The mid-late 1880s was a transformative period in which Charlotte juggled home duties with dress reform activism, periodical publication and the writing and research for her first book. Among her various other activities, she decided to teach Marie at home rather than sending her to school. Winnie was occupied by a nurse and later with simple lessons of her own. Neither daughter seemed particularly responsive to her teaching, but she persisted until 1892 when the girls went to board at St George's School in Edinburgh.

Marie had few happy memories of her early childhood. Her parents had decided on ‘an unconventional upbringing’, in which they would teach their daughter themselves.

Charlotte tried to draw on her training and experience as a teacher in Edinburgh and at Cheltenham College, believing she could teach her daughter to be great-minded. Hall remarks that ‘Charlotte, with the usual Scottish distrust of English education, refused to sully her daughter's mind by sending her one of the local schools’. There is some truth in this. Both Henry and Charlotte held strong moral and social views and did not want their children to be influenced by values they regarded as anti-intellectual. To complement Charlotte's efforts, Henry gave instruction in science. Hall identifies this as archaeology, an interest which captured Marie's enthusiasm and fuelled her later doctoral and postdoctoral research. Without any formal teacher training, Henry's enthusiasm for his subject made him a more memorable teacher, for Marie, than his wife's adherence to her notion of proper instruction.

Charlotte's method was ‘never to repeat the children's “clever things” before them, or to praise them unduly. So they developed and were able to speak without self-consciousness’.