Maury, who was born in Fredericksburg, Virginia, graduated from Harpeth Academy in 1825 and joined the US Navy as a midshipman. A leg injury in 1839 ended his sea career but, having made his reputation by his publication in 1836 of his Treatise on Navigation, he was chosen in 1842 to be superintendent of the Depot of Charts and Instruments in Washington. This post carried with it the directorship of the US Naval Observatory and Hydrographic Office. Maury largely ignored astronomical work, emphasizing instead the study of oceanography and meteorology, and consequently aroused the opposition of the scientific establishment centered upon Joseph Henry and Alexander Bache.

He resigned his position with the outbreak of the American Civil War (1861) to become a commander in the Confederate Navy. After the war he took on, in 1865, the post of Imperial Commissioner for Immigration to the doomed Emperor Maximilian of Mexico to establish a confederate colony. Following the collapse of the Mexican Empire he spent some time in England writing textbooks before he was permitted to return to America where he became, in 1868, professor of meteorology at the Virginia Military Institute, remaining there until his death.

Maury has often been described as the father of oceanography. He wrote one of the earliest works on the topic, The Physical Geography of the Sea (1855) and he demonstrated the rewards to be gained from an increased knowledge of the oceans. From 1847 he began to publish his Wind and Current pilot charts of the North Atlantic, which could shorten sailing times dramatically. Claims were made that as much as a month could be saved on the sailing time for the New York–California voyage. This knowledge was acquired by the study of especially prepared logbooks and the collection of data in a systematic way from a growing number of organized observers.

After 1849 Maury had the use of two research vessels and began a study of ocean temperature and a collection of samples of the ocean floor. He was thus able to publish his Bathymetrical Map of the North Atlantic Basin (1854) showing a profile of the Atlantic floor between Yucatan and Cape Verde.