The Queensland Government has succeeded in passing laws to tighten groundwater licence requirements for mines, while also appeasing the Indian mining giant Adani.

Labor backed down on aspects of controversial water laws that had angered the mining companies and managed to get the legislation through Parliament in the early hours of Thursday morning.

The Cairns and Cook independent MPs and the Parliamentary Speaker Peter Wellington sided with the Government to pass the Environmental Protection (Underground Water Management) and Other Legislation Amendment Bill 2016 and the amended Water Legislation Amendment Bill 2015.

The legislation requires miners to get a water licence to extract groundwater.

The Labor bill was in response to laws passed by the former LNP government that were due to take effect from December this year that scrapped that requirement.

In October, the State Government declared Adani's Carmichael coal mine project in the Galilee Bason in central Queensland to be "critical infrastructure" to try to fast-track its remaining approvals.

The Queensland Resources Council (QRC) criticised the ALP legislation as a last-minute, left-field development that had the potential to hold up planned projects.

Adani was also critical and claimed the change would give green groups more opportunities to hold up its massive Carmichael mine project in the courts.

Amendment gives Adani more certainty

But Queensland Environment Minister Steven Miles moved an amendment early this morning to give Adani more certainty.

The change means companies that had already undergone scrutiny through an environmental impact statement (EIS) and the Land Court would still require a water licence but would not have to go through the public objection process.

"This will be achieved by allowing associated water licence applications to be exempt from public notification if the mining project has already been through an EIS process and a Land Court objections hearing in which objectors tested the groundwater modelling undertaken by the project proponent with expert evidence of their own," Mr Miles said.

"That particular project has been through two very significant Land Court cases and so what we've said is if they can demonstrate that they have met the requirements of the water licence and all of those elements had been tested in previous Land Court hearings, then this water licence stage would not be appealable in the Land Court.

"It would still be subject to potential judicial review, but not a full Land Court challenge."

Bill creates transparent, streamline approach, Minister says

Mr Miles said the bill addressed the needs of disparate water users to create a transparent, streamlined and environmentally responsible approach to allocating underground water rights.

"For the community, the bill will ensure groundwater impacts are properly considered and can be scrutinised by the public and the courts," he said.

"For the resources industry, there is a streamlined process that better integrates groundwater assessment into the environmental impact assessment process.

"For landholders, the bill not only provides a positive step forward for improved groundwater management, it also will assist landholders to better negotiate make good agreements with resource companies."

While Adani is better protected, the changes would not help the Acland mine near Oakey, west of Brisbane, that is not as progressed.

Mr Miles said it had been the Government's position "that these projects should and would need a water licence".

"That's the situation that particular project is in and I have urged them to talk to the department and get started on that water licence process — there's no need for it to take too long," he said.

Government bowing to green groups, Opposition says

The LNP and Katter MP's opposed the law changes, accusing the State Government of bowing to green groups.

Opposition natural resources spokesman Andrew Cripps questioned why the Government amended the bill for Adani but would not help Acland.

"There is no material difference between these two projects and something is going on here that's not being explained properly, something's going on here that isn't being explained properly and the Minister ought to do so," Mr Cripps said.

Toowoomba North LNP MP Trevor Watts told Parliament the laws would hurt the Acland Mine near Oakey in his electorate and the wider community.

"Make no mistake the commencement of this bill will cost hundreds of jobs on the Darling Downs," he said.

"They should be ashamed of themselves. Those families working the cafes, those kids going to the schools. The families spend their money at the retail stores. "

Lockyer MP Ian Rickuss was also scathing.

"Really this is a company that we should be proud of as Australians, this this is a great Australian company and why they're being held up by this Labor Government beggar's belief," he said.

"But unfortunately it's all about their union mates — it's not about what's good, the progress of the state."

Natural Resources Minister Anthony Lynham said the Water Legislation Amendment Bill 2015 changed three Acts, including preventing some parts of the LNP's Water Resource and Other Legislation Amendment Act 2014 taking effect next month.

Dr Lynham told Parliament the legislation would reinstate the principles of ecologically sustainable development, prevent the introduction of the LNP's water development option, prevent the LNP's designated watercourses, allowing unregulated amounts of water to be taken from rivers and streams.