Family members identified the deceased as Michael Weir, 73, and Gerald Thom, of Youbou, B.C., who was in his 50s.
Transportation Safety Board spokesman Bill Yearwood said the plane, an "amateur-built" Avid amphibious aircraft, crashed shortly after it took off from the Nanaimo Airport in Cassidy, about 20 kilometres southeast of Nanaimo, at around 7 p.m. PT.
The single-engine two-seater went down on the Cottonwood Golf Course, which is adjacent to the airport.
Trent Kaese, owner and operator of the golf course, wasn't working at the time but arrived at the crash site about half an hour later.
He told CBC News that no one on the ground was injured, but golfers were using the 13th and 15th fairways when the plane came down between them, next to the pond at hole number 14.
"About half of the plane was left. Just the tail section of the plane was left. The rest of the plane was pretty much disintegrated where the impact had happened," Kaese said.
Yearwood says Mounties are interviewing those witnesses as police, along with the TSB and the B.C. Coroners Service, investigate the crash, but at this point he believes it is possible the pilot encountered a problem and lost control.
"I had a look at the site and there's no scars or significant markings from the accident," he said. "The debris field, the accident site, and the wreckage is contained in a very small area."
"The damage that's there right now is consistent with an impact that's very steep — a dive towards the ground, which is consistent with a loss of control at some point during the flight," he said.
Weather conditions were sunny and clear at the time of the fatal accident.
Yearwood said records show the two men had been actively flying the homemade aircraft in recent months.
Family members say Thom, who volunteered with shoreline cleanup projects and was recently awarded Citizen of the Year by the Cowichan Lake and District Chamber of Commerce, had been friends with Weir for 28 years.
Google Maps: Cottonwood Golf Course