The jury 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 felony waterboarding in the bathtub and five misdemeanors. Jurors reduced the second waterboarding charge to a misdemeanor and acquitted Morse of the suffocation charge.
Morse did not show any immediate reaction after the verdict. He was ordered to surrender his passport, but will remain out on bail until his sentencing hearing, set for April 11.
Morse faces a maximum of 10 years in prison, but a lesser sentence is likely. Under state sentencing guidelines, each misdemeanor carries a maximum of one year in prison, and often probation, while a felony charge typically carries 15 months.
Prosecutor Melanie Withers said she was "very gratified" by the verdict and that she was on her way to speak with the victim. Morse referred questions to his lead defense attorney, Joseph Hurley, who said he planned to appeal.
Hurley criticized a decision by the judge to allow jurors to see video interviews that the victim and her sister gave to authorities in August 2012. He said the unsworn statements improperly prejudiced the jury.
During the trial, defense attorneys argued that "waterboarding" was a term jokingly used to describe hair washing that the girl did not like.
Morse was charged with endangerment and assault after the girl ran away in July 2012 and told authorities of waterboarding and other abuse.
Morse, whose medical license was suspended after his arrest, has written several books and articles on paranormal science and near-death experiences involving children. He has appeared on shows such as "Larry King Live" and the "The Oprah Winfrey Show" to discuss his research, which also has been featured on an episode of "Unsolved Mysteries" and in an article in "Rolling Stone" magazine. Morse denied police claims that he may have been experimenting on the girl.
The girl's mother, Pauline Morse, 41, pleaded guilty last year to misdemeanor endangerment charges and testified against Melvin Morse. Pauline Morse was not in the courtroom Thursday.
Pauline Morse and her daughter, now 12, testified that Melvin Morse used waterboarding as a threat or a form of punishment. Waterboarding as used in the past by U.S. interrogators on terror suspects simulates drowning. Many critics call it torture.
According to testimony, the allegations of waterboarding surfaced after the girl ran away. The girl went to a classmate's home the morning after Morse grabbed her by the ankle and dragged her across a gravel driveway into the home, where she was spanked and warned of worse punishment the next day. When investigators questioned the girl, then 11, she told them about what she called waterboarding.
Prosecutors argued that in addition to being waterboarded, Morse subjected the girl to other abuse, including being forced to stand with arms outstretched for hours at a time; being confined to her room, where she had to use her toy box or closet as a toilet; and being deprived of food or force fed until she vomited.
Withers portrayed Melvin 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 said she chose to ignore the abuse, saying she was afraid of "undermining" Melvin Morse. She also testified that she did not have a close relationship with the girl for several years that encompassed the waterboarding, and that she did not pay her much attention.
The girl and her younger sister remain in foster care but are allowed supervised visits with Pauline Morse. Pauline Morse said she hoped her cooperation with prosecutors will bolster her chances of being reunited with her daughters.