A PRISTINE marine environment in the Western Isles has been designated a conservation area despite fierce opposition from local fishermen.

After years of agonising, the Scottish Government said yesterday the Sound of Barra, which is home to seals and fragile plants and algae that act as a nursery for commercial species such as scallops, cod and whiting, would be given Special Area of Conservation (SAC) status.

But there is concern that the strict regulation will significantly restrict local fishing activity, particularly for shellfish, and campaigners have warned the move will hit the island's economy.

Paul Wheelhouse, environment minister, insisted the concerns had been "taken into consideration". He said that for the first time the island community would lead the management of the Barra SAC, utilising the local knowledge of the waters around the island.

Mr Wheelhouse said: "Thanks to generations of careful stewardship by the local community, Sound of Barra is a diverse and precious environment, home to important seal populations with reefs and sandbanks that support many species. The concerns of the local community have been taken into consideration and we will be implementing a new bottom-up approach to the management structure to ensure as much local involvement as possible.

"I want all those with an interest to have the opportunity to work constructively together on securing a bright future for Sound of Barra and the wider region. I look forward to visiting again shortly to discuss the next steps with the local community."

The SAC was first proposed in 2000. Mr Wheelhouse yesterday said there would be boundary changes so the world famous Traigh Mhor beach airport is no longer within the SAC.

The campaign group Southern Hebrides Against Marine Environmental Designations (Shamed) was set up by islanders in 2009 to fight both the East Mingulay and the Sound of Barra SACs. Its members were appalled at ministers' decision to approve the former in 2011 and they demonstrated outside the Scottish Parliament in February last year.

Now the Sound of Barra will be put forward to the European Commission for inclusion in plans for an EU-wide network of SACs after the move was recommended by Scottish Natural Heritage (SNH) in November. Mr Wheelhouse asked for an independent review which concluded the scientific data was robust.

He said the outstanding beauty of Barra and its growing reputation as an important nature location could only be enhanced by SAC status, increasing tourism.

He said he understood local concerns, but he believed that "a viable local fishing industry can be fully compatible with SAC designation".

But Angus MacLeod, one of the founders of Shamed said every assurance they had been given had proved worthless.

Speaking from his fishing boat working in the Minches, he said: "The way things have been going with one door after another being slammed shut in our faces – SNH, the government, the petitions committee – but they just horsed on and did what they always intended to do since 2000." Mr MacLeod said it would hit the economy of the island. Fishermen had suggested local control over management of the Mingulay SAC last year but nothing had happened. "So we will believe community-led management of the Barra SAC it when we see it," he said.

The SNP MP for the Western Isles Angus MacNeil, who is a native of the island and still lives there, blamed Europe for the debacle.

He said: "Obviously, no one would have wanted this SAC.

"It has been a brainwave of faceless bureaucrats in the EU, who have shown disdain for the areas and communities involved by not even sending the most junior person from Brussels involved with this, to explain to the communities their reasoning and why they would potentially fine the Scottish Government if there was no SAC."

He said it was a classic example of what gave the EU a bad name.

However, Calum Duncan, of the Marine Conservation Society Scotland, welcomed the news.

"It's good news that the Scottish Government recognises that community support is vital in the designation of this site," he said.

He said there were 19 different types of reef habitat in the Sound of Barra and the sandbanks supported fragile features such as seagrass beds and probably the UK's largest maerl beds.

"Maerl, a fragile coral-like seaweed that forms beds on the seafloor, provides important nursery grounds for commercial species such as scallops, cod and whiting, but is susceptible to damage from some human activities like heavy towed fishing gears such as scallop dredges," Mr Duncan said.