Elisa Esposito, who was found in a river as an orphaned child with wounds on her neck, is mute, and communicates through sign language. She lives alone in an apartment above a cinema, and works as a cleaning-woman at a secret government laboratory in Baltimore at the height of the Cold War. Her friends are her closeted next-door neighbor Giles, a struggling advertising illustrator who shares a strong bond with her, and her co-worker Zelda, a woman who also serves as her interpreter at work.

The facility receives a mysterious creature captured from a South American river by Colonel Richard Strickland, who is in charge of the project to study it. Curious about the creature, Elisa discovers it is a humanoid amphibian. She begins visiting him in secret, and the two form a close bond.

The film features an original score from composer Alexandre Desplat.

Alexandre Michel Gérard Desplat (born 23 August 1961) is a French film composer. He has won two Academy Awards for his soundtracks to the films The Grand Budapest Hotel and The Shape of Water, and received seven additional Academy Award nominations, eight César nominations (winning three), seven BAFTAnominations (winning three), seven Golden Globe Award nominations (winning two), and six Grammy nominations (winning two).