[2] He was appointed to the United States Naval Academy from Wisconsin's 1st congressional district by John F. Potter.

[3] From 5 January to 24 April 1871, Cotton served aboard the screw frigate Tennessee on a visit to the Dominican Republic to explore establishment of an American naval base at Samaná Bay.

[1][3] From 24 April 1871 to 16 February 1874, he served as executive officer of the screw sloop of war Ticonderoga in the vicinity of Brazil.

From 15 September to 4 October 1876, he served as executive officer of the receiving ship Worcester at the Norfolk Navy Yard.

During this period, he also commanded the Anglo-American Bering Sea Patrol Squadron to combat seal poaching from 22 June to 5 October 1891.

From 24 August 1894 to 1 September 1897, Cotton was given command of the protected cruiser Philadelphia, which was serving as flagship of the Navy's Pacific Station.

She then conveyed more than 1000 prisoners of war to the United States, delivering the officers to the Naval Academy in Maryland and the enlisted men to the Portsmouth Navy Yard in New Hampshire.

Returning to Cuba, Harvard loaded the 33rd Michigan Regiment at Santiago and delivered the troops to Montauk Point on Long Island in August.

[3][4] Cotton served as commander of the European Squadron from 28 April 1903 until his retirement from active duty on 16 February 1904.

[4] On 7 July 1903, he visited Portsmouth, England aboard his flagship the battleship Kearsarge, accompanied by the protected cruisers Chicago and San Francisco and the schooner-rigged gunboat Machias.

[4][6] Their son Charles Stanhope Cotton Jr. (19 March 1870 – 11 October 1926) served as a captain in the Army Air Service during World War I.