During the Civil War, Stembel served in the Western Gunboat Flotilla during 1861 and 1862. He participated in the engagements of Lucas' Bend, September 9, 1861; Belmont, November 1861; Fort Henry, February 1862; and the bombardment and capture of Island No. 10 in March and April 1862. While commanding the "Cincinnati", Stembel was seriously wounded in an engagement with Confederate rams near Fort Pillow on May 10, 1862, and invalided in 1863.