Five species of seabirds across all the islands have declined by more than 20% in the last nine years.
The Lesser black-backed gull (-26%), Herring gull (-22%), Shag (-21%), Common tern (-85%) and Kittiwake (-72%) have all seen a fall in numbers, with the Kittiwake and Common tern now in danger of being lost as breeding species in Scilly.
The figures, reported by the Isles of Scilly Wildlife Trust, were discovered as a result of the latest all-island seabird survey completed in 2015/16, during which a total of 8,266 territories of 13 species of seabird were recorded from 55 rocks and islands, achieving complete coverage of all islands.
Nikki Banfield from the Wildlife Trust told Radio Scilly: "The kittiwake and the Common tern are really important indicators of how healthy our seas are and what’s happening around the islands but also globally. All of these birds are having issues globally as well so gulls in particular are protected.
"Nobody really knows a definite reason why they've declined, it’s a whole host of issues for the birds such as food source, nesting places, how far they have to travel to gather food for their chicks and then it’s predation by other species. And also obviously the human impact as well."
However, the Wildlife Trust said the news is not all bad. Since 2006 there has been a "marked increase" in the numbers of both Razorbill and Guillemot across the islands, while Puffin numbers have remained relatively stable. The Fulmer is also "doing very well".
Meanwhile, the removal of rats from St Agnes and Gugh through the Isles of Scilly Seabird Recovery Project has resulted in successful breeding of Manx shearwaters, with 10 stargazing chicks recorded in 2014 rising to 48 this year.
The Wildlife Trust and partners have just ratified the Isles of Scilly Seabird Conservation Strategy (2018-2023). The document "reviews previous strategies and progress achieved; bringing them up to date with revised objectives and outcomes while also detailing a five-year work programme".
The Strategy was produced by staff from the Isles of Scilly Wildlife Trust, RSPB, Natural England and Isles of Scilly IFCA and endorsed by all the Isles of Scilly AONB Partnership, which includes the Wildlife Trust, RSPB, Duchy of Cornwall Estate, Islands' Partnership, Council of the Isles of Scilly, Isles of Scilly IFCA and Isles of Scilly Bird Group.