The couple welcomed a baby boy Friday.
Morgan took to Instagram over the summer to share the family's heartbreak.
She wrote, "We are beyond devastated. Our baby girl, Emmy, passed away yesterday. Never in a million years did we think we would ever experience pain like this."
The couple turned their pain into a personal mission to promote water safety. The two have spoken to several media outlets trying to educate families about pool drownings.
Bode Miller's wife shares heartbreaking photo of dying daughter to raise awareness
Bode and Morgan also have a 3-year-old son and two other children from previous relationships.