The 30-year-old woman has been refused bail and is set to appear in Blacktown Local Court today.
Despite earlier estimates that the boy was 2-3 days old, police will now allege that he is seven days old and was placed into the drain on Tuesday, 24 hours after being born.
If the allegation is true it means he has survived in the drain for five days before being found by a passing cyclist on Sunday morning.
The baby is now in a serious but stable condition at the Westmead Children's Hospital.
Police suspect the baby was squeezed through the drain's narrow opening and dropped about 2.4 metres.
After he was found on Sunday, several people lifted the heavy slab covering the drain to get him out.
The baby is now in the care of the NSW Family and Community Services (FACS) Minister.
It will be up to the state agency to assess what now happens to him.