The findings of the study were released on Wednesday, resulting in a consortium of scientists developing a framework to help land and water managers restore the ecology of the Coorong.

If successfully implemented, the framework could also be applied to lakes Alexandrina and Albert.

The $5.3 million report recommends 300 gigalitres of water be allocated to the Coorong for environmental use each year.

Scientists say that amount of fresh water would be enough to influence the overall health of the Coorong and maintain salinity at safe levels.

South Australian Murray-Darling Basin Natural Resources Management Board project co-ordinator Glynn Ricketts said other means of reducing salinity, such as bioremediation, were effective but no substitute for fresh water.

"What we can do is re-set the system to prepare it for recovery," he said.

The study recommended the water in the Coorong's south lagoon, which has a higher salinity level than the ocean, be pumped out to sea and replaced with salt water.

It is understood the action, believed to cost between $15-20m, would have only short term negative impacts on that part of the coastline.

Justin Brookes, from the University of Adelaide, said species numbers in the system were under threat due to evaporation caused by climate change and high water extraction further up the system.

He said there had been a dramatic decrease in Ruppia Tuberosa - a plant species which acts as a food source for birds.

"As we start seeing a decline in food we have also seen a decline in fish and bird species," he said.

"The system is in decline, but is recoverable.

"This goes beyond economics and science - it goes to politics.

"The time is right to make a change because everyone is suffering under the current rules."

He said a last resort proposal made by the South Australian government to flood the entire Lower Lakes and Coorong region with sea water would result in the environment being traded off for short term gain.

"It would be very difficult to get the salt back out," he said.

"You couldn't do it without another barrage or weir and there is already too much infrastructure in the system.

"We've got ourselves into a position that is catastrophic."