Born in Princeton, New Jersey, at the age of fourteen he went to sea in the merchant service, and was in command of a trading schooner (a ship with two or more masts) at an early age. The American trading vessels of that period were supposed to be excluded by the navigation laws from commerce with the British West Indian Islands, though with the concealed or very slightly disguised assistance of the planters, they engaged in a good deal of contraband commerce.
The war between France and Great Britain tended to make trade difficult for neutrals. Bainbridge had therefore to expect, and when he could to elude or beat off, much interference on the part of French and British cruisers alike. He is said to have forced a British schooner, probably a privateer, which attacked him when on his way from Bordeaux to St Thomas, to strike, but he did not take possession. On another occasion he is said to have taken a man out of a British ship in retaliation for the impressment of an American seaman by HMS Indefatigable, then commanded by Sir Edward Pellew. When the United States navy was organized in 1798 he was included in the corps of naval officers, and appointed to the schooner Retaliation. She was on one occasion seized by the French but afterwards released.
As captain of the brig Norfolk of 18 guns, he was employed in cruising against the French, who were said to be as aggressive against American commerce as the English. He was also sent to carry the tribute which the United States still condescended to pay to the dey of Algiers, in order to secure exemption from capture for its merchant ships in the Mediterranean — a service which he performed punctually, though with great disgust. When the United States found that bribing the pirate Barbary states did not secure exemption from their outrages, and was constrained at last to use force, he served against Algiers and Tunis. His ship, the Philadelphia, ran aground on the Tunisian coast, and he was for a time imprisoned. On his release he returned for a time to the merchant service in order to make good the loss of profit caused by his captivity.
When the War of 1812 broke out between Great Britain and the United States, Bainbridge was appointed to command the frigate Constitution (44), in succession to Captain Isaac Hull. The Constitution was a very fine ship of 1533 tons, which had already captured the HMS Guerrière. Under Bainbridge she was sent to cruise in the South Atlantic. On the 29th of December 1812 he fell in with HMS Java, a vessel of 1073 tons, formerly the French frigate Renommée (40). She was on her way to the East Indies, carrying the newly appointed lieutenant-governor of Bombay. She had a very raw crew, including very few real seamen, and her men had only had one day’s gunnery drill. The United States navy paid great attention to its gunnery, which the British navy, misled by its easy victories over the French, had greatly neglected. In these conditions the fate of the Java was soon sealed. She was cut to pieces and forced to surrender, after suffering heavy loss, and inflicting very little on the Constitution. After the conclusion of the war with Great Britain, Bainbridge served against the Barbary pirates once more. During his later years he served on the board of navy commissioners.
Several ships of the Navy have since been named USS Bainbridge in his honor.