A community farm told the BBC that the discoloration of Canons Brook in Harlow, Essex had happened before.
The EA said it was investigating but that it had so far found no evidence of harm to wildlife.
Elliot Wollen, manager at Herts and Essex Community Farm, told the BBC: "It's a really vivid blue, you can't miss it at all and if you follow the brook down, it goes as far as you can see.
"This brook leads into the River Stort, so it's contaminating a huge area with this unknown substance."
Wollen said on previous occasions the brook had turned yellow, pink and red.
"Children play in these streams, people walk their dogs and they go into the water...it leads down to the River Stort and there's an outdoors pursuits centre where they are running holiday clubs at the moment," he added.
He said his farm had stopped using the water from that part of the brook to water crops and had moved upstream to extract water.
In a statement, the EA said: "Our specialist officers are investigating how Canons Brook in Harlow turned blue over the weekend, but thankfully have no current evidence of harm to wildlife or the environment."