After Virginia's fleet was integrated with the Confederate Navy, Barron was issued a commission as commander and appointed chief of the Office of Orders and Details on June 10. Barron would remain in that post until July 20, when Confederate Secretary of the Navy Stephen R. Mallory agreed to Barron's request to be assigned as commander of coastal defences of Virginia and North Carolina, an important port for Pamlico Sound-based Confederate privateers. Arriving at his headquarters on Fort Hatteras on August 28, Barron commanded the defense of both the forts Hatteras and Clark against Union Flag Officer Silas H. Stringham during the Battle of Hatteras Inlet on August 28–29. Barron was captured following the surrender of the two fortresses. Held at Fort Columbus on Governors Island in New York harbor, then at Ft. Warren, Boston harbor, Barron was eventually released in a prisoner exchange the next year.