Superior Court Judge Richard F. Stokes gave Melvin L. Morse a five-year sentence Friday, but ordered he could be put on probation after serving three years of it. Morse was led from the courtroom in handcuffs.
The judge denied motions made by Morse's attorney to delay the sentence because Morse is being treated for prostate cancer.
Morse was arrested in August 2012 after his stepdaughter ran away from home and told police he had forced her head under running water, making her think she would drown.
He pleaded not guilty and testified in his own defense in a January trial, but a jury found him guilty of six offenses, including first-degree reckless endangerment.
The jury deliberated for about six hours before returning its verdict against Morse on Feb. 13.
The girl's mother, Pauline Morse, 41, pleaded guilty last year to misdemeanor endangerment charges and testified against Melvin Morse.
Pauline Morse and her daughter, now 12, testified that Melvin Morse used waterboarding as a threat or a form of punishment.
Pauline Morse, her daughter and other prosecution witnesses painted Morse as a father figure who delivered harsh punishment to the girl seemingly at random while favoring her younger sister, who was biologically Morse's child.
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 and deprived of food.