On Tuesday, the man pleaded not guilty and asked for a jury trial.
After a jury was selected and following a brief recess, the father agreed to a plea bargain.
Assistant Washington County State's Attorney Gina Cirincion said the remaining charges would be dismissed if the father pleaded guilty to one count each of second-degree rape and second-degree child abuse.
Washington County Circuit Judge Frederick Wright sentenced him to 20 years on the second-degree rape charge and gave him a 15-year suspended sentence on the child abuse charge. The father also will be registered as a sex offender.
Circinion had asked the judge to impose the maximum 20-year sentence for second-degree rape and a consecutive 15-year suspended sentence for second-degree child abuse.
Cirincion said following the proceeding that she agreed to the plea so the children wouldn't have to testify.
The father told Wright he had suffered from mental health problems for years and was prescribed medication but didn't take it.
During sentencing the victims sat in the courtroom clutching their mother and stuffed animals.
His younger daughter, now 8 years old, was abused by her father while she was suffering from a severe heart condition, said Cirincion. She said the father knew of her condition and didn't care.
The stress of the abuse and possibility of having to testify accelerated the child's condition and she had to have heart surgery five years earlier than doctors had predicted, she said.
The girl is now doing well, said Cirincion.
The daughter suffered " a loss of innocence by the one man on the planet who was supposed to be protecting her," said Cirincion.
Defense attorney John Chillas told the judge his client has had "a history of mental illness for most of his adult life."
Wright said the father's behavior was "the most hurtful, harmful, hateful actions I've heard in 30 years I've been on this panel."
Wright said if the father had any contact with the victim it would violate the terms of the sentence and he would have to serve the additional 15 years.