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Malibu's Surf Rider Beach and Santa Monica Municipal Pier are also on the list.
Two Orange County beaches made the unhealthiest list as well: Poche Beach and Doheny Beach.
Heal the Bay said the contamination comes from storm-water runoff that overloads storm drains and sewage systems.
The group said when it rains, people should stay out of the water for at least three days.
"If we immerse ourselves only once in polluted waters, we can contract diseases like stomach flu. It can be upper respiratory infections, ear infections, it can be total body rashes," said Dr. Eliza Lefshitz from Heal the Bay.
To help solve this storm drain run-off problem, the city of Santa Monica is installing a new million dollar system that will divert contaminated water to a processing facility.
But beach-goer Victor Valdez and his son aren't waiting to see if it works.
"I think we're done, we're done," he said.
For the past 19 years, Heal the Bay has been analyzing water quality reports by local and state agencies, then grading beaches up and down the California coast.
Beaches in both Orange County and Ventura County rated very high in the latest report card.