Senator Xenophon, who was joined on stage by SA Greens senator Sarah Hanson-Young, a potential voting ally, said the Federal Government had to seek out the 350 gigalitres needed to flush the system and see it through next summer.

Adelaide University environmentalist David Paton, who has monitored the declining bird and animal life at the Coorong for 20 years, told the rally that the problem was the result of over-allocation and not of drought or climate change.

He said the Federal Government was potentially in breach of its obligations under the Environmental Protection and Biodiversity Conservation Act to manage the area, which was listed under the international Ramsar convention on wetlands.

"Changing the nature of those wetlands from the point of nomination, as is happening to the Coorong and the lakes, contravenes that piece of legislation," Dr Paton said.

He said an allocation system that gave away more water than came into the river was deeply flawed and not sustainable.

The Coorong had had no water from the river system for the past six years, he said.

An environmental allocation for the lakes had to be available every year, not just when the system was in dire straits.

Dr Paton attacked the recent Council of Australian Governments (COAG) agreement — hailed by the Federal Government as the saviour of the Murray — because it put off a decision until 2018 to suit Victoria and NSW.

He said it should be scrapped and replaced with a system decided by an independent body.

Alexandrina Council mayor Kym McHugh said Prime Minister Kevin Rudd should declare a national disaster with emergency powers put in place to buy, divert and release water.

"There is enough water in the system, we know that. He must find enough water and send it down to save our precious lakes."

Mr Rudd, Senator Wong, SA Premier Mike Rann and SA Water Security Minister Karlene Maywald were booed by protesters for declining invitations to speak.