During the decades that followed, Niblack served on many ships and held several interesting posts ashore including work with the Smithsonian Institution, duty in the Bureau of Navigation and a tour in the Office of Naval Intelligence. He won his first command, Iroquois, on 10 February 1904 and subsequently commanded some of the Navy’s most famous ships including Hartford and Olympia. He was naval attaché to Argentina, Brazil, Chile, Germany and The Netherlands, and served as a member of the General Board. When the United States entered World War I, he took command of Division 1, Atlantic Fleet, with Alabama as flagship on 5 April 1917, and was appointed rear admiral on 31 August. Niblack assumed command of Squadron 2, Patrol Force on 23 October and served in this post through the Armistice. He became Director of Naval Intelligence on 1 March 1919 and Naval Attaché in London on 6 August 1920.
As vice admiral, he commanded U.S. Naval Forces in European waters from 15 January 1921 to 17 June 1922. After commanding the 6th Naval District at Charleston, S.C., Vice Admiral Niblack retired 25 July 1923. He died at Monte Carlo, Monaco on 20 August 1929.