1896, Cluverius was posted to the cruiser . In 1897 joined the crew of . He was on board on 15 February 1898 when the ship suffered an explosion in Havana Harbor. Cluverius made his way out, splashing through water up to waist deep in the darkness, his path obstructed by wreckage. He joined other survivors on deck, and was rescued by SS City of Washington. He was one of only 89 survivors, of whom 18 were officers. The loss of Maine helped precipitate the Spanish–American War. Cluverius saw action during the conflict on a number of ships including , on which he participated in the Second Battle of Manzanillo and the bombardments of Santiago and Aquadores. Commissioned as an ensign, he served in the Philippine–American War on in 1900. He then served on the gunboat . In 1899, he became engaged to Hannah Walker Sampson, the daughter of Rear Admiral William T. Sampson. The families knew each other well, and Cluverius was an usher at the wedding of Hannah's sister Olive. On 5 April 1900, they were married in a ceremony at the Boston Navy Yard. Their marriage produced two daughters, Elizabeth (Betty) and Martha, and a son, Wat Tyler Cluverius III. Not only did their son become a naval officer, but both daughters married naval officers, John S. Crenshaw and William Sterling Parsons respectively. Both sons in law later became admirals. Cluverius served at the Naval Academy on court martial duty and as commander of the torpedo boat . He became commander of the gunboat in June 1901 and then in October. He joined the torpedo boat in 1902. The next year he was promoted to lieutenant and was posted to the battleship , the namesake of the ship whose sinking he had survived in 1898, as an engineering officer. He was involved with the 1904 sea trials of the cruisers and before becoming senior engineer of the monitor . In 1908 he became senior engineer of the newly commissioned . Shore duty followed in 1909 as a member of the Naval Examining Board of the Special Service Squadron. For a short time in 1910, Cluverius was navigator of , an old battleship now used as a training ship for midshipmen, before becoming Judge Advocate at the Court of Inquiry at the Philadelphia Navy Yard. He attended a conference of officers at the Naval War College in Newport,