Phelps commanded the "Eastport" during the Mississippi River campaigns. "Eastport" sailed from Cairo, Illinois, in late in August after being repaired and converted for duty on the Mississippi River between Island No. 10 and the mouth of the White River in Arkansas. She was back at Cairo, Illinois, for repairs when, on 1 October 1862, the "Eastport" and the other vessels of the Western Flotilla were turned over to the Navy and became part of the Mississippi Squadron.