The Shoreline Unified School District has canceled classes at Tomales High School, Tomales Elementary School and West Marin, Inverness and Bodega Bay schools.
"Most of our kids travel by bus and it's just not safe for those buses to be on bay roads today with all the flooding and potential flooding," Superintendent Stephen Rosenthal said.
He said he wasn't aware of any flooding early this morning, but that he expected some by midday.
Rosenthal also pointed out the danger of downed branches or trees.
"The ground's really saturated, so the chances of major trees falling, etc., are pretty good," he said.
Parents were notified of the closures by phone, he said.
Four of the schools are in Marin County, and Bodega Bay School is in Sonoma County. All are expected to reopen on Friday.