Watkins pleaded guilty to most of the charges in April 2014, and pleaded guilty to the rape charges later that year.
His victims were 7 and 8 years old when the offending began, which lasted into their teenage years.
Reading aloud their victim impact statements, they said Watkins had deeply affected their mental, physical and spiritual wellbeing.
One said she took antidepressant medication as a result of the abuse and would likely be on them for the rest of her life.
"I still get flashbacks and nightmares about what he did to me and I can no longer find comfort in church because that is where we met him and I associate church with my sexual abuse."
The other victim said for many years she felt ashamed of what had happened and had attempted suicide more than a dozen times.
She said at the time of the abuse she thought it was normal, until she was 11 and took sexual education classes at school.
"I felt worthless, ashamed, a waste of space and I hated myself.
"As the years went on I hid my secret and my feelings worsened, I was depressed all the time and self harmed."
She said she had since turned her life around and wanted to work to prevent this kind of offending happening to others.
"He may have taken my childhood but he has not taken my life and I want my daughter to grow up in a world where there are not people like him."
Justice Mark Woolford said Watkins had close ties with Rotorua churches and it was through this he established a relationship with the victims.
Justice Woolford said it was clear the offending had a significant and permanent impact on the girls.
"The victims were both particularly vulnerable being only 7 and 8 years old when the offending began and it was a gross breach of trust given the position of authority and trust you had with the family."
Justice Woolford said that trust allowed the offending to be prolonged over a number of years.