The San Francisco Estuary sustains thousands of species of fish, invertebrates, birds, mammals, insects, amphibians, plants and other life. However, human use and development in the Estuary region has led to degradation of its natural habitats and major declines in many populations. The San Francisco Estuary Project is working cooperatively with diverse organizations and agencies to protect these invaluable resources, restore habitats and promote environmentally sound management of the Bay and Delta.

The Estuary

San Francisco Bay and the Delta combine to form the West Coast's largest estuary. The Estuary conveys the waters of the Sacramento and San Joaquin rivers to the Pacific Ocean. It encompasses roughly 1,600 square miles, drains over 40 percent of the state (60,000 square miles), contains about 5 million acre-feet of water at mean tide, and redistributes 80-280 million cubic yards of sediment every year. The Delta and Estuary watershed provide drinking water to 20 million Californians and irrigate 4.5 million acres of farmland. Estuary waters also enable the nation's fourth largest metropolitan region to pursue many activities including shipping, fishing, recreation and commerce.

Life In and Around the Estuary

Apart from the seven million human residents around its shores, the Estuary and its watershed sustain diverse aquatic organisms and wildlife. About two thirds of the state's salmon pass through the Bay and Delta, as well as nearly half of the waterfowl and shorebirds migrating along the Pacific Flyway. The overlap between marine, freshwater and terrestrial ecosystems in the Estuary region creates a rich mixture of habitats and species. Many species exist in viable, interdependent food webs despite the presence of big cities, farms and industry. Many others are in long-term decline, succumbing to urban growth, pollution, water development, disease, predation, loss of habitat and other factors. Those who manage the Estuary region are now working to maintain an environment in which both humans and wildlife can flourish.

History

A few hundred years ago, observers reported that migrating birds blackened the sky over the Estuary. One visitor reported salmon runs so dense that Delta rivers looked like a silver "pavement."

Commercial hunting began in the late 1700s when trappers slaughtered thousands of otters in the Estuary. By Gold Rush times hunters were delivering millions of waterbirds and shorebirds (and their eggs) to the tables of a growing populace and egret plumes to hat makers. Commercial fisheries were soon harvesting millions of pounds of Dungeness crab, grass shrimp and salmon, and decimating delicacies such as the sooty crayfish and red­p;legged frog.

Eventually, excessive hunting, fishing, pollution and other human disturbance brought about dramatic declines of many fur bearing and game mammals, migratory waterfowl and other birds. Expanding agriculture and urban development soon enveloped most wildlife habitats. Oak woodlands fell to the ax, lush riparian habitats gave way to bare levees, marshes disappeared under salt ponds and farm crops, and waterways were channeled to make way for upstream shipping.

In the last half century other threats to wildlife emerged. Pesticides threatened bald eagles, pelicans, ospreys and peregrine falcons. Massive withdrawals of ground and surface water for agriculture, cities and industry altered local ecosystems.

Today, little space and few natural resources remain on Estuary shorelines to sustain the region's once abundant plant and animal populations. In the water, fish and other organisms face increasing threats of habitat alteration, disturbance and contamination.

Current Factors Affecting Wildlife and Aquatic Organisms

Habitat Loss and Fragmentation

During the last 140 years, the Estuary's native wildlife habitats have been drastically reduced to islands in a sea of cities, suburbs and farms. Habitat loss and degradation forces wildlife to concentrate in small, isolated areas, often increasing vulnerability to other threats.

Hunting

Hunting is the largest single mortality factor affecting waterfowl. To provide habitat and encourage population recovery, hunting is now carefully managed through regulations on limits, seasons and methods of take. Private gun clubs and hunters around the Estuary killed an average of 387,333 ducks per year between 1971-1980 (they also preserved some valuable habitat). Other hunted species include dove, pheasant, quail, rabbit and deer.

Fishing

Commercial over exploitation of certain species such as Chinook salmon and white sturgeon contributed to their declines in the early part of this century. Today, the Estuary still supports stable anchovy, herring and shrimp bait fisheries.

Disease

Diseases such as avian cholera and botulism kill thousands of waterfowl wintering in Estuary. Water management practices and sewage effluent discharges often cause or exacerbate waterborne disease problems. Susceptibility to disease increases when birds concentrate in small remaining habitats.

Predation

While predation usually provides important natural limits on prey species, many birds and animals live in such suboptimal conditions that they become dangerously vulnerable prey. Predators of particular concern today are the growing numbers of non-native red foxes, rats, opossums and feral cats that raid bird nests.

Contaminants

Environmental contaminants present in the Estuary in potentially harmful concentrations include trace elements such as cadmium, copper, mercury, selenium and silver, and chlorinated hydrocarbons including pesticides such as DDT and polychlorinated biphenyls such as PCBs. Primary sources of contaminants include urban and agricultural runoff, municipal and industrial discharges, river inflows, dredging and dredged material disposal, and spills. Contaminants can harm wildlife, fish and other aquatic organisms if they affect the food base or otherwise disrupt habitat required for survival.

Natural River Flow and Freshwater Diversion

Drought and water management practices reduce the flow of fresh water to the Estuary at certain times of the year and increase it at others. Impacts of reduced flows on fish include interruption of migratory patterns as a result of reverse river flows, entrainment of fish and important food sources in pump screens, loss of habitat and spawning areas, and reduced transport of species to downstream nursery areas. Impacts on birds and mammals include habitat loss and alteration.

Other Factors

Many other factors affect Estuary organisms and wildlife. Traffic across shoreline parks and refuges in the form of aircraft, human visitors and roaming pets disturbs wintering waterfowl. Power lines and wind energy generators block bird flight paths, resulting in collisions and electrocutions (500 birds a year in the Altamont Pass area). Dike building and maintenance disturb and destroy riparian habitats. Dredging and dredged material disposal in the Estuary disturb and smother bottom dwelling communities, and resuspends sediments and associated pollutants in the water column. Meanwhile, opportunistic introduced species continue to expand their populations and ranges, moving into degraded habitat areas, and often competing with, or preying on, native species.

Status and Trends

Primary Producers

Microscopic forms of plant life are the foundation of the aquatic food web. Primary producers such as bacteria and algae (phytoplankton) grow and drift in the water, to be eaten by zooplankton (floating and drifting animals), which are in turn consumed by juvenile fish and shrimp.

Trends<: There have been long-term declines in phytoplankton, becoming more severe as a result of intensive filtering by large populations of the introduced Asian clam Potamocorbula amurensis. There have also been massive blooms of the largely inedible alga Melosira granulata since 1980.

Zooplankton

These plankton include water fleas, opossum shrimp, copepods, rotifiers and other microscopic animals and are found throughout the water column. They are important food sources for small or larval fish.

Trends: Rotifiers (the smallest zooplankton), water fleas and copepods have sharply declined throughout the Delta over the last 20 years.

Benthic Organisms

The benthos is the zone at the bottom of the Estuary inhabited by mussels, clams, crabs, shrimp and other aquatic organisms. Many burrow in the mud and filter water and sediments for food.

Trends: Oyster and marine clam populations fluctuate, largely in response to harvest, pollution, and invasion of new species. The Asian clam population has exploded, which has lead to declines of other benthic organisms. One species of grass shrimp (Crangon franciscorum) continues to decline because of inadequate freshwater inflows and other factors. Dungeness crab populations are also in decline, primarily as a result of ocean temperature rise.

Planktivorous Fish

These filter-feeders are among the most plentiful fish in the Estuary. Some eat phytoplankton, others zooplankton. Northern anchovy, by far the most abundant planktivorous fish, consume 4.5 percent of its body weight in zooplankton each day.

Trends: Planktivorous fishes that spend significant parts of their life cycle in the Delta or Suisun Bay have declined. Marine dependent species such as the northern anchovy and Pacific herring remain stable. Delta smelt is now in precipitous decline, possibly due to increased water diversions and drought. There have also been long-term declines in longfin smelt and threadfin shad.

Predatory Fish

These fish prey on other fish. Some, like flatfish, lie on the bottom waiting for prey to swim within reach; others, like white croaker, chase crabs, shrimp, small fish and other prey. The two most abundant flatfish, English sole and starry flounder, are marine species that use the Bay mainly as a nursery.

Trends: Starry flounder have declined as a result of changing environmental conditions and toxic contamination. By contrast, white croaker populations have been growing since 1980, increasing their use of the Bay for spawning and expanding their range as marine conditions become more predominant. There has been little change in the abundance in other marine dependent species. However, fresh water dependent species such as white catfish and Sacramento splittail are declining. The invading chameleon goby (a small Asian species) is on the increase.

Anadromous Fish

Several planktivorous and predatory fish are anadromous, which means they live some or all of their adult lives in salt water but migrate to fresh water to spawn. Four runs of Chinook salmon migrate through the Bay and Delta each year. Other anadromous species include striped bass, American shad, white sturgeon and steelhead trout. Striped bass, though a non-native, is used as an important indicator species for the study of estuarine environmental conditions.

Trends: Natural spawning Chinook salmon have experienced severe declines largely due to dams and diversions. Winter-run Chinook salmon were recently placed on the threatened and endangered species lists. Striped bass have suffered record low populations, largely due to the effects of water diversion, but also as a result of inadequate food supplies, pollution and poaching. White sturgeon have been declining worldwide and exhibit increasing selenium levels in the Estuary.

Songbirds

Dozens of species of songbirds live around the Estuary including warblers, sparrows, larks and thrushes. Their habitats range from oak savanna and grassland to riparian forests where trees, cattails and other vegetation along waterways make excellent nesting sites.

Trends: Some species have declined due to loss of habitat, introduced predators and competitors.

Shorebirds

The Estuary is an important wintering and migratory stop-over site for shorebirds such as plovers, stilts, avocets and sandpipers. At least 34 species live, nest and forage for food along the Estuary's shore-many equipped with long bills and legs useful for foraging in the mudflats. The Estuary attracts more migrating shorebirds than any other wetland area in California. Spring counts indicate up to one million birds estuarywide.

Trends: The long-billed curlew is declining due to habitat loss and drought. The black-necked stilt, American avocet and Wilson's phalarope appear to have been increasing in response to tidal marsh conversion into salt ponds suitable for nesting and raising young. Many shorebird populations, including the endangered clapper rail and black rail, are suffering from red fox (a non-native species) predation.

Waterfowl

These birds seek out shallow, sheltered open water such as sloughs and bays, nesting and resting along shores and feeding on plants, seeds, snails, clams and insects. The Bay provides a major coastal wintering and migratory staging area for a variety of Pacific flyway ducks. Suisun Marsh and the Delta attract both dabbing and diving ducks, as well as geese, swans and cranes.

Trends: Total waterfowl numbers in the Estuary dropped from a record high of 1.3 million in 1977 to a low of 109,000 in 1982 (with a mean annual population over the same period of 390,532). Populations of dabbling ducks and geese are at an all time low due to drought, predation and habitat loss (both in the Estuary and its watershed, and in Canadian and Arctic nesting grounds).

Colonial Waterbirds and Seabirds

Gulls, terns, herons, egrets, ibises and cormorants feed in the open waters of the Bay and ocean and nest in colonies on isolated islands or salt pond levees. Because they primarily eat fish and other aquatic organisms, these birds are sensitive to contaminant accumulation in the food web.

Trends: Populations of the double-crested cormorant, California gull and western gull have all increased since they're able to exploit artificial habitats such as manmade salt ponds and garbage dumps. California least terns, Chtmlian terns, herons and egrets have experienced recent major nesting failures due to human disturbance, intensive land use and habitat contamination.

Raptors

Raptors have talons for grhtmling their prey, hooked beaks for tearing flesh, and extraordinary eyesight. Each year, more than 10,000 hawks, kestrels, harriers, vultures and other raptors migrate over the Estuary region.

Trends: All populations continue to decline, with only limited recovery from past depletions. Causes include food contamination, habitat loss, urban expansion, wind energy development and incompatible changes in agricultural practices.

Land Mammals

Many mammals live around Estuary including rodents, rabbits, bats, skunks, badgers, opossums, beavers, foxes, raccoons, bobcat and deer. Some rely on the Estuary watershed for habitat and freshwater; some fish for food in creeks, rivers and bays; some hunt for bird eggs in wetlands.

Trends: Many small native mammals and carnivores are in decline due to urban and agricultural growth. By contrast, many opportunistic introduced species populations such as the red fox, Norway rat and Virginia opossum are growing, readily adapting to urban environments.

Aquatic Mammals

Marine mammals such as California sea lions and harbor seals frequent the Estuary and its shores. Harbor seals must come on shore (haul out) to rest and give birth. Populations observed at the five primary haul out spots around the Estuary-Mowry Slough, Greco Island, Yerba Buena Island, Castro Rocks and the Corte Madera Ecological Reserve-range from 125 to 550.

Trends: Today's Bay seal population is around 700 and has not changed significantly since the mid 1970s. Sea lions are still recovering from past exploitation and increasing their ability to use habitats such as San Francisco's Fisherman's Wharf. River otters still frequent the Delta.

Amphibians and Reptiles

Numerous species of amphibians and reptiles once inhabited the Estuary's river channels, creeks, sloughs, lakes, ponds and seasonal wetlands. Amphibians may live on dry land but can only breed in water. Most amphibian and reptile populations fell victim to widespread urban and agricultural development which destroyed their habitats. Today, only limited populations of these snakes, salamanders, frogs, turtles and lizards remain.

Trends: Species that have experienced dramatic depletion include the California tiger salamander, red-legged frog, San Francisco garter snake and western pond turtle.

Current Issues:

Introduced versus Native Species

Over the years, many non-native species have been introduced into the Estuary region. Oysters, striped bass and red fox were introduced for commercial harvest, while the Asian clam probably arrived in ships' ballast water. As introduced species expand their range they often compete with, displace or negatively impact native species.

Conflicts resulting from non-native species can be found throughout the Estuary area. In the Suisun Bay, burgeoning Asian clam populations (up to 30,000 clams per square meter) are consuming so much phytoplankton they may be endangering the aquatic food supply. On the Estuary's shores, European starlings are aggressively competing for nesting holes, displacing titmice, nuthatches, and other birds; red foxes which escaped from Central Valley fur farms are eating endangered rail eggs; wild pigs are destroying native vegetation; and a native ant, the only known food of the rare coast horned lizard, is being displaced by an Argentinean relative. Efforts are now being made to control some of these introduced species and to encourage native species recovery.

Habitat Loss and Degradation

Human influences on aquatic, shoreline and surrounding habitats will continue to have a major impact on organisms and wildlife in the future. Specific future impacts on habitats will include:

• Loss of 10,000 acres of wildlife habitat per year to accommodate projected population growth.
• Loss of 36 percent of the Bay Area's 21,400 acres of remnant seasonal wetlands to development.
• Agricultural conversion to incompatible crops such as orchards and vineyards.
• Rapid erosion of the Bay's margin of tidal marshes, particularly on eastern edge of the South Bay where 3-16 feet of shore erode annually.
• Increasing contamination from industrial and domestic wastewater discharges. Despite improved treatment, the total volume of wastewater will rise in response to population growth.
• Probable continued conversion of tidal salt marsh to brackish (salt and freshwater mix) due to increasing South Bay sewage effluent discharge.
• Increased water diversion in Delta due to growing urban and agricultural demand.
• Increasing predation by red foxes, contributing to eventual extirpation of California clapper rail and least tern.
• Reduced wildlife use of wetland areas due to increasing human visitation and disturbance by domestic and feral animals.