Police said District Justice Larry Pentz arraigned Johnson and sent him to the Franklin County Prison in lieu of $50,000 bail. Johnson was still at the prison Tuesday night.
There is no phone directory listing for a William Johnson on Clay Hill Road.
Charging documents indicate that Johnson spent time with the girls at church, at one girl's home in Waynesboro and at his own home.
Johnson allegedly initiated sexual contact with the 12-year-old girl at least four times and with the 8-year-old girl at least twice, according to charging documents. Other times, he allegedly propositioned each girl.
In the summer of 2000, Johnson allegedly took the 12-year-old girl to his Clay Hill Road house "under the pretense that she was going to help him do some housecleaning," charging documents say.
A woman was reportedly sitting in a chair at the house. Johnson said the woman was his mother, but the girl later learned that the woman was Johnson's wife, who is legally blind, has diabetes and depends on him as a caretaker, charging documents say.
Upstairs, Johnson allegedly told the girl to sit on a bed, then pulled her pants and underwear down and opened his own pants. He got on top of her and had sexual contact with her, according to charging documents.
The girl allegedly told police that the first contact between her and Johnson occurred at the Five Forks Brethren in Christ Church in Waynesboro on a rainy evening around Easter 1999.
The girl was in a play at the church and Johnson was in the choir. He allegedly offered to dry her hair, then led her into a storage closet, where he pressed himself against her from behind, charging documents say.
Another alleged assault occurred around the summer of 2000 when Johnson allegedly offered to help the girl clean her bedroom at home.
Two of the three incidents involving the 8-year-old girl allegedly happened during games of hide-and-seek in April and May at the 12-year-old girl's home.
Johnson allegedly trapped the 8-year-old girl in a bathroom both times and urged her to perform oral sex on him.