The Mill on the Floss centers on the childhood and young adulthood of Maggie and Tom Tulliver, two siblings growing up in the fictional town of St. Ogg’s, Lincolnshire, England. The unnamed narrator, whose gender is never specified, dreams of Dorlcote Mill, the Tulliver family’s ancestral home, and sees a little girl playing outside. The little girl, it is later revealed, is Maggie Tulliver. Inside the house, Mr. Tulliver and Mrs. Tulliver are discussing Tom’s education. Mr. Tulliver admits that he never had much education himself, but wants to send Tom to school in the hopes that his son will go into business. On the recommendation of a family friend, Mr. Riley, decides to send Tom to study with Mr. Stelling, an Oxford-educated minister.
Maggie is delighted when Tom comes home from school for a visit, since she adores her older brother. However, upon his return Tom is angry with her because she failed to take care of his rabbits in his absence. He points out that he carefully saved up his money to buy her a gift, whereas she carelessly forgot to feed the rabbits and let them die. Maggie apologizes profusely and is very distressed at Tom’s anger, so he eventually forgives her.
Mrs. Tulliver’s sisters come for a visit as well. Maggie and Tom particularly dislike the bad-tempered Mrs. Glegg, who constantly criticizes them for being “naughty” and predicts they will come to a bad end. However, both children like playing with Lucy Deane, their sweet and pretty cousin. Maggie becomes so irritated with Mrs. Glegg’s criticisms of her long dark hair that she runs upstairs and cuts off her hair with scissors. However, she quickly regrets this, since she is then roundly mocked by all the adults. On this same ill-fated visit, Mr. Tulliver gets in an argument with Mrs. Glegg. As a result, Mr. Tulliver decides to try to pay back the three hundred pounds Mrs. Glegg has lent the family, since he doesn’t want to be beholden to anyone—and especially not his wife’s sister.
Mrs. Tulliver visit her sister Mrs. Pullet for help, hoping to end the quarrel between Mr. Tulliver and Mrs. Glegg. During the visit, however, Maggie makes a spectacle of herself. Jealous that Tom and Lucy are playing together without her, she pushes Lucy into the mud, horrifying the adults. Maggie feels so rejected that she decides to run away from home to live with the gypsies, who bring her back to her parents that same evening. Meanwhile, Mr. Tulliver visits his sister, Mrs. Moss, since she owes him a significant amount of money that he hopes to get back. However, he doesn’t have the heart to demand money from her, seeing her poverty and eight children to feed. Instead, he takes out a large loan in order to repay Mrs. Glegg.
At school with Mr. Stelling, Tom has a rather miserable time. He is ill-suited for Latin and geometry—the “gentlemanly” subjects that Mr. Stelling tries to teach him. Over the Christmas vacation, Mr. Tulliver initiates a lawsuit against a neighbor, Mr. Pivart, for allegedly infringing on his water power. Pivart is represented by a successful and crafty lawyer named Mr. Wakem. Mr. Tulliver has developed a deep-seated hatred of Wakem, so Tom is surprised when he returns to school to find that his fellow pupil is Philip Wakem, Mr. Wakem’s son. Unlike Tom, Philip has a natural aptitude for study. However, since Philip has a physical disability, Tom looks upon him with some contempt. When Maggie visits Tom before going to boarding school, she and Philip connect over their shared love of books. Tom has an accident while play sword-fighting and Philip helps nurse him back to health. Both Tom and Maggie’s school days come to an abrupt end, however, when Maggie tells Tom that Mr. Tulliver has lost the lawsuit with Mr. Pivart and will lose his mill, money, and property. He’s also fallen off his horse and is now so ill that he doesn’t recognize anyone save for Maggie.
Mr. Tulliver’s debts have now mounted so high that he has to declare bankruptcy and sell the family’s furniture. This is humiliating for Tom, who is the new head of the household, and very distressing to Mrs. Tulliver, who loves her linens, furniture, and other homewares. Despite these sufferings, Tom decides to respect Mr. Tulliver’s wishes and not call in the loan from Mrs. Moss. He even destroys the note proving that Mr. Tulliver ever lent money to Mrs. Moss, in order to protect her from the creditors. Determined to make his fortune and pay back the family debts, Tom then goes to visit his wealthy uncle Mr. Deane to ask for a job with the shipping company Guest & Co. However, his uncle says Tom will only get a job if he has accounting and bookkeeping skills, and that Tom’s gentlemanly education will be of little use to him.
Mr. Wakem decides to take revenge on Mr. Tulliver by buying Dorlcote Mill and retaining Mr. Tulliver as his employee. This arrangement is very humiliating, but Mr. Tulliver complies in order to support his family. However, he asks Tom to swear—by writing in the family Bible—that he will one day take revenge on the Wakems. After the bankruptcy, life at Dorlcote Mill is miserable. Mr. Tulliver is sullen and depressed, and Tom works all the time, obsessed with earning enough money to pay back the family debts. Lonely and desperate for companionship, Maggie begins secretly meeting with Philip in the wooded area behind the mill. Philip confesses that he loves her, and she tells him that she loves him too. However, after a year of these secret meetings, Tom finally finds out and is furious. Tom angrily confronts Philip and makes Maggie promise to never see Philip again without Tom’s permission.
A few weeks later, Tom tells the family that he has finally earned enough money to pay off the family debts—by investing in a shipping venture with his old friend Bob Jakin. Tom explains that the creditors will be paid back at a dinner at a local pub. That night, Mr. Tulliver is elated at this victory after four years of hard work and suffering. On the way back to Dorlcote Mill, he runs into Mr. Wakem and tells him that he refuses to work for him anymore. Mr. Tulliver’s long-suppressed rage finally bursts out, and he brutally attacks Mr. Wakem, beating him with his horsewhip. Shortly afterward, Mr. Tulliver collapses and becomes very ill. Just before he dies, he tells Tom to get back the “old mill.”
Since the loss of Dorlcote Mill, Tom has been lodging with Bob, and Maggie has taken a job as a schoolteacher. During a visit to Lucy’s house, Maggie meets the charming Stephen Guest, Lucy’s suitor and heir to the Guest & Co fortune. Maggie and Stephen are immediately attracted to each other, but attempt to repress their feelings out of consideration for Lucy and for Philip, who also visits the Deane household in an attempt to rekindle his romantic relationship with Maggie. Philip once again tells Maggie that he loves her and even persuades Mr. Wakem to sell Dorlcote Mill back to Guest & Co, making Tom the owner of the mill once again. But despite these attempts at reconciliation, Tom remains adamantly opposed to a marriage between Philip and Maggie.
Maggie, meanwhile, continues to struggle with her feelings for Stephen and with Philip’s increasing jealousy and suspicion. At a ball given at the Guest house, Stephen kisses her arm and she runs away from him. While she is staying with her aunt Mrs. Moss, Stephen visits her and tells her that he loves her, arguing that it is wrong for them to marry other people if they love one another. Maggie continues to resist, telling him that she cannot ensure her own happiness by making others unhappy. However, one day, Stephen and Maggie take a boat out on the river on their own. Stephen deliberately rows far away from St. Ogg’s and then proposes that he and Maggie elope and get married. Maggie is shocked, but agrees to take passage with him to Mudport, a nearby town. Once they arrive, however, she leaves him and takes a coach back to St. Ogg’s, despite his protestations that they have gone too far to turn back now.
Back in St. Ogg’s, a disgraced Maggie flees to Tom for comfort. However, he rejects her as a sister and tells her that he finds her behavior “disgusting.” Maggie thus takes lodging with Bob Jakin and her mother. She finds employment as a governess with Dr. Kenn, the kind local vicar, but is an outcast in St. Ogg’s. Since she has returned unmarried, people assume that she has slept with Stephen outside of marriage and condemn her for her conduct. Stephen writes a letter to Lucy exonerating Maggie from any part in the elopement, at which point Lucy visits Maggie and tells her she forgives her. Philip, too, writes a letter to Maggie in which he expresses his continuing love and assures her that he believes her side of the story.
One night, after days of heavy rain, Maggie wakes to find that the river has broken through the dams, and St. Ogg’s has flooded. She dashes to a boat and rows to Dorlcote Mill by herself to rescue Tom. Tom is astonished that his sister has come all alone to rescue him, and they have a moving reconciliation in the boat. As they embrace, however, they are caught in the current and drown. In a final conclusion, Stephen, Lucy, and Philip, visit the shared grave of Tom and Maggie Tulliver, which reads, “in their death they were not divided.”