Ottawa joined the South Atlantic Blockading Squadron for service in the waters of the Carolinas, Georgia, and Florida. During the Civil War she participated in nineteen operations against ships and shore installations from Hilton Head, South Carolina, to the St. Johns River in Florida. Ottawa also assisted the U.S. Army in the occupation of Bull's Bay, South Carolina, 11 February 1865. Other engagements took place with the batteries at Brown's Landing, St. Johns River, Florida, and at Palatka, Florida.