The film was shot aboard the ship Calypso. Cousteau and his team of divers shot 25 kilometers of film over two years in the Mediterranean Sea, the Persian Gulf, the Red Sea and the Indian Ocean, of which 2.5 kilometers were included in the finished documentary.

The film later faced criticism for environmental damage done during the filmmaking. In one scene, the crew of the Calypso massacre a school of sharks that were drawn to the carcass of a baby whale, which itself had been mortally injured by the crew, albeit accidentally (Cousteau had the ship driven into a pod of whales to get a close-up view, striking one whale in the process before the baby was lacerated by the prop). In another, Cousteau uses dynamite near a coral reef in order to make a more complete census of the marine life in its vicinity. Cousteau later became more environmentally conscious, involved in marine conservation, and was even called "the father of the environmental movement" by Ted Turner.