Part of the River Roch and a large stretch of the River Irwell between Salford and Manchester is blanketed in the unknown substance.
Residents suggested it looked like "leaking bubble bath" and expressed concerns for wildlife on the river.
EA officers are on site investigating and Salford City Council said it would "advise residents accordingly".
An EA spokesperson confirmed that its officers had been out on site yesterday “to investigate the pollution to find the source, stop the problem and understand how best to reduce any impacts on local communities and the environment”.
Water samples taken from both rivers have been sent to an accredited laboratory for analysis and the EA said it was waiting for results.
Mike Duddy, from Mersey Rivers Trust in Salford told BBC Radio Manchester it is believed someone has poured a pollutant down a surface water drain.
He advised the public not to enter the waterways after the "huge icebergs of foam" were discovered.