Many mothers with mental health issues are caught up in the child protection system and face the prospect of having their children removed from their care. The aim of this study was to determine prevalence and outcomes for mothers with mental health issues and their children in child maltreatment cases opened for investigation in Canada. The method was secondary analysis of the Canadian Incidence Study of Reported Child Abuse and Neglect (CIS-2003) core data. This CIS-2003 contains process and outcome data on a nationally representative sample of 11,652 child maltreatment investigations. Maternal mental health issues were noted in 2,272 (19.7%) cases opened for investigation. The most common child protection concerns were neglect, emotional maltreatment and exposure to domestic violence. A significant association was found between maternal mental health issues and child maltreatment investigation outcomes, with many potentially confounding variables held constant. Broad spectrum, multi-disciplinary services are needed to support mothers with mental health issues. Effective mental health care is vital but insufficient. Addressing trauma, strengthening social relationships and alleviating poverty are also key. Systemic advocacy is needed to ensure that mothers with mental health issues can access broad spectrum supports.