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In the upper reaches of the Brazilian Amazon, archaeologist Dr. Carl Maia and his team, including Luis, Zee and Chico, excavate a webbed claw from a wall of limestone. Carl rushes the claw to the nearby Instituto de Biologia Maritima, leaving Luis to guard their camp. At the institute, marine life specialist David Reed and his girl friend Kay, amazed with Carl's finding, bring the claw to their boss, Dr. Mark Williams, and the other institute doctors, including Dr. Thompson. After the men agree to fund a more thorough investigation, the group boards the boat of local sailor Lucas to reach the camp. Upon arriving, Carl is devastated to find that a mysterious creature has torn Luis to pieces. No one notices when a webbed hand creeps out of the water toward Kay's leg, disappearing when she walks away. Over the next eight days, the team digs up the limestone but finds nothing, causing Mark, who is eager for publicity-worthy finds, concern about wasted time and funds. One day, David deduces that a lagoon at the end of the river probably holds more fossils. Although Lucas recounts an eery legend about a half man-half fish creature, or Gill Man, that lives in the unexplored Black Lagoon, everyone boards the ship. On board, Mark watches jealously as Kay kisses David. They reach the lovely lagoon the next day, where the Gill Man watches David and Mark as they dive for rocks to test. While Carl discovers that the rocks match the makeup of the limestone, Kay swims out into the lagoon. The Gill Man, fascinated with her beauty, follows her through the water, once touching her foot gently. Before she notices his presence, however, the men call her back, and when the Gill Man pursues her, it becomes tangled in the boat's net. The men struggle to raise the net quickly, but the creature escapes at the last minute, leaving a talon behind. Mark is eager to find and kill the Gill Man, but David urges him to preserve the creature and its natural habitat. They dive, and when the Gill Man attacks them underwater, David takes a photograph and Mark shoots it in the back with a harpoon. On the boat, David chastises Mark, but when his photograph reveals only seaweed, Mark worries that no one will believe their story unless they bring back the Gill Man's body. While the other doctors argue over its existence, the Gill Man drags Chico over the boat and kills him. The next day, Lucas sprinkles the lagoon water with a drug he uses to sedate fish, but the Gill Man avoids the drugged waters. That night, the Gill Man climbs on board to grab Kay, and after her scream scares it back into the drugged water, David follows it, afraid the creature will suffocate underwater. The creature escapes into a grotto, with David close behind and the others on the shore in a rowboat. The Gill Man then circles around to the shore to grab Kay again, and when Tomas tries to stop it, the creature kills him but then collapses. David stops Mark from killing it, instead imprisoning it in a water tank on the boat. Mark's command for the team to leave immediately is vetoed by David, who insists that they stay to complete their experiments. Dr. Thompson stands guard over the creature while the scientists gather more data, but the Gill Man soon escapes his tank and slashes Thompson's face, leaving him near death. The next day, David announces that they cannot risk any more attacks and so must leave. This time, Mark insists that they stay to kill the Gill Man, but Lucas holds a machete to Mark's neck and starts the engine. On the way out of the lagoon, however, they discover that the creature has blocked the boat with a huge log, trapping them. When they cannot clear the log from above, David dives under the boat, followed by Mark, who still wants to kill the Gill Man. The moment it attacks, Mark shoots it with a harpoon. Only slightly wounded, the creature grabs Mark, and although David scares it away, he is too late to save Mark's life. On the boat, David devises a plan to shoot the rest of the drug directly at the creature, hoping to disable it long enough to clear the log. He dives down and surrounds the Gill Man with the drug. As soon as he moves the log and the boat can sail, however, the creature climbs aboard, grabs Kay and dives back into the water with her. David follows them into the grotto, where the still-groggy creature attacks him. Carl and Lucas appear in time to shoot the creature several times with bullets, after which David asks them not to shoot again. They watch in silence as the wounded Gill Man struggles into the water and slowly sinks out of sight.