Bay Nature magazineFall 2003


Four Threats to a Healthy Bay

October 1, 2003

Habitat Loss

On the fringes of the Bay lie the varied wetlands that feed and shelter the Bay’s wildlife. Chinook salmon, white croaker, and northern pintails feed in the shallow water as it fluctuates with the tides. Topsmelt, Pacific staghorn sculpin, and brine shrimp thrive in salt ponds that cover large portions of former tidal marsh. Dungeness crabs, clams and shrimp use stretches of mudflats that sit exposed between the open water and the shoreline while a million shorebirds feed on the living systems of diatoms, microalgae, protozoans, and other invertebrates. Leopard sharks, shiner perch, and great egrets cluster in salt marshes from sea level to high water lines.

Poets extol the verdant wealth of tropical rain forests and the coastal redwoods. Hardly at all do they praise the salt marsh bathed by tides where scented cordgrass and pickleweed create dense communities of wildlife and vegetation. Yet this ecological transition zone between deep water and land is among the most intricate and bountiful ecosystems in the world, called an “incubation crib” by Luna Leopold, geology professor emeritus at University of California at Berkeley.

Once viewed as useless swampland, these 10,000-year-old wetlands were drained and developed by California settlers. In the last century and a half, approximately 80 percent of the Bay’s 193,800 acres of tidal marshes has been lost. And probably no wild animal has suffered as much from this loss as the California clapper rail, a bird uniquely adapted to this once-common but now rare and fragmented habitat. Tens of thousands of these cinnamon-breasted waterbirds with distinctive downward-curving bills once lived in tidal salt marshes from Morro Bay to Humboldt Bay, well camouflaged with their olive-brown backs and barred flanks. On mudflats bordering the marshes and along the channels wending through them they’d feed on mussels, clams, worms, and small fish.

Then came the Gold Rush, and a growing population that began filling and diking these marshes for cities, croplands, pastures, and salt ponds. Hunters killed a seemingly endless supply of the chicken-size birds for sport or to sell to San Francisco restaurants. Today, only about 1,500 California clapper rails remain in the world, all of them living in and around San Francisco Bay.

In 1970, the federal government declared the California clapper rail endangered and environmentalists used the imperiled bird’s plight to get Congress to establish the San Francisco Bay National Wildlife Refuge. Even so, by the mid-1980s, rail numbers had plummeted to 500, so the U.S. Fish and Wildlife Service (FWS) was tasked with providing habitat for the rail—and the endangered salt marsh harvest mouse—in any restoration efforts.

The current campaign to turn diked ponds and pastures back into tidal marshes goes beyond saving the clapper rail. Tidal wetlands with native vegetation are essential nursery habitat for an array of invertebrates and fish, which feed on the nutrients provided by the plants and find shelter from predators along the banks and among the roots. Foraging animals eat less than 15 percent of the plant biomass in saltwater marshes. Yet when the plants die in the winter, up to 70 percent of the plant material is broken down into small particles and released into the water, where it becomes food for fish and shellfish. More than 300 species of birds and mammals, 130 species of fish, 40 species of reptiles and amphibians, and an even greater number of invertebrate and plant species depend on the estuary’s wetland and aquatic habitats for food, shelter, or completion of part of their life cycle, according to FWS.

Moreover, tidal marshes serve to filter pollutants, control floods, stabilize shorelines, and aid in the recharge of groundwater. Nowadays, thanks to the grassroots efforts to save the Bay and agencies such as the Bay Conservation and Development Commission, the Bay is no longer suffering from large-scale filling and diking. But just the presence of so many humans can make the remaining habitat difficult to use.

This is the challenge facing a bigger but just as skittish Bay resident, the Pacific harbor seal, which is losing habitat due to encroachment by humans. While harbor seal numbers are on the rise along coastal California, the Bay population has remained stagnant at around 600. Over the past century, these animals have abandoned many of their historic haul-out sites in the Bay.

Compared to the more mobile, less sensitive California sea lions that greet tourists at Fisherman’s Wharf, harbor seals are awkward and slow on land. So if there are humans around, they just won’t come ashore. And if people approach a haul-out site, the seals hit the water. Noisy boats and even quiet kayaks can scare them off, a serious matter for a marine mammal that needs to periodically haul out of the cold water to maintain a balanced body temperature. The development of healthy seal babies, which need to nurse frequently, can be jeopardized when the seals are flushed. Experts fear that disturbance from the growing human population will keep the seals away from usable haul-out sites—sloping terrain near deep water or channels—eventually forcing out the only marine mammal that lives in the Bay year-round.

In 1996, Dianne Kopec, coauthor with Jim Harvey at Moss Landing Marine Lab of a study on harbor seal population dynamics and toxic contaminants, heard that the California Department of Transportation was planning to retrofit the Richmond-San Rafael Bridge, a span that passes within 250 feet of Castro Rocks, the largest year-round haul-out and breeding site in the North Bay. Caltrans initially received an exemption from the Marine Mammal Act to go ahead with its work, which included the use of huge pile drivers. Aided by Stanford’s Environmental Law Clinic and the nonprofit firm Earthjustice, Kopec filed objections to the exemption, eventually forcing Caltrans to agree not to work near the rocks during the pupping and molting seasons (March through August) and to sponsor a monitoring program of the haul-out sites.

The parties involved agree that the seal pact shows that humans can have a safe bridge and at the same time make room for a Bay that embraces a healthy diversity of life. But, scientists caution, before they can strike this balance, they must first understand ecological principles at work in the Bay and in all the other places where human needs for another bridge, another housing development, or another airport runway might come up against a remaining fragment of habitat for wildlife.


Humans have been using the Bay as a dump and a sewer for as long as we’ve lived here, starting with the Ohlone, whose everyday life leftovers are preserved in shellmounds around the Bay. But as our products grow more and more toxic, the effect of these practices becomes more serious, making it harder for other species to live among us.

Every spring, from as far away as Colombia, North America’s largest tern, the Caspian, returns to breed by the Bay. Nesting in colonies, the terns scrape depressions on salt pond levees, islands, or relatively barren shorelines. More streamlined than gulls, these graceful birds with sleek black caps, sparkling white heads, and deep red bills feed on small fish, arthropods, and amphibians on the open Bay, salt ponds, rivers, and reservoirs. For their trouble, they’re poisoned with mercury, dioxin, PCBs, DDT, and a class of flame-retardant compounds called PBDEs (polybrominated diphenyl ethers), which are used in foam, computers, television sets, and textiles. According to scientists from the U.S. Geological Survey, Caspian tern populations in the South Bay are declining at the same time that high levels of mercury are being found in their eggs. The highest mercury levels found in animals from the Bay were in the eggs of Caspian and Forster’s terns that nest near the Cargill salt ponds at the mouth of the Guadalupe River (near Alviso).

The terns aren’t the only ones contaminated with mercury. California clapper rails, black-necked stilts, avocets, and snowy plovers are also affected. A study conducted by the U.S. Fish and Wildlife Service has found that nearly three-quarters of the eggs examined from black-crowned night heron nests in the Guadalupe watershed contained mercury exceeding thresholds known to kill the embryos of other bird species.

This should come as little surprise, as the largest single source of mercury to the Bay is the now-closed New Almaden Quicksilver Mine in the hills above San Jose. Some 120 years’ worth of accumulated mine waste from these productive mines has been gradually draining into the Guadalupe watershed. The Cargill salt ponds at the mouth of the watershed are part of the 16,500 acres that have recently been purchased with the intention of restoring them as wetlands. One-fourth of this acreage contains mercury, according to the San Francisco Bay Regional Water Quality Control Board. Once it gets into the wetlands, the mercury is converted to methyl mercury, the most toxic form of the element. Methyl mercury readily binds with proteins in plants and animals and is passed up the food chain. Exposure to methyl mercury can damage an animal’s nervous, excretory, and reproductive systems. Early life stages are the most sensitive.

Many species of fish-eating birds that visit the Bay on their migrations along the Pacific Flyway are at risk. The Bay’s 1,600 square miles of wetlands and open water are home to at least 800,000 waterbirds at any one time and to more than a million during the peak of migration. Seventy percent of the birds that migrate along the Pacific Flyway spend some time every year by the Bay.

What food they find here may not earn the state’s seal of approval. Sport fish in the Bay routinely exceed state health guidelines for PCBs, mercury, dioxin, dieldrin, and selenium, according to the latest results from the Regional Monitoring Program conducted by the nonprofit San Francisco Estuary Institute (SFEI). Researchers have also found PBDEs in all samples from frequently caught and consumed Bay fish: white croaker, shiner surfperch, leopard shark, California halibut, white sturgeon, striped bass, and jacksmelt.

The California Environmental Protection Agency has issued a fish advisory for the Bay and Delta, warning people not to eat more than two 8-ounce meals a month of sport fish, or any striped bass longer than 35 inches. Pregnant women, nursing mothers, and children under age six should be even more careful.

There has been little study of the effect of all these pollutants on the health of the fish themselves. Scientists fear that the mercury, which can decrease brain size and delay physical and mental development in human babies, may kill fish hatchlings and impair reproduction in sensitive species. But tests to show the effects of toxic chemicals on white croakers have been inconclusive so far, and funding for additional studies has been hard to come by.

Marine mammals are also exposed to danger when they eat fish from the Bay. Unfortunately, harbor seals can’t read agency warnings and they don’t have alternative sources for their diet of fish. Ecologist Jay Davis of SFEI’s Regional Monitoring Program notes, “The state says humans should eat no more than two meals a month of Bay fish. But the seals are eating 90 meals a month of Bay fish, and they’re mammals like us.” Recent studies of seal blood and blubber have shown elevated levels of a variety of common Bay contaminants, including a hundredfold increase of the flame-retardant compounds. Recent studies also show elevated levels of PBDEs in the breast tissue of Bay Area women, though this is likely from sources other than fish consumption. Tissue samples from the 1960s showed no PBDEs at all.

Concerned about the rapid rise of this class of chemicals, which are similar in structure to persistent PCBs, the California legislature passed bills in August phasing out two common forms of PBDEs. This is one small but important step toward keeping contaminants from polluting the Bay in the future. Yet the task that lies ahead is daunting. New chemicals come on the market every year, while the banned chemicals already in the Bay take decades to get flushed out or buried by sediments. As scientists restore thousands of acres of tidal marsh and open new habitat to crustaceans, shorebirds, and waterfowl, they need to make sure that the welcome banquet they’re preparing isn’t a deadly one.

Freshwater Flow

Altering the flow of rivers wasn’t a new concept in the 1930s. After all, California Indians had temporarily dammed creeks to make it easier to catch salmon returning to spawn.

But the massive federal and state water projects completed in the 1940s through the 1970s reached a scale so unprecedented that they permanently changed the ecosystem of the largest estuary on the west coast of North America. The Sacramento-San Joaquin River system, which drains 40 percent of the landmass of California, poured 8.7 million acre-feet of water into the Bay in the dry year of 1934. In the dry year of 1994, the Bay got 6 million acre-feet, 60 percent of the prewater project dry-year flow. The difference: a vast network of canals, pumps, and dams, which send a huge portion of the water to farms and homes in Central and Southern California. A creature that has paid dearly for that overall change is the humble Delta smelt, a three-inch-long fish of no interest to either sport or commercial fishers.

Septuagenarian Bay Area natives remember when the Delta smelt was so common that they could dip cupped hands into the water and draw out the small, slender fish. They were everywhere, from Suisun Bay in the Delta down into the South Bay. Now they’re so rare they have triggered federal lawsuits and changed the very way their native Delta operates.

The state and federal governments listed the Delta smelt as threatened under the federal Endangered Species Act in 1993. UC Davis fisheries biologist Peter Moyle prepared the listing petition with the American Fisheries Society, after chronicling a steep decline in smelt numbers during the early 1980s. Professor Moyle traced the decline to two main factors: decreased freshwater flows from inland rivers, resulting in an upstream shift of the brackish zone where fresh water from the mountains meets salty ocean water, and the operation of massive water pumps in the Delta, which were sucking in the fish.

Delta smelt evolved to live in the brackish mixing zone. In the winter, maturing fish moved upstream into fresher waters in upper Suisun Bay and the lower reaches of the Delta, congregating there before they spawned. They used the channels and dead-end sloughs, depositing their eggs on submerged tree branches or in open water over sand and rocks. The juvenile smelts, feeding on planktonic crustaceans, then moved downstream to brackish waters, in some years passing through the Carquinez Strait to San Pablo Bay and even as far down as the Central and South Bay, depending on flow conditions.

Studies by Moyle and others have demonstrated the link between the abundance of Delta smelt and the number of days when ample fresh river water pushes the fresh-saltwater mixing zone down into Suisun Bay. The shallower, warmer, lighter waters of Suisun Bay provide a more plankton-rich nursery than the deeper, colder channels of the Delta. As their rearing environment changed, the smelt suffered, along with a number of other species that had evolved to rely on the special conditions of the Bay-Delta estuary. These include the Sacramento splittail, longfin smelt, starry flounder, and the Bay’s only species still fished commercially, Pacific herring. Runs of young chinook salmon, leaving the Sacramento and San Joaquin Rivers where they were spawned, also need generous freshwater flows to get past water project intake pumps to the ocean.

The diminished flow from the Delta affects all of the Bay, according to the U.S. Geological Survey. The quiet southern reach gets saltier, and pollutants that tend to cling to floating and settled sediments don’t get flushed, absent the vibrant flow from spring floods. In addition, without ample river flows to hold it back, salty water encroaches on the part of the Delta from which Contra Costa County pumps part of its drinking supply.

The protective provisions of the Endangered Species Act, triggered by the listing of the Delta smelt, have required resource agencies to alter the amount and timing of water exports from the Delta to Southern and Central California cities and San Joaquin Valley growers. However, in 2003, Central Valley growers and water districts filed a lawsuit against the U.S. Fish and Wildlife Service (FWS), demanding that the smelt’s endangered status be reviewed as required under the original settlement. The suit cited improved average counts for the fish in recent years. A federal judge has now directed FWS to complete a new review.

Fisheries biologist Tina Swanson, who studies the smelt for the nonprofit Bay Institute, says it would be unwise to remove protections for the fish based solely on a single five-year period of data, the time indicated in the fish’s recovery plan. The little fish remains very vulnerable, and a string of dry years could well push it over the edge, she warns. According to Swanson, in such dry years only 40 percent and 60 percent of the water from rain and snowmelt in the Sacramento-San Joaquin river system gets to the Bay. In 2001, the last year for which records are available, 60 percent of the water made it past the pumps, dams, canals, and reservoirs and into the Bay. During the critically important spring flood period, the Bay received only a quarter of the flow that would have reached it without artificial diversions.

This reduced flow in 2001 took a toll on the fish, according to Bay Institute research, which found abundance of native fish to be just half of what it was 30 years ago. During the 1980s and early 1990s, a period of both prolonged drought and increased water diversions, Bay fish abundance declined by 80 percent. Since its low point in the early 1990s, abundance hasn’t significantly increased. Hardest hit was Suisun Bay, where native fish populations in 2001 were just 15 percent of the average measured only 20 years earlier.

Environmentalists fear that it’s going to get even harder to preserve healthy freshwater flow to the Bay. Recent U.S. Interior Department decisions have caused California to lose a significant amount of Colorado River water. In response, the Metropolitan Water District (“Met”) of Southern California, which serves 18 million customers, has already started buying water from Sacramento Valley growers. Barry Nelson, who has followed California water issues for two decades, first with Save the Bay and now for the Natural Resources Defense Council, says, “We know what’s happening here. Met is trying to figure out how to get more diversions from the Bay and Delta system to replace the Colorado River water. We’re concerned there will be more pressure from Southern California to divert more water in a way that could damage the Bay.” Yet with the threat of more pumping, a new union of old opponents—Delta farmers, North Coast tribes, Sacramento Valley agriculture advocates, fishers, and Bay Area environmentalists—is emerging. “People are saying, ‘Enough already!'” says Nelson. “Before the state and federal projects pump more from the Delta, they need to comply with—and stop obstructing—legal requirements to protect Northern California ecosystems.”

Invasive Species

Four decades ago an Oakland teenager’s fascination with what he called an “accidental zoo” of exotic aquatic life in Lake Merritt laid the foundation for a startling finding: San Francisco Bay is one of the most invaded estuaries in the world. James T. Carlton is now director of the maritime studies program at Mystic Seaport in Connecticut, the nation’s largest maritime history museum. Back in the early 1990s, he teamed up with then-UC Berkeley doctoral student Andrew Cohen (now at the San Francisco Estuary Institute) to chronicle the invasion of the Bay and Delta by more than 250 introduced aquatic organisms. Their ground-breaking 1995 paper showed how these alien species had profoundly affected the diversity and abundance of the Bay’s native life.

Carlton was the first scientist to look at the scale of marine invasions on a regional basis. His interest began 40 years ago when, at age 15, he collected organisms at Lake Merritt and brought them to the California Academy of Sciences for identification. By age 24, he had completed a comprehensive survey of aquatic life in the saltwater lake, finding that almost all the organisms had come from elsewhere in the world. That work became part of his 1979 doctoral dissertation on the ecology of introduced marine and estuarine invertebrates on the Pacific Coast.

Carlton and Cohen’s work brought to public attention for the first time the extent of the incursion of exotic species into the San Francisco estuary. One of the key species they discussed was the Asian clam, Potamocorbula amurensis. Most likely introduced through discharged ballast water from a cargo ship, the clam was proliferating in the Bay by 1987 at an alarming rate. It is such a heavy grazer that, according to the U.S. Geological Survey, the population is capable of filtering the entire water column at least one to two times a day in the shallow reaches of the Bay. The clam has reduced the primary production of phytoplankton fivefold, creating an environment of chronic food limitation for aquatic wildlife such as native shrimp, other crustaceans, and zooplankton.

As well as eating the food of copepods and mysid shrimp, the clams also eat their young, leading to a sharp decline in their abundance and range. In addition, the Asian clam concentrates selenium, which is then passed on to the animals that feed on it, such as sturgeon, staghorn sculpin, and scaup. Unfortunately, the mollusk is now a permanent Bay resident, primarily in the North Bay. In the South Bay, it has appeared, disappeared, and reappeared in a pattern that still mystifies scientists. The largest populations are found on soft sediments in subtidal waters in a wide range of salinity.

While the Asian clam is busy disrupting the estuary’s food chain, the nonnative Atlantic salt marsh cordgrass (Spartina alterniflora) is wreaking havoc with its tidal marshes, pushing out its less aggressive cousin, Pacific cordgrass (Spartina foliosa), a crucial building block of the Bay’s native marshes. Pacific cordgrass and a natural mix of pickleweed, jaumea, salt grass, and alkali heath form a complex habitat that supports nesting birds, fish, and invertebrates. When the cordgrass dies, it decays into nutrient-rich food for fish and invertebrates.

In 1970, a consultant working for the U.S. Army Corps of Engineers on the Alameda Flood Control Project imported Atlantic cordgrass and planted it in an attempt to create a new marsh in what is now Coyote Hills Regional Park. In the three decades since, the exotic grass has emerged as an aggressive invader, choking out the native cordgrass and other marsh plants. To make matters worse, the invader has interbred with the native cordgrass to form new hybrids that spread even faster.

The Atlantic cordgrass and its hybrids grow more densely, more rapidly, and twice as tall as the native cordgrass. Because it tends to grow in a thick mat, researchers are concerned that the exotic grass will eventually choke off the sloughs that bring water into the marshes, the very lifeblood for food and habitat for such birds as the California clapper rail and the Alameda song sparrow. The changed marsh structure could well affect the way sediments collect and circulate, in turn affecting the invertebrates and other species at the bottom of the Bay’s food chain.

Already the exotic grass and its hybrids have sprung up on some 500 acres spread over about 5,000 acres, mostly concentrated in the South Bay north of the Dumbarton Bridge. This encroachment is posing a major challenge for scientists planning for tidal marsh restoration on the salt ponds purchased from Cargill earlier this year. Scientists fear that if left unchecked, the Atlantic cordgrass will opportunistically colonize the ponds when dikes are breached. No simple and effective methods for eradicating it have been found. Resource managers have dug it up, covered it, burned it, and even used herbicides in limited spots. All these methods have serious drawbacks. Scientists are now debating whether to launch a major herbicide assault on the invader as a way to avert the permanent extinction of South Bay tidal marshes.

The die may already be cast. When measuring the wet weight of organisms in or on the Bay floor, scientists now estimate that up to 90 percent are nonnative. In its 10-year study released last May, the San Francisco Estuary Institute concluded that the great influx of alien species is now as serious a disruption to life in the Bay as chemical pollution. It’s unlikely that resource managers can successfully eradicate organisms already proliferating in the Bay, according to Cohen. So what’s left is to concentrate on keeping out newcomers.

Unfortunately, Cohen points out, the rate of invasions has been increasing. Between 1850 and 1970, an average of one new species was established in the estuary every 46 weeks; since 1970, the rate has jumped to one new species every 15 weeks. A giant reed called Arundo donax grows in the Napa River, Sonoma Creek, and San Pedro Creek, producing towering stalks and deep roots, guzzling three times the water of native plants. The Chinese mitten crab has already spread to the Delta, where it threatens to clog water systems and burrow into levees. Atlantic green crabs, which may have come to the Bay in seaweed packing with bait worms from Maine, prey on bivalves, polychaetes, and small crustaceans and threaten to displace the native Dungeness crab.

Scientists and environmentalists agree that state and federal laws on the books have been ineffective in guarding against these invasions and that more needs to be done. The California Legislature is expected to extend a 1999 law that forbids oceangoing vessels from discharging untreated ballast water into state waters. And a federal law requires that ships report any exchange of ballast water, yet it doesn’t require an exchange before entering coastal zones or bays. Overall, there is little monitoring and enforcement, and just this September the federal Environmental Protection Agency denied a petition by several environmental groups requesting that the agency regulate invasives as pollutants under the Clean Water Act.

Reflecting on his and others’ work researching the estuary’s invasive species, Carlton observes that the Bay is a prime example of the concept of the reticulate mesh of nature. “You can’t tweak one little part of nature,” he says, “without it having some other effect that you can’t even imagine.”

About the Author

Jane Kay is the environmental writer for the San Francisco Chronicle. She has reported extensively on San Francisco Bay for nearly two decades.

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