The state government has taken a step towards flooding the Lower Lakes with seawater by applying for approval from the Federal Government.

The Minister for the River Murray Karlene Maywald said that this is a requirement of the $10 million management strategy to avoid the lakes becoming acidified and is "a last resort".

"I stress that this is not a decision to let seawater into the Lower Lakes but is part of the preparations required in case drought continues … and action is required to prevent widespread acidification in the region," she said.

However even this initial step to seawater inflow has angered many people including the Alexandrina Council who will write to Prime Minister Kevin Rudd asking him to intervene and reject the application.

The council’s chief executive officer, John Coombe, said seawater would unleash an environmental disaster in the lakes.

"We do not know what seawater will do to this freshwater environment," he said.

"With this decision the state government signals it will walk away from our freshwater lakes".

Ms Maywald said the strategy has outlined triggers for alkalinity and water levels at the Lower Lakes, which will determine if action needs to occur.

The trigger is calcium carbonate at levels of 25 milligrams per litre or if water levels reach 1.5 metres below sea level in Lake Alexandrina or 0.5 metres below sea level in Lake Albert.

"If these triggers are likely to be reached and if there is not enough freshwater inflows to maintain the Lower Lakes, as a last resort, a minimum quantity of seawater would need to be introduced through the barrages to manage the risk and avoid acidification," she said.

Member for Hammond, Adrian Pederick, also believes that seawater is not the answer and that maintaining the lakes with freshwater above acidification levels is critical to the survival of the whole system, not just the lakes.

"What is needed is a strategy to secure water to avert an ecological disaster. What we have is a plan to monitor its deterioration up to a point where seawater has to be let in, this in itself threatens the long term survival of the lakes," he said.