A World Heritage-protected lake system south-west of Sydney has been "stuffed" by coal mining in the area, a scientist behind newly published research says.

The Tahmoor Colliery has mined near the Thirlmere Lakes, two of which are currently empty, for almost 40 years.

Operators have mined with approvals and under strict regulations - but this has not stopped the damage, according to one of the groundwater experts behind the report.

"Whatever constraints we set 30 years ago have not been good enough," said research co-author Philip Pells, who is also a former mining consultant.

"We have severely impacted, and I would say stuffed this national park. And we have to do something about it."

Dr Philip Pells and Steven Pells have been gathering data on the lake's sensitive catchments for over four years.

Given recent rainfall events water levels were disturbingly low, the pair found.

"There is a strong body of evidence now that the groundwater lost to the coal mine has impacted on the lakes," Dr Philip Pells said.

"Instead of them filling up after significant rainfall events, they have hardly come up at all."

Trees encroach across dry lake

Two of the largest lakes in the system sit empty, and despite recent rains water levels in three other lakes remain low.

Groundwater expert Dr Philip Pells at Thirlmere Lakes testing the groundwater. ( ABC News: Greg Miskelly )

University of New South Wales (UNSW) wetland ecologist Professor Richard Kingsford said gum trees were encroaching on the dry lakes.

"What we are seeing here in terms of the vegetation is the slow death of a wetland," he said.

The Thirlmere Lakes are remnants of a 15-million-year-old riverbed, and according to Professor Kingsford, hold a rich geology.

"You have this amazing sediment, which can then be looked at historically," he said.

"To find out when were the fires around here? When did different plants arrive?"

As well as being a haven for water birds, the lakes were once popular with swimmers and canoeists.

But in recent years the falling waters have triggered a scientific debate as to whether dry conditions or human influences are at play.

New evidence shows coal mine has impacted lakes

Professor Kingsford and fellow environmental scientist Samira Schadler used historic photos and data to develop 3D models of three main lakes.

The analysis shows a systemic fall in water tables following the start of long-wall mining.

Dead water lilies on the dried-out lake bed at Lake Nerrigorang, south-west of Sydney. ( ABC News: Greg Miskelly )

"This was a long-term decline, and the decline happened relatively soon after coal mining started in the 1980s," Professor Kingsford said.

Despite agriculture in the area it was "clear that there was a smoking gun in terms of coal mining, and there were also groundwater bores, and more of them over time," Professor Kingsford said.

The losses are not suspected to be caused by subsidence or cracking.

The nearby Tahmoor Colliery has extracted an average of 1,200 ML of water a year, amounting to almost 500 Olympic swimming pools, causing seepage from the lakes.

Glenmore, which took over Tahmoor Colliery in 2013, said the company operated responsibly.

"The closest longwall activity at Tahmoor occurred at more than double the distance within which mine-induced subsidence would be expected, and our current operations are more than 13 kilometres from the lakes," a statement said.

Research to the contrary of official inquiries

The new research stands at odds with two official inquiries, held in 2010 and 2012, which both suggested periods of drought and low-rainfall could be behind water impacts.

NSW Environment Minister Mark Speakman said the research was "plausible", but Government scientists were seeking more definitive data into water levels.

"We know that over the last 100 years the lakes have dried out from natural causes, it would seem drought and low rainfall," he said.

"The jury is out as to whether there are man made causes that aggravate that.

"But we need more data, more research, and that's what the Chief Scientist, DPI Water (Department of Primary Industries) and the OEH (Office of Environment and Heritage) are working on. And once we have that data a more reliable response will follow."

The OEH said it hoped wet weather would restore the lakes.

"Current monitoring shows that there is still water in the peat beneath the bed of the lake and presumably the water will rise again once we get back to wetter weather."