A lonely, mute cleaner named Eliza (Sally Hawkins) has few friends, other than her co-worker, Zelda (Octavia Spencer). They both work in a hidden, high-security government laboratory.

Eliza likes to wander around the laboratory and discover what the scientists are working on. She comes across an amphibious creature kept in a small tank of water and realizes that the creature can not only communicate, but is intelligent and has emotions. 

She develops a relationship with the creature, who was captured in the Amazon before being brought to the laboratory for experimentation. When she discovers that the scientists, including Strickland (Michael Shannon), plan to kill him in order to study him, she decides it's time to help her new friend escape.