Scapa Flow and North Orkney, covering a total area of 529 square kilometres, have been designated marine Special Protection Areas (SPAs).
The Scottish Government said the move largely completes the network of SPAs across Scotland’s seas, with 14 sites now protected.
It is the result of ten years of gathering and assessing evidence to support the designation of marine areas critical for 31 species of marine birds, which include the great northern diver and Slavonian grebe.
SNP environment minister Mairi McAllan announced the new sites on a visit to Orkney.
She said: “Scotland has some of the most beautiful, diverse and important marine ecosystems in the world and it is imperative that we protect and enhance them.
“Designations such as these ensure some of the most vulnerable seabird species and their habitats are afforded the protection they need not just for today, but for future generations.
“Scotland’s marine environment is also crucial for supporting the sustainable recovery of our maritime industries and these designations will play a pivotal role in it.
“This marks the culmination of a great deal of work and I would like to thank everyone involved for their efforts, for the designations in Orkney, which largely completes Scotland’s SPA network.”
Enhancing marine environmental protection formed part of the co-operation agreement between the SNP and Greens in Holyrood.
James Stockan, leader of Orkney Islands Council, said: “This has undoubtedly been a long-running process, but one which provides a great example of the value of robust negotiation and constructive discussion between the Scottish Government and Orkney Islands Council.
“Having challenged the initial proposals, we worked alongside Government officials to reach a mutually agreeable solution that was more in keeping with Orkney’s needs.
"We believe that the designations are now more accurate and achieve a dual purpose of supporting future development of our vital maritime industries, whilst also protecting our local ecosystems.”
The two new SPAs add to the protected area network, which covers 37 per cent of the Scottish inshore and offshore region.