"The truth about SeaWorld is right here in our parks and people," the company said in the ad, which appeared Friday.
"Our guests may enter our gates having never given much thought to the remarkable animals in our oceans," the ad said. "When they leave with a greater appreciation for the importance of the sea, educated about the animals that live there and inspired to make a difference, we have done our job."
CNN said "Blackfish" traces a 39-year history of killer whales in captivity, leading up to the 2010 death of SeaWorld trainer Dawn Brancheau by Tilikum, a 12,000-pound orca previously associated with the deaths of two other people.
"Blackfish" filmmaker Gabriela Cowperthwaite has said the documentary team's research shows the whales suffer from boredom and stress, and are unsuitable for life in captivity.
However, SeaWorld in its ad said it last captured a whale in the wild 35 years ago. The company also said it does not separate whale calves from their mothers except for "the rare occasion that a mother killer whale cannot care for the calf herself,"
Seaworld rejected claims its whales have shorter lifespans than those living in the wild, CNN reported.