Carter was a member of the first graduating class from the United States Naval Academy at Annapolis, Maryland. He resigned as a lieutenant from the United States Navy on April 25, 1861, two weeks after the siege of Fort Sumter, South Carolina. Two days later, Carter entered the new Confederate navy. He was sent to New Orleans to convert a sidewheel steamer, the Ed Howard, into a war vessel. He was given command of the gunboat, which he renamed the Polk, presumably after former U.S. President James K. Polk of Tennessee. Carter assisted in the evacuation of New Madrid, Missouri, and saw action at Tiptonville, the seat of Lake County, in the northwestern corner of Tennessee. On the Yazoo River, Carter torched the Polk on June 26, 1862, to prevent its capture by Union forces. Thereafter, Carter was ordered to contract for and to supervise the building of one or more gunboats on the Red River on October 3, 1862. He built the ironclad gunboat Missouri at Shreveport, in northwestern Louisiana, which he launched on April 14, 1863. Carter was placed in command of the Missouri and of the naval defenses in western Louisiana in the fall of 1863. Low water levels in the Red River prevented the Missouri from participating in the defense of western Louisiana when the army of Union General Nathaniel P. Banks and the fleet of Admiral David Dixon Porter advanced on Shreveport in April 1864.
In March 1865, the Red River rose sufficiently to permit Carter to take the Missouri downstream to Alexandria, the seat of Rapides Parish in central Louisiana, where the gunboat, officers, and crew surrendered to the United States Navy on June 3, 1865, some two months after Robert E. Lee signed the surrender at Appomattox Court House, Virginia.
Carter was promoted to Captain in the CSN by the end of the war.
Carter remained in Louisiana after the end of the war. He operated a cotton plantation in Bossier Parish, located across the Red River from Shreveport, during the period from 1866 until 1871, when financial reverses caused him to abandon the project. At some time prior to 1872, Carter married the former Henrietta G. Thompkins in Louisiana. He died in Shirley, Virginia.
- "Alumni Lookup". United States Naval Academy Alumni Association and Foundation. https://www.usna.com/SSLPage.aspx?pid=1303&reid=E28S8zGKMMs%3d&bbsys=0&bbrt=0. Retrieved 2009-02-15.
- Snowden, p.6
- "Jonathan H. Carter", A Dictionary of Louisiana Biography, Vol. 1 (1988), p. 156
- Jeter, Katherine Brash (1996). A Man and His Boat: The Civil War Career and Correspondence of Lieutenant Jonathan H. Carter, CSN. Lafayette, LA: Center for Louisiana Studies, University of Louisiana. ISBN 1-887366-07-5.
- Snowden, Yates, and Cutler, Harry G., History of South Carolina, 1920
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