The years of World War II were decisive for the history of diving. After the armistice of 1940, the family of Jacques-Yves Cousteau, Simone Melchior, with whom he had two sons, Jean-Michel (born 1938) and Philippe (1940–1979), took refuge in Megève, where he became a friend of the Ichac family who also lived there. Jacques-Yves Cousteau and Marcel Ichac shared the same desire to reveal to the general public unknown and inaccessible places — for Cousteau the underwater world and for Ichac the high mountains. The two neighbors took the first ex-aequo prize of the Congress of Documentary Film in 1943, for the first French underwater film: Par dix-huit mètres de fond (18 meters deep), made without breathing apparatus the previous year in the Embiez islands (Var) with Philippe Tailliez and Frédéric Dumas, using a depth-pressure-proof camera case developed by mechanical engineer Léon Vèche (engineer of Arts and Métiers and the Naval College).

In 1943, they made the film Épaves (Shipwrecks), in which they used two of the very first Aqua-Lung prototypes. These prototypes were made in Boulogne-Billancourt by the Air Liquide company, following instructions from Cousteau and Émile Gagnan. When making Épaves, Cousteau could not find the necessary blank reels of movie film, but had to buy hundreds of small still camera film reels the same width, intended for a make of child's camera, and cemented them together to make long reels.

Having kept bonds with the English speakers (he spent part of his childhood in the United States and usually spoke English) and with French soldiers in North Africa (under Admiral Lemonnier), Jacques-Yves Cousteau (whose villa "Baobab" at Sanary (Var) was opposite Admiral Darlan's villa "Reine"), helped the French Navy to join again with the Allies; he assembled a commando operation against the Italian espionage services in France, and received several military decorations for his deeds. At that time, he kept his distance from his brother Pierre-Antoine Cousteau, a "pen anti-semite" who wrote the collaborationist newspaper Je suis partout (I am everywhere) and who received the death sentence in 1946. However, this was later commuted to a life sentence, and Pierre-Antoine was released in 1954.

During the 1940s, Cousteau is credited with improving the aqua-lung design which gave birth to the open-circuit scuba technology used today. According to his first book, The Silent World: A Story of Undersea Discovery and Adventure (1953), Cousteau started diving with Fernez goggles in 1936, and in 1939 used the self-contained underwater breathing apparatus invented in 1926 by Commander Yves le Prieur. Cousteau was not satisfied with the length of time he could spend underwater with the Le Prieur apparatus so he improved it to extend underwater duration by adding a demand regulator, invented in 1942 by Émile Gagnan. In 1943 Cousteau tried out the first prototype aqua-lung which finally made extended underwater exploration possible.