John Lee of the Transportation Safety Board says the single-engine Cessna 185 left the airport in Fort McMurray on Friday for a trip that was supposed to be a short flight to a remote lake south of the city.
Lee says the amphibious plane was privately registered but the purpose of the flight was to conduct geological survey work in the region.
"An over-flying helicopter saw the plane partially submerged and inverted in the lake," Lee said Saturday.
Lee said the helicopter wasn't connected to the work being done by the plane, but just happened to be passing over the same area.
Rescue personnel from Cold Lake, Alta., recovered the body of the pilot who RCMP say was the only occupant.
An RCMP dive team, meanwhile, has also been sent to search for the pilot of a DeHavilland DHC-3 Otter that was located in water Friday near Ivanhoe Lake, N.W.T.
Cpl. Barry Ledoux said Saturday afternoon that the pilot, who was the only person aboard the flight, had not yet been found.
Safety Board investigator Peter Hildebrand said an investigation team likely wouldn't know more about what caused the Otter to crash until Mounties complete their search and the plane can be removed from the water.
"It's not totally submerged but we're still looking at 10 to 15 feet at some depths," Hildebrand said.
"We can't get at it the way it is. We're going to depend on machinery and a helicopter to lift it."
RCMP say the aircraft took off from Scott Lake, Sask., Thursday night and a Royal Canadian Air Force Hercules aircraft located it Friday.
Transport Canada says operated by Transwest Air.
The identities of the pilots in either crash have not been released.
Lee said investigators didn't know yet whether the pilot who died near Fort McMurray on Friday was conducting aerial survey work, or was planning to do the survey work after landing on the remote lake.