Officers are searching Yerrabi Pond in Gungahlin for Pranav Vivekanandan after the bodies of a woman and a young boy were discovered in the water.
The dead woman is thought to be the mother of the deceased boy and his missing brother.
Officers found the bodies after a member of the public saw them in the water, while investigators later recovered a vehicle from a car park nearby.
Police hold grave concerns for Pranav and they have pleaded for assistance from the public in the event he is alive and someone knows his location.
Divers have been searching the water while other officers scour surrounding bushland.
"It's obviously a tragic situation, it's still very early days and it's unfolding," Detective Superintendent Hall O'Meagher told reporters on Saturday.
"We're making inquiries with the family of these deceased people. They're assisting us with our inquiries at this time.
"Our thoughts go out to them and also to the responding police who have had to deal with this tragic circumstance."
Police describe Pranav as being of Indian appearance, about 110cm tall, with short, dark hair and dark brown eyes.
He might be wearing an orange T-shirt, light-coloured shorts and a jacket.
The cause and manner of the deaths are not yet known and investigations are ongoing.
"We're asking for any member of the public who has information in relation to the circumstances of this matter to come forward and call Crime Stoppers," Det Supt O'Meagher said.
Yerrabi Pond is a popular recreation spot in Canberra's north. It has a playground, walking and cycling paths, and a skate park.
Lifeline 13 11 14
Kids Helpline 1800 55 1800 (for people aged 5 to 25)
27°C