After graduation from the Naval Academy in 1932, Waters served in the heavy cruiser USS Augusta (CA-31) and destroyer USS Downes (DD-375) before taking postgraduate training in ordnance engineering. He then went to England as a special naval observer in the period when Britain was engaged in hostilities but the United States was not yet in the war. That led directly to his assignment to set up the Navy's first mine disposal school in Washington after his return. He served later in the light cruiser USS Memphis (CL-13) and on the staff of Vice Admiral Jonas Ingram, both in the South Atlantic and when Ingram commanded the Atlantic Fleet. Waters was skipper of the destroyer USS Laffey (DD-724) during the Bikini atomic bomb tests in 1946. He later commanded the attack transport USS Glynn (APA-239) and Destroyer Squadron Two. While commanding the Naval Weapons Station at Yorktown, Virginia, he was selected for rear admiral and then served as Commander Destroyer Flotilla One. After duty as Commander Mine Force Pacific Fleet and Naval Base Los Angeles, he began a long tour of duty as Oceanographer of the Navy, up to his retirement in 1970.