A statement this week from Brazil's National Observatory named the underground river Hamza and said it represents one of two different draining systems for the large rainforest region.
A team of scientists led by Elizabeth Pimentel came to the conclusion from studying 241 wells drilled by the state oil giant Petrobras in the Amazon region.
Even though the two rivers cover a similar path they have differences. The underground river flows at a far slower pace and empties into the ocean deep underground.
"It is likely that this river is responsible for the low level of salinity in the waters around the mouth of the Amazon," the statement said.