In the early 1960s, during the height of the Cold War, Elisa Esposito, a mute and isolated woman, works as a night-time cleaner at a high-security government laboratory in Baltimore. Elisa's life is simple and routine, her interactions limited to her co-worker Zelda, who serves as her interpreter at work, and her neighbor Giles, a struggling advertising illustrator. One day, the facility receives a classified experiment, an amphibious creature captured in the South American rivers, which is held in a water tank and studied for possible advantages in the space race against the Soviet Union.

Elisa discovers the creature and feels an immediate connection as she shares her own experience of being misunderstood and not being able to communicate traditionally. She spends time with the amphibious being, secretly visiting him in the lab, and forming a unique bond through music, hard-boiled eggs, and sign language. Her affection for the creature grows, leading her to take great risks to ensure his well-being. Meanwhile, the creature's primary captor, a ruthless government agent, is determined to exploit him, viewing the creature as nothing more than a tool for furthering his own career and the United States' dominance in the Cold War.