Although the opening titles claim the film was based on "the diary of the monk Gaspar de Carvajal", director Werner Herzog has stated that there is no historical basis for the story and that the monk's diary was invented to lend it more credence. However, a diary of Carvajal does in fact exist, but Carvajal was not part of any expedition with Aguirre, but rather part of one 20 years earlier to the interior.
According to director Werner Herzog, Klaus Kinski threatened to abandon the film entirely at one point during the shooting. 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. Kinski stated in interviews that Herzog wielded a pistol to emphasize the threat, but Herzog denies this.
Near the end of the shooting, Werner Herzog thought he had lost all the negatives that the film was shot on. He later discovered that the shipping agency at the Lima airport had completed all paperwork that accompanied the transportation of the film cans, but had not actually shipped them. The cans were thought lost for several weeks before the oversight was revealed.
Most of the film, as well as several other features by Werner Herzog, was shot on a 35mm camera that he stole from his film school. He readily admits to the theft but also attempts to justify it with the significance of the films he's made with the camera.
Many of the scenes depicted in the film were unrehearsed and unstaged, and the dividing line between the cast acting in character and simply reacting to their situations as people became very blurry. For example, in one of the opening scenes, when the carriage holding Aguirre's daughter 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.
Werner Herzog claims to have written the screenplay in two and a half days. He wrote a good portion of it while traveling with his soccer team, during games and on bus rides. Following one game, the team was very drunk, and the player seated behind Herzog vomited on his typewriter, ruining many pages of the script. Herzog was unable to salvage the pages, and tossed them out the window. He was also unable to recall what he'd written on them.
During one scene set in a native village, Klaus Kinski hits one of the crewmen over the head with his sword. The blow nearly killed the man, and only his helmet saved his life.
This was the first Werner Herzog film with Klaus Kinski. It was the start of an extremely stormy, and sometimes violent, professional relationship that lasted 15 years,
During a particularly rowdy night of production, Klaus Kinski repeatedly fired a Winchester rifle into an occupied tent. 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.