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Up to 60 tonnes of the invasive fish has been estimated to have died after being left exposed when the Banrock Station wetlands were drained over summer.
South Australian Research and Development Institute scientists monitored the carp during the environmental project at Kingston-on-Murray.
As the wetlands drained and the area was allowed to dry out to mimic its natural cycle, the carp swam into deeper parts of the wetlands against the water flow.
They swam in the opposite direction to the native fish which, sensing the dropping water level, immediately sought refuge in the river proper.
The carp were left high and dry when the remaining pools within the wetlands evaporated. Scientists estimated "thousands" of the fish had since been found dead in the mud.
Institute scientist Dr Ben Smith said many of the smaller carp had probably been eaten by predators, such as foxes and pelicans.
"They are not adapting to the wetting and drying like the native fish," Dr Smith said.
"In the past there's been too much effort spent on just trying to kill the carp with whatever ways we can and not learning their biology and looking for weakness in them.
Source: Adelaide now