The novel is divided into three volumes.

Part One (Chapters 1 to 15): Gilbert Markham narrates how a mysterious widow, Mrs Helen Graham, arrives at Wildfell Hall, a nearby mansion. A source of curiosity for the small community, the reticent Mrs Graham and her young son Arthur are slowly drawn into the social circles of the village. Initially Gilbert Markham casually courts Eliza Millward, despite his mother's belief that he can do better. His interest in Eliza wanes as he comes to know Mrs Graham. In retribution Eliza spreads (and perhaps creates) scandalous rumours about Helen. With gossip flying, Gilbert is led to believe that his friend Mr Lawrence is courting Mrs Graham. At a chance meeting on a road Gilbert strikes the mounted Lawrence with a whip handle, causing him to fall from his horse. Though she is unaware of this confrontation, Helen Graham still refuses to marry Gilbert, but when he accuses her of loving Lawrence she gives him her diaries.

Part two (Chapters 16 to 44) is taken from Helen's diaries, in which she describes her marriage to Arthur Huntingdon. The handsome, witty Huntingdon is also spoilt, selfish and self-indulgent. Before marrying Helen he flirts with Annabella, and uses this to manipulate Helen and convince her to marry him. Helen, blinded by love, marries him, and resolves to reform him with gentle persuasion and good example. After the birth of their only child, however, Huntingdon becomes increasingly jealous of their son (also called Arthur), and his claims on Helen's attentions and affections.

Huntingdon's pack of dissolute friends frequently engage in drunken revels at the family's home, Grassdale, oppressing those of finer character. Both men and women are portrayed as degraded. In particular, Annabella, now Lady Lowborough, is shown to be unfaithful to her melancholy but devoted husband.

Walter Hargrave, the brother of Helen's friend Milicent Hargrave, vies for Helen's affections. While he is not as wild as his peers, he is an unwelcome admirer: Helen senses his predatory nature when they play chess. Walter tells Helen of Arthur's affair with Lady Lowborough. When his friends depart Arthur pines openly for his paramour and derides his wife.

Arthur's corruption of their son — encouraging him to drink and swear at his tender age — is the last straw for Helen. She plans to flee to save her son, but her husband learns of her plans from her diary and burns the artist's tools with which she had hoped to support herself. Eventually, with help from her brother, Mr Lawrence, Helen finds a secret refuge at Wildfell Hall.

Part Three (Chapters 45 to 53) begins after Gilbert's reading of the diaries. Helen bids Gilbert to leave her because she is not free to marry. He complies and soon learns that she has returned to Grassdale because her husband is gravely ill. Helen's ministrations are in vain, and Huntingdon's death is painful since he is fraught with terror at what awaits him. Helen cannot comfort him, for he rejects responsibility for his actions and wishes instead for her to come with him to plead for his salvation.

A year passes. Gilbert pursues a rumour of Helen's impending wedding, only to find that Mr Lawrence, with whom he has reconciled, is marrying Helen's friend Esther Hargrave. Gilbert goes to Grassdale, and discovers that Helen is now wealthy and lives at her estate in Staningley. He travels there, but is plagued by anxiety that she is now far above his station. By chance he encounters Helen, her aunt and young Arthur. The two lovers reconcile and marry.