Shooting a documentary about a long-lost Indian tribe on the Amazon River, director Terri Flores (Lopez) and members of her crew, including cameraman Danny Rich (Ice Cube) and Professor Steven Cale (Stoltz), come across stranded snake hunter Paul Sarone (Voight) and help him, believing he knows how to find the tribe they're searching for, but Sarone acts strangely and the crew suspect something. When Cale is bitten by a poisonous wasp which entered his mouth (leaving him unconscious for nearly the rest of the film), Sarone takes command of the boat...and the crew.
They are then forced to help him achieve his true objective; hunting down and capturing a record-breaking Green Anaconda he had been tracking. During the process, several members of the crew are killed before the snake itself is shot dead and Sarone incapacitated by the newly awakened Cale.
Later on, Terri and Danny, two of the surviving members of the crew, are captured when Sarone catches up to them. He dumps a bucket of animal blood on them and then uses them as bait in an attempt to capture a second, larger Anaconda.
The anaconda, Terri and Danny are caught in a net by Sarone, but escape when the snake breaks free. The survivors cut their bonds and break free as Sarone himself is killed by his quarry. The snake becomes trapped in the smoke stack, which Danny ignites and it seems to have died. As Terri and Danny recuperate on a nearby dock and the snake appears one final time. Danny beats the anaconda with an axe until it is finally slain.
Afterwards, the survivors of the expedition reunite on the ship, and as they float down the river, accidentally locate the natives they were originally searching for. They realize Sarone was right and begin filming their documentary as the movie ends.