14 year-old Ellis (Tye Sheridan) lives on a makeshift houseboat on the banks of a river in Arkansas with his parents, Mary Lee (Sarah Paulson) and Senior (Ray McKinnon). He sneaks out early one morning to meet his best friend, Neckbone (Jacob Lofland). Neckbone, also 14, lives with his uncle, Galen (Michael Shannon), who makes a hardscrabble living diving for oysters. The two boys set out to an island on the Mississippi River, where Neckbone has discovered an unusual sight-a boat, suspended high in the trees, a remnant of an extreme flood some time in the past. They climb the tree and into the boat only to find fresh bread and fresh footprints. Realizing that they are not the only ones who have discovered the treehouse boat, they decide to leave. When they reach the shore, they find the same footprint in their boat. And that's when they meet Mud (Matthew McConaughey). Mud is a gritty, superstitious character; his clothes are dirty, his tooth is cracked, and he needs help. He tells the boys he will give them the treehouse boat, his current hideout, in exchange for food. Neckbone is reluctant, but Ellis brings food to Mud, and they develop a tentative friendship. Ellis learns that Mud has killed a man in Texas, and police and bounty hunters are looking for him, but Mud is more concerned about reuniting with his longtime love, Juniper (Reese Witherspoon). Ellis, who has recently developed his own crush, agrees to help Mud escape with Juniper. Ellis and Neckbone carry out bold schemes in an effort to protect Mud and relay messages to Juniper, who is holed up in a fleabag motel, under constant surveillance by Carver (Paul Sparks), a Texas bounty hunter. Carver and his gang are intent on capturing Mud, on orders from the cold-blooded King (Joe Don Baker). As the boys risk everything to reunite these seeming mythical lovers, Ellis's own ideas about love and romance are challenged by the strains in the relationships closest to him: his parents' marriage is dissolving while he himself falters in his efforts to impress May Pearl (Bonnie Sturdivant). Through it all, Ellis struggles to look for an example of love that he can believe in, learning about the unspoken rules and risks of love and the reality of heartbreak.
In Arkansas, 14-year-old Ellis lives in a floating house with his mother Mary Lee and his father Senior. Ellis helps his father selling fish with his best friend Neckbone. Ellis and Neckbone find a motorboat stranded on the top of a tree in an island on the Mississippi River since a flood and they plan to fix the boat for them. One day, they climb the tree and they find fresh meal inside the boat meaning that someone is living in "their" boat. They leave the place and meet a man named Mud near their boat. Soon they learn that the passionate Mud killed a man that had beaten up his girlfriend Juniper and now the father and the brother of the deceased man are hunting him down. Mud makes a deal with the romantic Ellis and Neckbone to help him to reunite with Juniper. But when Ellis meets Mud's stepfather Tom, he has a different opinion about the love of Juniper with Mud.
Two young boys encounter a fugitive and form a pact to help him evade the vigilantes that are on his trail and to reunite him with his true love.
- Two teenage boys in the Arkansas delta, Ellis and Neckbone, travel to a small island in the Mississippi River where Neckbone found a boat stuck high in a tree, likely from a flood. They intend to make it their own. They realize someone is living in it and meet Mud a fugitive who grew up in the area. He wants to reunite with his old girlfriend Juniper and then skip town. Mud explains he killed a man who had impregnated Juniper and who then pushed her down a flight of stairs, causing her to lose the child. The boys decide to lend Mud a helping hand, working to free the boat and get it working again, in exchange for Mud's .45 pistol. Mud also tells them about Juniper, whom he claims to love. He describes her as having a nightingale bird on her hand, and Neck and Ellis spot her at the local Piggly Wiggly. When they follow her, they interrupt abuse of her by another man. Ellis charges the man and shoves him off Juniper, but is punched and gets a black eye. Juniper thanks Ellis for saving her.
The police are searching for Mud, but the boys don't give away his hiding place. Notified by his surviving son that Mud is in the area, King Carver, the vengeful father of Mud's victim, arrives in town. The Carvers pay off the police and hire a small militia to find and kill Mud.
Meanwhile, Ellis is dealing with personal troubles. His parents are heading for divorce, which threatens their old river houseboat, owned by his mother. No longer used as residences by the owners, the boats are being taken off the river, due to recently passed laws.
Ellis falls for a high school girl named May Pearl and thinks he's in love. Mud looks to Tom Blankenship, an older father figure from his childhood, for help. Tom lives across the river from Ellis, so he is easy to find. Tom is disturbed that Mud is in trouble again over Juniper and refuses to help.
Stealing machine parts and other supplies from junkyards, the boys help Mud repair the boat and rebuild the engine. Mud has a plan to leave with Juniper, get to the Gulf and make it to Mexico. They also locate Juniper, but at the last minute she decides not to leave with Mud, and breaks his heart by having an affair with another man. Ellis also suffers heartbreak when May Pearl rebuffs him in front of her friends.
When he returns to the island, Ellis angrily calls Mud a liar and says he made Ellis a thief . Running away, Ellis falls into a creek with water moccasins and is bitten. Mud and Neckbone get Ellis to the mainland and Mud takes the boy to the hospital. Recognizing the wanted man, one of the hospital employees calls the police who, in turn, tips off King.
Mud and Neckbone get the repaired boat into the water. Mud gives Neckbone his pistol but not the bullets. As Mud wants to say good-bye to Ellis, Neckbone takes him to Ellis's houseboat, where he is recovering. While Mud is there, Carver and his posse arrive and start shooting. From across the river and the roof of his houseboat, Tom uses his old sniper rifle to pick off several attackers. Mud saves Ellis and tries to get away, but appears to be shot before disappearing into the river. After all the posse members are dead, including Carver, the police arrives. One trooper calls King and delivers the message that his other son is dead.
Ellis's parents separate and when his mother moves to a town apartment, their houseboat is taken off the river. Seeing attractive teenage girls there, Ellis renews his sense of hope. He is uncertain of Mud's fate but believes again he has some redeeming value.
Tom finds Mud in the river, alive, and treats his wounds. The duo uses the repaired boat to travel down the Mississippi, where it opens out to the Gulf, they made it!