At AAAS Pacific Division Meeting, Researchers Detail Mounting Perils for San Francisco Bay


Research by the U.S. Geological Survey and others shows that if water levels in the San Francisco Bay rise 140 centimeters by the end of the century, thousands of acres (in blue) of natural tidal marshes, agricultural land, and urban areas would be vulnerable to inundation. [Image courtesy of the San Francisco Bay Conservation and Development Commission. See a full selection of the commission's inundation maps, including explanations and disclaimers.]

SAN FRANCISCO—Some 35 years ago, a crew from the PBS science show "Nova" joined a team of scientists from the U.S. Geological Survey as the researchers worked to piece together one of the earliest systemic views of the San Francisco Bay. They explored its physics and its biology, and along the way analyzed a daily flood of discharged sewage, high concentrations of heavy metals, and the demise of shellfish, birds, and other native Bay species.

Today, some of the most troubling conditions described in that 1974 documentary have been abated. But during a day-long symposium at the AAAS Pacific Division annual meeting, a new generation of researchers described a new generation of challenges that imperil the Bay—the continuing loss of native species, incursions by non-native species, and rising concentrations of fire retardants and other chemicals.

The overarching challenge, some said, may be Earth's changing climate, which could raise Bay water levels by four feet or more by the end of the century. Even a smaller rise in the water level could inundate thousands of acres of low-lying developed areas on shore, damage or submerge sensitive tidal marshes that harbor endangered wildlife, and force the expenditure of billions of dollars for protective levees.

"As snowpacks diminish in the upstream watershed, and as sea level rises at the Golden Gate, salinity in the estuary will increase and wetland and shallow-water habitats will be threatened, with potentially strong adverse ecological impacts," said Noah Knowles, a research hydrologist with the U.S. Geological Survey. "Levee systems around the Bay and in the upstream Delta will face a much higher likelihood of widespread failure. These types of changes will pose enormous challenges to both the cities and agricultural areas of the San Francisco Bay region."


John Largier

"The bay is changing," added symposium organizer John Largier, professor of coastal oceanography at the University of California-Davis' Bodega Marine Laboratory, "and so too is our understanding of change. Direct anthropogenic effects such as sediment management, habitat loss and water contamination continue in parallel with climate-change trends in sea-level and land runoff, and with decadal fluctuations in ocean-driven conditions. The challenge for science is to identify the primary threats to the sustained delivery of ecological goods and services—and to provide the insight to enable optimal decisions for the Bay ecosystem."

The AAAS Pacific Division held its 90th annual meeting from 14-19 August at the California Academy of Sciences and San Francisco State University, drawing more than 475 scientists, engineers, teachers, students, journalists, and others with a diverse selection of symposia and workshops. Marking the 150th anniversary of the publication of Charles Darwin's On the Origin of Species, the meeting focused on how nature changes through evolution, and how humans must build a sustainable relationship with nature to ensure the future health of all life.

But the events at the meeting included a broad range of issues: the search on Earth and beyond for "weird life," or life that does not share a bio-chemical heritage with known plants and creatures; project-based science learning; recent advances in pharmacology and toxicology; and communicating science to the public.

The Bay symposium was a centerpiece of the meeting, convening more than a dozen top scientists from the U.S. Geological Survey (USGS), San Francisco Estuary Institute (SFEI), and California universities to present their latest research about the past and future health of biggest estuary on the Pacific Coast. While the Bay is the center of a complex and far-reaching ecosystem that is constantly in flux, studies of sediment flow, phytoplankton concentrations, eel grass distribution, tidal marshlands, and other markers all suggest that the Bay is struggling to cope with an increasing load of environmental change caused by human activity.

A Vital Organ for Life in Northern California

Most tourists—and many among the 7 million people who live in the region—know the San Francisco Bay as one of the most beautiful estuaries in the world. But they don't always see its complexity, the way in which it knits together ecosystems from the inland mountain ranges to the Pacific Ocean.

It's a single system of interconnections and interdependence, where great, still-mysterious climatic fluctuations such as the Pacific Decadal Oscillation or the North Pacific Gyre Oscillation help determine the fate of grasses that grow on the Bay's shallow floor or populations of fish and crab in Bay waters. As an integrated system, the Bay is like a vital organ supporting life throughout Northern California and beyond.

Fresh water from the Sierra Nevada snowpack streams down the west-facing slopes of the range, joining into rivers and deltas that eventually empty into the Bay. About 40% of California's total area drains to the Bay, said Knowles, who is based in Menlo Park, California.

At the same time, tides pull salty Pacific water into the Bay, where it combines with fresh water before the briny mix is expelled back into the ocean. "Central Bay is the cross-roads, directing flows north of south or back out to sea," said Largier. "Yet we know little about how changes in sea level, river inflow, sediment deposition/erosion and ocean fluctuations will alter these links with the ocean."

The environment supports an abundance of life in the waters and shores of the Bay, and the sky above. More than a million birds a year stop at the Bay as they migrate along the Pacific Flyway.

People, too, have been drawn to the Bay. As far back as 10,000 years ago, indigenous people lived in what is now the Bay Area. By the time of the first Spanish explorations in the 16th Century, the area was home to an estimated 200,000 to 500,000 people—most from the Coastanoan, Coast Miwok, Yokut, and Wintun tribes.

But with the arrival of new settlers beginning in the 19th century, land use and exploitation for agriculture, mining and other purposes began to disrupt the Bay's delicate balance. Farmers filled in tidal marshes and cut channels to drain seasonally flooded lowlands. Miners searching for gold and other riches washed whole hillsides into the Sierra's rivers, and this sediment was carried into the Bay.

As the population grew, development destroyed an estimated 85% of the Bay's original marshlands. The Bay also absorbed millions of gallons of household sewage and toxic contaminants produced by manufacturing and other enterprise. Dams built to control floods, generate electric power, and provide water for homes and farms changed the flow of fresh water into the Bay.

As a result, dozens of plant, insect, and animal species—from shrimp and salmon to turtles, butterflies, and California clapper rails—declined in the Bay environment throughout the 20th century.

In the 1960s and '70s, scientists, environmental advocates, and others began to detail the damage, and they helped guide a movement to understand and restore the healthy function of the estuary system. In 1977, 1980 and 1994, the AAAS Pacific Division held symposia on the state of the Bay and produced reports that still provide benchmarks and valuable insight to new generations of researchers.


Jay A. Davis
[Photo courtesy of San Francisco Estuary Institute]

The Power of Deep Forces

Speakers told the AAAS Pacific Division audience that the conservation and restoration efforts have had some significant impact on the quality of Bay waters. Since 1999, more than 10,000 acres of marshland have been restored, with many more projects underway or planned. Populations of the California clapper rail have inched up.

Jay A. Davis, an environmental scientist at the San Francisco Estuary Institute, said that problems associated with sewage discharge have largely been solved. So too with levels of silver in the water. Concentrations of copper and nickel have declined and now are below thresholds of concern, Davis said.


James Cloern, a USGS aquatic ecologist.
[Photo courtesy of U.S. Geological Survey]

James Cloern, a USGS aquatic ecologist, said that beginning in 1999, researchers began to document record high populations of English sole, Dungeness crab, and other marine species in the Bay from 1999 through 2005. A 10-species index, tracked from 1980-2008, found "a clear increase in the abundance of these marine species after 1996."

Can that be attributed to improved conditions in the Bay? Apparently not—Cloern linked that trend to the North Pacific Gyre Oscillation, a climatic pattern reported for the first time last year by researchers at Georgia Tech. The pattern is linked with increased salinity, cooler sea surface temperatures, and increased upwelling of nutrients in the California Current of the Northeast Pacific.

While that North Pacific climate shift appears to be natural, research suggests that Earth's rising temperature intensifies the effect of the new climate pattern.

Cloern called the link between the North Pacific Gyre Oscillation and rising Bay marine populations "striking." And, he added: "We have to recognize that climate change is manifest in many ways, not just the sea warming and the sea-level rising."

The Coming Flood?

The likelihood of rising seas—and rising water levels throughout the estuary—is a source of growing concern to Bay Area policymakers. And at the AAAS Pacific Division symposium, several researchers suggested it could have a profound disruptive impact on the Bay ecosystem—and on the Bay Area's communities and economy.

"A formidable challenge is to improve our ability to predict morphologic [structural] and environmental change as global warming accelerates sea-level rise and alters weather patterns that shape the estuary," USGS oceanographer Bruce Jaffe wrote in the abstract for his presentation.

Knowles, offering a synopsis of various climate models, said that temperatures could rise by 2 to 9 degrees Celsius by 2100, with most setting the increase at 3C to 6C. Some models predict little or no change in Bay Area precipitation, while others forecast "significant" drying, he said. Some foresee less snow and more rain in warm Sierra winters—with increased likelihood of floods downstream.

At the same time, Knowles said, warming over the Pacific Ocean will melt sea ice and expand the water. That could help drive a 4.5-foot rise (140 centimeters) in Bay water levels.

"This," he said, "is a problem."

Knowles noted that waters could flow into important agricultural lands and into heavily developed areas. San Francisco International Airport and Oakland International Airport could be submerged, he said, as could the island community of Alameda; the South Bay shore near cities like Palo Alto, and areas near downtown San Francisco.

If waters rose undeterred, they would submerge tidal marshlands that buffer the shore from high winds, high tides, and winter storms. If the rising waters erode the Bay Area's already fragile levees, future floods may be even more serious, he said.

Knowles said that one mitigation approach likely to be considered by policymakers would be to spend millions—perhaps billions—on new and rebuilt levees to hold delta and Bay waters in check.

Dan Hanes, a USGS oceanographer and former professor of civil and coastal engineering at the University of Florida, is skeptical that the Bay Area could engineer its way to a solution. The best option for some areas may be simply moving to higher ground, he suggested.

According to Hanes, Bay Area residents may not have to wait long before getting a glimpse of the future. With water levels already 20-30 centimeters higher now than a century ago and a storm-spawning El Niño climate system emerging in the Pacific, and with storm surge likely to compound cyclical high tides, the augurs are in line for a challenging winter.

"It's likely we're going to experience a flood soon," he said. "If that happens, then for a few weeks to a few months we will get to see what sea level in the Bay will look like in the next 50 to 100 years."

Not Sexy, but Critically Important

Faced with such momentous risks, sediment hardly seems a central concern. But for many researchers who study the health of San Francisco Bay and the potential impact of climate change, sediment tells a critically important story.

Historically, sediment flowing naturally to the Bay from the Sierra Nevada and other mountain ranges has provided important nutrition to marine life and provided essential material for the formation of tidal marshes at the Bay's rim. Some of the sediment has made its way outside the Golden Gate, where currents shape it into an underwater barrier that protects against storm-driven wind and waves.

But when the Gold Rush of the mid-19th century triggered mass migration to the area, a cycle of disruption was set in motion.

Before mining started in earnest, an estimated 2 million cubic meters of sediment came out of the Sierra Nevada into the Bay, Jaffe said. But in the mid- and late 1800s, that rose to 14.1 million cubic meters per year. Between 1850 and the 1980s, more than 250 million cubic meters of sediment was deposited into the Bay, he said.

After mining played out, the trend reversed. Rivers were dammed to store water for farms and thirsty communities; they captured tons of sediment every year. Levees were built to prevent flooding, and that further reduced sediment flow. Dredging for ports, shipping and other purposes removed 50 million cubic meters of sediment beginning in the 1950s, Jaffe said.


David Schoellhamer, a USGS research hydrologist, sampling Miner Slough in February 2009.
[Photo courtesy of U.S. Geological Survey]

Just in the past 15 years, researchers have recorded a 36% decrease in concentrations of suspended sediment, said David Schoellhamer, a USGS research hydrologist. The prevalence of fauna and flora in the Bay has declined and their distribution has shifted.

For example, Schoellhamer said, smelt populations have declined, perhaps because they prefer more turbid waters. The clarity of the water may allow more sunlight to penetrate, leading to the larger spring blooms of phytoplankton in recent years, along with unusual autumn and winter blooms.

The effects of diminished sediment seem evident outside the Bay, too. Centuries of sediment transport from the Sierras through the Bay to the Pacific continental shelf had helped build up the Ebb Tide Delta—a large, relatively stable, radial-shaped underwater ridge. But, Hanes said, the ridge has lost an estimated 92 million cubic meters of sediment in just the past 50 years. Erosion of the Pacific beaches has been unusually heavy in recent years. Hanes said the reduced flux of sediment from the Bay may be at least partly to blame for the shrinking Ebb Tide Delta; rising seas and larger Pacific waves over the past 30 to 40 years may also play a role, he said.

Tipping Points and "Cascading Threats"

Decreased sediment, increased phytoplankton, reduced carbon dioxide—researchers see these trends as evidence that the fundamental chemistry of the San Francisco Bay is turning less hospitable to its historic diversity of plant and animal life. Edwin Grosholz, a benthic ecologist at the University of California-Davis, warned of "cascading threats" that could transform the Bay.

But an array of trends make understanding elusive and Bay protection exceedingly difficult.

Where great progress has been made in reducing sewage discharges and the concentration of many heavy metals, researchers have come to understand the risk posed by other contaminants.

Toxic mercury, dioxin, and polychlorinated biphenyls (PCBs) are among the Bay's most serious contaminants now, said Davis, the environmental scientist at the San Francisco Estuary Institute. Mercury has entered the food chain, leading to a consumption advisory for Bay fish, and it could have an impact on reproduction for some creatures. Further, Davis said, those compounds have been trapped in the sediment over the last several decades—and can be released by storms and shifting currents.

While PCB concentrations are declining, he explained, "we're so far above the threshold it's likely that in 20 years, we'll still be under a dark cloud." Levels of dioxins, which have been linked to cancers and reproductive damage, are far above safe concentrations and will likely remain so for at least 20 years.


USGS biologists Cory Overton (left) and John Takekawa weighing a California clapper rail.
[Photo courtesy of U.S. Geological Survey]

Meanwhile, new contaminants are appearing in the Bay. For example, polybrominated diphenyl ethers, or PBDE, are flame retardants widely used in textiles, computer equipment, motor vehicles, and building materials. They're similar to PCBs—they pose health risks because they can accumulate in the food chain, and in human tissue. Two of the three major classes of PBDEs have now been banned in California, but parts of the Bay have PBDE concentrations not seen elsewhere in the world, Davis said.

Inevitably, researchers look to this more hostile chemistry for clues to changing wildlife population patterns. John Takekawa, a USGS wildlife biologist, told the audience of significant declines in a variety of birds that have historically visited or lived in the Bay environment: the brant goose, the canvasback duck, and the song sparrow, among others.

At the same time, Takekawa said, the population of native California gulls has increased "exponentially."

Grosholz, in his presentation, said that more than 250 invasive species are now established or gaining a foothold in the Bay: cordgrass, kelp, and clams, even goldfish and catfish.

The San Francisco Bay is "among the most invaded estuaries in the world," Grosholz said. "The question is how much more invaded the Bay will be in the future—and how we will manage those invasions."

Whether their expertise is sediment, endangered birds, or climate change, other researchers and policymakers, are asking the same question. For any estuary, change is a constant, but how can humans manage a huge and vital ecosystem that's changing or stressed at so many points?

Continued research will advance understanding, and that will help guide well-informed management, researchers said at the symposium. Engagement with policymakers, businesses, and the public will be critical.

Indeed, strong progress in understanding and mitigating problems has already been achieved. And compared to many urbanized estuaries along the California coast, San Francisco Bay still offers major restoration opportunities, said Robin Grossinger, an environmental scientist at the San Francisco Estuary Institute. In the end, he and others suggested, managers seeking to restore the Bay's health must nurture its vast natural resilience.

Said Grossinger: "San Francisco Bay, despite all of the challenges, has an enormous amount of resources left."