Global warming has been wreaking havoc on the reef, contributing to an unprecedented bleaching event this year that saw much of it whiten and almost a quarter of corals die.
The reef, which teems with marine life, is also under pressure from farming run-off, with the 560 square kilometre Springvale Station near Cooktown in northern Queensland one of the worst culprits.
Queensland Environment Minister Steven Miles said Springvale contributed huge amounts of sediment run-off to the northern part of the Barrier Reef, the worst hit by the bleaching caused by warming sea temperatures.
Run-off from the land carries sediment to the reef where it blocks light, smothers marine organisms and reduces coral and seagrass growth.
"We need to make sure the reef has the best chance to recover from this (bleaching) event by making sure water flowing from the catchments is as clean as possible," he added.
"That includes stepping up effective erosion control measures on the gullies and rivers in far northern Queensland."
Scientists have said parts of the 2,300-kilometre long reef will take at least a decade to recover, and the World Wide Fund said good water quality was key to its survival.
"Never before has a government bought land to protect the water quality of the Great Barrier Reef," said WWF-Australia spokesman Sean Hoobin in hailing the decision as "unprecedented".
"Large volumes of mud wash off this station and out into reef waters which stresses the coral.
"Action to reduce sediment pollution from Springvale will help the surviving coral to bounce back.
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