The Australian coral reefs were great hazards to early seafarers. Even today, with highly accurate navigation equipment and powerful engines, boats and even ships still run aground within the Great Barrier Reef. For example, in 2010 the bulk coal carrier Shen Neng became grounded on Douglas Shoal of the Great Barrier Reef, east of Rockhampton. Navigating the waters must have been far more difficult for explorers like James Cook and Matthew Flinders, who had to command sailing vessels that were at the mercies of the winds and tidal currents. This was particularly the case when navigating the intricacies of the Great Barrier Reef. On 1 June 1770 Cook's vessel, HM Bark Endeavour, became firmly fixed on a reef, yet he was able to refloat it, make hasty repairs, sail to the mainland and there careen it on a river bank at present-day Cooktown. With the repairs complete he sailed the short distance to Lizard Island and climbed its granitic hill, 300 m high, to search for a way out of the reefs, taking a bearing on a channel to the safety of the open sea. Matthew Flinders, following Cook in early European exploration along the northeastern coastline, directed steerage of the Investigator from the masthead. Both men and their vessels survived their encounters with the reef.

Not so fortunate were those on the Pandora, which was carrying mutineers from the Bounty home to England for trial. In 1791 she struck Pandora Reef, at the entrance to Torres Strait, and was dragged across it through the night before being tipped into 34 m depth of water the next morning.