Maggie Tulliver is the impetuous, clever younger daughter of the Tullivers of Dorlcote Mill in St. Ogg's. Maggie frustrates her superficial mother with her unconventional dark coloring and unnatural activeness and intelligence. Maggie's father often takes Maggie's side, but it is Maggie's older brother Tom upon whom she is emotionally dependent. Maggie's greatest happiness is Tom's affection, and his disapproval creates dramatic despair in Maggie, whose view of the world, as all children's, lacks perspective.
Though Tom is less studious than Maggie appears to be, Mr. Tulliver decides to pay for Tom to have additional education rather than have him take over the mill. This decision provokes a family quarrel between Mr. Tulliver and his wife's sisters, the Dodsons. Mr. Tulliver is frustrated by the snobbish contrariness of the Dodsons, led by Mrs. Tulliver's sister Mrs. Glegg, and vows to repay money that Mrs. Glegg had lent him, thereby weakening her hold on him. He has lent almost an equal sum to his sister and her husband, the Mosses, but he feels affectionately toward his sister and decides not to ask for money back, which they cannot pay.
Mr. Stelling, a clergyman, takes Tom on as a student, and Maggie visits him at school several times. On one of these visits, she befriends Mr. Stelling's other student—the sensitive, crippled Philip Wakem, son of her father's enemy, Lawyer Wakem. Maggie herself is sent to school along with her cousin, Lucy, but is called home when she is thirteen when her father finally loses his extended lawsuit with Lawyer Wakem over the use of the river Floss. Mr. Tulliver is rendered bankrupt and ill. Tom returns home as well to support the family, as the Dodson's offer little help. The mill itself is up for auction, and Lawyer Wakem, based on an idea inadvertently furnished to him by Mrs. Tulliver, buys Dorlcote Mill and retains Mr. Tulliver as a manager in an act of humiliating patronage.
Even after Mr. Tulliver's recovery, the atmosphere at the Tullivers' is grim. One bright spot is the return of Bob Jakin, a childhood friend of Tom's, into Tom and Maggie's life. Bob, a trader, kindly buys books for Maggie and one of them—Thomas a Kempis's The Imitation of Christ—influences a spiritual awakening in her that leads to many months of pious self-denial. It is only after Maggie reencounters Philip Wakem on one of her walks in the woods that she is persuaded to leave her martyrish dullness in favor of the richness of literature and human interaction. Philip and Maggie meet clandestinely for a year, since Maggie's father would be hurt by their friendship as he has sworn to hold Lawyer Wakem as his life-long enemy. Philip finally confesses to Maggie that he loves her, and Maggie, at first surprised, says she loves him back. Soon thereafter, Tom discovers their meetings, cruelly upbraids Philip, and makes Maggie swear not to see Philip again.
On a business venture with Bob Jakin, Tom has amassed enough money to pay off Mr. Tulliver's debts to the family's surprise and relief. On the way home from the official repayment of the debts, Mr. Tulliver meets Lawyer Wakem and attacks him, but then Mr. Tulliver falls ill himself and dies the next day.
Several years later, Maggie has been teaching in another village. Now a tall, striking woman, she returns to St. Ogg's to visit her cousin Lucy, who has taken in Mrs. Tulliver. Lucy has a handsome and rich suitor named Stephen Guest, and they are friends with Philip Wakem. Maggie asks Tom for permission to see Philip, which Tom grudgingly gives her. Maggie and Philip renew their close friendship, and Maggie would consider marriage to Philip, if only his father approved. Lucy realizes that Tom wishes to purchase back Dorlcote Mill, and she asks Philip to speak to his father, Lawyer Wakem. Philip speaks to his father about selling the mill and about his love for Maggie, and Lawyer Wakem is eventually responsive to both propositions.
Meanwhile, however, Stephen and Maggie have gradually become helplessly attracted to each other, against both of their expectations and wishes. Maggie plans for their attraction to come to nothing, as she will take another teaching post away from St. Ogg's soon. Stephen pursues her, though, and Philip quickly becomes aware of the situation. Feeling ill and jealous, Philip cancels a boat- ride with Maggie and Lucy, sending Stephen instead. As Lucy has proceeded down river, meaning to leave Philip and Maggie alone, Stephen and Maggie find themselves inadvertently alone together. Stephen rows Maggie past their planned meeting point with Lucy and begs her to marry him. The weather changes and they are far down the river. Maggie complacently boards a larger boat with Philip, which is headed for Mudport. They sleep over night on the boat's deck and when they reach Mudport, Maggie holds firm in her decision to part with Stephen and return to St. Ogg's.
On her return to St. Ogg's, Maggie is treated in town as a fallen woman and a social outcast. Tom, now back in Dorlcote Mill, renounces her, and Maggie, accompanied by her mother, goes to lodge with Bob Jakin and his wife. Despite public knowledge of Stephen's letter, which acknowledges all the blame upon himself, Maggie is befriended only by the Jakins and the clergyman Dr. Kenn. Lucy, who has been prostrate with grief, becomes well again and secretly visits Maggie to show her forgiveness. Philip, as well, sends a letter of forgiveness and faithfulness.
Stephen sends Maggie a letter renewing his pleas for her hand in marriage and protesting the pain she has caused him. Maggie vows to bear the burden of the pain she has caused others and must endure herself until death but wonders to herself how long this trial, her life, will be. At this moment, water begins rushing under the Jakin's door from the nearby river Floss, which is flooding. Maggie wakes the Jakins' and takes one of their boats, rowing it down river in a feat of miraculous strength toward Dorlcote Mill. Maggie rescues Tom, who is trapped in the house, and they row down river towards Lucy. Before they can reach Lucy's house, the boat is capsized by debris in the river, and Maggie and Tom drown in each other's arms. Years go by and Philip, and Stephen and Lucy together, visit the grave.