The son of a customs officer, Bligh joined the Royal Navy (Royal Navy, The) in 1770. After six years as a midshipman, he was promoted to sailing master of the Resolution and served under James Cook (Cook, James) on the great captain's third and final voyage to the South Seas (1776–79). After returning to England, he married Elizabeth Betham, with whom he had four daughters and twin sons (the boys died in infancy), and entered private service as a commander of merchant ships in the West Indies.

The Bounty voyage was undertaken at the request of Caribbean plantation owners, who were seeking a subsistence food for their slaves. English botanist Sir Joseph Banks (Banks, Sir Joseph, Baronet) (a veteran of Cook's first Pacific voyage) recommended feeding them Tahitian breadfruit. An unenthusiastic Admiralty agreed to refit the 215-ton Bethia as the Bounty and to commission Bligh as her commander. Bligh's competence was unquestioned, but the circumstances of his command and his feelings about the voyage were dangerously complex. Despite performing well on the Resolution, Bligh felt that his contribution to the expedition had been overlooked after the death of Cook, and he had great ambitions to command a brilliant scientific expedition of his own. He took a drastic pay cut when he reentered the Royal Navy and was bitterly disappointed not to have been promoted to a post captaincy for the expedition. Finally, he chose to serve as both captain and purser, a decision that, given his preoccupation with financial matters, would prove tragic.

The Bounty set out for Tahiti in December 1787. Bligh soon realized that the incompetence of his officers, delays by the Admiralty, and the ferocity of the weather around Cape Horn (Horn, Cape) would dash his hopes for a superb expedition. Proceeding to Tahiti by the Cape of Good Hope (Good Hope, Cape of), he finally reached his destination in October 1788. He would have to stay five months at Tahiti to ensure that the breadfruit cuttings would set.

By April 4, 1789, when the Bounty left Tahiti for England, the crew members were eager to get home, but Bligh had become enraged at their poor seamanship. He had fallen out with his first mate and longtime friend, Fletcher Christian (Christian, Fletcher), tormenting him to the point that Christian planned a suicidal escape from the Bounty by raft. A determined group of nine men persuaded him to take the ship instead. On April 28, 1789 (April 27, ship's time), Christian and his supporters mutinied. Bligh and 18 loyal men were put into a 20-foot (6-metre) launch with some navigational instruments and five days' food. A tragic stop at a nearby volcanic island, Tofua, where one of them was killed by natives, resolved Bligh to sail directly for Timor, 3,600 miles (5,800 km) away. It was a voyage of extreme hardship, brilliant navigation, and mutual hatred, as the launch party blamed one another for the mutiny and their plight. Bligh and his men reached Timor on June 14, 1789. Continuing to Batavia (Jakarta) on the island of Java, they found transportation to England, finally arriving there in March 1790. The Bounty, meanwhile, returned to Tahiti and left several mutineers there. Christian and eight others then sailed to Pitcairn Island, where the small colony they founded went undiscovered until 1808 and where their descendants still reside.

Upon learning of the mutiny, the Royal Navy dispatched the Pandora to Tahiti, where it captured three mutineers. Bligh himself put back to sea in the Providence in 1791, determined to complete his mission. However, it was a fatal choice for his public reputation, as he was not in England for the trial and execution of the mutineers, and accusations about his command went unanswered. In his Narrative of the Mutiny, published a few months after his return to England, Bligh argued that the hedonistic delights of the South Seas were the cause of the mutiny. Christian's brother Edward, a professor of law at the University of Cambridge, replied in a pamphlet that interviews with the Bounty crew revealed many flaws in Bligh's command. The abolition movement (abolitionism), which also had no sympathy for the expedition, circulated the journal of boatswain's mate James Morrison, which contained very damning stories of his former captain's extravagant behaviour. (Morrison was condemned to hang for the mutiny but was later given King's Mercy.)

Despite the notoriety of the mutiny (the title “Bounty Bastard” dogged him for the rest of his life), Bligh received several other commands, served as governor of New South Wales from 1805 to 1810, and was promoted to rear admiral in 1811 and vice admiral in 1814. His courage, navigational skills, and intelligence cannot be denied. He was commended at the Battle of Camperdown (1797) by Lord Nelson and performed well at the Battle of Copenhagen (1805). Bligh's three visits to Tahiti gave him a knowledge of its language and customs that was probably not equaled among Europeans in the 18th century. He is credited with the discovery of some 13 Pacific islands, and he was elected to the Royal Society of London (Royal Society) in 1801.

But Bligh never overcame a fatal inability to control his relationships with his men. While he was captain of the Director, his crew took part in the general mutiny of the fleet at the Nore (Nore, The) (in the Thames estuary) in 1797. In 1805 he was court-martialed, but acquitted, for abusive language. In 1808, while governor of New South Wales, his bad relations with the New South Wales Corps helped spark the Rum Rebellion, during which Bligh was arrested by his own military officer, Major George Johnston, and kept under guard for a year before being sent home by his successor, Lieutenant Colonel Lachlan Macquarie. It was not the extravagance of Bligh's physical punishments that caused problems but his mode of inflicting them. He was not physically violent. In fact, statistics show that Bligh used corporal punishment less than any other captain in the Pacific. However, he was verbally and personally abusive and was given to extravagant, aggressive gestures. Even worse, he violated the privileges and privacies that sailors relied upon to counterbalance naval discipline and the rigours of life at sea. Ironically, for a captain who has been the subject of countless plays and novels, Bligh never learned to manage the theatre of command.