SA Premier Mike Rann has said the State Government wants the most stringent environmental process possible before any decision is reached, and will only take the action as a last resort to prevent acidification.

Federal Environment Minister Peter Garrett says the EIS will consider the potential impact of South Australia's proposal on the ecological character of the protected wetlands, threatened species and migratory species.

Other long-term options for protecting South Australia's Lower Lakes system from acidification would also be considered, Mr Garrett told reporters in Sydney today.

"Today's decision means that South Australia's proposal will be subject to a high standard environmental impact assessment," he said.

"There will be sufficient opportunity for the public to comment on that proposal and all the relevant environment matters that attach to South Australia's proposal will be fully and comprehensively considered.

"The EIS will be required to be drawn up and formulated by South Australia according to terms of reference that are set by me and by my department."

Mr Garrett said he expected the EIS would take months to complete.