Autopsies are now being conducted to confirm the identity of the bodies.
The 18-year-old Schmegelsky and 19-year-old McLeod were wanted in connection to three deaths in northern B.C. last month.
The travelling couple were found dead on July 15 on B.C.'s Alaska Highway 97, south of Liard Hot Springs.
"The search is over", Manitoba police announced on Twitter.
His body was found near the suspects' vehicle, which was abandoned and set on fire, near the Fox Lake Cree Nation reserve near Gillam.
Bryer Schmegelsky and Kam MacLeod have sent Canadian law enforcement on a trying chase through rough terrain for weeks now.
This is the damaged aluminum boat found by #rcmpmb officers on the shores of the Nelson River during a helicopter search on friday afternoon.
The Manitoba RCMP's Underwater Recovery Team was called into Gillam to search a section of the Nelson River on Sunday.
The forest was so thick that linking arms and traversing ground, as is normally done in search operations, was out of the question, MacLatchy said.
The vehicle used by the two teenagers suspected of murdering Lucas Fowler and his girlfriend was found torched.
The bodies were found around 10 a.m. on Wednesday, said RCMP Asst.
Assistant Commissioner MacLatchy said the nightmare is over for affected families and communities ensnared in the Canada-wide manhunt.
"While there were no confirmed sightings since July 22, our officers never gave up in their search efforts - following up on every lead, considering all options, and using every available resource".
She said "strong public engagement and support" had been key to the hunt and thanked all Canadians for "remaining vigilant". Still, she said RCMP were not giving up the hunt to find the suspects.