ULAN, Moolarben and Wilpinjong coalmines have been granted temporary variations to their water licences to allow effectively unlimited saline discharges after heavy rain.
Environmentalists and some residents have complained about the licence variations, but the state government said they were justified.
A spokesman for the Department of Environment, Climate Change and Water said Mid-Western Council had declared "a natural disaster area" and "controlled discharges" of mine water were better than "uncontrolled ones".
The spokesman said Wilpinjong's storage dams were full, threatening the "catastrophic failure of a dam wall".
He said Ulan needed the licence variation to allow it to pump water out of its flooded underground mine.
But Julia Imrie, of Goulburn River Stone Cottages, said the recent rain was not unprecedented and "the decision to allow uncontrolled discharge into the river over many months is a short-sighted, ill-advised, negligent action".
Bylong Valley Protection Alliance secretary Craig Shaw said the mines discharged their saline water into the Goulburn River, which joined the Hunter River at Denman.
Ulan's licence variation runs until March 31, Moolarben's licence runs until February 7 and Wilpinjong's licence runs until January 31.
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