Deep in the Amazonian rainforest, a group of scientists discovers a fossilized hand that appears to belong to a link between land and sea creatures. Intrigued by the possibility of uncovering an evolutionary missing link, the team, led by ichthyologist Dr. David Reed, mounts an expedition to find the remainder of the skeleton. Accompanying Reed are his girlfriend and colleague, Kay Lawrence, the financier of the expedition, Mark Williams, and the captain of the boat, Lucas. They set out on a boat named the Rita, heading deep into the uncharted waters of the Black Lagoon.

As the scientists begin their research in the lagoon, they soon learn that they are not alone in these mysterious waters. The team encounters a strange, amphibious being— a living member of the species they believed to be long extinct. While Reed is motivated by scientific curiosity and hopes to study the creature peacefully, Williams sees an opportunity for fame and insists on capturing it. The creature, displaying intelligence and curiosity, becomes infatlyated with Kay, leading to a series of escalating encounters between human and non-human. The expedition soon turns into a struggle for survival, with the crew forced to defend themselves against the unknown dangers lurking below the lagoon's surface.