The National Resources Access Regulator has found that over 40,000ML of water was taken out illegally in one year

The huge amount of overdrawn water is the equivalent of 16,000 Olympic swimming pools worth of water, and is prompting a crackdown on water holders who take more than their share.

NRAR's Director of Regulatory Initiatives Ian Bernard said they would not be taking it likely.

"There's an outdated practice whereby people treat their water accounts like bank accounts, occasionally going into the red by taking more than they've been allocated and simply paying it back later. That practice is against the law," he said.

"Only six per cent of water accounts were found to have overdrawn their accounts, which tells us that most people are doing the right thing ... But this small number of rule breakers have a big impact on our water resources and can cause significant harm to industry, communities, culture and the environment."

Officers are now looking into data from 2022-23, searching for overdrawn accounts.

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Mr Bernard had a stark warning for waterholders who might be tempted to skirt around the regulator.

"World-class technology and intelligent data allow us to be anywhere at any time, with the click of a button ... If you overdraw your water account, NRAR will know about it, and you can expect to hear from us," he said.

"Water users have a responsibility to learn and follow the rules. Breaking them is simply not worth the risk."

One landholder in Carrathool was found to have overdrawn their account by over 2000 megalitres, and was forced to pay over $100,000 in fees and reparations - including an $80,000 payment to Hay Shire Council.

The holder was also required to pay for the extra water, surrender several licenses and conduct weekly manual water meter readings for three years - in addition to paying NRAR $35,000 in legal costs.

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