The House system, School crest and motto, and the School prayer and hymn are vital parts of St Mary's rich history and identity. 

As part of the House system, each girl is placed in one of six houses - Craig, Hackett, Lefroy, Riley, Wardle or Wittenoom - where past family connections are continued. 

As well as being the vehicle for extracurricular activities and competitions, the Houses are important in the development of leadership, values and ethics. Each House has a prefect who, together with captains and the guidance of a Head of House, lead the House through the year's activities. Each year group and House also raises funds for worthy causes and those in need. 

Each year group has a Head of Year who takes on an important pastoral care role, monitoring student welfare and development, and interacting with students on a regular basis. The Head of Year also organises important activities for the groups.