OF all the people battling over the Murray-Darling basin, South Australians present themselves as the righteous ones - the ones who would see the river system returned to its most pristine state.

State Premier Jay Weatherill led the campaign last week, arguing that the Murray-Darling Basin Authority's plan was not even a good starting point for an agreement on the river. It did not adequately recognise South Australia's responsible use of the river and it did not place the burden of returning the river to good health upon the upstream states. While South Australia had capped its take from the river 40 years ago, he said the other states had taken additional water.

South Australian independent Senator Nick Xenophon joined the chorus, as did the Federal Opposition's water spokesman, another South Australian, Senator Simon Birmingham.

One of the stated objectives of the Murray-Darling Basin Plan is to ensure sufficient flow to flush salt and nutrient from the basin and keep the Murray mouth open to the sea in most years. The proponents of the plan would like to see Lake Alexandrina, near the mouth of the Murray, as a freshwater haven.

But historically, was Lake Alexandrina naturally freshwater?

Not according to Dr Jennifer Marohasy, who argues that the lower lakes were estuarine before the erection of Murray mouth barrages. These barrages are a series of 593 independent gates across five structures, creating a barrier 7.6 kilometres long and holding the lake above sea level.

Marohasy, and the media running her views, copped flak from the ABC's Media Watch a fortnight ago, with presenter Jonathan Holmes arguing her views did not reflect mainstream scientific opinion.

The ABC's Counterpoint responded by giving Marohasy a forum to argue her case. And a feisty performance it was. There was no evasion in her answers. She was as direct as anyone could be.

Web material uploaded by Media Watch, but not broadcast, shows that initially Media Watch asked Marohasy if she accepted that the vast majority of recognised experts on the lower lakes disagreed with her conclusion that they were estuarine before the erection of the barrages.

''No,'' she replied, and she quoted from a paper published by a number of scientists, including Professor R.P. Bourman. ''Originally a vibrant, highly productive estuarine ecosystem of 75,000 hectares, characterised by a mixing of brackish and fresh water with highly variable flows, barrage construction has transformed the lakes into freshwater bodies with permanently raised water levels …''

Instead of broadcasting this, Media Watch chose to quote Professor Bourman saying, ''The [Marohasy] paper appears to be a Crusade against the barrages and the scientists who have actually carried out their unbiased science there, rather than a sound scientific paper.''

Now, it seems to me that there are two different issues here. One is the historic, geographic fact: were the lakes estuarine and salty in the pre-barrage past, or were they freshwater?

That should be something scientists can establish. Media Watch acknowledged that one expert, Professor Peter Gell of the University of Ballarat, broadly supported Marohasy.

The program also quoted Professor Richard Kingsford of the University of NSW, who disagreed. In additional papers provided to the Sunday Canberra Times, Professor Bourman also disagrees. He and Professor Nick Harvey of the University of Adelaide state that Lake Alexandrina was predominantly fresh for the past 6,000 years.

But the Bourman quote chosen by Media Watch raised an entirely different matter, one beyond the actual historic state of the lakes - that is, the political question of what should be done now.

Marohasy believes the barrages should be open and the lakes turned into a marine environment. Bourman, Harvey and Kingsford believe they should not.

Bourman and Harvey point out that originally South Australia received all of the flow of the River Murray. It now gets less than 25 per cent and the state's allocated use is a mere seven per cent. The only solution, they say, is to increase the flow or the river will die. To turn the lakes into an arm of the sea would be to destroy the freshwater ecosystem.

What is to be done is a political matter. It appears most South Australians want the barrages maintained. They like keeping the river's fresh water just as much as most of the people up river. Adelaide and parts of south-east South Australia depend on water pumped from the barrage-protected lakes.

In a week's time the Murray-Darling Basin Authority will have completed its 20 weeks of consultation on its plan. This consultation came on top of the previous nine months of talking. Added to that, the plan allows for seven years to 2019 to give everyone time to adjust to the changes required to implement the new system.

With all the floods in the eastern states you would think that if ever there was a time to reach an agreement, this must be it. But South Australian Premier Jay Weatherill has already announced that his government will not support the plan and other states are threatening legal action.

With this sort of response, it will take all of Prime Minister Julia Gillard's renowned negotiating skills to get a deal. Opposition Leader Tony Abbott might enjoy watching the Government struggle over this. But he might be wiser to help Gillard reach a compromise.