The 22-year-old St. Lawrence College student went missing in the city the night of Oct. 15 or in the early morning of Oct. 16.
A passerby came across the body at about 5:15 p.m. Saturday in Anglin Bay behind the provincial court building.
Officers and residents had combed the city looking for the young man since he went missing.
Const. Steve Koopman, a media relations officer with the Kingston Police, said it wasn't the outcome everyone was hoping for.
"It's hit everybody hard, the police force in totality, more specifically our major crime unit, our detectives have been working on it pretty much every day, they've put some other cases aside. We really appreciate the family's support even though there was such a huge distance with that," said Koopman.
Police told CBC News that they have sent Kilabuk's body to Ottawa for an autopsy. They will wait for those results before releasing the cause of death.
Detectives from the major crimes unit are investigating. They ask anyone with information about the night Kilabuk went missing or about how his body came to be in Anglin Bay to contact them.
Kilabuk was from Pangnirtung, Nunavut.