Cousteau was born on 11 June 1910, in Saint-André-de-Cubzac, Gironde, to Daniel and Élisabeth Cousteau. He had one brother, Pierre-Antoine. Cousteau completed his preparatory studies at the prestigious Collège Stanislas in Paris. In 1930, he entered the École Navale and graduated as a gunnery officer. After an automobile accident cut short his career in naval aviation, Cousteau indulged his interest in the sea.

In Toulon, where he was serving on the Condorcet, Cousteau carried out his first underwater experiments, thanks to his friend Philippe Tailliez who in 1936 lent him some Fernez underwater goggles, predecessors of modern diving masks. Cousteau also belonged to the information service of the French Navy, and was sent on missions to Shanghai and Japan (1935–1938) and in the USSR (1939).[citation needed]

On 12 July 1937 he married Simone Melchior, with whom he had two sons, Jean-Michel (born 1938) and Philippe (1940–1979). His sons took part in the adventures of the Calypso. In 1991, one year after his wife Simone's death from cancer, he married Francine Triplet. They already had a daughter Diane Cousteau (born 1980) and a son Pierre-Yves Cousteau (born 1982), born during Cousteau's marriage to his first wife.

The years of World War II were decisive for the history of diving. After the armistice of 1940, the family of Simone and Jacques-Yves Cousteau 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 Embiez (Var) with Philippe Tailliez and Frédéric Dumas, without forgetting the paramount part played, as originator of the depth-pressure-proof camera case, by the mechanical engineer Léon Vèche (engineer of Arts and Métiers and the Naval College).

In 1943, they made the film Épaves (Shipwrecks): for this occasion, they used the aqua-lung, which continued the line of some inventions of the 19th century (Rouquayrol's and Denayrouze's Aerophore) and of the early 20th century (Le Prieur). 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 snorkel diving with a mask, snorkel, and fins with Frédéric Dumas and Philippe Tailliez. In 1943, he tried out the first prototype aqua-lung — designed by Cousteau and Émile Gagnan — which finally made extended underwater exploration possible.

In 1946, Cousteau and Tailliez showed the film "Épaves" to Admiral Lemonnier, and the admiral gave them the responsibility of setting up the Groupement de Recherches Sous-marines (GRS) (Underwater Research Group) of the French Navy in Toulon. A little later it became the GERS (Groupe d'Études et de Recherches Sous-Marines, = Underwater Studies and Research Group), then the COMISMER ("COMmandement des Interventions Sous la MER", = "Undersea Interventions Command"), and finally more recently the CEPHISMER.

In 1948, between missions of mine clearance, underwater exploration and technological and physiological tests, Cousteau undertook a first campaign in the Mediterranean on board the sloop Élie Monnier, with Philippe Tailliez, Frédéric Dumas, Jean Alinat and the scenario writer Marcel Ichac. The small team also undertook the exploration of the Roman wreck of Mahdia (Tunisia). It was the first underwater archaeology operation using autonomous diving, opening the way for scientific underwater archaeology. Cousteau and Marcel Ichac brought back from there the Carnets diving film (presented and preceded with the Cannes Film Festival 1951).

Cousteau and the Élie Monnier then took part in the rescue of Professor Jacques Piccard's bathyscaphe, the FNRS-2, during the 1949 expedition to Dakar. Thanks to this rescue, the French Navy was able to reuse the sphere of the bathyscaphe to construct the FNRS-3.