They were alerted after several calls from members of the public who had seen what they thought was sewage gushing into the Silchester Brook and Foudry Brook near the village.
Three environment officers and two fisheries experts are at the scene tonight but there was concern at reports that people had been removing dead fish from the water and the Agency is asking that they be left where they are until the full extent of the pollution has been established.
Environment officer Ben Govan said: "This is a serious incident which has affected a long stretch of the Foudry Brook and Silchester Brook.
"Environment officers are currently on site collecting evidence and sampling, and we have staff taking further samples from the river and doing some ecological monitoring.
"We would like to thank members of the public for informing us of this incident promptly, and will fully investigate the causes and impact of what has clearly been a serious incident."
It is understood the Agency has traced the source of the pollution and will take charge of the clwean-up and salvage operation.
The public can report pollution incidents by calling the Environment Agency's emergency hotline on 0800 807060.