Non-Labor parties and independent senators approved the moves this week, including one proposal to block Victoria's controversial north-south pipeline project.

But the Greens confirmed that the amendments to legislation enabling the Commonwealth takeover of the Murray-Darling Basin would require those cities that take drinking water from the river be "weaned off".

At a joint news conference, Opposition water spokesman Greg Hunt, Greens senator Rachel Siewert and independent senator Nick Xenophon called on the Government to pass the amendments in the lower house.

Mr Hunt said the Government should negotiate with the other parties on the fate of the Water Amendment Bill, to which the Senate amendments are attached.

"We make an honest and sincere gesture to them — come and talk," Mr Hunt said.

However, Water Minister Penny Wong's office indicated the Government would try to block the amendments made in the upper house.

It is believed Liberal members are not prepared to scuttle the bill completely, and if it returns to the Senate without the amendments they could relent on some, including the pipeline amendment.

But this could set up a showdown with their partners, the Nationals, who indicated yesterday they would hold firm on the amendments on a second vote in the Senate.

Victorian Water Minister Tim Holding said the Opposition parties were playing "reckless politics" with the state's water security.

"I can't understand why Greg Hunt thinks it is OK for Adelaide to take water from the Murray River, but it is somehow outrageous for Melbourne to do so when the water that will come down that pipeline comes from savings," Mr Holding said.

Victorian independent Craig Ingram warned that the amendments could threaten revitalisation of the Snowy River.

He said the amendments could make redistribution of water to the river illegal.