Following the outbreak of the Civil War, Wainwright was promoted to commander on 24 April 1861 and commanded , flagship of Admiral David G. Farragut's West Gulf Blockading Squadron. During the passage of the forts below New Orleans, Louisiana on the night of 24 and 25 April 1862, he performed gallant service in extinguishing a fire on "Hartford" while continuing the bombardment of the forts. Commended by Admiral Farragut for his actions, Wainwright later participated in the squadron's operations below Vicksburg until taken ill with fever.