Coast Guard Lt. Mark Leahey says that 68-year-old Harry Holzhauer of Tigard, Ore. was operating the pleasure craft when it collided Saturday afternoon with the MS San Francisco, which was headed from Sausalito to San Francisco with about 500 passengers.
A second victim who was transported to a local hospital continues to suffer from serious injuries.
Coast Guard investigators are trying to determine who was at fault.
Golden Gate Transit spokeswoman Mary Currie says the ferry briefly was taken out of service to be investigated, then put back in service Sunday.
She says all five crew members aboard will be drug tested and placed on administrative leave.