The park, initially called Sea World of Texas, was developed by Harcourt, Brace and Jovanovich (now Houghton Mifflin Harcourt). Built for $170 million, it opened on May 27, 1988, and 75,000 people attended the opening. It had 3.3 million visitors in its first 12 months of operation, placing it among the Top 10 attractions in Texas. At the time of its debut, it was billed as "the largest educational, marine-life theme park in the world."

On November 26, 1988, Kayla (stage named "Baby Shamu") was the first orca born at the park. At the time of her death on January 28, 2019, she resided at SeaWorld Orlando.

In 1989, Harcourt, Brace and Jovanovich (heavy in debt and fighting a hostile takeover) sold its SeaWorld and Boardwalk and Baseball theme parks to Anheuser-Busch, Inc. Plans to build a second Boardwalk and Baseball park adjacent to Sea World San Antonio were abandoned.

Under Anheuser-Busch ownership, the park closed less popular attractions consisting of the Texas Walk, Cypress Gardens West, Joplin Square, U.S. Map Plaza, and the Garden of Flags and added its Budweiser Clydesdales to the park.

In 2008, Anheuser-Busch merged with InBev; soon after, in 2009, the newly merged company sold the SeaWorld parks to the Blackstone Group. In 2017, Blackstone sold its stake to China's Zhonghong Group.

In March 2016, SeaWorld Entertainment announced that the current generation of orcas at it parks would be the last. SeaWorld San Antonio currently houses 5 orcas. It was also announced that the theatrical orca shows would be phased out and replaced with more naturalistic Orca Encounters. SeaWorld San Antonio's Orca Encounter opened on February 22, 2020.

In 2024, Catapult Falls, the world's first launched flume ride, opened to the public. In the fall of 2024, SeaWorld San Antonio announced that they would retheme their Sesame Street Bay of Play area to SeaWorld Rescue Jr., a similar concept to the one at SeaWorld San Diego. On March 8th, 2025, SeaWorld Rescue Jr. area opened to guest, with new and rethemed rides such as Beach Rescue Racers, Ocean Quest Express, Tide Pool Tumble, Seabird Swing, and Ocean Rescue Carousel.