Police were called to a home on Coleridge Park Drive in the city's Westwood area at about 8 a.m. CT and located the children — a two-month-old and a two-year-old — inside.
They were rushed to hospital in critical condition and later died from their injuries. Police have not elaborated on the type of injuries they had.
No one else was home, which is now surrounded by police tape.
Police are now searching the city for the mother, Lisa Gibson, 32.
Many of the first responders are going to need counselling after what they discovered this morning, a police spokesperson told reporters.
Police also said they have spoken to the father but are urging the public to alert them if they see Gibson.
A fire official told CBC News that she is believed to be wearing pyjama pants and is distraught.
Police have been seen looking through parks in the area and along the riverbank, where there have been three reported sightings of Gibson.
A police boat has also been seen patrolling the river.