Men capture the creature from the Black Lagoon and make him an aquarium attraction, from which he escapes.

In the upper Amazon, two employees of Jacksonville, Florida's Ocean Harbor marine center, Joe Hayes and George Johnson, set out to capture the notorious Gill Man, a dangerous half-fish, half-man creature. The captain of the expedition, Lucas, who was with a team that spotted the Gill Man the previous year, warns the cocky men that the creature will bring only harm to mankind. They explain that, since the Gill Man is a prehistoric creature that may be the missing link between marine and terrestrial life, he is invaluable to science, but Lucas believes that he is a demon. The next day, the team reaches the Black Lagoon and Joe dives into the water to search for the Gill Man. Within moments, the creature attacks, and the group barely manage to rescue Joe. They then detonate dynamite over the surface of the water, which stuns the Gill Man and causes him to float up, where he is easily trapped. In a coma, the Gill Man is brought to Ocean Harbor, where Joe walks him around a shallow tank, hoping to revive him in the same way that sharks are resuscitated. Watching in the tangle of tourists is lovely graduate student Helen Dobson, who is gathering material for her master's thesis in ichthyology. Hours later, the Gill Man stirs, and within minutes jumps over the side of the tank, pulling technicians into the water. As the tourists scatter in panic, the team captures the Gill Man with a net and then shackles him to the bottom of the tank. Soon, the creature is the center's main attraction, and animal psychologist Prof. Clete Ferguson travels to Florida to head the team of scientists investigating the Gill Man's behavior and link to humankind. After he and Helen experience an instant attraction, Clete is happy to include her in his research team. One night, Helen accepts Clete's invitation to dinner, and although Joe is envious, he accepts his defeat with grace. Clete's first experiment aims to condition the Gill Man to respond to commands, and to this end, he and Helen enter the tank, attract the Gill Man with food, then shock him with a cattle prod after Helen tells him to "stop." Their work is successful, but the Gill Man grows fascinated with Helen, especially when she stops at the window outside his tank each night to watch him. Further studies, including one in which the Gill Man's brain waves are studied, reveal that the creature is anatomically very similar to humans. One day, Clete and Helen take a break on the beach, where Helen muses about her future plans, realizing that she must eventually choose between a career and a family. Clete reveals that he has a personal interest in her decision and kisses her, stopping only when her dog, Chris, bounds onto their towel. That night, Helen visits the Gill Man's tank, sympathetic to his unmistakable sadness. Clete finds her and informs her that he now believes that it is too risky for her to join him in the creature's tank, but she scoffs at his concern. The next day, they are in the tank when suddenly the Gill Man attacks Clete, backing off only after Helen commands him to stop. Clete escapes, but then the creature tears at its bonds and leaps out of the tank, causing the Ocean Harbor guests to flee in terror. Trying heroically to stop the creature, Joe is killed, and in the ensuing chaos, the creature escapes into the sea. Four days later, conflicting reports place the Gill Man anywhere from Maine to the Amazon, but in reality he is still in Florida, wandering outside Helen's hotel room. That night, while Helen showers, Chris hears the creature outside and howls, attracting Clete's attention. He and Helen search the grounds but cannot find the dog, and Clete distracts a grieving Helen by planning a cruise for them the next day. Although Clete must soon return to his university for three months, the couple plans to marry as soon as he returns. During the cruise, Clete and Helen swim all day, not realizing that the creature swims just below them. That night, while they dance at a nightclub by the docks, the Gill Man reaches up for Helen's foot, but they move away just in time. Soon after, however, he follows them into the club and grabs Helen, pulling her into the sea with him. Clete joins the Coast Guard in a hunt, but they find no information until two students spot Helen's unconscious body on a deserted beach and, upon investigating, are attacked by the Gill Man. The Coast Guard swarms to the beach, where a team soon spies Helen's body at a different location. The creature, which cannot leave the water for long, tries to protect his love, but she soon revives, and Clete rescues her. As soon as she is safely in Clete's arms, he shouts at the creature to stop. After the creature obeys, the police open fire on the Gill Man, who crawls back into the water and, wounded, sinks to the bottom of the ocean.