It has also been told to stop breeding orcas in captivity in a ruling from the California Coastal Commission.
They gave the park permission to double the size of its orca enclosures on the condition that breeding and bringing in new whales stopped.
It comes after criticism of the way the whales are treated there, something SeaWorld has always rejected.
Animal rights activists have welcomed a ruling by the California Coastal Commission, an agency that makes big decisions on major building projects in that area of America.
SeaWorld had put in plans to spend $100m (Â£65m) to expand its orca facility, which the commission approved.
But their decision came with several conditions. SeaWorld cannot add any new whales from the wild to its San Diego tanks, and none of the 11 orcas currently at the park will be allowed to breed there.
SeaWorld said it was disappointed with the ruling. They issued a statement that said: "Breeding is a natural, fundamental and important part of an animal's life and depriving a social animal of the right to reproduce is inhumane."
Groups that have criticised the park said they were pleased with the decision.
The group, People for the Ethical Treatment of Animals, said: "The commission's action ensures that no more orcas will be condemned to a nonlife of loneliness, deprivation and misery."
The breeding ban will not apply to the 13 other whales at SeaWorld attractions in San Antonio and Orlando.

Police said the incident happened at 10:30 BST near the village of Tockwith, which is 10 miles (17km) west of York.
North Yorkshire Police said it was believed the aeroplane had suffered engine failure.
Sgt Andy Graham, who attended the crash, praised the "great piloting skills resulting in no injuries".
More on this and other North Yorkshire stories

The union announced in August that Glasgow Warriors boss Townsend would replace Cotter in June.
Former Clermont head coach Cotter has subsequently secured a return to France with Montpellier for next year.
"Holistically, I understand," said Cotter, who has named his squad for November's autumn Test series.
"As a competitor, you're always disappointed if you're doing something and you want to go somewhere and you've got objectives in mind, naturally, but that's the deal and that's done.
"The decision was made to put Gregor in place. I think it's a good decision and the executives made their decision. I respect it and just move on."
Cotter, whose side face Australia (12 November), Argentina (19 November) and Georgia (26 November) in his last autumn internationals as Scotland head coach, says the "big year" ahead should keep the players focused.
"There's more important things than just us," he said of himself and Townsend. "It's a Lions year, there's places to be taken on that trip in June against New Zealand.
"The players are professional and they'll be wanting to play well for their club, whether it's Glasgow, and then shifting through to international stuff - whether it's a young player or established players.
"Look at [Edinburgh hooker] Ross Ford. It could be his 100th game [for Scotland]. Those sort of things take precedence.
"It's not about us, it's about the bigger picture."
SeaWorld has been banned from bringing wild killer whales to its park in San Diego, America.
[NEXT_CONCEPT]
A pilot escaped without injury after making an emergency landing in his light aircraft next to a river in North Yorkshire.
[NEXT_CONCEPT]
Vern Cotter is "disappointed" he is leaving his job as Scotland head coach but "respects" Scottish Rugby's decision to appoint Gregor Townsend.