The two were arrested within about an hour of each other Thursday.
Border Patrol agents saw immigrants near the pipe's Rio Grande outflow grate.
They radioed other agents, who followed underground voices toward Brownsville's downtown.
Agustin Sanchez Cruz was arrested after agents opened a manhole cover and coaxed him and three others out of the pipe. The other immigrants said he was the guide.
About an hour later, bike patrol agents waiting by the manholes spotted Ramon Acosta Hernandez climbing out to the street. They arrested him after a brief chase.
Acosta Hernandez was charged with smuggling four other immigrants, though it was unclear where the others were apprehended.
A federal magistrate Monday set bond for both at $50,000.
The attorney appointed to defend Sanchez Cruz said she had not had time to review the case and had no comment. Acosta Hernandez's attorney did not immediately return a call late Monday afternoon.
The Rio Grande drainage pipe has been identified as a smuggling route, and the Border Patrol notified the city of Brownsville that the outflow grate was being compromised, said Border Patrol spokesman John Lopez.

