Someone spotted the body from the docks and called police at about 10:30 a.m., police Capt. Steve Clark said.
It appears he had been in the water for about eight hours, he said.
There is no indication of foul play, Clark said.
Clark said the man had been living on a boat in the harbor over the past year but also had a home in Santa Cruz County.
It's likely he fell overboard from his boat into the water, which was "extremely cold," Clark said.
There were hand marks along the side of his boat, and it appears the man had tried to catch himself, Clark said.
"His body had traveled through the harbor a good distance," Clark said.
The man's cell phone was found on the dock by the boat.
The coroner's office will determine whether the man was intoxicated at the time of his death, Clark said.