The bleak forecast came in a five-yearly report released by the Great Barrier Reef Marine Park Authority. Climate change remained the biggest threat to the site, the report said.
But poor water quality from land-based run-off, coastal development and fishing also posed challenges, it said. "Even with the recent management initiatives to reduce threats and improve resilience, the overall outlook for the Great Barrier Reef is poor, has worsened since 2009 and is expected to further deteriorate," the report released on Tuesday said.
Greater reduction of all threats at local and regional levels was needed to stop the decline and improve the reef's ability to recover, it said.
'No quick fixes': The Great Barrier Reef is the world's largest coral structure, rich in marine life. It stretches for more than 2,600km (1,680 miles) along Australia's eastern coast, containing 400 types of coral, 1,500 species of fish and 4,000 types of mollusc.
It is a Unesco-listed World Heritage Site, but in recent years the UN body has warned that it could be put on its World Heritage in Danger list because of its worsening condition.
Conservationists also fear that proposed development on the Queensland coast, including a planned coal port expansion at Abbott Point, could further harm its health.
In its report, the GBRMPA said that investment in some areas of reef management had yielded positive results, for example in reducing pollutant loads entering the reef.
It also highlighted examples of species that were making a comeback after years of decline, such as humpback whales and estuarine crocodiles.
But it said that climate change was already affecting the reef - causing coral bleaching and ocean acidification - and was "likely to have far-reaching consequences in the decades to come".