He was born on Jult 25, 1835 at Saint Etienne, and entered the French Navy, and after voyaging in Brazilian waters and the Pacific, he obtained a post on the staff of Admiral Charner, who from 1860 to 1862 was campaigning in Cochinchina.
After some time spent in France, Garnier returned to the East, and in 1862, he was appointed inspector of the natives in Cochinchina, and entrusted with the administration of Cholon, a suburb of Saigon. It was at his suggestion that the marquis de Chasseloup-Laubat determined to send a mission to explore the valley of the Mekong River, but as Garnier was not considered old enough to be put in command, the chief authority was entrusted to Captain Ernest Doudard de Lagrée. In the course of the expedition - to quote the words of Sir Roderick Murchison addressed to the youthful traveller when, in 1870, he was presented with the Victoria Medal of the Royal Geographical Society of London - "from Kratie in Cambodia to Shanghai 5392 miles were traversed, and of these, 3625 miles, chiefly of country unknown to European geography, were surveyed with care, and the positions fixed by astronomical observations, nearly the whole of the observations being taken by Garnier himself".
Volunteering to lead a detachment to Dali, the capital of Sultan Suleiman, the sovereign of the Muslim rebels in Yunnan, Garnier successfully carried out the more-than-adventurous enterprise. When shortly afterwards Lagree died, Garnier naturally assumed the command of the expedition, and he conducted it in safety to the Yangtze River (Chang Jiang), and thus to the Chinese coast. On his return to France, he was received with enthusiasm. The preparation of his narrative was interrupted by the Franco-Prussian War, and during the siege of Paris, Garnier served as principal staff officer to the admiral in command of the eighth sector. His experiences during the siege were published anonymously in the feuilleton of Le Temps, and appeared separately as Le Siege de Paris, journal d'un officier de marine (1871).
Returning to Cochinchina, he found the political circumstances of the country unfavourable to further exploration, so accordingly, he went to China, and in 1873 followed the upper course of the Yangtze River to the waterfalls. He was next commissioned by Admiral Dupré, governor of Cochin China, to found a French protectorate or a new colony in Tonkin. On 20 November 1873 he took Hanoi, the capital of Tonkin, but a month later he was slain in a fight with the Black Flags. His death caused the French to abandon Hanoi after signing a treaty with the Vietnamese. The French took Hanoi again in 1882, but Garnier was blamed by the government for the disaster.
Garnier's chief fame rests on the fact that he originated the idea of exploring the Mekong, and carried out the larger portion of the work.