Joshua Tabor admitted to police he had used the CIA torture technique because he was so angry.
As his daughter 'squirmed' to get away, Tabor said he submerged her face three or four times until the water was lapping around her forehead and jawline.
Tabor, 27, who had won custody of his daughter only four weeks earlier, admitted choosing the punishment because the girl was terrified of water.
Human rights activists demonstrate waterboarding in front of the Justice Department. A soldier father stands accused of waterboarding his daughter because she couldn't recite the alphabet
The practice of waterboarding was used by the CIA to break Al Qaeda suspects at Guantanamo Bay. Detainees had water poured over their face until they feared they would drown. President Barack Obama has since outlawed the practice.
Tabor, a soldier at the Lewis-McChord base in Tacoma, Washington, was arrested after being seen walking around his neighbourhood wearing a Kevlar military helmet and threatening to break windows.
Police discovered the alleged waterboarding when they went to his home in the Tacoma suburb of Yelm and spoke to his girlfriend.
She told them about the alleged torture and the terrified girl was found hiding in a closet, with bruising on her back and scratch marks on her neck and throat.
Asked how she got the bruises, the girl is said to have replied: 'Daddy did it.'
During a police interview Tabor allegedly admitted grabbing his daughter, placing her on the kitchen counter and submerging her face into a bowl of water.
Sergeant Rob Carlson said the punishment was carried out because the girl would not recite the alphabet.
Police have not revealed Tabor's military service, but his base is home to units that have served in Iraq and Afghanistan.
Tabor has been charged with assault and ordered to remain on his base and have no contact with his daughter or girlfriend, who has not been named. He is due to appear in court this week.
The girl has been taken into care. Her natural mother lives in Kansas but Tabor had been granted custody by a court.