support the sustainable development of fish farming.

Sepa announced decisions to allow development in the least sensitive locations, as well as providing an “effective and efficient framework” for risk assessment and management.

The sea lice framework includes the creation of wild salmon protection zones and sea lice risk models.

The protection zones will be formed in “migration bottlenecks” in coastal waters on the west coast and Western Isles.

Fish farm operators in these areas will be subject to tighter levels of sea lice control, with additional monitoring, engagement and adaption if required.

The framework for protection of wild salmon will be applied when determining applications for proposed new farms and for increases in the number of fish at existing farms in migration zones.

Rural Affairs Secretary Mairi Gougeon said: “Salmon is one of Scotland’s most iconic species and I am grateful for Sepa’s support in developing this framework.

“Our Vision for Sustainable Aquaculture values the role of aquaculture in producing world-renowned healthy and quality seafood, whilst recognising that its delivery and development must be sustainable.

“The framework will support sustainable development of fish farming worth more than £1 billion to our economy, ensuring our communities continue to realise the benefits of aquaculture by guiding development to the least-sensitive locations and protecting the environment, whilst making the development process more efficient and effective.”

Peter Pollard, Sepa’s head of ecology, said: “We know wild salmon populations are in crisis, and safeguarding their future requires co-ordinated action and a broad range of interests working together.

“As part of an international community working to address this shared challenge, we’re one of the first countries to take action to manage the risk posed by sea lice from fish farms to wild salmon.

“Scotland is emerging as a pioneer in sustainable aquaculture and we’re confident in the industry’s ability to adapt to the changing regulatory landscape, as it has done successfully before now.”

Sepa said it has engaged extensively with leading scientists in Scotland and Norway, other regulators, fish producers, environmental NGOs, coastal community groups and wild fishery interests to create the rules.

The framework will be implemented in phases and will sit alongside Sepa’s wider regulation introduced in 2019, which already controls all discharges from marine finfish farms to the water environment.

Tavish Scott, chief executive of Salmon Scotland, said: “We support regulation based on fact, evidence and sound science.

“The Scottish Government commissioned Professor Russel Griggs to conduct an independent regulatory assessment, his recommendations were accepted by ministers for better, more streamlined regulation.

“Now the sector faces more regulation, additionally, Sepa cannot explain how it will measure success. We support measures to address the decline in the population of wild salmon in Scottish waters.

“The Scottish Government has previously identified more than 40 pressures on wild salmon stocks, of which sea lice is just one. We are still waiting to see what Government and its many agencies are going to do on the other identified pressures.

“The Salmon Scotland board meets next week and will consider the Sepa plan in full.”