A witness on shore reported seeing the man become separated from his motor boat and fall into the river at about 4 p.m.
Emergency crews responded to the scene, east of Sedro Woolley, and searched by air and water. They found the boat - but not the missing man, said Joel Pratt, operations chief of Skagit County Search and Rescue.
The search was called off at nightfall Saturday and resumed again Sunday morning.
This is a developing news story. More information will be posted as it becomes available.