NTS owns and manages St Abb's Head on the Berwickshire coast, home to one of the largest mainland seabird breeding colonies in the UK. But the steep rocky inlets of the headland have also become popular for visiting sub-aqua enthusiasts because they have some of Britain's finest underwater scenery.
Boats bring thousands of people close to the cliffs every year so they can dive to see the sights. But conservationists say this is disturbing the birds, including nesting kittiwakes and guillemots, and could drive them from their nests.
The alarm has been raised by Graham White, an environmental author who lives in nearby Coldstream. He visited St Abb's Head to watch the birds earlier this month and was horrified by what he saw.
"What I witnessed was a dive boat 'derby' of 40-foot, 900-horsepower vessels making high-speed runs across the mouths of the nesting fiords and dropping off divers deep within the fiords. Over a dozen boats of various sizes were roaring about, ploughing through rafts of guillemots."
White raised his concerns with NTS, the government wildlife agency, Scottish Natural Heritage (SNH), and bird charity the RSPB. As a result, NTS convened a meeting on June 13 with dive boat operators, and there are now plans to draw up a voluntary code of practice.
This has been welcomed by White, but he questions whether it will be enough. "The only powers which NTS holds at St Abb's are powers of persuasion and education," he told the Sunday Herald. "When it comes to being an effective environmental watchdog, a guardian of wildlife, it seems this dog is toothless. "
As well as being a national nature reserve, St Abb's Head has three other official designations meant to ensure its wildlife is protected under law. It is a special protection area for birds, a special area of conservation and a site of special scientific interest.
White said: "All of these designations place conservation of wildlife and landscape as their primary objective, but these values seem to have been surrendered to tourism, diving and economic development at St Abb's."
The NTS said it was aware that the number of dive boats had increased in recent years.
The trust's conservation director, Terry Levinthal, said: "We recently convened a meeting of local skippers to highlight our concerns. This was positive and it was agreed that we would work with them and SNH to put together and promote a voluntary code of practice for boats operating in the area."
SNH said the "vast majority" of dive boat operators were sensitive to the need to avoid disturbing seabirds. It confirmed that it was in discussion with NTS about the management of the reserve.
Dive boat operators pointed out that they had to make a living.
Paul Crowe from Dive St Abb's said: "Yes, we do dive close to the rocks - it's where the best scenic diving is. But we do it carefully, and do not disturb any wildlife in the process.
"I have been a dive boat operator for the last 10 years and in my opinion there has never been a decrease or increase in the amount of birds."
But Kara Brydson from RSPB Scotland said seabird populations across Scotland were in steep decline. She said: "If it is the case that birds at this internationally important and protected site are being kept away from their nests, then we will ensure that all action is taken to stop illegal or unacceptable behaviour."