At the start of the American Civil War, Wells was suffering from exhaustion and exposure from this travels, coupled with depression from the recent death of his beloved brother-in-law, with whom he had sailed for twelve years.

Consequently, he spent three months in the Pennsylvania Hospital for the Insane in Philadelphia where he was diagnosed as having Melancholia, being released on October 11, 1861, to return to active duty.

He was appointed executive officer of the USS Susquehanna and took part in the capture of Port Royal, South Carolina, on November 7, 1861.

During this time he sent a letter to the United States Secretary of War, Edwin M. Stanton, that accused Maj. Granville O. Haller, former commander of George B. McClellan's headquarters guard, of sentiments disloyal to the Union.

Later that year, he was transferred to the East Gulf Squadron and served the rest of the war under David Dixon Porter on the James River.

[4] Wells died at his residence in Washington, D.C., from heart disease,[5] and was buried in Philadelphia's Laurel Hill Cemetery, Section M, Lot 22.