A survey by the Murray-Darling Basin Authority has found the numbers of migratory shorebirds in the Coorong and Lower Lakes at the mouth of the basin have been dwindling.
Ecologist David Paton from the University of Adelaide said the increased growth of dense algae has made it difficult for the birds, as it affects the vegetation that they rely on to grow.
Mr Paton said the damage, which he suspects may have been caused by drainage water runoff from farms in the area, is likely to be irreversible.