The theme of morality and guilt in The Mill on the Floss usually centers on the character of Maggie. George Eliot creates a female character who bucks against the idea of being "traditional" and uses her intelligence to make decisions based on being a free human being, not just a free woman. Her father and brother attempt to shame her and rein her in, but to no avail. She is not content to be silent and sent off to marry to support the family name.
Once her family is bankrupt, Maggie's moral character becomes a bit lost. She loses her father's affection and has two relationships that fail due to morality and the hindrance of the social order of the time. Maggie's experiences throughout the novel come into direct conflict with the British moral backbone that most novels stemmed from at the time. So in this novel, the character struggles with dual moral ethics both to rebel against social rationalities and never to forget responsibilities, that is, her guilt toward her family and her "place" as a woman in this society.