Kate Grenville's The Secret River is a sweeping tale of the founding of Australia and the moral choices that created a nation. The Secret River tells the story of William Thornhill, a poor waterman from London who is deported, along with this family, to New South Wales in 1806. The novel opens on William's first night in the convict settlement in Sydney. As William sits outside the mud hut, an Aboriginal man materializes out of the darkness. Scared for his family, William yells at the man, “be off!” The man doesn't move. Instead, he angrily repeats William's words, “be off!” In this scene, Grenville sets the stage for the conflict at the center of the novel: the battle for control of the land between the white settlers and the Aborigines. Neither people want anything to do with other. They each wish the other would go away. However, the white settlers are trapped by their status as convicts and cannot leave, and the Aborigines feel a spiritual connection to the land and will not voluntarily abandon it.
The novel then jumps back in time to William's childhood in London. Born into poverty in Southwark, William works as an apprentice to Mr. Middleton, a waterman on the Thames. Williams spends seven years rowing up and down the river, transporting the gentry from one side to the other. He develops a hatred of the gentry and their superior ways. He keenly feels the unjustness of his inferior social position and strains against the limitations of his class. He works himself into the ground in an effort to gain the security that Mr. Middleton and his house on Swan Lane represent.
William falls in love with Mr. Middleton's daughter, Sal. They get married the day that William becomes a free man. William continues to work as a waterman, building a life for his family. As master of his own boat, a wedding present from Mr. Middleton, William feels that he has left the dire poverty of his childhood behind. However, tragedy soon strikes. A month-long cold snap freezes the Thames. William cannot work, and the couple quickly goes through their savings. Mrs. Middleton falls ill, and Mr. Middleton spends all of their money trying to cure her. Mr. Middleton then succumbs to a fever, and Mrs. Middleton dies soon after. William and Sal are left destitute. The bailiffs confiscate the house on Swan Lane and the boats.
William must go to work as a waterman for another master. He does not earn enough to support his family and is forced to steal. Without the goods that William skims off the top, his family would starve. William is caught trying to steal a consignment of Brazil wood and sentenced to death. Thanks to Sal's efforts, his sentence is commuted to deportation to the convict settlement in New South Wales. A second child, Dick, is born on the voyage to Australia, joining older brother Willie.
Despite their initial shock at the run-down settlement, the Thornhill's adapt to life in the colony. William works as a waterman in the Sydney harbor and uses his old tricks to skim off rum from the barrels and barrels that pass through the harbor. Sal opens a little bar in one side of their hut, called The Pickled Herring. William receives his ticket of leave after twelve months in the colony. When his employer, Mr. King, hires a new clerk who pays close attention to the goods, William decides to quit before he gets caught stealing. He goes to work for Thomas Blackwood, an acquaintance from London, who owns a boat and plies the trade between Sydney and the settlements along the Hawkesbury river.
On his first voyage up the Hawkesbury, William falls in love with a piece of land that he names Thornhill's Point. He is determined to one day claim the land and build a stable and secure life for himself and his family. Also on this first voyage, William encounters Smasher Sullivan, a mean-mouthed settler who deals violently with any Aborigines who step foot on his land. Blackwood intensely dislikes Smasher and disagrees with his racial hatred of the Aborigines. Blackwood has learned to respect the Aborigines and advocates living in peaceful co-existence, based on his philosophy of give a little/take a little.
Blackwood decides to retire to his piece of land up the Hawkesbury, and William borrows money from Mr. King to buy his boat. William and his son Willie take up the trade and earn a good living for the family. With their situation improving, William tells Sal about his dream to claim Thornhill's Point. At first, Sal resists. She does not want to live in the wilderness, but only to earn enough money that they can someday return home in style. Eventually, she agrees to give William five years, and the family moves to Thornhill's Point.
William begins having problems with the Aborigines from the first day of arrival. A clan of Aborigines lives in the area, and they do not recognize William's ownership of the land. The Thornhill's and the Aborigines live in an uneasy peace until the Aborigines strip William's original patch of corn. William physically fights with the Aborigines at the corn patch, hurting several of the women and firing a shot at Long Jack. The Aborigines retaliate by torching the corn patch. Sal insists on leaving Thornhill's Point. She does not want her children in danger, and she knows that the Aborigines will not willingly relinquish their claim to the land. William is desperate. He cannot conceive of abandoning his dream.
In the middle of their argument about whether to stay on Thornhill's Point, William notices smoke from another settlement down the river. He takes the boat to help Saggity, whose land is being attacked by the Aborigines, while Sal packs their belongings. Saggity has been speared by the Aborigines, and William is forced to take him to Windsor, a township on the Hawkesbury. Saggity dies soon after they arrive, and his death becomes a war cry for the settlers. Led by Smasher Sullivan, they agree to put an end to the native problem once and for all. William is not a violent man, and he does have an understanding of the Aborigines' humanity. However, the only way that Sal will agree to stay on Thornhill's Point is if the Aborigines are dispersed. He agrees to take part in the attack.
The settlers sail up to the Aborigine camp near Thomas Blackwood's place. The slaughter is bloody and merciless, with children clubbed to death and their throats slit. Whisker Harry, the elder of the Aborigine clan, spears Smasher Sullivan. William, who has yet to fire his gun, turn and shoots Whisker Harry. The Aborigines disappear into the trees and no longer bother the settlers along the Hawkesbury.
William becomes a prosperous land owner and trader. He builds a grand stone house on Thornhill's Point, and the new settlers consider him a member of Australia's new gentry. William acquires all the trappings of wealth, but his success does not come without a price. After the bloody dispersal of the Aborigines, his young son Dick leaves him to live with Thomas Blackwood. Dick cannot accept his father's participation in the slaughter, and he never speaks to William again. Long Jack is the only Aborigine left on the land. Permanently disabled by a gunshot wound, he sits on Thornhill's Point challenging William's ownership of the land. Grenville ends the novel with the image of William scanning the horizon for a glimpse of a shape of man, symbolizing the haunting specter of the Aborigines that hangs over white Australia.