The report by the Environment Protection Authority (EPA) also concludes that ground water use in the northern Adelaide plains and parts of the state's south-east and surface water use in some parts of the Mount Lofty Ranges are unsustainable.
SA Environment Minister Jay Weatherill says the Government will consider the 41 report recommendations.
"The health of rivers, streams and wetlands of the River Murray flood plain is declining due to the extraction of water increasing salt levels, drought and non-delivery of environmental flows," he said.
"The Coorong and lower lakes are in the poorest condition ever recorded.