Campaigners hope move will eventually bring an end to shows involving the marine animals.
France has officially banned the breeding of killer whales and dolphins in captivity.
The government has also banned the captivity of all whales, dolphins and porpoises, except for orcas and bottlenose dolphins.
Pools must also be made significantly larger with no direct contact between the animals and the public.
Aquariums and water parks have six months to comply to the rules, and must expand their pools within three years.
The new rules came about after SeaWorld announced the last birth of a killer whale after it decided to stop breeding orcas following animal rights protests.
Segolene Royal, French environment minister, signed a version of the bill on Wednesday, but decided the rules needed to be “more radical” after learning “some animals were drugged” in aquariums, her ministry told AFP.
Jon Kershaw, the head of the Marineland Antibes park in the French Riviera, told local media the ban was a “bombshell” for businesses like his.