The site of patrimony currently consists of four sites: Ness of Brodgar is an archaeological site between the Ring of Brodgar and the Stones of Stenness that has provided evidence of housing, decorated stone slabs, a massive stone wall with foundations, and a large building described as a Neolithic "cathedral".

[7][8] Although it is not part of the World Heritage Site, the Ness of Brodgar "contribute[s] greatly to our understanding of the WHS" according to Historic Scotland, which manages most of the site.

[9] In 2008, UNESCO expressed concern about plans by the local council to "erect three large 72 metres wind turbines to the north-west of the Stones of Stenness and the Ring of Brogdar" that might damage the site.

The report by Historic Environment Scotland, the Orkney Islands Council and others concludes that the entire World Heritage Site, and in particular Skara Brae, is "extremely vulnerable" to climate change due to rising sea levels, increased rainfall and other factors; it also highlights the risk that Skara Brae could be partially destroyed by one unusually severe storm.

[11] The first application of the Climate Vulnerability Index to a Cultural World Heritage property took place at the Heart of Neolithic Orkney in April 2019.