[4][5] With the onset of the American Civil War in April 1861, Colhoun returned to U.S. Navy service, becoming an acting lieutenant on 24 September 1861.

He next commanded the monitor USS Saugus from 1864 to 1865, engaging Howlett's Battery on the James River in Virginia on 21 June and 5 December 1864 and taking her into action in North Carolina in both the First Battle of Fort Fisher in December 1864 and the Second Battle of Fort Fisher in January 1865.

[8][9] After the war, Colhoun had special duty at New York City in 1866 before serving as Fleet Captain of the South Pacific Squadron from 1866 to 1867.

On 15 January 1881, he relinquished command of the navy yard and was on special duty until 1882 as inspector of vessels in California.

[17] Colhoun died suddenly of heart failure in Washington, D.C., late on the evening of 17 February 1897.