The little boy, aged under two, was discovered by his parents in the Little Para River at Paralowie just after 9am after going missing from their family home.
He had gone out with an older sibling but only one of them returned.
By the time the youngest was found in the water, he was unconscious.
Paramedics raced to the scene and performed CPR.
Witness Trista Koleff said she saw the mother “in tears” and later watched attempts to resuscitate the child.
“I feel really sorry for that family, I really do,” she said.
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A car belonging to the family was left teetering on the edge of the embankment as the parents rushed to get to the child.
Mandy Farndale also saw the dramatic moment.
“They realised that he was there, so they rushed … it was spur of the moment. They just wanted to get out,” she said.
The boy was rushed to the Royal Women’s and Children’s Hospital where he remains a critical condition.
South Australia Police are checking security camera footage form nearby houses.