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 1947, Chief Petty Officer Maurice Fargues became the first diver to die using an aqualung while attempting a new depth record with the GERS near Toulon.
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.
The adventures of this period are told in the two books The Silent World (1953, by Cousteau and Dumas) and Plongées sans câble (1954, by Philippe Tailliez).
In 1949, Cousteau left the French Navy.
In 1950, he founded the French Oceanographic Campaigns (FOC), and leased a ship called Calypso from Thomas Loel Guinness for a symbolic one franc a year. Cousteau refitted the Calypso as a mobile laboratory for field research and as his principal vessel for diving and filming. He also carried out underwater archaeological excavations in the Mediterranean, in particular at Grand-Congloué (1952).
With the publication of his first book in 1953, The Silent World, he correctly predicted the existence of the echolocation abilities of porpoises. He reported that his research vessel, the Élie Monier, was heading to the Straits of Gibraltar and noticed a group of porpoises following them. Cousteau changed course a few degrees off the optimal course to the center of the strait, and the porpoises followed for a few minutes, then diverged toward mid-channel again. It was evident that they knew where the optimal course lay, even if the humans did not. Cousteau concluded that the cetaceans had something like sonar, which was a relatively new feature on submarines.
Cousteau won the Palme d'Or at the Cannes Film Festival in 1956 for The Silent World co-produced with Louis Malle. With the assistance of Jean Mollard, he made a "diving saucer" SP-350, an experimental underwater vehicle which could reach a depth of 350 meters. The successful experiment was quickly repeated in 1965 with two vehicles which reached 500 meters.
In 1957, he was elected as director of the Oceanographical Museum of Monaco. He directed Précontinent, about the experiments of diving in saturation (long-duration immersion, houses under the sea), and was admitted to the United States National Academy of Sciences.
In October 1960, a large amount of radioactive waste was going to be discarded in the Mediterranean Sea by the Commissariat à l'énergie atomique (CEA). The CEA argued that the dumps were experimental in nature, and that French oceanographers such as Vsevelod Romanovsky had recommended it.
Romanovsky and other French scientists, including Louis Fage and Jacques Cousteau, repudiated the claim, saying that Romanovsky had in mind a much smaller amount. The CEA claimed that there was little circulation (and hence little need for concern) at the dump site between Nice and Corsica, but French public opinion sided with the oceanographers rather than with the CEA atomic energy scientists. The CEA chief, Francis Perrin, decided to postpone the dump.
Cousteau organized a publicity campaign which in less than two weeks gained wide popular support. The train carrying the waste was stopped by women and children sitting on the railway tracks, and it was sent back to its origin.
A meeting with American television companies (ABC, Métromédia, NBC) created the series The Underwater Odyssey of Commander Cousteau, with the character of the commander in the red bonnet inherited from standard diving dress) intended to give the films a "personalized adventure" style.
In 1970, he wrote the book The Shark: Splendid Savage of the Sea with Philippe, his son. In this book, Costeau described the oceanic whitetip shark as "the most dangerous of all sharks".
In 1973, along with his two sons and Frederick Hyman, he created the Cousteau Society for the Protection of Ocean Life, Frederick Hyman being its first President; it now has more than 300,000 members.
Three years after the volcano's last eruption, on 19 December 1973, the Cousteau team was filming on Deception Island, Antarctica when Michel Laval, Calypso's second in command, was struck and killed by a propeller of the helicopter that was ferrying between Calypso and the island.
In 1976, Cousteau uncovered the wreck of HMHS Britannic. He also found the wreck of La Therese in Crete island
In 1977, together with Peter Scott, he received the UN International Environment prize.
On 28 June 1979, while the Calypso was on an expedition to Portugal, his second son, Philippe, his preferred and designated successor and with whom he had co-produced all his films since 1969, died in a PBY Catalina flying boat crash in the Tagus river near Lisbon. Cousteau was deeply affected. He called his then eldest son, the architect Jean-Michel Cousteau, to his side. This collaboration lasted 14 years.