Todd Iwamoto, 40, of Mountain House, was thrown overboard when his boat struck a railroad crossing in Old River at about 11:30 a.m. Saturday, Contra Costa County sheriff's spokesman Jimmy Lee said.
Sheriff's deputies from Contra Costa and San Joaquin counties, the U.S. Coast Guard and local firefighters and police searched the waters extensively by boat and air throughout the day.
They found Iwamoto's body in the river near the accident site at about 5:15 p.m., Lee said.
The sheriff's office is still investigating how the crash happened and is looking into the possibility that the boat had struck something else before the rail crossing, Lee said.
Anyone with information about the crash has been asked to call the Contra Costa Sheriff's Office Marine Patrol at (925) 427-8507 or email tipsso.cccounty.us.
