At 3:20 p.m. officials tweeted their radar is indicating heavy rain that "will cause flooding."
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"Excessive runoff from heavy rainfall will cause flooding of highways, streets, and underpasses as well as other drainage areas and low lying spots," officials said.
RELATED: Flooding, power outages shut down parts of San Francisco Muni
Officials did not say how long the warning will be in place.
The flooding is already having an impact on public transportation.
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Muni reports service is impaired due to floods at some stations.
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