A River Runs Through It begins with the narrator, Norman Maclean, describing what it was like to grow up in Missoula, Montana, as the son of a Scottish Presbyterian minister who holds two things sacred: God and fly-fishing. Norman and his brother, Paul, spend much of their time out of school in church services and studying the Bible. But their father also introduces them to the complex, intricate art of fishing, in which one must learn to read the river and attempt to listen to its words. Their family is close-knit, and somewhat suspicious of the outside world. Norman and Paul only fight once, and when their mother tries to separate them, she falls down, and the two are chastened into never fighting again. Paul, though, retains a fighting streak. From a young age, he is incredibly stubborn, and enjoys betting on anything—as he gets older, he begins to gamble. Norman spends his teenage summers working for the United States Forest Service, while Paul is a lifeguard, giving him time to fish in the evenings. Paul has come to be the expert fisherman among the two, and his greatest goal is to not let work interfere with his fishing. He becomes a newspaper reporter in Helena, the capital of Montana.
In the summer of 1937, when the bulk of the novella takes place, Paul is living in Helena, while Norman lives with his wife Jessie’s family in Wolf Creek. Norman’s mother-in-law, Florence, has just told Norman that Jessie’s brother Neal will be arriving shortly from the West Coast, and she’d love for him to fish with Norman and Paul. Norman runs into Paul outside a bar, though it’s not yet noon. Neither Norman nor Paul like Neal, whom they consider an outsider and a failed Montanan, but they love Florence, so they agree to fish on the Elkhorn with Neal. The two brothers go fishing together the next morning. On the way Paul tells Norman about getting into a car crash (probably while drunk) and of the fine he’ll have to pay—he tells it as a joke, but Norman isn’t sure how seriously to take it. Still, Paul regains the upper hand when they’re fishing, as Norman admires his technique of “shadow casting.” Norman stays with Paul for the night, but Paul goes out on the town, and Norman later gets a call in the middle of the night to come down to the jail. Paul had gotten into a fight with a man who had insulted the girl he was with, a part-Native American woman whom Norman calls “Mo-nah-se-tah.” Norman drives them home, and then drives back to Wolf Creek himself, trying to figure out how he might be able to help Paul.
A few days later Neal arrives on the train wearing two sweaters and carrying a monogrammed suitcase—certainly not a regular sight in Wolf Creek, Montana. As soon as he can, Neal tries to sneak off to a bar, and Norman goes with him, since Jessie has asked him to keep an eye on her brother. There they meet Long Bow, a regular at the bar, and Old Rawhide, the town whore. Neal slowly starts sidling up to Old Rawhide, at which point Norman says he’ll make it an early night. The next morning Paul is at their door bright and early for the fishing trip. Florence is slightly embarrassed that Neal is still in bed, having had a late night—though Paul says he didn’t go to bed at all. The three men pile into the truck with Jessie’s other brother Ken, Jessie, and Florence, to go down to the Elkhorn. Once again, Jessie admonishes Norman to keep an eye on Neal, but as soon as they go downstream together, Neal says he’s going to stay at a certain bend, and soon nods off. Enraptured by the day, Norman soon forgets about Neal, and joins Paul in fishing. Finally, as storm clouds are approaching, he thinks to go back to look for Neal. He searches for him along the river with rain pelting down, but doesn’t find him. When he and Paul get back to the truck, Neal is safe and dry inside, while the women are angry with Norman for having abandoned Neal.
Realizing that Jessie is unhappy with him, Norman suggests that he go away for a few days, and spend some time fishing with Paul. Jessie agrees. Norman drives up to Helena, but when the brothers drive to their regular summer cabin and its nearby river, it turns out that Neal and Old Rawhide have followed them, and Neal claims that now he wants to fish with the brothers right now. It’s midday and too hot for good fishing, and Neal has forgotten his rod, but Paul has no patience for such lack of care, so he makes them get into the car anyway. Neal and Old Rawhide have brought liquor and are increasingly tipsy. Norman and Paul leave them, bury some beers in the cold river for afterward, and find their own fishing holes, where they fish as long as they can until the heat grows unbearable. But on their way back, the beers aren’t there. The brothers are almost back to the car when they catch sight of two naked, red bodies lying on a sandbar: Neal and Old Rawhide have drunk all their liquor, all the beers, and are fast asleep, with horrific sunburns developing. Norman and Paul drive them back to town in silence, drop off Old Rawhide, and return home, where Paul leaves Norman to face the women (Jessie, Florence, and Ken’s wife Dorothy). They immediately get Neal into bed, and Norman and Jessie, though they begin to fight, are soon reconciled. The other women repeat that they love Norman as well.
Feeling absolved, Norman, following Jessie’s suggestion, goes back to Helena to finish his fishing trip with Paul. Paul suggests they stop by their parents’ home and invite their father along. They do so, and their parents seem thrilled to see them—especially Paul—but are upset when Paul slips out after dinner to the bars. Still, the next morning, he is ready to fish before Norman or his father. The three of them fish a number of holes together. At first, Norman is more successful than his brother, and this gives him a burst of pride and joy, but Paul soon regains the upper hand. After a while, Norman decides he’s finished, and sits by his father, who’s reading the Bible. They both watch Paul try to reach his limit, admiring his skill and artistry.
The present-day Norman who is narrating this story, long after the event, notes that he often thinks about this fishing trip, since it was the last time he would fish with Paul. Not long afterward, Paul would be beaten to death and left outside an alley. Norman and his father ask each other over and over again if there was anything they could have done, but never reach an answer. All they can truly understand is that Paul was an incredible fisherman and artist. As an old man, Norman continues to fly-fish, reveling in the beauty and rhythm of the sport, but he continues to be haunted by his past.