Known as Murujuga, the Archipelago is made up of 42 islands as well as reefs, shoals, channels and straits and is the traditional home of five Aboriginal language groups.
It was formed 7,000 years ago when rising sea levels flooded what were once coastal plains.
The underlying rocks are among the oldest on earth, formed in the 'Archaean' period more than 2,400 million years ago.
"Excavations on Rosemary Island, one of the outer islands, have uncovered evidence of one of the earliest known domestic structures in Australia, dated between 8,000 and 9,000 years ago," said Jo McDonald, from University of Western Australia (UWA).
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For the site to gain a World Heritage listing, the team needed to learn more about deep-time archaeology, the contemporary cultural values of Aboriginal people and to understand how they managed their cultural sites across the string of islands, researchers said.
"As well as containing more than one million rock engravings of great scientific and cultural significance, the Archipelago is home to one of the country's largest industrial ports," she said.
"We anticipate that this extraordinary rock art estate will produce some spectacular insights into what life was really like in deep history," McDonald said.