RCMP announced the charges Thursday, six months after the death of a toddler on the Peguis First Nation.
The girl died last July after being brought to hospital with "trauma-related injuries", an RCMP release said.
The toddler's mother was charged with second-degree murder and failing to provide the necessities of life.
The father was charged with manslaughter and failing to provide the necessities of life.
The girl's stepsister also faces charges of manslaughter and failing to provide the necessities of life.
All three adults were arrested earlier this week and were being held in custody.
The dead child had some involvement with Manitoba's child welfare system, although the government would not provide details.
A publication ban was imposed by the court on Thursday that appeared to prohibit the identities of those charged as well as the name of the victim.
Rachel Morgan, press secretary to Family Services Minister Kerri-Irvin Ross, said the case would be investigated.
"On learning of the death of or serious injury to a child known to or in the care of (a family services) agency, the agency initiates an internal review of the events and circumstances leading the child's death or serious injury," Morgan wrote in an email.
The independent provincial office of the children’s advocate will also investigate what services were provided.
Manitoba's chief medical examiner has the authority to call an inquest if warranted, Morgan added.