Growing up in a family with one member being affected by mental health problems or substance abuse is an adverse childhood experience which can lead to socioeconomic and health-related impairments in later life. Furthermore, the risk of child maltreatment is increased in affected families, which often adds to the individual risk factors. However, the interdependence between the particular risk factors is not well understood. To examine the correlation between mental health problems or substance abuse and child maltreatment within families and long term consequences for affected children, a cross sectional population representative survey in Germany (N = 2,531) has been conducted. The risk of child maltreatment was 5 to 5.6 times higher if mental illness and 4.9 to 6.9 times higher if substance abuse of a family member was reported. Furthermore, the risk of health problems, including obesity, decreased life satisfaction, lower income, low educational achievement, unemployment and living without a partner was increased if participants grew up in a family affected by mental health problems or substance abuse. All associations were mediated significantly by child maltreatment. These results point towards an urgent need for greater awareness for child protection issues in families affected by mental health problems or substance abuse.