The baby, who is only a few days old, was in a serious but stable condition in Sydney's Westmead Children's Hospital, police said in a statement.
A group of cyclists were riding along a bicycle lane beside the M7 Motorway in the Sydney suburb of Quakers Hill when they heard a baby's cry coming from the drain, police said.
They managed to lift the heavy concrete lid off the drain, which is 2.5 meters deep and saw the baby wrapped in a hospital blanket at the bottom.
"It was disturbing how the child was placed in the drain," said Quakers Hill Police Inspector David Lagats, who estimated the baby was 2-3 days old.
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"We all thought the worst, but the baby was still alive," he added.
The boy had no signs of physical injury, but was malnourished, Lagats said.
They found the mother this afternoon by checking hospital records and by knocking on the doors of homes in the neighborhood, police said.
They did not release the mother's name, but said she was from Quakers Hill. She was taken for questioning.
They did not say how long the child had likely been left there.
There has been no rain in Sydney for several days, so the drains are dry. But rain is forecast for tonight.