[10] After returning from the expedition, Merrell – who was promoted to lieutenant on 21 March 1871[11][12] – served at the Naval Torpedo Station in Newport, Rhode Island, from 1872[13] to 1875, then aboard the screw frigate USS Swatara in the North Atlantic Squadron from 1875 to 1877.

[18] He then served in the Asiatic Squadron aboard the protected cruiser USS Baltimore from 1893 to 1895,[19] and from 1895 to 1896 was a member of the State Department Commission charged with investigating anti-foreign riots in Sichuan in the Chinese Empire.

[20] Merrell was promoted to commander on 1 November 1896[21] and was inspector in the 13th Lighthouse District from 1896 until January 1898, when he joined the staff of the Naval War College in Newport, Rhode Island.

He then served aboard the protected cruiser USS Montgomery from 1899 until 1900, when he became equipment officer at the Norfolk Navy Yard in Portsmouth, Virginia.

[23] Relinquishing command of Oregon, Merrell returned to Newport, Rhode Island, to become the 11th President of the Naval War College on 24 May 1906.

The most notable event of his presidency was the suspension by direction of President Theodore Roosevelt of the 1908 summer course on 8 July so that the General Board of the United States Navy, the bureau chiefs of the United States Department of the Navy, and the college's staff and students could participate in a "Battleship Conference" at the college, with Roosevelt himself visiting to chair the conference for a day on 22 July 1908.

[29] Merrell fell ill while visiting his daughter and son-in-law in New London, Connecticut, late in 1916, and died in their apartment on 8 December 1916.