Farrand served at Pensacola Navy Yard, and held various appointments in the Confederate States Navy in 1861 until his appointment at Savannah station in 1862. He was put in charge of commanding naval defenses at Drewry's Bluff, Va., 1862. From Virginia, he went to Alabama to serve at the Selma Naval Foundry. In 1863, he commanded in Mobile after Admiral Buchanan was wounded and taken prisoner by Union forces in August 1864.
