Attached to Monticello, blockading the North Carolina coast, Howorth accompanied Lt. William B. Cushing on a reconnaissance up the Cape Fear River to Wilmington 23–24 June 1864, gaining valuable information about Confederate defenses.
In October, Howorth joined Cushing’s expedition up the Roanoke River to sink Confederate ram Albemarle. Both the ram and the launch carrying the Federal sailors were destroyed and while Cushing and one other man escaped, Howorth and others were captured. In his report Cushing noted: “Acting Master’s Mate William L. Howorth, of the Monticello, showed, as usual, conspicuous bravery. He is the same officer who has been with me twice in Wilmington harbor. I trust he may be promoted, when exchanged . . . .”
In February 1865, Howorth was exchanged and promoted acting master. Honorably discharged in October, he reentered the Navy in 1866 and was appointed ensign 12 March 1868. He resigned 4 April 1869.