The sheriff's office received a call at 12:50 a.m. from someone reporting that there was a man in the water near Werner Dredger Cut just north of Discovery Bay. The man was splashing around and yelling for help, Lee said.
A short time later, the witness saw the man go under.
The sheriff's office's marine patrol and helicopter responded, along with the U.S. Coast Guard and began searching for the man.
Investigators first found a submerged 11-foot fishing boat in the area, but they didn't find the man.
They continued searching until divers found the man's body at about 7:30 a.m.
The man has been identified as a 35-year-old resident of Antelope, an unincorporated area of Sacramento County, but the sheriff's office was not releasing his name this morning because his family hadn't been notified of his death, Lee said.
An autopsy is scheduled for today to determine a cause of death.