While Nicholson was aboard State of Georgia, the ship blockaded Wilmington, North Carolina, and fought engagements with Confederate fortifications guarding the city.

[4][5] On 30 September 1869, Nicholson was appointed from the District of Columbia as a midshipman and entered the United States Naval Academy in Annapolis, Maryland.

Promoted to ensign on 16 July 1874, he served aboard the sidewheel steam frigate USS Powhatan in the North Atlantic Squadron from 1875 to 1877.

He returned to sea aboard the new steam sloop-of-war USS Mohican in the Pacific Squadron from 1885 to 1888, and was promoted to lieutenant on 17 January 1886.

[6][7] In December 1897, Nicholson reported for duty aboard the battleship USS Oregon, and he served as her chief navigation officer during her spectacular voyage from the United States West Coast around Cape Horn to Cuba at the outset of the Spanish–American War in 1898.

[13] In 1903 he was assigned to the new protected cruiser USS Tacoma, then under construction at Union Iron Works in Mare Island, California, and became her first commanding officer when she was commissioned on 30 January 1904, remaining aboard her until December 1905.

After the conclusion of the voyage in 1909, President William Howard Taft appointed him on 1 December 1909 for a four-year tour as Chief of the Bureau of Navigation in Washington, D.C.[5][16][17][18] Nicholson was promoted to rear admiral on 19 May 1911.

[19] In mid-1911, he was chosen to end his tour at the Bureau of Navigation early and succeed Rear Admiral Joseph B. Murdock as commander-in-chief of the U.S. Asiatic Fleet as of November 1911, but United States Secretary of State Philander C. Knox requested that Murdock be kept on as fleet commander to allow continuity during unrest in China related to the Xinhai Revolution of that year.

Meanwhile, United States Secretary of the Navy George von Lengerke Meyer had already selected Nicholson's successor as Chief of the Bureau of Navigation.