Beaches may be washed away, hundreds of metres of coastline eroded and the barrages swamped by waves.
But climate change is not likely to breach the barriers that keep the Lower Lakes from draining into the Coorong or the sea, according to the Department of Environment, Water and Natural Resources (DEWNR).
Two DEWNR staff members presented information on the topic to a long-nosed fur seal working group in October.
Coastal programs team leader James Guy said the University of Sydney had modelled the likely impact of a 1.5-metre rise in sea levels during the late 2000s, and that more frequent storm surges and more pronounced erosion would result by the end of this century.
But he also warned that more recent projections by the National Oceanographic and Atmospheric Administration in the United States suggested sea levels could increase by as much as 2.5 metres by 2100.
He said the Coast Protection Board was planning to keep new developments away from risky areas, to protect existing properties, and to allow coastal ecosystems to adapt to the new realities they would face.
However, the board was concerned that the community was not worried about the issue, and that "the demand to protect existing communities might exceed capacity to do so".
Queried about the comments, a DEWNR spokeswoman simply said climate change was having no significant impact in the Coorong and Lower Lakes "at the moment".
She said preliminary analysis had shown the barrages would need to be closed more often, particularly in winter, as sea levels rose to prevent salt water flowing into the lakes.
"DEWNR, with its partners, will continue to monitor and assess South Australia's landscape to manage climate change impacts," she said.
A 2014 climate change adaptation plan for the Murray-Darling Basin in SA suggested the barrages would need to be made taller within 10 years, or relocated within 30 years, to stop seawater regularly coming into the Lower Lakes.