Routine testing by health officials found a high level of contamination in the Marina Lagoon at Parkside Aquatic Park and Lakeshore Park, county health systems spokeswoman Jan Ogar said.
The beaches were closed Dec. 22 and will remain off-limits for recreational use until further testing can be conducted, which won't happen until Monday.
The closures do not apply to the beach areas of the parks, just their adjacent waters, Ogar said.
The health department had also temporarily closed Rockaway and Lindamar beaches in Pacifica last week after high levels of bacteria were found, but those beaches have since reopened after testing showed that the levels had dropped enough to allow surfers, swimmers and kayakers back in the water safely.
The bacteria levels spiked when heavy rain caused sewer drainage systems to overflow into downstream ocean beaches and lagoons, health officials said.
The county health department routinely tests water for bacteria such as E. coli and coliform, and enacts temporary closures whenever unsafe levels are detected.