Born in Albany (Bibb County), Georgia on December 2, 1860, Marbury Johnston was the son of Thomas H. and Lamara Hill Johnston. After graduating from the U. S. Naval Academy in 1882, Johnston was assigned to the USS Yantic. In 1883, he was transferred to the USS Swatara. The following year, Johnston was promoted to ensign and transferred to the training ship USS Portsmouth. In 1887, Johnston was assigned to the Fish Commission Steamer USS Albatross, a research vessel. After three years on the Albatross, he was transferred to the Office of Naval Intelligence, where he served for a year, then served two years on the USS Concord. Promoted to lieutenant, junior grade in 1894, he spent the next few years under various assignments (the USS R. S. Franklin, the War College and Torpedo School, the San Francisco, the New Orleans, and the Cassius) before being placed in command of the Nero in 1899. He served a year aboard the Prairie as executive officer; then in quick succession, he served aboard the Vermont, the Columbia, the Dolphin and the Montgomery.

In 1902, Johnston was assigned as assistant to the U. S. minister at La Guyara, Venezuela. Six months later, he became naval attache at Caracas, Venezuela, a post in which he served for six months. Returning to Washington, D. C., Johnston was promoted to lieutenant commander and given command of the Second Torpedo Flotilla. From 1907 to 1908, he again served aboard the Albatross, this time as the ship's commander. His command was transferred to the USS Galveston in 1908. The following year, Johnston was assigned to Navy Yard Puget Sound, and in 1910, he became captain of the Navy Yard at Portsmouth, New Hampshire. The following year, Johnston was promoted to captain and placed in command of the USS Georgia. In 1913, Johnston attended a long course at the Naval War College. In 1914, he reported for duty as commandant of the New Orleans Navy Yard and Station, a post in which he served until 1917, when he was given command of a patrol force, and soon thereafter was placed in command of the Atlantic Fleet's Squadron 2, Cruiser Force, and promoted to rear admiral. From 1918 to 1921, he served as commandant of the 15th Naval District, adjacent to the Panama Canal Zone. In the latter year, Johnston became director of naval communications and president of the Naval Examining and Retiring Board, the post at which he served until his retirement in 1924.

A lifelong bachelor, Johnston by 1930 was living with his sister and brother-in-law, Rebecca and Robert Toombs in Randolph County, Georgia. Marbury Johnston died on March 15, 1934, and was buried in Riverside Cemetery, Macon, Georgia.