Pathologist Claudia Szentiks said a necropsy of the four-year-old bear who died suddenly two weeks ago showed he was suffering from encephalitis, an irritation and swelling of the brain that was likely brought on by an infection.
Szentiks also rejected allegations from animal-rights groups that he was traumatized by living in a zoo environment, saying that there were no indications of any chronic stress.
She added that even if Knut had not drowned after his collapse, he would not have survived the damage from the encephalitis.
Knut died March 19 in front of visitors at Berlin zoo, turning around several times and then falling into the water in his enclosure. Polar bears usually live 15 to 20 years in the wild and even longer in captivity.
Knut, who was born in December 2006 at the zoo, rose to celebrity status as an irresistibly cute, fluffy cub.
Knut was rejected by his mother at birth - along with his twin brother, who only survived a couple of days. He attracted attention when his main caregiver, Thomas Doerflein, camped out at the zoo to give the button-eyed cub his bottle every two hours.
The bear went on to appear on magazine covers, in a film and on mountains of merchandise.
Doerflein, the zookeeper who raised him, died in 2008 of a heart attack.