The Hunter's unusual ecology derives from its geographic location, bridges as it does tropical and subtropical zones. It also connects coastal and inland NSW through a break in the Great Dividing Range.

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Georgina Woods, a spokeswoman for the Lock the Gate Alliance, said the report's findings indicate how mining is potentially affecting farming in the region, especially during the current dry spell.

"This represents a major impact on agriculture in the region, and is even more devastating during a severe drought like that we are experiencing at present when farmers are under pressure already," Ms Woods said.

The assessment also highlighted the potential impact of the Bylong coal mine, a thermal coal project proposed for a region east of Mudgee.

The report found the groundwater drawdown could affect about 500 square kilometres, 137 of which are within the Blue Mountains World Heritage Area.

"The World Heritage Area sets aside [a region] needing our highest possible conservation," Ms Woods said. "Having an underground mine right next to it is not keeping with our obligations."

Ms Woods said the report's findings suggest the government should pause in its approval of the new mines, particularly for Bylong Valley.

A spokesman for the Department of Planning and Environment said the government would give the report "careful consideration"

"All new mine proposals are subject to rigorous assessment and approval processes under the EP&A Act, which includes careful consideration of all cumulative dust and noise emissions and cumulative impacts on surface water and groundwater systems," the spokesman said.

Stephen Galilee, chief executive of the NSW Minerals Council, said the report was a high-level study that included some hypothetical projects like Drayton South that won’t be proceeding.

"Overall, the results show the impacts of mining are relatively small within the context of the bioregion," Mr Galilee said, noting Hunter River flow impacts are likely to be between 1 per cent and 1.6 per cent.

However, Jeremy Buckingham, the Greens resources spokesman, said coal mining in the Hunter had had a "massive impact" on the region's rivers and groundwater.

"The Greens believe that protecting valuable water assets should be prioritised before coal mining," Mr Buckingham said.

"Before coming to government the Liberal leadership donned 'Water Not Coal' T-shirts and Barry O’Farrell promised to stop mining in 'All drinking water catchments – no ifs, no buts a guarantee,'" he said.

"The government has since abandoned this promise and we see mines such as Wallarah 2 and Bylong getting approved despite the severe impact on water."