The heroine of this story is Maggie, the impetuous, dark-haired daughter of the Tullivers of Dorlcote Mill, near St. Ogg's. As a child she rebelliously shears off her dark curly hair which contrasts with her cousin Lucy's blond, manageable hair. While her mother and aunts of the Dodson family criticize her disorderly conduct, Maggie's father takes Maggie's side. Most of all she seeks the approval of her older brother Tom.
After Tom is sent to study with clergyman Stelling, Maggie visits him and befriends the sensitive, crippled Philip Wakem, son of her father's archenemy, Lawyer Wakem. The pugnatious Tulliver sues and loses his lawsuit with Wakem over river usage. Tom and Maggie are called home. Their life collapses with their father's bankruptcy and incapacitation. Tom is forced to work to support the family, as the well-off Dodson's offer little help, and Maggie, as a young girl, is unemployable. Dorlcote Mill is up for auction and Lawyer Wakem, in an act of humiliating patronage, purchases it, retaining Tulliver as manager.
In her total isolation and loneliness, Maggie attempts a pious self-denial which is interrupted only after reencountering Philip Wakem on one of her walks in the woods. He persuades her to leave self-renunciation in favor of literature and friendship and helps her complete her education. Since Maggie's father would be hurt by her friendship with the son of his sworn enemy, Philip and Maggie meet clandestinely for a year. Philip finally confesses love to Maggie, and Maggie returns that love. However, Tom discovers their meetings, insultingly rebukes Philip, and makes Maggie swear not to see Philip again without his consent.
Bob Jakin, Tom's childhood friend, also reenters the scene after the loss of the mill, first supplying Maggie with books - one of which, Thomas a Kempis's The Imitation of Christ, had influenced her asceticism - and then by offering Tom a business venture. Tom manages thereby to amass enough money to pay off his father's debts to the relief of his proud father. After officially announcing repayment, Tulliver assaults Lawyer Wakem, but then dies the next day.
Since her father's death, Maggie has obstinately refused to live with her aunts and has been teaching in another village. She returns to St. Ogg's to visit her cousin Lucy, who has taken in Mrs. Tulliver. Lucy introduces Maggie to her rich suitor Stephen Guest who is immediately struck by Maggie's dark beauty. Since both Guest and Lucy are friends with Philip Wakem, Maggie asks Tom for permission to meet Philip, and Tom grudgingly consents. Maggie and Philip renew their friendship, and Maggie tells Lucy that she would consider marrying Philip, if only his father, Lawyer Wakem, would approve. Lucy, hoping to bring this about, decides to help Tom get back Dorlcote Mill. She asks Philip to speak to his father about selling the mill. Philip does so but also relates to him his love for Maggie and desire to marry her. Reluctantly, Lawyer Wakem consents to both propositions.
Nevertheless, Stephen and Maggie are hopelessly attracted to each other and every meeting reaffirms this. As Stephen pursues her, Maggie – out of fear of hurting Lucy and betraying Philip – decides to accept another teaching post and leave St. Ogg's. Though Lucy remains blind to this change in Stephen and Maggie, Philip grows aware of it. He cancels a planned boat-ride with Maggie and Lucy, sending Stephen instead. As good-hearted Lucy has proceeded down river, romantically intending to leave Philip and Maggie alone on the boat-ride, Stephen and Maggie are now thrown together. Stephen rows Maggie past their planned meeting point with Lucy but is chastised by Maggie. The weather changes menacingly and they travel further downriver. Maggie and Stephen board a larger boat headed for Mudport. They sleep overnight on the boat's deck and when they reach Mudport, Stephen asks Maggie to elope with him. Though Maggie is torn between her attraction to Stephen and her love for Lucy and Philip, she decides to return to St. Ogg's, believing that her refusal, in line with her previous ascetic notions, would lead to their forgiveness.
After her return to St. Ogg's, the narrow, tradition-bound society treats Maggie as a fallen woman and social pariah. She seeks refuge with her brother Tom, now back in Dorlcote Mill, but encounters rejection. Accompanied by her mother, she finds lodging with Bob Jakin and his wife. Meanwhile, Stephen writes from Holland, acknowledging all blame. Despite public knowledge of that letter, Maggie is befriended only by the Jakins and the clergyman, Dr. Kenn. Two bright stars enlighten her gloom. First, Lucy, recently recovered from her grief, secretly visits Maggie to show her forgiveness. Philip sends her a letter of forgiveness and faithfulness.
Stephen sends Maggie a letter again pleading for her hand in marriage and protesting the pain she has caused him. However, Maggie returns to self-denial and vows to bear the burden of the pain she has caused others. Just then, water from the river Floss floods through the door. Maggie wakes the Jakins and takes one of their boats, rowing it downriver in a feat of bravery toward Dorlcote Mill. Maggie rescues Tom and they row towards Lucy, but the boat capsizes. Maggie and Tom – in an act of final reconciliation - drown in each other's arms.
Five years later, Philip, and Stephen and Lucy together, visit their graves.