A rich misanthropic miser who has made his fortune from London's rubbish dies, estranged from all except his faithful employees Mr and Mrs Boffin. By his will, his fortune goes to his estranged son John Harmon, who is to return from South Africa to claim it, on condition that he marries a woman he has not met, Miss Bella Wilfer. The implementation of the Will is in the charge of the solicitor, Mortimer Lightwood, who has no other practice.
Before the son and heir can claim his inheritance, he goes missing, presumed drowned, at the end of his journey from South Africa to London. A body is found in the Thames by Gaffer Hexam, a waterman who makes his living from retrieving corpses and robbing them of valuables before rendering them to the authorities. The body is identified from papers in the pockets as that of the heir, John Harmon. Present at the identification is a mysterious young man, who gives his name as Julius Handford and then disappears.
By the terms of the miser's will, the whole estate then devolves upon Mr and Mrs Boffin, naive and good hearted people who wish to enjoy it for themselves and to share it with others. They take the disappointed bride of the drowned heir, Miss Wilfer, into their household, and treat her as their pampered child and heiress. They also accept an offer from Julius Handford, now going under the name of John Rokesmith, to serve as confidential secretary and man of business, at no salary. He uses this position to watch and learn everything about the Boffins, Miss Wilfer, and the aftershock of the drowning of the heir John Harmon. A one-legged ballad seller, Silas Wegg, is engaged to read to Mr Boffin in the evenings, and he tries to take advantage of his position and Mr Boffin's good heart to obtain other advantages from the now-wealthy dustman.
Gaffer Hexam, who found the body, is accused of murdering John Harmon by a fellow-waterman, Roger "Rogue" Riderhood, who is bitter at having been cast off as Hexam's partner on the river and who covets the large reward offered in relation to the murder. Hexam is shunned by his fellows on the river, and excluded from The Six Jolly Fellowship-Porters, a public house frequented by them on the river. Hexam's young son, the clever but priggish Charley Hexam, leaves his father's house in order to better himself at school, and train to be a schoolmaster, encouraged by his sister, the beautiful Lizzie Hexam. Meanwhile, Lizzie stays with her father, to whom she is devoted.
Before Riderhood can claim the reward for his false allegation against Hexam, Hexam is found drowned himself. Lizzie Hexam becomes the assistant of a doll's dressmaker. But she has caught the eye of the briefless and languid barrister, Eugene Wrayburn, who noticed her when accompanying his friend, the Harmon solicitor Mortimer Lightwood, in pursuit of Gaffer Hexam upon the accusation of Riderhood. Wrayburn falls in love with her. However, he has a violent rival in Bradley Headstone, the schoolmaster of Charley Hexam, who is set on marrying her, and believes that Wrayburn will make her his mistress but not his wife. Lizzie Hexam flees both men, getting work up river outside London.
Mr and Mrs Boffin adopt a young orphan, previously in the care of his grandmother, Betty Higden. Mrs Higden minds children for a living, assisted by the gangling foundling known as Sloppy. She has a terror of the workhouse. When Mrs Higden is found dying by Lizzie Hexam, Lizzie is thereby introduced to the Boffins and to Bella Wilfer. But Lizzie has been tracked down by Eugene Wrayburn and also by Bradley Headstone. Headstone violently assaults Wrayburn and leaves him for dead, but Lizzie finds and rescues him. Wrayburn, thinking he will die anyway, marries Lizzie, in order to save her reputation. When he survives, he is glad that this has brought him into a loving marriage, albeit with a social inferior. He had not cared about the social gulf between them, but Lizzie had and would not otherwise have married him.
Rokesmith has clearly fallen in love with Bella Wilfer, but she cannot bear to accept him, determining that she will marry only for money. Mr Boffin appears to be corrupted by his wealth, and becomes a miser. He also begins to treat his secretary Rokesmith with contempt and cruelty. This rouses the sympathy of Bella Wilfer, and both she and Rokesmith are turned out of the Boffin household. They marry, and live happily although poor.
Meanwhile, Bradley Headstone has tried to put the blame (for his murderous assault of Wrayburn) on Rogue Riderhood, now working as a lock gate keeper, by dressing in similar clothes when doing the deed. Riderhood realises this, and is also aware of the assault, and blackmails him. Headstone and Riderhood wrestle, and both fall into the canal and drown.
The one-legged parasite Silas Wegg has, with the articulator of bones Venus, discovered a will subsequent to the one which has given the Boffins the whole of the Harmon estate. By the later will, the estate goes to the Crown. Wegg and Venus decide to blackmail Boffin with this will.
It becomes clear to the reader that John Rokesmith is, in fact, the missing presumed drowned heir, John Harmon. He had been robbed of his clothes and possessions by the man later found drowned, and wrongly identified as him. Rokesmith/Harmon has been maintaining his alias in order to see Bella Wilfer before committing to marry her as required by the terms of his father's will. Now that she has married him believing him to be poor, he can throw off his disguise.
He does so, and it is revealed that Mr Boffin's ill treatment of him and his miserliness was part of a scheme to test Miss Wilfer's motives and affections, a test she has triumphantly passed.
When Wegg (abandoned by Venus) attempts to clinch his blackmail on the basis of the later will disinheriting Boffin, Boffin turns the tables by revealing a still later will, by which the fortune is granted to Boffin even at young John Harmon's expense. But the Boffins are determined to make John Harmon and his bride Bella Wilfer their heirs anyway, and so all ends well, except for the villain Wegg, who is carted away by Sloppy.