A report from the CSIRO on the Murray-Darling river system, using the most complete modelling ever undertaken there expects the Murray mouth to close every second year by 2030.

Some farmers will miss out on their full water allocations 80% of the time by 2030 if so.

The Queensland Farmers Federation (QFF) says the state faces some tough decisions about water use and irrigation over the next three years.

QFF spokesman John Cherry says it highlights some areas of over-extraction in Queensland.

"Look, it shows that we do face some major challenges with climate change in the Murray-Darling Basin moving forward, although the climate change impacts for Queensland will be less than they will be for the southern part of the basin," he said. "It also shows that some of our groundwater areas in the Condamine and the border rivers are suffering from levels of over-extraction and there will need to be reform in those areas."

The Lower Lakes, already at risk of acidification, will be forced on to drought rations of water every eight years as global warming takes hold.

"The largest share of the hydrological impact of climate change under current water-sharing arrangements would occur at the end of the Murray River -- that is, inflows to the Lower Lakes and the Coorong," the report says.

Climate Change and Water Minister Penny Wong said, "The report makes for sobering reading when it comes to water availability...it reminds about the costs of inaction, it reminds us that there are enormous costs to a changing climate and communities are already feeling that.  We are facing a critical situation in the Murray-Darling Basin after years of over-allocation and drought and in the face of climate change.”

"The drought has highlighted how far we've pushed some of these ecosystems…but even when the drought breaks there's going to be an ongoing challenge to provide secure, safe water in a healthy environment unless we make some changes," said lead author of the Project's report, Tom Hatton, Director of the CSIRO's Water for a Healthy Country Flagship in NSW.

His team's research also finds groundwater is being used at an unsustainable rate in many areas of the Basin.

"[I]t's absolutely something that is fundamental for us to be able to go forward as a nation and plan a reallocation of water to our rivers," said John Williams, from the NSW Natural Resources Commission.

Ken Mathews, CEO of the National Water Commission in Canberra, agrees. "In the past Australia hasn't managed the Murray-Darling system as well as we could because we haven't properly understood its capacity, its hydrology, the connection between surface flows and groundwater, and the aggregate effects of drought, floods and climate change - as well as the varying demands of each state and territory for its water," he said. "We now have this information and that's critical to properly managing a river system that supplies at least 40 per cent of Australia's agricultural production. We can now better understand the possible effects of climate change on water availability in the Basin and plan for its impacts."  THE END.