In 1861, Dahlgren's superior at the Washington Navy Yard resigned to join the Confederate navy, and President Abraham Lincoln wanted to name then-Commander Dahlgren to the post of commander of the Washington Navy Yard. By law, however, that position could only be held by an officer with a rank of captain or above. Lincoln successfully persuaded Congress to pass a special act legalizing Dahlgren's appointment to the yard, and, in July 1862, Dahlgren was promoted to the rank of captain and made chief of the Bureau of Ordnance. In February 1863, Dahlgren was promoted to rear admiral and took command of the South Atlantic Blockading Squadron. In 1864, he helped William Tecumseh Sherman secure Savannah, Georgia.