At the Battle of Port Royal later that year, troops under his command at Fort Beauregard and Fort Walker came under attack by ships of the Union Navy, including the USS "Pocahontas", commanded by his brother, Percival Drayton. Thomas Drayton's son, Lieutenant William Drayton, also fought with the Confederates in defense of the forts. After a lengthy bombardment, both forts fell to the Union attackers, who subsequently occupied much of the region. They gained an important deepwater port in coastal Carolina. For the remainder of the war Union naval operations against First Battle of Charleston Harbor and the Union Blockade were both supported by the port.