Madame Bovary opens during Charles Bovary's childhood. An outcast in his new school, Charles does not fit in, and he suffers ridicule. As he grows older, we learn that he is fairly dull and lacks talent in his chosen profession, medicine. Charles becomes a poor doctor who does not earn much respect from his peers. His mother remains very influential in his life decisions; she pushes him into medicine and persuades him to marry a widow. The widow dies soon after the wedding, leaving Charles much less money than he expected.
Soon after his first wife's death, Charles falls in love with Emma, the daughter of one of his patients. After much time, Charles finally asks her father for Emma's hand in marriage. An elaborate ceremony takes place. After marrying, Charles and Emma move to Tostes, where Charles sets up his meager practice. Unfortunately, Emma soon finds herself disillusioned with her country life, having aspirations of greater romance and luxury. After Emma and Charles attend a ball thrown by a wealthy nobleman, she becomes obsessed with the idea of living a more elaborate and sophisticated existence. Eventually her obsession takes over, sending her into a depressive state. During this period of illness, Emma becomes pregnant and Charles decides to move to a new area with the hope of improving Emma's health and realizing a positive future for his family.
Charles establishes his new practice in Yonville. Homais, the town pharmacist, considers himself an expert on all subjects and greatly enjoys pontificating to excess. Emma and Charles also meet Leon, a law clerk bored with rural life. Emma finds many similarities between herself and Leon, foreshadowing their eventual affair. In Yonville Emma gives birth to a daughter, Berthe. She is disappointed not to have borne a son, and her sadness persists. During this time romantic feelings develop between Emma and Leon, but as soon as Emma becomes aware of his feelings, she develops a powerful sense of guilt. To counteract this overwhelming emotion, she devotes herself to acting as an excellent mother and wife. Observing Emma's efforts, Leon believes his love will forever be unrequited, so he leaves for Paris to study law. Upon his departure, Emma again falls into a state of severe depression.
Soon after Leon moves away, Emma and Charles attend an agricultural fair where Rodolphe, a wealthy neighbor, declares his love to Emma with the goal of simply seducing her. The two begin a passionate affair, and Emma is often careless with her behavior. However, Charles does not suspect anything, believing his wife loves him dearly, while truly she is disgusted by his lack of success and class. In an attempt to boost his professional reputation, Charles and Homais attempt an experimental surgery to treat the club-footed man Hippolyte. Emma encourages this project, believing it will lead to Charles's fame and therefore a more luxurious and extravagant life. But the treatment is disastrous and, sadly, another doctor must be brought in to amputate the leg. Wallowing in Charles's constant failures and mediocrity, Emma renews her passion for Rodolphe, even borrowing money to buy him extravagant gifts. Eventually, Emma suggests that she and Rodolphe begin a new life together, but Rodolphe only has only viewed Emma as a conquest and entertainment. Therefore, in a letter delivered on the scheduled day of their rendezvous, he refuses to elope and ends the relationship. Heartbroken after believing Rodolphe truly loved her, Emma falls into a terrible illness, barely escaping death.
In attempting to heal Emma's mysterious illness and pay off her debts, Charles falls into financial trouble. Despite the expense, he takes Emma to an opera in Rouen, a nearby city, believing the trip will enliven her spirits. While in Rouen, Emma and Charles happen to run into Leon. The old romantic feelings between Emma and Leon are quickly rekindled and emboldened in the aftermath of her experience with Rodolphe, so Emma soon begins an affair with Leon. Under the guise of taking piano lessons, Emma repeatedly travels to Rouen to meet Leon. Meanwhile, she falls deeply indebted to the moneylender Lheureux and grows careless in her adulterous behavior to the point where she is almost discovered many times.
Soon Emma grows bored with Leon because he is afraid to take risks to show his love for her. Emma grows increasingly demanding; meanwhile, her debts mount. Lheureux soon orders seizure of Emma's property, and terrified that Charles will discover her secrets, Emma grows frantic. She appeals to anyone she can think of for loans, including Leon, the town's businessmen, and even Rodolphe. Upon her offer of prostitution, Rodolphe refuses to help her and Emma grows truly mortified. Aware of the impending revelations of dishonest behavior, Emma sees no option but to remove herself from the world. She commits suicide by eating arsenic, dying an agonizing and painful death.
At first, Charles idealizes the memory of his wife. But he eventually discovers her letters and keepsakes from Rodolphe and Leon, and finally he confronts the truth of her infidelity. Having grown into an antisocial hermit, Charles dies alone in his garden of an apparent heart attack. Berthe, now an orphan, is sent to work in a cotton mill.