Air force Capt. Trevor Reid says the man reported mechanical difficulties with his eight-metre boat in Douglas Channel on Thursday afternoon before losing contact.
He says the Air Force sent a Buffalo airplane and Cormorant helicopter from Comox, B.C., to assist in the coast guard's search but their efforts were hampered by winds of between 50 and 70 kilometres an hour.
The search was called off for the night, resumed in the morning, and Reid says coast guard members aboard a fast-response boat spotted the man's partially submerged vessel just after noon on Friday.
Reid says crew aboard the Buffalo found the man, who was wearing an orange floater jacket, and pinpointed his location on shore with a smoke marker.
He says coast guard members took the man to Kitimat, and that he was in good condition.
"When we first sighted the individual, we thought we were looking at an orange gas can near a log," Capt. Andrew Doepner, aircraft commander, said in a news release.
"We flew over at 1,000 feet and saw him waving to us in his orange jacket. He did everything right. He had the right clothing and called the right people."