Some colonies are said to be on the edge of survival
Kittiwakes, Arctic terns and Arctic skuas have had a terrible breeding season which could see them wiped out in the UK, according to RSPB Scotland.
The environmental group claims changes in food supply, which may be linked to climate change, could threaten the future of these species.
There have been virtually no chicks reared to fledging in the far north of Scotland, where breeding grounds are.
Scotland hosts 45% of the EU's breeding populations of seabirds.
Some cliffs - which used to support huge colonies - are now in steep decline.
Great skuas, gannets and cormorants have experienced modest increases in their numbers, while herring gulls have remained stable.
RSPB Scotland said recent reports of significant declines in plankton biomass point to major changes to ocean ecosystems in the Atlantic, which could be affecting seabirds.
SEABIRD BREEDING PROBLEMS
Kittiwake: Declines in breeding pairs of 50% in Mull of Galloway and up to 89% on Orkney on previous years
Arctic skua: Reserves on Shetland and Orkney saw a 30% decline in nesting pairs, with only three chicks fledged
Arctic Tern: Reports suggest virtually no young Arctic terns were fledged this year from Orkney or Shetland
It said that although direct evidence was still lacking, increased winter sea surface temperatures disrupting the food chain are thought to be driving the declines.
Douglas Gilbert, an ecologist with RSPB Scotland, said: "The outlook for some species such as Arctic skua, kittiwake and Arctic tern is dire, and there are problems with other species like guillemots and puffins in some areas too.
"Unless conditions change to allow these birds the chance of successful breeding, the long-term future for them is bleak.
"The evidence that this is linked to changes in sea surface temperatures is now growing."
RSPB Scotland has called on the Scottish Government to ensure that it puts the environment at the heart of the forthcoming Scottish Marine Bill in the light of what it calls the worrying declines.