The San Francisco Bay — with a shoreline half as long as the entire coast of California — is a draw for people who love water sports from swimming to kayaking to windsurfing. But some beaches on the Bay are contaminated by fecal pathogens, threatening the health of those who come for fun in and on the water. Now, spurred by new regulations for bacteria on our beaches, cities are cleaning up the waterfronts that drain into these troubled shores.

Water that is polluted by feces can contain more than 100 kinds of human pathogens, including bacteria, parasites, and viruses. Pathogen-contaminated water — or even just its spray — can infect ears, eyes, and skin, as well as gastrointestinal and respiratory systems. According to the Centers for Disease Control and Prevention, those most at risk are pregnant women, children, and people with weakened immune systems.

We’ve come a long way from the days when cities dumped raw sewage into the Bay. But most of the region’s sanitary sewers and wastewater treatment plants were built in the 1950s and ’60s, and many are showing their age. “A lot of the development was in the post-war boom, and sewer pipes are at the end of their usable life,” said Ian Wren, a scientist with San Francisco Baykeeper, a nonprofit focusing on pollution in the Bay.

Most of these old sewer lines are made of sections of clay pipe laid end-to-end. These connections were tight initially, but now there are gaps between many of the pipe sections because even small earthquakes can dislodge them, particularly in areas built on fill. On the Peninsula, for example, three-quarters of clay sewer pipes are cracked, Wren said. And leakage from these pipes often makes its way down storm drains and into the Bay. “Sanitary sewer and storm drain pipes were generally laid next to each other, forming a direct conduit from one to the other,” he said.

In addition, heavy rains can overwhelm sewer systems, leading to overflows. Wren estimated that during the exceptionally wet winter of 2010-2011, more than 26 million gallons of sewage-contaminated water spilled into the Bay. Other sources of fecal contamination in waterways include animal droppings and urban runoff.

Unlike other water pollutants, pathogens are alive. “Bacteria have a way of growing when conditions are right,” said Jan O’Hara of the San Francisco Bay Regional Water Quality Control Board, adding that these microorganisms can flourish in shallow, warm shorelines. In the spring of 2016, the Water Board adopted the first-ever regulations for bacteria in beaches along the Bay. The regulations are based on fecal bacteria, which are simple to measure and so are used as proxies to indicate when water is contaminated by other fecal pathogens.

Currently, six beaches on the Bay fail to meet the new standards for bacteria: Marina Lagoon in San Mateo; Candlestick Point, Aquatic Park, and Crissy Field in San Francisco; and China Camp and McNear, which are near San Rafael. In the first phase of the new regulations, these cities must “find and fix” leaking sewer pipes within a quarter mile of these beaches, O’Hara said, adding that they have three years to do this. Cities can also curb stormwater flows to the Bay, which carry bacteria from sources including leaky sewer pipes, portapotties, and homeless encampments.

When the three years are up, cities will assess their efforts to see if their beaches “get an A,” O’Hara said. If not, the next step will be extending the find and fix for leaky sewer pipes to within half a mile of the contaminated beaches. O’Hara is hopeful that there will be at least a few good beach report cards soon. “It’s possible that some could get an A within three to five years,” she said. “Cities are being very proactive.”

That’s partly because “we knew this was coming,” said Sarah Scheidt, the City of San Mateo’s regulatory compliance manager. Cities are also eager to get their beaches off the list of those polluted with bacteria. Heal the Bay, a nonprofit based in Santa Monica, publishes annual report cards for bacterial contamination on California beaches, spotlighting the ten worst in its “Beach Bummer” list. “We were in the Beach Bummer list for at least five years and this year we came off it,” Scheidt said.

Why, then, is San Mateo’s Lagoon Beach on the Water Board’s list of bacteria-contaminated beaches? The two lists are based on different methods of assessing bacterial pollution. Notably, Heal the Bay includes several types of fecal bacteria. In contrast, the Water Board focuses on one type called Enterococcus that has “recently been tied to health issues in marine waters,” O’Hara said.

To get Lagoon Beach off the Beach Bummer list and, hopefully, off the Water Board list, Scheidt has done everything she can think of. Monitoring salinity in sanitary sewer manholes can reveal cracks in sewer pipes as well as connections between sewer lines and storm drains. The latter were made before sewage treatment plants went in and are “not on maps,” Scheidt said.

Animal droppings are also a priority because Canada geese live year-round on Lagoon Beach. A contractor picks up goose droppings twice a week, collecting 450 pounds in five months. And another contractor brings dogs that chase geese off the beach (but are trained not to harm the birds). In addition, the city has a permit to addle goose eggs, which entails coating them with vegetable oil so they don’t hatch. “The geese are not migrating the way they should be, so they’re a nuisance,” Scheidt explained. “We addle more than a thousand eggs a year.”

People can do quite a bit to help too, she said. One way is not feeding the geese, which might encourage them to move on when it’s time to migrate. Other ways of helping include picking up pet waste in yards and on public walkways near the beach, and using less fertilizer on yards near the beach. “When nutrients are high in the lagoon, algae grows and harbors bacteria,” Scheidt said. People can also maintain the sewer laterals from their homes to municipal sewer lines. The laterals are not under municipal jurisdiction and “people don’t think about it until it’s a problem,” she said. Signs of a problem include drains that aren’t working properly.

Another option is a comprehensive fix to our sanitary sewers. “Society has to make a decision about these things no one wants to pay for,” Baykeeper’s Ian Wren said. “We don’t want sewage backed up into homes or running down streets.”