The SA Government recently asked for pre-approval to allow salt water into the lakes but said the action would only be taken as a last resort.

A public consultation period on the move closed today with Environment Minister Peter Garrett now having until December 31 to consider calling for a full risk assessment.

Senator Hanson-Young said Mr Garrett should continue to take public submissions but should also call for the wider investigation.

"It's absolutely imperative that we look at what all of the risks are," she told reporters today.

"We need to know whether flooding the lakes with salt water will have an impact on the groundwater in the region.

"We need to be looking at what the impacts are on the long-term sustainability of the ecology.

"What will happen to all these precious species of flora and fauna in what is an internationally recognised site?"

The federal member for Mayo, Jamie Briggs, whose electorate covers the lower lakes, said the 10-day consultation period on SA's application was too short.

"For a decision like this, a once-in-a-century decision, to have 10 days consultation is just not good enough," he said.

Mr Briggs said the lakes were also showing some signs of recovery after some better rainfall in late July and August.

Under the advance approval strategy, the SA Government outlined a series of triggers that would lead to releasing sea water through the barrages at the Murray mouth.

Those triggers included a fall in the water level of Lake Alexandrina to 1.5 metres below sea level, and to 0.5 metres below sea level in Lake Albert.

"If these triggers are likely to be reached and if there is not enough fresh water to maintain the lower lakes, as a last resort, a minimum quantity of sea water would need to be introduced through the barrages to manage the risk and avoid acidification," River Murray Minister Karlene Maywald said last week.

"It would be just enough sea water to maintain the water level at a critical threshold to avoid acidification, not flooding and refilling the lower lakes completely."