As an ensign, Jones was commended for his bravery and skill in helping to save Nipsic (AT-33) from sinking during the great Samoan hurricane of 1889. During the Spanish-American War, he served in Dorothea on patrol duty off Cuba. In 1912, he commanded Rhode Island (BB-17); in 1913, the Washington Navy Yard; and, during World War I, patrol units and a division of the Transport Force. He received the Distinguished Service Medal for outstanding service.
From June 1921–December 1922, Adm. Jones was the last Commander in Chief, United States Atlantic Fleet, before the title was discontinued until 1941. He then served as a member the General Board and retired in 1927, but served as naval advisor at the Geneva Disarmament Conference in 1927 and the London Naval Conference of 1930.
A prominent member of the Society of the Cincinnati, Admiral Jones died 1 January 1938.