Millions of litres of highly toxic water is escaping from a derelict coal mine into Sydney's drinking water catchment, according to new scientific research.

Dr Ian Wright, one of Australia's leading water scientists, tested waste water from the derelict Berrima Colliery, and said pollution levels are the highest he's ever seen.

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

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

The underground mine water flows into the Wingecarribee from this single drainage pipe – currently dispensing 2.6 megalitres, or about an Olympic swimming pool – each day. ( ABC News: Greg Miskelly )

Dr Wright said the contamination was "internationally significant", with heavy metals in the Wingecarribee River far exceeding safe environmental levels.

Levels of zinc are especially high — more than 120 times the normal baseline level.

KEY REPORT FINDINGS Median concentrations of nickel (430 ug/L), manganese (12667 ug/L) and zinc (1400 ug/L) are at extremely high levels

Median concentrations of nickel (430 ug/L), manganese (12667 ug/L) and zinc (1400 ug/L) are at extremely high levels 89% of aquatic insects sampled in the vicinity of discharge have been wiped out (Ephemeropetera, Plecoptera and Trichoptera species)

89% of aquatic insects sampled in the vicinity of discharge have been wiped out (Ephemeropetera, Plecoptera and Trichoptera species) Overall pollution has increased despite the mine's closure in 2013

Overall pollution has increased despite the mine's closure in 2013 Other contaminants include high levels of acidity, salinity, iron and sulfates.

The mine's owners, Boral, declined a request for interview, but told the ABC the company is aware of Dr Ian Wright's work and have cooperated with him to provide 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 said.

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

The mine is currently under "care and maintenance" provisions and Boral are in the process of seeking approval to rehabilitate and abandon the mine.

Concerns over fishing food chain

Paul Miller believes fishing will be impacted by the pollution of the Wingecaribee River. ( Supplied: Paul Miller )

"From a fisherman's point of view we're concerned about the insects the fish thrive on, the food-chain," said Paul Miller, president of Fly Fishers in the Southern Highlands.

"Good clean healthy fish must be good for your diet.

"But fish that are contaminated with some elements, that can't be good for you."

Another cause for concern is the fact that river water flows to dams which feed Sydney's water supply.

Community activist Peter Martin said authorities must now carefully consider the danger posed by new mines close to the water catchment.

"When it comes to big resource projects, governments, the mining companies blindly ignore real impacts on the environment, on the communities," he told the ABC.

"I think this is a huge wake-up call.

"I mean, this river is extremely polluted and it'll come as a real shock to the locals, the level of pollutions here.

"Obviously, we've got to stop it from happening in the future."

EPA welcomes research

The Environmental Protection Agency (EPA) was approached for comment, and told the ABC that the contamination "only emerged" in late 2015.

The Wingecaribee River is a highly protected river and part of Sydney's drinking water catchment. ( ABC News: Greg Miskelly )

A spokesperson told the ABC that it welcomes the research, and will work with Dr Wright and other stakeholders "to look at the best course of action" on the mine.

Dr Wright said the Berrima Mine study holds lessons for the regulation of other coal mines around Australia.

And he warned the flow of pollution out of the abandoned mine could be incredibly long-lived.

"This can go for decades," he said.

"There are bronze-age mines in the northern hemisphere that are polluting centuries later.

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