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Rodents, Rivers and Runoff: Why Parts of the Bay Area Flood, Where the Water Goes and How Animals Adapt

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Three images in a triptych, one features two people standing in a flooded street, next is a map of San Francisco with color coded areas that have been filled in, the third is a fat ground squirrel sitting back on its haunches.
Mission District residents work to unclog a drain; a map of the San Francisco shoreline in 1895; a rotund California ground squirrel in Briones Regional Park. (Beth LaBerge, KQED/Courtesy of Oakland Museum of California/Courtesy of Erin Person)

Read a transcript of this episode here.

Rain — California has seen a lot of it so far this year in the form of multiple atmospheric river storms that have hammered the Bay Area. That got the Bay Curious team wondering about some of the questions we’ve received over the years about water — where it flows and how we’re affected by it. This week we have a three-question lightning round.

1. When it rains in the Bay Area, and the water runs to the gutter, does it go directly into the bay?

This question came to us from listener Eric Bauer. For most cities in the Bay Area, the answer is yes. Depending on where you live, gutters in your street will take stormwater or other runoff to creeks that lead out to the bay without any kind of treatment. Instead, many cities put signs on the curb urging residents not to put pollutants in the drain.

The one exception to that is San Francisco. The city has what’s called a combined sewer system, and other than a section of Old Sacramento, it’s the only one in California. This means rainwater and runoff go into the sewer system, along with whatever is coming from the pipes in our homes, and is subject to the same level of water treatment before it is released.


The vast majority of the time, this system works great, and the environment is spared from the chemicals, oil and other unsavory substances that get washed from San Francisco streets. During normal conditions, the system can handle a lot of water — up to 500 million gallons of sewage plus runoff, with an additional 200 million gallons of storage.

Close up image of a storm drain on a street corner. Someone is sweeping debris away from it.
Stormwater drains are part of San Francisco’s combined sewer system, which treats both sewage and storm runoff. (Beth LaBerge/KQED)

But every system has its limits. On the most recent New Year’s Eve, a storm dropped 5.46 inches of rain on San Francisco in one day, equivalent to over 4 billion gallons of water. That led to some sewage being discharged without full treatment — not just in San Francisco, but throughout the Bay Area. Collectively, the nine counties discharged some 62 million gallons of raw or partially treated sewage into waterways.

How do we keep that from happening again, as storms like these become more common as the climate changes? One idea is creating more “green infrastructure” by capturing or diverting some of that water before it gets into the sewer system. That could be in the form of cisterns to collect water for use in drier times, opening up more green space or creating permeable asphalt to allow water to soak into the soil below.

2. Are there really underground rivers in San Francisco?

A listener named Norm wrote to us asking about an oft-repeated story about San Francisco’s secret, underground rivers. He mentioned a 2021 quote from the director of the San Francisco Municipal Transportation Agency citing an “underground river” as part of the reason the city’s Central Subway completion was delayed.

By definition, a creek or river is free-flowing water that follows a channel, like a creek bed, either on the surface or in an underground cave. So are rivers really down there?

Time to do some myth-busting.

“We don’t have caves underground for creeks to flow through, other than the sewer,” says writer and natural history educator Joel Pomerantz. “So really, the misimpression that there’s an old creek here and it’s still down there somewhere is not accurate.”

A man wearing blue jeans, a sweater and a knitted cap leans forward on a railing, with a colorful mural on the wall behind him.
Joel Pomerantz stands near Mission Playground. In the early days of the city, this area held a large freshwater marsh and estuary. (Amanda Font/KQED)

But there is a connection between areas that are prone to flooding and where creeks used to flow.

It’s no secret that much of San Francisco is built on fill, and the most visible of those areas are along the edges of the city. But inland waterways have been covered up over time, too. A few years ago, Pomerantz created the “Seep City” map, which traces waterways that existed when San Francisco first became a city. That includes the bays, but also numerous creeks and large areas of marshland and estuaries.

At one time, much of the Mission District was marshland fed by the Arroyo Dolores, a waterway that ran from Twin Peaks down the center of 18th Street and through the northern corner of modern-day Dolores Park. That led to a larger saltwater marsh and slough that fed into Mission Bay.

Those waterways have since been filled, but the topography of the land hasn’t changed.

“I mean, if you think of the shape of the land,” says Pomerantz, “and if you’re a bicyclist, especially, like I am, you notice the shape of the land because you’re avoiding the hills. That’s what the water does.”

In addition to gravity leading rainwater down to those lower-lying sections of the city in the form of storm runoff, groundwater is also seeping through the soil to pool in those areas.

So when it’s raining really hard, says Pomerantz, the combination causes flooding. San Francisco’s large concentration of groundwater, coupled with increasing atmospheric river storms and the potential for sea level rise, could pose a big problem for the city. A new study finds that rising groundwater has huge implications for future flooding events.

3. What happens to the ground squirrels when it floods? Do they drown?

Our final question comes from listener Emily Robertson. In light of the massive flooding many cities have dealt with recently, Emily was worried that California ground squirrels might be getting flooded out of their burrows — or worse, drowning.

For the answer to this question, we turned to Jennifer Smith, a behavioral ecologist who studies social mammals, and specializes in squirrel behavior. For nearly a decade, Smith has been leading a research team in a long-term study of California ground squirrels in Briones Regional Park in Martinez. The team safely traps and marks the fur of individual animals so they can study their behavior and social patterns over time.

A small, fuzzy, and very cute juvenile ground squirrel pops out of a burrow. Another squirrel is partially visible behind it.
A young California ground squirrel peers out of its burrow in Briones Regional Park. (Courtesy of Jenn Smith)

They’ve also been able to map what the ground squirrel’s burrows look like. It turns out they’re well-prepared for the possibility of flooding.

“It may look like that burrow entrance will go directly down, and it might go a foot down or something, but it actually spreads out underground,” says Smith. “And part of the design is to have horizontal rather than vertical burrows. The horizontal nature of the underground structure is quite resistant to rainfall.”

The burrows branch out into numerous sections that can be extended if they become wet. So when the rains are thundering above, the ground squirrels stay nice and dry in their complex, multilevel burrows. They’re even good at withstanding intentional flooding: People who consider ground squirrels pests may stick a hose in the burrow to attempt to drive the squirrels from their home. But observations show that doesn’t really work.

“The squirrels are very, very faithful to their home,” says Smith. “They’ve invested a lot. They’ve constructed it, and they’ll usually stay. So we know from those types of studies that’s not a very effective method.”

In fact, because ground squirrels typically live in family groups, a family may stay in the same burrow for many generations.

Note: In researching this story, we asked if you had any questions about squirrels in the Bay Area. So many of you did that we’re working on an episode all about squirrels! It’s not too late to get your squirrel questions in. Submit them in the Bay Curious question box below. 


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