Mr Miller, the most successful skier in US history with six Olympic medals including gold at the 2010 Vancouver Games, said he was “beyond devastated”.
In a statement posted to social media he said: “Our baby girl, Emmy, passed away yesterday.
Never in a million years did we think we would experience a pain like this.
“Her love, her light, her spirit will never be forgotten. Our little girl loved life and lived it to its fullest every day.”
The tot was found by her mother Morgan Beck Miller, who is pregnant with the couple’s third child, during the party last weekend.
The professional beach volleyball player leapt into the water and pulled her out, but the little girl was unresponsive.
Paramedics took her to hospital but she could not be saved.
Mr Miller, 40, and Ms Beck Miller, 31, were married in 2012.
Their son Nash was born in 2015.
The winter sports legend also has a 10-year-old daughter and a five-year-old son from previous relationships.
Mr Miller has won four World Championship titles.
He retired last year and attended the Pyeongchang Games as a commentator.
Fellow Olympic skier Lindsey Vonn tweeted: “Devastating news. My deepest condolences to you and your family.”