At Dark Waters, a sacred area belonging to Native Americans, the tranquility is shattered when a teenager is killed by a grotesque, plant-like monster. The next day, newcomer sheriff Kyle Williams arrives in Bywater, where he encounters deputy sheriff Fraser. Fraser reveals a chilling truth: the previous sheriff is among 47 people who have mysteriously disappeared since oil magnate Fred Schist acquired the ancient tribal lands from shaman and Seminole leader Ted Sallis, the first of the missing. Schist contends that Sallis legally sold off the land, claiming he fled with the cash, which has raised suspicions among the locals who oppose his drilling activities. Meanwhile, the notorious and treacherous Rene Laroque is actively sabotaging Schist's operations.
As Williams delves deeper into the ongoing mysteries of the community, he encounters a string of brutal murders, where victims are discovered with plants grotesquely growing from their bodies. Renowned photographer Mike Ploog and shaman Pete Horn introduce him to local lore, implying that the magical guardian spirit of the swamp might play a role in the unfolding tragedy.
With tensions escalating, Williams and Fraser embark on a canoe expedition to explore the swamp further, only to stumble upon the corpse of the former sheriff. Medical examiner Val Mayerik confesses that the prior sheriff pressured him into labeling the murders as mere alligator attacks, despite his belief in something more sinister at play.
Simultaneously, Schist sends the Thibadeaux brothers, local criminals, on a mission to hunt down Laroque. However, the malevolent swamp creature intervenes, leading to their demise. When Williams is captured by Laroque, he learns that Laroque had an instrumental role in aiding Schist's property deal, and that the antagonist's actions are inciting the wrath of the guardian spirit. Despite Fraser's attempts to aid Laroque, tragedy strikes when the Man-Thing emerges, resulting in Fraser’s death.
After waking from his unconscious state, Williams is met by Ploog, who has captured blurry images of the monster but is sternly warned by Williams not to return to the swamp. During a pivotal day, Williams conducts interviews with Horn and Schist, alongside local schoolteacher Teri Richards. A budding romantic connection forms between Williams and Richards, while Horn attempts to pacify the Man-Thing through prayer, only to sacrifice his own life in the futile effort as the monster remains unyielded.
That evening, the plot thickens further when Mayerik discovers evidence during the autopsy that ties Schist to a dark crime. As he attempts to communicate this crucial information to Williams, he finds him unreachable, leading Richards to venture into the swamp with news of the findings. In a cruel twist of fate, Ploog falls victim to Schist's malevolence as he uncovers the horrifying truth of the monster.
With desperation mounting, Williams and Richards set out to find Laroque, but just as they reach the drilling tower at Dark Waters, an intense conflict unfolds. As bullets and chaos ensue, Laroque, desperate to destroy the tower, gets injured while Williams is similarly wounded.
In a gripping climax, the Man-Thing arrives and exacts furious revenge upon Schist, brutally eliminating him by filling him with oil. However, the creature soon sets its sights on Williams and Richards. In the end, Laroque's selfless sacrifice leads to an explosive confrontation, resulting in the Man-Thing's retreat back into the land, permitting Williams and Richards to escape, albeit scarred by the harrowing events at Dark Waters.
