Dr. William Barton leads an expedition to capture the Gill Man, a dangerous half-man, half-fish creature that lives in the Amazon’s Black Lagoon. Bill and his young wife Marcia join the rest of the team, including geneticist Dr. Thomas Morgan, biochemist Dr. Borg, lab technician Dr. Johnson and guide Jed Grant, who warns the group that the Gill Man is too deadly to control, regardless of their state-of-the-art equipment and a new sedative called rotonol. During the trip, the rakish Jed attempts to seduce Marcia, who continually spurns him. After they finally reach the Amazon, Jed takes the men to the home of Morteno, a local man who was brutally attacked by the creature. Back at the boat, Bill reveals his plan to mutate the Gill Man’s blood in order to form a new, more advanced form of life, which he hopes will be more suited to life in space. Horrified, Tom warns Bill that they cannot bypass nature, but only make it safer for humankind. Once in the Black Lagoon, a bored Marcia insists on diving with Tom and Jed, despite Bill’s attempts to stop her. While Tom and Jed search underwater for the Gill Man, Borg identifies the Gill Man on the sonar, but he has grown craftier since his last experience with humans, and so eludes their grasp. After Marcia dives too far down, she collapses, but Tom rescues her from the water and the Gill Man. He carries her to her cabin, where he counsels her not to take risks, and she explains that when she married Bill she was only a teenager, and now it is too late to live the life she wants. After Tom leaves, a jealous Bill enters and warns her never to leave or make a fool out of him. That night, the crew follows the Gill Man into a narrow waterway, where they are forced to drop anchor and move onto a small speedboat. They track the creature further into the water, then drop the rotonol, but a misstep results in a small fire, which burns the creature. After he passes out, the crew bring him into the lab, where they cover his burns with bandages but note that his gills have been destroyed and he can no longer take in much oxygen. Just before the creature suffocates, Bill realizes he has small lungs, and performs a tracheotomy to help him breathe. The operation is a success, and the next day, the doctors discover a layer of human skin under the Gill Man’s burnt scales. Further tests reveal that first the creature’s metabolism and then his eyes are also mutating to become more human. Over the next few days, while Tom urges Bill to treat the Gill Man with kindness, Bill warily notes Jed’s interest in Marcia. One day, the doctors discover that the Gill Man is growing fingers where he once had flippers, and during a celebratory party that night, Tom states that although the creature's skin has changed, his nature has not, and that they “all stand at the crossroads between the jungle and the stars.” After Bill grows inebriated, the party breaks up, and he later raves at Marcia that she is untrustworthy and “worthless.” In the middle of the night, Jed discovers a despondent Marcia pacing the hallway and aggressively pursues her. In the lab, the Gill Man, now clothed, revives and manages to unlock the door. Hearing Marcia plead for Jed to leave her alone, the creature comes to her rescue, knocking out Jed and then heading for the water. The men wake and Tom, realizing that the Gill Man can no longer breathe in the water, dives in after him and wrestles him until the creature passes out. Under Tom’s watch, the team treats the Gill Man gently, and the creature grows more docile. Soon after, they reach Bill’s waterside ranch in Sausalito, California, where the Gill Man walks placidly into a cage, from which he can see the house and the ocean. Bill forces Marcia to stay in her room, and one night, as he and Tom argue about the creature’s capacity for change, Bill sneers at the notion that violence stems from fear and rants that loyalty is often returned with infidelity. Later, Tom tells Marcia that Bill is disturbed, but she feels helpless to change him, and sympathizes with the caged Gill Man. When she leaves for a swim, Bill calls her a tramp, and the Gill Man watches as an unwelcome Jed joins her at the shore. Just then, a mountain lion leaps into the creature’s cage, and frightened, the Gill Man attacks it viciously. When everyone runs to the cage, Bill sees Jed’s wet hair and, agitated, later insists that he leave. Jed taunts Bill about Marcia, and Bill flies into a rage and kills him, in view of the creature. After Bill dumps Jed’s body in the creature’s cage, the creature, inflamed by the violence, breaks free and pursues Bill into the house. After a prolonged chase, the Gill Man throws Bill off the balcony and then escapes from the ranch. The next day, the scientists gather, and although Borg bemoans the fact that the experiment failed, Tom points out that the creature did not revert to his base instincts until after he was provoked. While Tom promises to visit Marcia soon, they receive notice that the Gill Man has been spotted heading toward the coast.