During the Civil War, in April 1862, he was recommended for promotion for gallantry for his actions on board the screw steamer while serving as executive officer, as that ship led Admiral David Farragut's starboard column past Fort Jackson and Fort St. Philip. He was promoted to lieutenant commander on July 16, 1862, and placed in command of the gunboat on the Mississippi River. While commanding "Katahdin", Roe defeated Confederate general John C. Breckinridge's attack on Baton Rouge, Louisiana.