During this period, he resumed his study of the Chinese Junk and published several papers on the subject as well as commissioned a local carpenter at Weihaiwei to make scale models.
[2] In 1940, he became a flying instructor in the Fairey Swordfish aircraft, based at Toulon, where he was also involved in bombing raids on the Italian coast.
The German occupation of France in June forced Waters to evacuate to Algeria and then Malta, where he flew with 830 Naval Air Squadron.
Flying from Malta on the night of 13–14 August 1940, he was making a low-level torpedo attack on German shipping at Augusta, Sicily, when he became disoriented after flares went out and crashed his "Stringbag" aircraft into the harbour.
Through a friendship that he developed with the wealthy American sportsman, former wartime naval officer, and book collector, Henry C. Taylor, Waters began his studies of the history of navigation.
He published "The Rutters of the Sea" in 1967 and the "Art of Navigation in England and Elizabethan and Early Stuart Times" in 1958, books that Taylor had instigated as well as financially supported, even providing school fees for Waters's new family after David married his brother William's widow, Hope, in 1946.