The film is about two detectives who investigate a series of grisly murders in and around an isolated university campus in the French Alps. With a $14 million budget, the movie went on to gross $60 million from a worldwide theatrical release. Despite its box office success, one of its stars, Vincent Cassel admitted, "I can't help explain the film because I didn't understand it! We cut out everything in the film that was explanatory, therefore 'boring' [according to the director]. You end up with a film that's not boring but you don't understand it [at] all."
Detective Superintendent (Commissaire Principal) Pierre Niemans (Jean Reno), an investigator well known in Paris, is sent to the small rural university town of Guernon in the French Alps to investigate a brutal murder. The victim's body is found bound in the fetal position and suspended high on a cliff face, his eyes removed and his hands cut off. Niemans learns that the victim was a professor and the University's librarian, Remy Callois, and he seeks out a local ophthalmologist for an explanation to the removal of the eyes. Dr. Cherneze, once on the University staff, explains that the school's isolation led to in-breeding amongst the professors, with increasingly serious genetic disorders. Recently the trend has reversed, with the local village children becoming ill and the college babies remaining healthy. Cherneze hints that the killer is leaving Niemans clues to their motive by removing the body parts that are unique to each individual - the eyes and hands. Niemans questions the Dean and examines the librarian's apartment, where he finds images of athletic "supermen" juxtaposed with texts on genetic deformities. The Dean's assistant (and son) Hubert translates the title of Callois' Ph.D. thesis as, "We are the masters. We are the slaves. We are everywhere. We are nowhere. We control the crimson rivers."
Coincidentally Detective Inspector (Lieutenant de Police) Max Kerkerian (Vincent Cassel) is in the nearby town of Sarzac investigating the desecration of the grave of Judith Herault, a girl who died in 1982, and the theft of her photos from the local primary school. The girl was killed in a horrific highway accident, witnessed by her mother, who was so traumatized she took a vow of darkness in a nunnery. The mother tells Kerkerian that when Judith was ten she fell ill, and they went to get help in Guernon where she was born; she claims they were then attacked by "demons" and, when they fled, her daughter was killed in the road accident. She says the pictures were stolen to erase her daughter from history, and that her face is a threat to the demons who have returned to complete their mission. She tells him it all began in Guernon.
Niemans questions Fanny Ferreira (Nadia Farès), a glaciologist and student, who is immediately suspect because of her climbing ability. Despite her contempt for the school and its arrogant professors, she works for the university to steer away frequent avalanches, and is incensed when Niemans implies she might withhold evidence to protect the school. She tells him that anyone with good equipment could've hoisted the body up the cliff, and brushes off his obvious attraction. Soon after, the pathologist reports that it was acid rain in Callois' eye sockets, which has not fallen in the area since the seventies. Niemans enlists Fanny to take him up the glacier to get ice samples to compare with the acid rain in Callois' eyes. On a hunch, Niemans follows a glacial melt tunnel to a cave that contains a second body, frozen into the ice.
Kerkerian traces a car from the accident to Phillip Sertys in Guernon and meets Niemans while attempting to break into Sertys' apartment. Sertys is the body in the ice, a doctor that worked in the maternity ward at the University hospital. They find Judith's stolen photograph as well as evidence that Sertys was breeding and training fighting dogs - and then they find the dogs, and Niemans the "supercop" is momentarily paralyzed by fear, until Kerkerian coaxes him through.
Sertys was also mutilated, and his eyes replaced with glass prosthetics, "Like you would find at an eye doctor's" remarks the pathologist, leading Niemans to race back to Cherneze's practice. The doctor is already dead, and they almost catch the killer, who fights off Niemans and races away after deliberately emptying Niemans' gun into the wall but not hitting him. Kerkerian gives chase but the killer escapes. Returning to the scene, where the killer has written "I will trace the source of the crimson rivers" in Cherneze's own blood above his body, they learn the prints on Niemans' gun belong to Judith Herault.
Kerkerian goes back to search the grave in Sarzac, which is empty except for a picture, while Niemans goes to Fanny's home. Niemans tells her that although he sees her as physically capable of committing the crimes he doesn't believe her to be guilty. When he returns to the university, the local police captain tells him that Callois' thesis is full of Nazi-style eugenics, suggesting perfection can be achieved by breeding athletically gifted and intellectually gifted children together.
Kerkerian returns with the photo which Niemans recognizes as Fanny and, on the way to her house, they narrowly avoid being run off the road by the Dean's son as they piece together the story. Due to the poor bloodlines and genetic mutations in the faculty's inbred offspring, the doctors at the hospital had been swapping healthy village children with the university children. Sertys, they deduce, must have swapped Fanny for Judith, and Callois arranged the matches in the college's breeding program. Once at Fanny's house they find the missing hands and eyes of the victims in her basement, but Fanny is now gone and so are her grenades. Niemans gives the order to evacuate the university while he and Kerkerian travel up the mountain to find Fanny.
The duo confront Fanny only to be set upon by Judith, who is her identical twin. Judith tells Fanny to kill Niemans, but she refuses, and instead turns the gun on her sister. At the same time Kerkerian fires at Judith, but hits Fanny in the shoulder and the gunshots trigger an avalanche. Judith is swept away and the rest are buried in the snow until a rescue team arrives with search dogs. Fanny is airlifted to hospital while Kerkerian asks Niemans to explain his fear of dogs.
Exteriors were shot on location near Grenoble in the communes of Albertville, Livet-et-Gavet, Avrieux, Apprieu, Bourg d'Oisans, Vallorcine, Vinay and Virieu sur Bourbre.
The university was actually the Onera Modane-Avrieux wind tunnels Centre at Villarodin-Bourget, Savoy 45°12′49.53″N 6°43′1.90″E. The glacier scenes were filmed on the Mer de Glace beneath Mont-Blanc and above Argentiere in the Chamonix Valley, Haute-Savoie. The house on stilts by the river can be seen here 45°6′26.45″N 5°55′59.27″E.
The Crimson Rivers was nominated for five César Awards: Best Director, Best Cinematography, Best Music, Best Editing, and Best Sound. It also received one European Film Awards nomination for Best Director and two nominations for Best Actor (Jean Reno and Vincent Cassel). It was also nominated for the Golden Seashell at the San Sebastián International Film Festival.