As a Lieutenant, he served in Vandalia in Commodore Matthew C. Perry's Opening of Japan from 1853 to 1855.
During the Civil War he served in Pocahontas and Pensacola, and commanded the Isaac Smith, Shamrock, Manhattan, and Mohongo.
In 1861, under the command of Percival Drayton in activities near Charleston, he was made supervisor of a colony of over 100 former slaves on Otter Island in December 1861.
As Commodore from August 1873, and Rear Admiral from October 1881, he commanded the European Squadron from 16 September 1881 to February 1883.
Nicholson retired on 10 March 1883 and died at his home in New York on 28 October 1887.