The 64-year-old is the alleged leader of a drug trafficking organisation that smuggled tens of thousands of kilos of cocaine, according to the office of Loretta Lynch, US Attorney for the Eastern District of New York.
Nicknamed "El Abuelo" ("The Grandfather" in Spanish), he was extradited from Panama on Friday and arraigned before US Magistrate Judge Lois Bloom on Sunday, it said.
Juarez "led a large-scale maritime and land transportation operation responsible for trafficking multi-ton quantities of cocaine from Central America, through the waters of the Atlantic Ocean to the coast of Mexico" from the early 1990s until his arrest in March 2012.
Juarez also allegedly worked with major Colombian and Mexican drug traffickers including the Beltran-Leyva cartel and the Sinaloa cartel.
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In the mid-2000s, his group was responsible for transporting more than 35,000 kilos of cocaine for the Beltran-Leyva cartel alone, according to court filings.
In addition, at the height of its activity, it allegedly handled some eight tons of cocaine a month in conjunction with the Sinaloa cartel, prosecutors added.