Waterloo Regional Police allege the suspect gave the children an over-the-counter eye care product that can cause abnormal drowsiness, low blood pressure, respiratory problems and decreased heart rates in young children.
The woman operated a home daycare in Kitchener from 2009 to 2011 and investigators are concerned there may be more alleged victims.
"The accused had access to children during the period in which she operated the informal daycare, so as a precaution for public safety we want to make the public aware that anyone who maybe subscribed to her services at some point and has had a child who has become sick with similar symptoms (should) give police a call," said Waterloo Regional Police spokesman Olaf Heinzel.
The suspect in March was caring for a friend's child who was taken to hospital with "serious physical symptoms" such as breathing difficulties, drowsiness and a decreased heart rate, police said.
The child recovered but had to be taken back to hospital at a later date with similar symptoms.
Detectives discovered that another child who had been under the woman's care in July 2010 had similar symptoms, and recovered after a few days in hospital, police said.
Christine Allen, who also goes by Christine Keilbar, is charged with two counts each of aggravated assault and administering a noxious substance.
Heinzel wouldn't name the specific eye care product or say why they allege it was given to the children.
"We can't speak at this point as to why the individual may have administered this product," he said.
"It's still too early in the investigation and it's now before the courts. That will be something that will be determined through the process in the court system."
The daycare did not have a name, Heinzel said, and it's not known how many children Allen cared for during the three years it operated.
Allen was arrested over the weekend and was ordered to remain in custody after a first court appearance. She is set to appear in court again Wednesday in Kitchener.
Heinzel could not say if she has a lawyer yet.