But environmentalists have questioned why it appears the other charged were dropped.

The Environment Protection Authority prosecuted the US-owned miner's subsidiary Metropolitan Collieries after heavy rains led to significant spills of coal material into Camp Gully Creek at Helensburgh.

This creek flows into the Hacking River and through the national park; coal wash material was found throughout the length of the park as far as the Audley weir.

A directions hearing was held last Friday in the Land and Environment Court and a Peabody spokeswoman said the miner pleaded guilty to three charges .

Two related to the pollution and two others relating to failing to properly maintain the site were collapsed into one, the third charge.

Peabody, which has a licence to discharge waste water into the creek, has since committed to a series of improvements at the mine site, aimed at preventing a repeat of the spills.

The spokeswoman said maintaining the confidence of the community was a top priority for the miner.

"Our team at Metropolitan Coal has worked tirelessly in co-operation with the EPA to implement a comprehensive program of structural improvements to surface water management facilities and upgrades to water monitoring equipment and procedures to help improve the management of record-breaking rain events like those experienced in the past few years," she said.

"That program of work continues.

"Peabody is 100 per cent committed to continuing to operate our Metropolitan mine in the Illawarra, mining responsibly and providing jobs and critical steel making coal for NSW."

Peabody declined to specify whether or what charges were dropped, referring the question to the EPA.

The EPA claimed it could not detail the specific charges as the matter was still before the court.

It's a win for the EPA which will obtain a conviction without having to go to a hearing, but Catherine Reynolds from the Sutherland Shire Environment Centre, whose members were involved discovering and reporting spills, said penalties would be reduced with charges dropped.

"We were very glad when the EPA brought five criminal charges against Peabody, each with a maximum fine of $1 million," she said.

"On Friday the company pleaded guilty to three of those charges, which is good news. But the EPA has chosen to drop the final two charges, and it is not clear why.

"It immediately drops the maximum penalty we can hope to see to $3 million, which is meaningless to a company that size.

"It's highly unlikely that the river can ever be restored to its natural pristine state."

Ms Reynolds said there was still coal waste in the river today.

"Our stream watch group went up to Camp Gully Creek and the Hacking River again recently, and these waterways are still full of coal waste sediment," she said.

"Even if the water looks clear, you only have to put your hand in the sand, swirl it around and the water turns black. The coal in the river is visible for kilometres."

The EPA spokesperson said the case was not finalised.

"The NSW Environment Protection Authority is proceeding with the court case against Metropolitan Collieries Pty Ltd, who have pled guilty to three charges," an EPA spokesperson said.

"These include two charges for water pollution offences in September and October 2022, and one charge relating to breaches of their Environment Protection Licence."