Jonsy McCain, a twelve-year-old tomboy, lives on an inlet of the Mississippi River with her grandmother Vadie McCain, who raised the girl after her father, Billy McCain, was imprisoned for robbery and murder thirteen years earlier. Jonsy, an industrious youngster, helps her grandmother run a bait and tackle shop at their riverfront house, and spends her free time trying to repair an old boat named the River Rat. One day, Sheriff Cal stops by to notify Vadie that Billy will be paroled soon. The news is unexpected and Vadie appears concerned, because she has lost touch with her son, while Jonsey has never met her father. After arriving, Billy is distant as he readjusts to being back on the river where he grew up. The inquisitive Jonsy is not shy about asking her newfound father personal questions, but Billy is not forthcoming. Vadie informs Billy that Joyce, Jonsy’s irresponsible mother, wrote from Memphis, Tennessee, a few years before, wanting to reconnect; however, Vadie discouraged it because she was afraid of losing her granddaughter. As Billy struggles to come to terms with his past, Vadie declares she never gave up on him and longs for him to be part of the family again. Billy agrees to help Jonsy fix up the River Rat and buys an old engine from Poley, the shifty, local salvage man. In Jonsy’s presence, Poley mentions the rumor that Billy and his partner-in-crime Whitey hid the robbery money downriver, but Billy reminds Poley that the cash burned, along with Whitey, in the car wreck. As they work on the boat together, Billy and Jonsy become closer. When the boat is ready, Billy suggests they take a trip down the Mississippi River to Memphis. Under the terms of his parole, Billy obtains permission to leave the county from Dr. “Doc” Cole, the prison psychiatrist in charge of rehabilitation. Before leaving, Billy receives a visit from Doc Cole and takes him for a ride in a skiff to talk privately. The two men engage in an intense argument. As the parolee tussles with the doctor, both men fall overboard. When Billy returns to shore alone, he pushes Doc Cole’s car into the river. Meanwhile, Doc Cole survives and stumbles onto the bank, where Poley finds him and attempts to steal his wallet. Rousing himself, the doctor offers to pay Poley to help him and sleeps at the salvage man’s riverfront shack. The next day, Billy and Jonsy set out for Memphis in the revamped boat, but soon discover that Wexel, a precocious nine-year-old African-American boy, has stowed away. The boy, who is a frequent presence around Vadie’s shop, mentions he was scared at the sight of a man in a white suit walking out of the swamp last night. Billy appears anxious since Wexel’s description fits Doc Cole. After the doctor’s car is discovered missing, Poley suspects Cole is concealing the real reason for his visit and mentions the rumor of Billy’s hidden robbery money. Doc Cole denies any knowledge of the money, then strangles Poley. In an attempt to frame Billy for the murder, the doctor places a trinket with Billy’s initials in the dead man’s hand. Meanwhile, on the riverboat, Billy tells his daughter about the murder and robbery thirteen years ago: One night, Billy, Joyce, and Whitey broke into the decaying mansion of an elderly widow, who was rumored to be rich. As Whitey and Billy discovered empty cat food boxes filled with cash underneath the woman’s bed, the widow woke and tried to shoot the two boys. Whitey did not hesitate to grab the gun and kill her. Joyce screamed, and the boys left her behind at the mansion while they escaped with the money and made their way down river to Louisiana. After going ashore and stealing a car, police intercepted them, and Whitey died when the vehicle crashed and exploded during the pursuit. Billy tells Jonsy that the money was left behind and burned inside the car. She is distressed to hear that her father was wrongly charged for the widow’s murder because Joyce made a deal and testified against him. After docking in Memphis, Billy pays a surprise visit to Joyce and tries to reconcile with her, but she dismisses him. During her parents’ conversation, Jonsy overhears Billy mention that the robbery money did not burn, but was hidden. Angry that her father lied to her, Jonsy confronts him as they walk back to the dock. Billy explains he made a deal with Doc Cole in prison; the corrupt doctor would authorize Billy’s parole in exchange for acquiring the hidden money. However, during their recent argument on the skiff, the doctor threatened to send Billy back to prison if he did not receive the money soon. Billy thought he accidentally killed the doctor, but apparently Cole survived. Billy warns Jonsy that the doctor is capable of murder. At the dock, Cole is waiting with a gun and forces Billy to lead him to the money, while insisting they bring along Jonsy and Wexel on the “treasure hunt.” Meanwhile, Sheriff Cal discovers Poley’s corpse in a patch of poison ivy. On the boat, Doc Cole indicates to Jonsy that Billy, not Whitey, shot the elderly woman. The young girl appears to doubt her father’s story, until Billy reassures her that he is telling the truth and is not a murderer. During a thunderstorm, the group takes shelter on a deserted stretch of beach. Doc Cole has developed a severe poison ivy rash on his face and hands. When the doctor reveals that Poley is dead and a trinket will implicate Billy in the murder, the two men fight for control of the gun. As lightning strikes nearby, Doc Cole aims the pistol at Billy and the children. Forced to reveal the location of the money, Billy recounts how he escaped the car wreck and ran toward a nearby Cajun cemetery, where he hid the cash in a coffin that was about to be entombed. Billy tells Doc Cole the name of the Louisiana cemetery, La Croix Cassee, but hesitates to reveal the name on the grave. Suddenly, a burning barge that was struck by lightning careens toward the beach. Grabbing Wexel, Billy flees with Jonsy to the boat, while Doc Cole runs inland. The following night, Billy and the two youngsters arrive at the cemetery in Louisiana and remove the money from the coffin. However, Doc Cole is waiting for them and stabs Billy in the shoulder with a metal object. Gripping the money, Doc Cole tries to capture Jonsy and Wexel, but Billy recovers enough to knock the doctor to the ground. As Cole scurries away, a Cajun man appears and takes Billy and the two children to the police station, where Billy receives medical treatment. Jonsy is worried her father will be implicated in another murder until Sheriff Cal arrives in Louisiana and reassures her. Further weakened and disfigured by the poison ivy rash, Doc Cole is escorted into the police station in handcuffs. Billy and Jonsy return home on the River Rat.