The privately owned Lindon harbor, 2130 W. 600 South, is at the south end of the freshwater lake.
The man's wife told police she had been trying to contact her husband by cellphone but had not reached him.
"There is no indication of exactly what has happened to him," Cannon said. "We don't know if the boat became disabled and he walked to shore or if he fell off and is still in the water. He may be on the shoreline and injured somewhere and we just don't know it."
Cannon said the water temperature of the lake could be as cold as 40 degrees this time of year.
Crews totaling about 40 personnel from the sheriff's office and the state parks office were expected to continue the search until midnight Saturday.
The search effort included a shoulder-to-shoulder search of the water in the area where the boat was found and a foot search of the nearby shoreline. The Utah Department of Public Safety helicopter was also slated to fly the over the lake with infrared radar, which picks up radiating heat, Cannon said.
The search was expected to resume about 7 a.m. Sunday, Cannon said.