The man and woman appeared in provincial court in Dauphin, Man., on Tuesday afternoon, charged with numerous offences that include sexual assault, making child pornography, forcible confinement and failing to provide the necessities of life.
The woman was released on $2,000 bail.
RCMP say they received reports of child abuse on Aug. 7 in Manitoba's Parkland area. Manitoba's Parkland is a large area in west central Manitoba north of Brandon. It joins up with Saskatchewan's Parkland area northeast of Regina.
Investigators found a total of three girls, all under the age of 10, living in appalling conditions.
"What we discovered was quite shocking," RCMP spokesperson Tara Seel told CBC News.
"We discovered often that the children were not fed, they were locked in their rooms for most of the day, and the two older girls were also forced to perform sexual acts."
The girls were also physically assaulted and one girl was even beaten with a belt, according to court documents, which said the abuse allegedly began in September 2011. That was about when their birth mother died.
All three girls have been taken into care by Child and Family Services but they are currently staying with family members.
Some relatives told CBC News their current priority is to protect the girls and to get counselling for them.
Neighbours said the children's father was mysterious, unfriendly and made it known to stay off his property.
RCMP did not release the names of the accused or say where in the Parkland region the abuse allegedly took place in order to protect the children's identities.
Having grown up in rural Nova Scotia, Canada, about 30 miles from Halifax, I was somewhat aware of sexual abuse that occurred within families - fathers sleeping with their daughters, brothers raping their sisters. It was disgusting then and it's disgusting now.
How do you reach men and boys like that? How do you teach them to treat their daughters and sisters with respect? So many, like these people, live in remote areas and are often poorly educated and non-communicative. How do you reach them?