On March 23, 1863, he assumed command of , for duty in the Mississippi Squadron. In that gunboat, he participated in Yazoo River operations during April and May. Then on June 7, he supported a Union garrison at Milliken's Bend, Louisiana in holding off some 4,000 Confederate troops. Moving on to Vicksburg, he commanded a battery of heavy guns mounted on scows in exposed positions before the city, June 19 – July 4. After the capture of the river stronghold, he was given command of the 3d Division, Mississippi Squadron.