The tender will be the first part of a $350 million process to purchase water in Queensland as announced at last month's Council of Australian Governments meeting.

The Federal Government started purchasing water earlier this year with a $50 million tender securing 35 billion litres in water entitlements.

Water Minister Senator Penny Wong said the program would ensure rivers and wetlands would "get a greater share of water when it is available".

"After 12 years of inaction under the previous government, we are the first Federal Government to enter the water market to tackle over-allocation in the Murray-Darling Basin," she said.

Senator Wong said the impacts of drought and climate change were hitting hard across the Murray-Darling Basin, with critical human needs for towns and cities relying on the Murray for drinking water taking first priority in the southern Basin.

"In the southern Basin in particular, there is very little water available for the rivers or for farmers due to continued low inflows and the need to make sure we can meet critical human needs," she said.

Sen Wong said that while there was no easy solution for the Murray-Darling Basin, purchasing water in Queensland would benefit wetlands and rivers in the northern Basin and increase flows down the Darling River.

In wetter years, increased flows to the Darling River will make their way down to the Murray River, she said.

However, at the moment the Darling River is so dry that increased flows to that river are unlikely to reach the Murray River.

"Unfortunately, there is currently just not enough water in the system to do everything we want to do," Sen Wong said.