As the narrator recounts the story of creation from Genesis, vivid imagery unfolds on the screen, setting the stage for the thrilling adventure ahead.
In the remote jungles of the upper Amazon, Dr. Carl Maia (Antonio Moreno) makes a groundbreaking discovery: a fossilized claw. He eagerly informs his native workers of the significance of his find, expressing his need to return to the coastal institute for assistance in uncovering the remainder of the fossil. However, lurking just beyond their line of sight, a claw similar to the one found surfaces momentarily before vanishing into the river.
At the institute, Dr. David Reed (Richard Carlson) arrives and is surprised to encounter Maia, who reminisces about their days together when Reed was still a student. Reed explains that they are currently studying lungfish. Their conversation swiftly transitions to Maia's inquiry about Kay Lawrence (Julie Adams), prompting Reed to reveal that she has never managed to sway him into marriage. Maia shows Reed a photo of the fossil, convinced it dates back hundreds of millions of years, igniting Reed's enthusiasm to return to the river and extract more from the site.
After discussions at the institute confirm the fossil's potential as a strong amphibian, consensus leads to a decision for a larger expedition to recover the fossil. Night falls at the campsite, where workers prepare for sleep, only for one to be met with a grisly fate as a mysterious creature infiltrates their tents and kills the two occupants.
Fast forward, the expedition team boards the Rita, a rather uncomfortable motor vessel, as Captain Lucas (Nestor Paiva) provides chilling insights about the lethal wildlife surrounding the Amazon. Upon arrival at the campsite, they are met with horror—everything has been destroyed, and the crew members are dead, leading them to theorize that a jaguar is to blame.
Despite this ominous discovery, the crew begins the tedious task of recovering the fossil, but after eight long days, the effort yields no results. Reed suspects the fossil might have been washed downstream into a lagoon, known as the Black Lagoon. Captain Lucas warns them, sharing local legends about a gill man that resides beneath the waters, further heightening the tension.
Amidst the perilous atmosphere, Reed and Kay share a tender moment, discussing their future together as they maneuver the boat toward the lagoon. As Reed and Dr. Williams (Richard Denning) prepare to dive and explore the lagoon, they unknowingly become the objects of fascination and predation for the creature lurking just out of view. Their shared tension escalates when Kay, attempting to break up the rivalry, takes a refreshing swim.
Unbeknownst to her, the creature mirrors her movements underwater, brushing against her leg in an unexpected encounter that piques its curiosity even further. On board, chaos ensues as the net they are deploying suddenly tears, revealing a large fang or claw, leading Kay to question what truly touched her while she swam.
In an ill-fated attempt to hunt the enigmatic creature, Williams disregards Reed's objections and goes diving, where they finally catch a glimpse of the creature but fail to capture it. Lucas informs the team about a native poison that draws fish to the surface, and they agree to deploy it across the lagoon. Although a plethora of fish surface, the creature remains elusive.
As night deepens, they witness the terrifying sight of bubbles rising from the depth, indicating the creature is near. When the creature attacks one of the crew members on deck, panic ensues. Finally, armed with the resolve to capture the creature, Reed and Williams venture forth, only to stalk the cave where the beast resides and track its footprints.
The tension escalates further when the creature attempts to abduct Kay, resulting in chaos when it succumbs and collapses due to its injuries. The team hastily constructs a makeshift cage to contain the creature, while Kay and Dr. Thompson (Whit Bissell) discuss their hopes for the future. However, the creature shatters its confines and attacks Thompson, who valiantly retaliates despite sustaining grave injuries.
Faced with loss and conflict, the team decides it's best to leave the lagoon after suffering four fatalities. As they attempt to navigate their way out, they are thwarted by a suddenly emerged snag, believed to have been caused by the creature itself to hinder their departure. In mounting frustration, Reed takes a plunge into the water, only to be ambushed by the creature. Amidst a fierce combat, Reed calls for help, leading to a chaotic struggle that sees Williams dragged under.
In a gripping climax, the team attempts to use poison once more to incapacitate the creature while they navigate the obstruction. Reed's determination and courage shine through as he finally succeeds in neutralizing the creature with poison, just as it re-emerges, angering it further.
As the boat clears the lagoon, they remain unaware of the creature quietly boarding. However, when it seizes Kay and pulls her underwater, Reed pursues, armed with a spear gun. A battle for survival ensues, leading to the creature’s painful retreat under duress, leaving a tortured outcome that sparks a lingering sense of respect for the creature's struggle. The expedition concludes with Reed’s decision to allow the creature to retreat back into its domain, possibly retreating to its depths to confront the finality of its fate.
