Medications for the heart (milrinone) and gout (allopurinol), as well as cosmetic and industrial chemicals, were among hundreds of thousands of substances detected in the reptiles' bloodstream as part of an ongoing conservation project.
Scientists said exposure to the substances had caused side effects in the turtles, with indications of inflammation and liver dysfunction.
"Humans are putting a lot of chemicals into the environment and we don't always know what they are and what effect they are having," said Amy Heffernan of the University of Queensland.
Researchers tested turtles at Cleveland Bay and Upstart Bay along the Queensland coast, as well as the more remote Howicks islands in the reef's north as part of the "Rivers to Reef to Turtles" project led by WWF-Australia.
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The 2,300-kilometre long barrier reef, a World Heritage site, is already under pressure from farming run-off, development, crown-of-thorns starfish and climate change, suffering its most severe bleaching on record last year.
WWF-Australia said the turtles could be used as a bio- monitoring tool to find out what chemicals were entering reef waters and what their impact on marine life could be.
The chemical, oxybenzone, was causing "gross deformities" in baby coral, the study said.