In 1896, Clark was promoted to captain. In March 1898, he assumed command of the battleship Oregon (BB 3) at the Mare Island Naval Shipyard, San Francisco. When war with Spain was deemed inevitable, he received orders to proceed to Key West, Florida with all haste. After a voyage of more than 14,000 miles around Cape Horn, the first of its kind by US Navy warship, Oregon joined the American fleet in Cuban waters on 26 May.
On 3 July 1898 at the Battle of Santiago, Captain Clark commanded his ship in the destruction of the Spanish squadron of Almirante Pascual Cervera y Topete, for which he was advanced in seniority and appointed Rear Admiral on 16 June 1902.
Rear Admiral Clark died of heart failure on 1 October 1922 at his home at Long Beach, California.