The men launched before midnight Saturday and were reported missing when they failed to return, according to officials.
Their bodies were recovered Sunday morning. Officials said both men were wearing life jackets.
Battalion Chief Bret McTigue of the Marin County Fire Department warned about the dangers of the waterway.
"The area of Tomales Bay and the mouth of Tomales Bay in particular is one of the most dangerous waterways imaginable in California coastlines, so if you are coming out, you need to do your homework," McTigue said.
Fire officials are urging boaters to carry a marine radio and wear a life jacket.