The actress, who played Septa Unella in seasons five and six of the hit fantasy series, reveals she was originally supposed to be raped by Hafbor Julius Bjornsson's character the Mountain but writers came up with an even more harrowing torture scene.
"I think they'd had so many complaints about the rape of Sansa (Sophie Turner's character) that they chose not to go with it," Hannah tells Collider. "Unbelievably, they changed it quite at the last minute."
The new scenes featured waterboarding - a torture technique used by professional criminals and those seeking the truth from terrorists and the like.
"I think they possibly changed it when I was mid-air flying to Belfast (to film the scene) because suddenly I got sent these new sides that said I would need a wetsuit top," Waddingham adds. "I thought they'd sent me the wrong bits."
"They were like, 'Oh, it's going to be waterboarding instead.' And I was like, 'But we're not actually doing waterboarding.' And they were like, 'No, no, no, we are.' "
Waddingham was bound to a wooden table in the scene with "proper big straps" for hours as Lena Headey's character Cersei poured wine into her face.
"Definitely other than childbirth, it was the worst day of my life," she explains. "Lena was uncomfortable pouring liquid in my face for that long, and I was beside myself. But in those moments, you go, 'Do you serve the piece and get on with it?' or do you chicken out and go, 'This isn't what I signed up for.' "
She admits she wasn't happy with the episode's director, Miguel Sapochnik, after finishing filming for the day, "(He said), 'The crew have just been saying we are actually really waterboarding you here,' and I was like, 'Yup, you don't need to tell me that!' " she adds. "I had bruises already coming up, like I'd been attacked."
"It (the scene) definitely gave me claustrophobia around water. It's quite full on being waterboarded for 10 hours."