RCMP Sgt. Chris Swain said the boy was found unresponsive in the pool at around 10:30 a.m. PT on Sunday, and then flown to hospital in critical condition.
The parents were at home at the time, but are not suspected of harming the child intentionally, he said.
"Although still underway, the investigation has so far revealed that this is a tragic accident and not the result of any type of criminal behaviour," Swain said in a written statement.
On Wednesday morning, North Cowichan and Duncan RCMP and the B.C. Coroners Service announced that the young boy had passed away in hospital.
"There was a lot of intervention and he did manage to make it to B.C. Children's [Hospital] but, unfortunately, he had been in the water too long and in the end did not survive," B.C. Coroners Service spokeswoman Barb McLintock said.
Police said the Coroners Service has now taken over the investigation.