The pair announced their pregnancy last month.
Ahead of his second dance of the night with partner Emma Slater, the Dawson's Creek alum shared that his wife, Kimberly, had miscarried on Saturday. They were expecting their sixth child together.
"My wife, Kimberly, and I went through every expecting parent's worst nightmare. We lost the baby," an emotional Van Der Beek said. "The little soul that we had expected to welcome in our family took a shortcut to whatever lies beyond. You never know why these things happen. That's what I've been telling my kids. All you know is that it brings you closer together."
"It breaks you open. It opens up your heart, it deepens your appreciation. It makes you more human. I really didn't think I would be dancing tonight, but Kimberly from her hospital bed said to me, 'I am not done watching you dance.' Kimberly, I love you," he continued.
Van Der Beek explained that he'd be dancing to "Take Me To Church" by Hozier. "That song has taken on a whole new meaning for me this week," he shared. "Kimberly, I'm dancing for you, I'm dancing for us, so here we go, babe."
The actor, who shares five kids -- Olivia, 9, Joshua, 7, Annabel, 5, Emilia, 3 and Gwendolyn, 1 -- with his wife then delivered a stunning Foxtrot on the dance floor, ending his routine in tears. He received praise and admiration from the judges, and stopped to hug his crying daughter in the audience on his way up to the star lounge.
"Kimberly, I love you. Thank you," Van Der Beek said in a tearful message to his wife. "You're amazing, thank you."
He received a total score of 27 out of 30 for his dance.
Van Der Beek opened up more about his wife's miscarriage on Instagram. "Wrecked. Devastated. In shock. That’s how we’re feeling right now after the soul we thought were going to welcome into our family in April... has taken a short cut to whatever lies beyond this life," he wrote. "We’ve been through this before, but never this late in the pregnancy, and never accompanied by such a scary, horrific threat to @vanderkimberly and her well-being. Grateful that she’s now recovering, but we’ve only just begun unpacking the layers of this one."
"Thank you to all of our friends and co-workers (and dance partners) who have shown up for us so beautifully during this time. As many of you have said, 'There are no words...' and it’s true. Which is why in a time like this it’s enough to know that you’re there. Grieving AND counting our blessings today," he added.
See more on Van Der Beek in the video below.