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Flinders first sailed to Australia in 1795 for the British Navy aboard the ship called the "Reliance." He and his friend George Bass (the ship's surgeon) bought an 8-foot-long boat called the "Tom Thumb" in order to explore the treacherous coastline of southern Australia. They first sailed south of Sydney (to Botany Bay) and rowed up the Georges River. During the years 1795 to 1798, they mapped much of the southeast coast of Australia and sailed completely around the island of Tasmania. Flinders returned to England on the "Reliance" in 1800.

In 1801, Flinders returned to Australia as captain of the 334-ton ship called the "Investigator." He first sighted land at Cape Leeuwin (the southwest tip of Australia). On this second trip, he mapped Australia's entire southern coast, from Cape Leeuwin to the Spencer Gulf (which he sailed up) to the Bass Strait (named for his friend George Bass, it separates mainland Australia from the southern island of Tasmania). On July 22, 1802, he sailed to the east coast of Australia, mapping the coastline from Port Jackson (where Sydney is located) up to the Gulf of Carpentaria. He continued west and then south, sailing completely around Australia; he returned to Port Jackson on June 9, 1803, even though his boat was leaking badly. This was the first time anyone had sailed around Australia.

On his way back to England in the autumn of 1803 (on a different ship, the "Cumberland"), Flinders had to make a stop for ship repairs at Île de France (now called Mauritius) in the western Indian Ocean. Thinking he was a spy, the French kept him prisoner for 6 1/2 years and stole his charts and papers (he was released when the British took over the island). He didn't arrive home until 1810, and reached home sick and a forgotten man. He wrote an account of his travels, called "Voyage to Terra Australis Undertaken for the Purpose of Completing the Discovery of that Vast Country," and died the day after it was published.