A cotton farmer has pleaded guilty to illegally pumping water from the Murray-Darling Basin, after he was charged following an ABC Four Corners investigation.

Key points: The charges came after an ABC Four Corners report into water theft

The charges came after an ABC Four Corners report into water theft Anthony Barlow's property is near the Queensland border

Anthony Barlow's property is near the Queensland border Court proceedings against Mr Barlow's parents have been dropped

Anthony Barlow's hearing in the Land and Environment Court started in Sydney today, where the cotton grower backflipped on an earlier decision to fight the charges.

He was charged with pumping water while metering equipment was not working and pumping water during an embargo in northern NSW.

The court proceedings came after the ABC Four Corners report, which uncovered allegations of illegal pumping at Mr Barlow's Mungindi property near the Queensland border.

Mr Barlow's parents had also been charged with pumping water during the embargo, but those charges were today dropped.

A cotton farm in NSW. ( ABC News )

The case is one of two being prosecuted by Water New South Wales after the Four Corners investigation, which also sparked an overhaul of water management in the state.

The NSW Government has established an independent regulator, the Natural Resources Access Regulator (NRAR), to boost transparency and public trust.

NRAR chief regulatory officer Grant Barnes said the new body had investigated more than 300 tip offs from the public in its first six months.

Outside court, he said the state had picked up its act.

"I think other basin states are watching closely, New South Wales, and how we are addressing water compliance," Mr Barnes said.

He said the industry needed to change and that people in NSW did not want people stealing water from the basin.

'No place for water thieves' in NSW

The New South Wales Minister for Primary Industries, Niall Blair, hailed the guilty plea as a victory for tougher compliance, saying there was "no place for water thieves" in the state.

"It brings down the good name of all of those who have been doing the right thing and it undermines confidence in the system, so good riddance to those who want to do the wrong thing," he said.

"We are coming after them and this prosecution is just an example of that."

Mr Blair said he would consider tougher penalties for special cases.

"I'll keep going. If I need to keep going to make sure we stamp out these rogue operators — the minority — we will."

He said the guilty plea sent a strong message to those looking to exploit the state — and nation's — water.

"At the moment I am confident we have the resources in play to make sure that those that are doing the right thing are protected and those that are doing the wrong thing are weeded out," he said.

Water New South Wales also condemned water theft, while and the New South Wales Irrigators Council issued a statement saying it respected Mr Barlow's decision to pursue the case, and that the industry relied on strong compliance.