Nicolson was promoted to lieutenant on May 20, 1812, while serving aboard the brig USS Flambeau, part of the Mediterranean Squadron during the Second Barbary War.
During the War of 1812, he served as fourth lieutenant aboard the USS United States during the battle with HMS Macedonian.
He also served as first lieutenant on USS Peacock under Commandant Lewis Warrington, and took part in the victory over HMS Epervier off the coast of Florida.
After the British vessel surrendered, Nicolson took Epervier back to the United States as a prize of war.
Nicolson, who filled the vacancy left by the death of Isaac Chauncey, served in the position from May 12, 1840, until April 29, 1841.