Concerned ramblers have alerted the Environment Agency after finding the water running through a woodland stream had turned bright green.
The discoloration was noticed in Fairywell Brook in Fairywell Woods in Timperley on Thursday morning.
A picture of the bright green stream was shared on Facebook by Diane Plunkett and sent to the Mersey Rivers Trust.
Reports were made to Trafford Council and the Environment Agency.
Some posters speculated the colour was because of harmless tracking dye, which is used to track the flow of water. Others thought it might be paint.
The river runs between the Redbrook Road estate in Timperley and Wythenshawe Hospital.
The green discoloration appeared to have gone by the afternoon when the M.E.N. visited the spot.
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In August, residents in Radcliffe found the River Irwell suddenly turned green.
The Environment Agency was called in to investigate.
A similar discoloration occurred on the same stretch of river in 2014 when scientists blamed pollution caused by calcium carbonate.
A spokesperson for Trafford Council said: “The striking colour comes from a plant-based dye that we’ve used to trace the drains from work been doing on Dobbinetts Lane.
“The dye is harmless, won’t pollute the watercourse and will soon disappear.”