Two teenage boys, Ellis and Neckbone, are exploring the Arkansas delta when they venture to a small island in the Mississippi River. There, they discover a boat precariously lodged in a tree, likely left there by a flood. Rather than simply claiming it for themselves, they soon encounter Mud, a fugitive who has deep ties to the area. Mud reveals that he is desperately trying to reconnect with his former girlfriend, Juniper, after having killed the man who harmed her. The boys, struck by his story, agree to assist Mud in fixing the boat in return for his .45 pistol.
Mud paints a picture of his love for Juniper, describing a distinctive nightingale tattoo on her hand. The boys catch a glimpse of her at the local Piggly Wiggly and witness her being mistreated by another man. Driven by bravery, Ellis intervenes, only to receive a black eye for his efforts. Grateful for his intervention, Juniper thanks Ellis, intensifying his feelings.
As the boys protect Mud from the police who are hunting him down, a new threat emerges. King Carver, the furious father of Mud's victim, arrives with intentions to exact revenge. He mobilizes the local law enforcement and a militia to track down Mud.
Meanwhile, Ellis grapples with his own challenges at home, as his parents' impending divorce looms over him, jeopardizing their family river houseboat. A new crush, May Pearl, captures his heart, but he soon discovers it might not be true love when she rejects him in front of her friends. Feeling lost, Ellis turns to Tom Blankenship, an old father figure for Mud, who ultimately decides not to help.
With determination, Ellis and Neckbone scavenge for parts to assist Mud in repairing the boat, while Mud dreams of a new life for himself and Juniper in Mexico. However, as they finally locate Juniper, she heartbreakingly chooses to remain behind, shattering Mud's visions of escape and leaving Ellis feeling equally dejected when May Pearl spurns him.
After a heated confrontation, Ellis runs away in anger, only to be bitten by a water moccasin in a creek. Mud and Neckbone rush him to the mainland for medical attention. Unfortunately, their presence attracts unwanted attention from the authorities, leading to a violent confrontation with King Carver and his crew. As chaos erupts, Tom steps in to protect Ellis, using his sniper skills to keep the attackers at bay. In the fray, Mud goes missing, sinking into the waters with a gunshot wound as the aftermath leaves tragedy in its wake.
Following the skirmish, with Ellis's family life crumbling and their houseboat taken away, he tries to muster hope with the presence of new friends. Uncertain about Mud’s fate, Ellis begins to find a flicker of optimism. Meanwhile, Tom discovers that Mud has survived and treats his injuries. Together, they set out on the repaired boat, embarking on a journey down the Mississippi, finally reaching the Gulf—a testament to hope, resilience, and the bonds of friendship.
