Water scientists say millions of litres of toxic water is escaping from a derelict coal mine into Sydney's drinking water catchment.

Leading expert Dr Ian Wright has tested waste water from the derelict Berrima Colliery, and is very concerned at the findings.

“I've been studying coal mines and water pollution associated with coalmines for nearly 20 years in the Sydney basin,” he told the ABC.

“This is the worst. And it's counterintuitive, to many, to me indeed, that the mines shut down and the pollution has got worse.”

Dr Wright said heavy metals in the Wingecarribee River far exceeded safe environmental levels, with levels of zinc more than 120 times the normal baseline level.

The mine's owners, Boral, have reportedly been cooperating with the investigators by providing them with data and assistance.

“We will now consider his findings, but note that from our initial review they do not appear to accord with other monitoring conducted downstream of his sampling points and as a result, will likely contradict other recent independent research commissioned by Boral,” a Boral spokesperson told reporters.

“This is something Boral will consider further as part of the development of its final closure plans.”

The mine is under “care and maintenance” provisions, and Boral says it is in the process of seeking approval to rehabilitate it.

Dr Wright warned that the flow of pollution out of the abandoned mine could go on “for decades”.

“There are bronze-age mines in the northern hemisphere that are polluting centuries later,” he said.

“I'm sorry to say I have no idea, but I suspect this will be going for centuries.”