Cousteau faced criticism for some of the practices used during his filmmaking, including instances of dynamiting coral reefs to obtain dramatic footage. Critics argued that these actions caused unnecessary damage to fragile ecosystems.

After Jacques's death, there were publicized conflicts between The Cousteau Society and Jacques's son, Jean-Michel Cousteau, regarding the use of the Cousteau name and brand. These disputes highlighted differing visions for the future of ocean conservation efforts.

The Calypso, while a symbol of ocean exploration, was criticized for its significant fuel consumption and the potential environmental impact of its operations. This raised questions about the balance between exploration and environmental responsibility.

The secrecy surrounding his marriage to Francine Triplet and the existence of their children while Simone was still alive generated considerable controversy and tarnished Cousteau's public image.