She says rain will not end drought conditions across Southern NSW if the government "allows special interests to secretly siphon off" water before it reaches the river.

Yet Federal Water Minister Keith Pitt and Senator Perin Davey said the move was made well within the rules.

On February 7 the government announced it would restrict the harvesting of overland flows in the northern Murray-Darling Basin for the first time.

But the ban was lifted just days after, allowing several large cotton properties to take the first flows in years

"Government ministers keep saying only rain with fix our problem... Well, with the rain this month we've seen a secret regulation change that allowed rainwater to be diverted for private use," Mrs Dalton said.

Mrs Dalton further criticised NSW Water Minister Melinda Pavey for "preventing the water from reaching the Darling River."

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Emails obtained by the Guardian show the NSW Department of Planning, Industry and Environment asked irrigator groups for "urgent" advice on water infrastructure damage their members would see if water flowed across their land.

However by the time the emails were sent, the exemption had already been made.

"This regulation change was made in secret, with no consultation, and no details released to the public," Mrs Dalton said.

Mr Pitt said his understanding was that "NSW was acting within the rules." Ms Pavey's department stated she had not played a role in the move, and Mr Pitt said "further discussions" were going to take place.

"I understand NSW was acting within the rules, as are Queensland, and I look forward to having a further discussion with the shareholding minister," he stated.