It's 1519 Spain and Tulio (voice of KEVIN KLINE) and Miguel (voice of KENNETH BRANAGH) are two petty con men who've just won a map to El Dorado, the legendary city of gold. Before they have much time for celebration, however, their gambling ruse is discovered and they inadvertently become stowaways on a ship in Spanish explorer Cortes' fleet that's bound for Cuba.
After a daring escape and much time at sea in a small longboat, the two con men, along with Cortes' intelligent steed, Altivo, wash up on a tropical island. Recognizing the environs from their map, the three set off looking for the hidden city, but instead encounter a native woman, Chel (voice of ROSIE PEREZ), and a small contingent of armed soldiers who were pursuing her.
Mistakenly believing Tulio and Miguel to be gods, the soldiers take the men to El Dorado where they meet the Chief (voice of EDWARD JAMES OLMOS), and his high priest, Tzekel-Kan (voice of ARMAND ASSANTE), who wishes to use their arrival as a means of overthrowing the Chief. Everyone but Chel believes the men to be true gods, and she becomes a partner of sorts in their plan to return to Spain with all of the gold that's been showered upon them.
As the men try to keep up their ruse over several days as the workers build them a ship to return to the "heavens," Tulio and Miguel must not only contend with their true identities being revealed as well as Tzekel-Kan's evil plans, but also the growing differences between them and the possibility of Cortes' arrival in their luscious jungle abode.