Autopsies have not yet been performed, and police have not released any information on what they believe happened.
Drew DeVoursney, 36, and his girlfriend Francesca Matus, 52, were reported missing by their friend Joseph Milholen, who went to Matus' home in the Corozal district of Belize on Friday to take her to the airport because she was scheduled to fly home to Toronto.
Milholen told local police that he could not find her at her home, DeVoursney's bicycle was parked in her driveway and her car was gone.
Milholen told local authorities that the last time he saw the pair was last Tuesday at a bar in Corozal Town.
"That's the hardest part. It's just that we don't know anything. We don't know where he is or what's going on," Char DeVoursney, Drew DeVoursney's mother, told local ABC News affiliate WSB-TV of Atlanta, before the two were found.
David DeVoursney, the brother of Drew DeVoursney, told WSB-TV before Monday's discovery that what happened to the couple "is a complete mystery."
Global Affairs Canada, a department of the Canadian government, previously told ABC News that it was aware of reports of a missing Canadian citizen in Belize and that it was providing consular assistance to her family and was in contact with local authorities.
An official at the U.S. State Department said it was aware of the reports as well but had no further comment.
ABC News' Kirit Radia and Anne Laurent contributed to this report.