S.F. Bay shows signs of progress in biennial report

Y. Mogadam cools his heels in the bay at Marina Park in Emeryville, Calif. on Wednesday, Sept. 9, 2015. The Bay Area endured a third straight day of record breaking heat. Y. Mogadam cools his heels in the bay at Marina Park in Emeryville, Calif. on Wednesday, Sept. 9, 2015. The Bay Area endured a third straight day of record breaking heat. Photo: Paul Chinn, The Chronicle Buy photo Photo: Paul Chinn, The Chronicle Image 1 of / 7 Caption Close S.F. Bay shows signs of progress in biennial report 1 / 7 Back to Gallery

The erstwhile murky waters of San Francisco Bay are mostly clean enough to swim in, and the fish are essentially edible if you can shrug off the mercury and PCBs left over from mining and industry, a state-of-the-bay report revealed Thursday.

The Pulse of the Bay report released by the San Francisco Estuary Institute compiled data on water quality, habitat, chemicals and bacteria into its biennial report, which also predicted water quality and the general outlook for the bay 50 years from now.

The results show that water quality is generally fair to good, but pollutants in the water are trouble for swimmers from time to time, especially during the winter. Aquatic habitat is improving, according to the report, with most chemicals measuring below the threshold of concern. Still, mercury pollution, PCBs, trash and invasive species are conspiring to muck up the works.

“It seems there is a ring of contamination focused in certain areas, but concentrated on the edge of the bay,” said Jay Davis, a senior scientist with the Estuary Institute, which conducted the study as part of a collaborative regional monitoring program.

Old chemicals linger

The bay’s biggest toxic bogeymen are left over from past exploitations. Mercury was used in gold mining during the Gold Rush, and there were mercury mines along the coast range throughout the 1800s, specifically the New Almaden quicksilver mine in the Capitancillas range in Santa Clara County.

PCBs, which were widely used in electrical equipment and building materials until they were banned in 1979, also still linger.

Davis said the water around the Oakland and Richmond harbors and Hunters Point have high concentrations of PCBs. The chemical also lingers in high concentrations along the shoreline on the western side of the South Bay.

He said mercury is still seeping down from rivers and creeks and working its way into San Francisco Bay. Concentrations in sediment are highest in San Pablo Bay, he said. Meanwhile, mercury entombed in the bay mud, possibly combined with mercury emissions from coal-fired plants in Asia, continues to find its way into the food web. Fishermen have long been advised to limit their consumption of California halibut and striped bass caught in the bay as a result of mercury contamination.

Surprisingly, the report found that chinook salmon and jacksmelt caught in the bay are safe to eat.

“Once mercury and PCBs spread across our watershed, they don't degrade,” said Davis, noting that PCBs have been tracked for 20 years and mercury levels have been monitored for 40 years. “We see no reduction. There is no sign of decline.”

One needn’t go back in history to find sources of pollution, though. The garbage and sewage that washes into the bay every year remains a big problem, the researchers reported. Swimming conditions were deemed poor on two of 28 beaches studied during the summer and six of 28 in the winter, mainly because of bacteria that poured out of storm drains and from leaking sewer pipes.

Worst places to swim

The worst place to swim, according to the report, was Marina Lagoon, including Aquatic Park and Lakeshore Park, in San Mateo County, which was polluted all year. The other risky swim areas — at least during periods of wet weather when there is heavy runoff from storm drains — were Oyster Point, Coyote Point and Kiteboard Beach in San Mateo County and Candlestick Point in San Francisco.

Davis said some species are also being negatively impacted by invasive species, trash, especially plastic, and pollutants.

The study documented a big reduction in flame retardants known as polybrominated diphenyl ethers, or PBDEs. High concentrations of PBDEs were found in the bay over the past two decades, prompting a decision in 2006 to begin phasing out the chemicals.

“We've seen sharp declines over the past 10 years,” Davis said. “This is one of the best success stories in the management of the estuary.”

The Pulse report includes projections from six marine scientists on how the bay will look in 50 years. They predict storm water runoff and wastewater, including the stuff that flows into the sewer from toilets, will be recycled and turned into drinking water by then, eliminating discharges into the bay all together.

"There won't be wastewater anymore in 50 years,” Davis said. “The water will be used as a resource.”

The improvements in water quality will be counteracted somewhat by climate change, which will reduce flows of freshwater from the mountains into the bay by 2065, the experts say.

The sea level will also rise, deepening the bay, engulfing much of the present-day shoreline, increasing water temperatures and changing the hydrology of the estuary, according to the report.

“All these things will cause the food web to be different, and there could be big changes in species,” Davis said. “The bay is on track to getting cleaner, but it’s a mixed bag because sea level rise and the changes to the ecology of the bay will make it hard on our native species.”

The Pulse of the Bay report, released every other year for the past 24 years, was prepared as a companion to an even more comprehensive State of the Estuary report coming out next week.

Peter Fimrite is a San Francisco Chronicle staff writer. E-mail: pfimrite@sfchronicle.com Twitter: @pfimrite