The jury in Georgetown, Delaware, deliberated for about six hours before returning its verdict against Melvin Morse, 60.
Morse was charged with three felonies - two for alleged waterboarding and one for alleged suffocation by hand. He was convicted of one - waterboarding in the bath - and five misdemeanours. Jurors reduced the second waterboarding charge to a misdemeanour and cleared Morse of the suffocation charge.
Morse, who showed no reaction as the verdict was read, was ordered to surrender his passport and will remain on bail until his sentencing on April 11.
He faces a maximum of 10 years in prison, but a lesser punishment is likely under state sentencing guidelines. Each misdemeanour carries a maximum of one year in prison but typically results in probation. The felony reckless endangerment conviction for waterboarding carries a maximum of five years in prison, but a presumptive sentence of 15 months.
Prosecutor Melanie Withers said she was "very gratified" by the verdict, and was on her way to speak to the victim, now 12.
Morse declined to comment and referred questions to his lawyers. "He maintains his innocence to this day," said one of them, John Brady.
Morse's lead defence lawyer, Joseph Hurley, said he planned to appeal.
The girl and her mother, Pauline Morse, told the court that Melvin Morse used waterboarding as a threat or a form of punishment. Waterboarding has been used in the past by US interrogators on terror suspects to simulate drowning and many critics call it torture.
The defence argued that waterboarding was a term jokingly used to describe hair washing the girl did not like.
But Ms Withers portrayed Morse as a brutal and domineering "lord and master" of his household, abusing the girl for years while her mother acquiesced in silence.
Pauline Morse, 41, said she chose to ignore the abuse and was afraid of "undermining" Morse. She also said she did not have a close relationship with the girl for the several years that encompassed the waterboarding and that she did not pay her much attention.
Pauline Morse pleaded guilty last year to misdemeanour endangerment charges and gave evidence against Melvin Morse. She was not in court when the verdict was returned.