The novel is set in the early years of the 19th century. Silas Marner is a member of a small Calvinist congregation in Lantern Yard, a slum street in an unnamed city in Northern England. He is falsely accused of stealing the congregation's funds while watching over the very ill deacon of the group. Two clues are given against Silas: a pocket-knife and the discovery of the bag formerly containing the money in his own house. Silas is proclaimed guilty and the woman he was to marry casts him off, and later marries his best friend, William Dane. With his life shattered and his heart broken, he leaves Lantern Yard and the city.

Marner heads south to the Midlands and settles near the village of Raveloe, where he lives as a recluse, existing only for work and the gold he has hoarded from his earnings. When it is stolen by Dunstan ('Dunsey') Cass, a dissolute younger son of Squire Cass, the town's leading landowner, Silas sinks into a deep gloom, despite the villagers' attempts to aid him. Dunsey disappears, but little is made of this not unusual behavior, and no association is made between him and the theft.

Godfrey Cass, Dunsey's elder brother, also harbors a secret. He is married to, but estranged from, Molly, an opium-addicted woman of low birth. This secret threatens to destroy Godfrey's blooming relationship with Nancy, a young woman of higher social and moral standing. On a winter's night, Molly tries to make her way into town with her two-year-old child to prove that she is Godfrey's wife and ruin him. On the way she takes opium, becomes disoriented and sits down to rest in the snow, child in arm. The child wanders from her mother's still body into Silas' house. Upon discovering the child, Silas follows her tracks in the snow and discovers the woman dead. Godfrey also arrives at the scene, but resolves to tell no one that she was his wife.

Silas decides to keep the child and names her Eppie, after his deceased mother and his sister, Hephzibah. Eppie changes Silas' life completely. Symbolically, Silas has been robbed of his material gold but has it returned to him in the golden-haired Eppie. Godfrey Cass is now free to marry Nancy, but continues to conceal the existence of his first marriage—and child—from her, while continuing to aid Marner in caring for Eppie with occasional financial gifts.

Sixteen years pass, and Eppie grows up to be the pride of the town with a very strong bond with Silas, who through her has found inclusion and purpose in life. Meanwhile, Godfrey and Nancy mourn their own childless state. Eventually, the skeleton of Dunstan Cass - still clutching Silas' gold - is found at the bottom of the stone quarry near Silas' home, and the money is duly returned to Silas. Shocked by this revelation, and coming to the realization of his own conscience, Godfrey confesses to Nancy that Molly was his first wife and that Eppie is his child. They hope to raise her as a gentleman's daughter, which for Eppie would mean forsaking Silas.

The mystery of the robbery that caused Silas' exile from Lantern Yard is never solved, as Silas' old neighbourhood has been "swept away" and replaced by a large factory and no one seems to know what happened to Lantern Yard's inhabitants. However, Silas contentedly resigns himself to the fact that he now leads a happier existence among his family and friends. In the end, Eppie marries a local boy, Aaron, son of Dolly, and both of them move into Silas' new house, courtesy of Godfrey. Silas' actions through the years in caring for Eppie have provided joy for everyone and the extended family celebrates their happiness.

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