Among them is popular Linda Mar State Beach in Pacifica. It received a grade of "F" when it comes to water quality.
It is ranked the worst in the Bay Area and the third worst of all California beaches.
"There are multiple cases of sewage spills in the area. Sometimes that happens because there may be a connection between the storm sewer and the sewerage system. There might be overflows during an intense rain and that can discharge some bacteria," said Annalisa Moe of Heal the Bay.
This is the second year in a row the beach has made the list.
"It's never bothered me. Maybe it will keep some people away, so it isn't so crowded," said Marti Haskins of Pacifica, a regular beach goer.
Some had a change of heart about staying here.
"I'm kind of thinking twice about staying in longer. But since I am here I will enjoy the Bay," said one man.
Two other beaches made the top 10 beach bummer list: Aquatic Beach in San Mateo and Keller Beach in Richmond.
"Your risk of gastro-intestinal disease increases as the grades go down," said Moe.
Heal the Bay says heavy rainy seasons means more bacteria-ridden runoff that gets carried into the sea.
It''s not all bad news.
Beaches in San Francisco, Marin and Sonoma all scored very high. And beaches in the East Bay were average.
The good news is most of the problems occurred during the rainy season. The grades for the beaches in the summer months is actually quite high.