Fears that coal exports and oil and gas exploration would jeopardise the reef prompted the Unesco delegation's visit.
Environmentalists have urged the government to suspend mining development until a government review is completed.
The reef is home to 400 types of coral and 1,500 species of fish.
The Great Barrier Reef, which holds Unesco World Heritage status, lies off the coast of the state of Queensland, which is the largest producer of coal in the country.
The Unesco team is scheduled to visit the reef for a week before making recommendations to the World Heritage committee. They will also meet members of the government.
Environmentalists are concerned that an increase in coal production and the shipping traffic that would follow could affect the Great Barrier Reef's World Heritage status.
They want the government to suspend all new developments while a state and federal review of the health of the reef is carried out.
Greenpeace Australia Pacific's senior climate and energy campaigner John Hepburn said the mining industry was threatening the reef's future.
"The Great Barrier Reef is in danger from the coal industry and the fossil fuel boom that is happening, but it is a reckless expansion that will have direct impacts both in terms of the dredging as well as the increased shipping, as well as the impact of climate change on the Great Barrier Reef," he said.
The BBC's Phil Mercer says the exploitation of oil and gas is driving industrial expansion along much of Australia's most famous wilderness area, including plans for the world's biggest coal port near the town of Bowen.
The Australian government has imposed strict guidelines to ensure water quality and protect marine life during development.
But the reef presents a familiar conundrum for resource-rich Australia - the demands of a powerful and lucrative mining industry against the needs of the environment, our correspondent adds.
A UN team has arrived in Australia to investigate possible damage to the Great Barrier Reef by the mining industry.