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According to Werner Herzog, Klaus Kinski threatened to abandon the film entirely at one point during the shooting over Herzog's refusal to fire a sound assistant. Herzog says he threatened to kill Kinski and then turn the gun on himself if Kinski left - and later declared he was quite prepared to do so, knowing that the authorities would write it off as a hunting accident. Kinski stated in interviews that Herzog wielded a pistol to emphasize the threat, but Herzog denies this.
During a particularly rowdy night of production, Klaus Kinski, irritated by the noise from a hut where cast and crew were playing cards, repeatedly fired with a Winchester rifle into it. One of the bullets took the tip of an unnamed extra's finger off. Werner Herzog immediately confiscated the weapon and it remains his property to this day.
Many of the scenes were unrehearsed and unstaged, blurring the line between the cast acting in character and simply reacting to their situations. In one opening scene, when the carriage holding Ursúa's mistress tips over and threatens to collapse, a hand comes in from the right side of the frame to assist the actors in steadying their hold. That hand belongs to director Werner Herzog.
The complete crew consisted of eight people.
In his commentary, Werner Herzog explained how he manipulated star Klaus Kinski into giving the performance he wanted. Kinski wanted to express Aguirre's madness at the end of the film with very loud shouting. Herzog had him do that for an hour and a half until Kinski grew tired. Then, he was very quiet and much more contained.
According to Werner Herzog's commentary, he paid the men who were to provide the monkeys at the end of the film only half of what they asked for, thinking they would try to run off with the money. The dealers took the money, then sold the monkeys to someone else, and prepared to fly them to Florida. In desperation, Herzog pretended he was a veterinarian and said the monkeys didn't have their vaccination documents. After filming, he released the monkeys into the wild.