The Adventures of Huckleberry Finn opens with Huck telling his story. Briefly, he describes what he has experienced since, The Adventures of Tom Sawyer, which preceded this novel. After Huck and Tom discovered twelve thousand dollars in treasure, Judge Thatcher invested the money for them. Huck was adopted by the Widow Douglas and Miss Watson, both of whom took pains to raise him properly. Dissatisfied with his new life, and wishing for the simplicity he used to know, Huck runs away. Tom Sawyer searches him out and convinces him to return home by promising to start a band of robbers. All the local young boys join Tom's band, using a hidden cave for their hideout and meeting place. However, many soon grow bored with their make-believe battles, and the band falls apart.
Soon thereafter, Huck discovers footprints in the snow and recognizes them as his violent, abusive Pap's. Huck realizes Pap, who Huck hasn't seen in a very long time, has returned to claim the money Huck found, and he quickly runs to Judge Thatcher to "sell" his share of the money for a "consideration" of a dollar. Pap catches Huck after leaving Judge Thatcher, forces him to hand over the dollar, and threatens to beat Huck if he ever goes to school again.
Upon Pap's return, Judge Thatcher and the Widow try to gain court custody of Huck, but a new judge in town refuses to separate Huck from his father. Pap steals Huck away from the Widow's house and takes him to a log cabin. At first Huck enjoys the cabin life, but after receiving frequent beatings, he decides to escape. When Pap goes into town, Huck seizes the opportunity. He saws his way out of the log cabin, kills a pig, spreads the blood as if it were his own, takes a canoe, and floats downstream to Jackson's Island. Once there, he sets up camp and hides out.
A few days after arriving on the island, Huck stumbles upon a still smoldering campfire. Although slightly frightened, Huck decides to seek out his fellow inhabitant. The next day, he discovers Miss Watson's slave, Jim, is living on the island. After overhearing the Widow's plan to sell him to a slave trader, Jim ran away. Jim, along with the rest of the townspeople, thought Huck was dead and is frightened upon seeing him. Soon, the two share their escape stories and are happy to have a companion.
While Huck and Jim live on the island, the river rises significantly. At one point, an entire house floats past them as they stand near the shore. Huck and Jim climb aboard to see what they can salvage and find a dead man lying in the corner of the house. Jim goes over to inspect the body and realizes it is Pap, Huck's father. Jim keeps this information a secret.
Soon afterwards, Huck returns to the town disguised as a girl in order to gather some news. While talking with a woman, he learns that both Jim and Pap are suspects in his murder. The woman then tells Huck that she believes Jim is hiding out on Jackson's Island. Upon hearing her suspicions, Huck immediately returns to Jim and together they flee the island to avoid discovery.
Using a large raft, they float downstream during the nights and hide along the shore during the days. In the middle of a strong thunderstorm, they see a steamboat that has crashed, and Huck convinces Jim to land on the boat. Together, they climb aboard and discover there are three thieves on the wreck, two of whom are debating whether to kill the third. Huck overhears this conversation, and he and Jim try to escape, only to find that their raft has come undone from its makeshift mooring. They manage to find the robbers' skiff and immediately take off. Within a short time, they see the wrecked steamship floating downstream, far enough below the water-line to have drowned everyone on board. Subsequently, they reclaim their original raft, and continue down the river with both the raft and the canoe.
As Jim and Huck continue floating downstream, they become close friends. Their goal is to reach Cairo, where they can take a steamship up the Ohio River and into the free states. However, during a dense fog, with Huck in the canoe and Jim in the raft, they are separated. When they find each other in the morning, it soon becomes clear that in the midst of the fog, they passed Cairo.
A few nights later, a steamboat runs over the raft, and forces Huck and Jim to jump overboard. Again, they are separated as they swim for their lives. Huck finds the shore and is immediately surrounded by dogs. After managing to escape, he is invited to live with a family called the Grangerfords. At the Grangerford home, Huck is treated well and discovers that Jim is hiding in a nearby swamp. Everything is peaceful until an old family feud between the Grangerfords and the Shepherdsons is rekindled. Within one day all the men in the Grangerford family are killed, including Huck's new best friend, Buck. Amid the chaos, Huck runs back to Jim, and together they start downriver again.
Further downstream, Huck rescues two humbugs known as the Duke and the King. Immediately, the two men take control of the raft and start to travel downstream, making money by cheating people in the various towns along the river. The Duke and the King develop a scam they call the Royal Nonesuch, which earns them over four hundred dollars. The scam involves getting all the men in the town to come to a show with promises of great entertainment. In the show, the King parades around naked for a few minutes. The men are too ashamed to admit to wasting their money, and tell everyone else that the show was phenomenal, thus making the following night's performance a success. On the third night, everyone returns plotting revenge, but the Duke and King manage to escape with all their ill gotten gains.
Further downriver, the two con men learn about a large inheritance meant for three recently orphaned girls. To steal the money, the men pretend to be the girls' British uncles. The girls are so happy to see their "uncles" that they do not realize they are being swindled. Meanwhile, the girls treat Huck so nicely that he vows to protect them from the con men's scheme. Huck sneaks into the King's room and steals the large bag of gold from the inheritance. He hides the gold in Peter Wilks's (the girls' father) coffin. Meanwhile, the humbugs spend their time liquidating the Wilks family property. At one point, Huck finds Mary Jane Wilks, the eldest of the girls, and sees that she is crying. He confesses the entire story to her. She is infuriated, but agrees to leave the house for a few days so Huck can escape.
Right after Mary Jane leaves, the real Wilks uncles arrive in town. However, because they lost their baggage on their voyage, they are unable to prove their identities. Thus, the town lawyer gathers all four men to determine who is lying. The King and the Duke fake their roles so well that there is no way to determine the truth. Finally, one of the real uncles says his brother Peter had a tattoo on his chest and challenges the King to identify it. In order to determine the truth, the townspeople decide to exhume the body. Upon digging up the grave, the townspeople discover the missing money Huck hid in the coffin. In the ensuing chaos, Huck runs straight back to the raft and he and Jim push off into the river. The Duke and King also escape and catch up to rejoin the raft.
Farther down the river, the King and Duke sell Jim into slavery, claiming he is a runaway slave from New Orleans. Huck decides to rescue Jim, and daringly walks up to the house where Jim is being kept. Luckily, the house is owned by none other than Tom Sawyer's Aunt Sally. Huck immediately pretends to be Tom. When the real Tom arrives, he pretends to be his younger brother, Sid Sawyer. Together, he and Huck contrive a plan to help Jim escape from his "prison," an outdoor shed. Tom, always the troublemaker, also makes Jim's life difficult by putting snakes and spiders into his room.
After a great deal of planning, the boys convince the town that a group of thieves is planning to steal Jim. That night, they collect Jim and start to run away. The local farmers follow them, shooting as they run after them. Huck, Jim, and Tom manage to escape, but Tom is shot in the leg. Huck returns to town to fetch a doctor, whom he sends to Tom and Jim's hiding place. The doctor returns with Tom on a stretcher and Jim in chains. Jim is treated badly until the doctor describes how Jim helped him take care of the boy. When Tom awakens, he demands that they let Jim go free.
At this point, Aunt Polly appears, having traveled all the way down the river. She realized something was very wrong after her sister wrote to her that both Tom and Sid had arrived. Aunt Polly tells them that Jim is indeed a free man, because the Widow had passed away and freed him in her will. Huck and Tom give Jim forty dollars for being such a good prisoner and letting them free him, while in fact he had been free for quite some time.
After this revelation, Jim tells Huck to stop worrying about his Pap and reveals that the dead man in the floating house was in fact Huck's father. Aunt Sally offers to adopt Huck, but he refuses on the grounds that he had tried that sort of lifestyle once before, and it didn't suit him. Huck concludes the novel stating he would never have undertaken the task of writing out his story in a book, had he known it would take so long to complete.