Dahlgren's eldest son Charles Bunker Dahlgren (1839–1912), who had studied steam engineering, joined the U.S. Navy at the start of the Civil War and served with distinction, receiving several promotions and ending as the rank of captain, though he declined offers to continue in federal service after the war. Among other incidents, Charles Dahlgren commanded the siege battery of IX inch Dahlgren shell-guns which destroyed the powerful Confederate batteries at the Battle of Vicksburg, and served under his father during the blockade of Charleston.