Ahead of more rain, the city continues to distribute sandbags. At least 400 have been given out so far.
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On Valencia Street, flooded storm drains led to water coming inches from some storefronts. Linda Yee said it was like a river.
"From my window, I could see the flow of the water going that way and the leaves were right there and it was really moving," said Lee.
MORE: TIMELINE: Rain continues through Wednesday, flooding some Bay Area roads
On 18th and Folsom streets, many businesses have layers of water barriers with sandbags outside of some stores and metal or wooden panels blocking the storefronts.
"It's a low line area so the public utilities commission for San Francisco puts up flood barriers. Those went up over the weekend. They always go up when there are big rains expected and that tries to mitigate the problems of flooding in that area," said Rachel Gordon with San Francisco Public Works.
Larry Russo was ready with sandbags.
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"We are used to the water coming down from the Twin Peaks area. We always put out the sandbags and we were lucky yesterday," said Russo.
Others were not as lucky. Raul Escobar was on the phone with his insurance company while public works employees worked around his car.
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"The tree fell on top of my truck," said Escobar and added, "I thought to myself, well I won't be able to move my car now. I can't go back to work."
The city's department of emergency services says they are ready.
"We held a coordination call earlier today complete with the national weather service. We received a very throughout briefing from the National Weather Service in terms of what to expect in duration on the next storm and intensity of the next storm," said Adrienne Bechelli, deputy director for Emergency Services.
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In the meantime, residents and businesses in low areas are continuing to add more flood barriers.
"We expect it to so whatever hopes we have, we are always going to be prepared," said Russo.