The most recent test results show a high level of contamination in the ocean at Linda Mar Beach in Pacifica and in the bay off Aquatic Park and Lakeshore Park in San Mateo, county health systems spokeswoman Jan Ogar said.
The waters will remain closed to recreational use until further testing can be conducted, which will not take place until Monday.
The closures do not apply to the beach areas of the parks, just their adjacent waters, Ogar said.
The health department had temporarily closed Rockaway Beach in Pacifica, which has since seen bacteria levels drop to safe levels and was reopened for recreational use, Ogar said.
Heavy rain from the weekend storms was blamed for the spike in bacteria levels, which occurred when sewer drainage systems overflowed into downstream ocean beaches and lagoons.
The county health department routinely tests water for bacteria such as E. coli of coliform and puts temporary closures in place whenever unsafe levels are detected.