Findings:

• Before 1848, human impacts on the Estuary's water quality and its ability to sustain biological resources were minimal.
• Hydraulic gold mining caused the first major human-induced alteration of the Estuary. By the early 1900s, more than one billion cubic yards of mining debris had silted in hundreds of miles of streams and the bottom of parts of San Francisco Bay by as much as three feet. Although the debris exacerbated flooding and impeded navigation, some of the deposited sediment enabled the spread of tidal marshes in thc Bay.
• By the turn of this century, levee construction in the Delta and along the shore of the Bay had enabled the conversion of more than half of the Estuary's tidal wetlands to farmland and urban uses
• The human population in the twelve Estuary counties has increased from about one million in 1920 to more than seven-and-a-half million today. Currently, the Bay Area is the fourth-most-populous metropolitan area in the United States. By the year 2005, nearly nine million people will reside in the twelve Estuary counties, and almost three million more will inhabit the Central Valley watershed.
• Urban expansion has converted thousands of acres of farms, rangeland, and forests to towns and cities. This has increased the Estuary's pollutant loads and has lowered the region's ability to support wildlife.
• The Estuary provides thousands of water-dependent jobs in commercial shipping, fishing, and other industries. Jobs in agriculture and in other sectors throughout the state depend on supplies of high-quality fresh water from the Estuary watershed.

Until the mid-l800s, the Estuary's waters and biological resources were essentially undisturbed by human development. Following the influx of gold seekers in the 1850s, human activities began to change the Estuary in major ways. Hydraulic mining carried more than one billion cubic yards of silt and gravel from thc Sierra Nevada into the Delta and San Francisco Bay. Land reclamation in the Delta and along the edge of the Bay converted more than 750 square miles of tidal marsh into agriculture and other uses. Farming and ranching altered large expanses of upland vegetation.

In this century, especially during thc past four dccades, urbanization has been the major influence on the lands around the Estuary. Large-scale residential and commercial development replaced small farms and pasture on the flatlands adjacent to San Francisco Bay. The construction of highways and freeways and associated leapfrog suburban development have become major features of the landscape. Much of this development converted or degraded important habitats, particularly tidal wetlands, and increased the loading of pollutants in urban runoff. Today, more than 30 percent of the land in the nine counties surrounding San Francisco Bay has been urbanized, as has more than 10 percent of the land in the three Delta counties.

"By the year 2005, nearly nine million people will reside in the twelve Estuary counties, and almost three million more will inhabit the Central Valley watershed."

The increase in urban land around the Estuary reflects the growth of the human population. More than 7,500,000 individuals now live in the twelve Estuary counties, making the region the fourth-most-populous metropolitan area in the United States. With more than two million additional people in the Central Valley, about one-third of California's population now lives on land that drains into the Delta and Bay. The number of people living within the Estuary's entire watershed is projected to increase to twelve million by 2005. Population growth is expected to be greatest in San Joaquin, Solano, and Sacramento counties.

Population growth is expected to result in the loss of productive agricultural land and, to a lesser extent, rangeland and forest land. Between 1990 and 2005, approximately 275 square miles of land will be urbanized in the twelve Estuary counties. In the Central Valley watershed, urban land is projected to increase by 454 square miles during the same time period. These changes will reduce the acreage of valuable farmland, wetlands, and riparian areas (the land immediately adjacent to rivers and streams) and will inerease the amount of human-produced pollutants entering the Estuary.

Decline of Biological Resources
Findings:

• The Estuary's habitats--its open water, wedands, and uplands--sustain the estuarine ecosystem.
• During the past 140 years, most of the wetland habitats--mudflats, tidal and seasonal marshes, and riparian woodland-- have been drastically diminished, while the Bay's open water has been redueed by one-third. More than one-half of the native upland habitat has been converted to urban land.
• Since the mid-1970s, the abundance of phytoplankton has declined in the Estuary's northern reach (San Pablo and Suisun Bays), due in part to decreased freshwater flows, increased water transparency, and the establishment of the voracious, non-native clam Potamocorbula in Suisun Bay. With this decrease in phytoplankton, zooplankton production has been low, thus reducing the availability of food for several species of young fish.
• The number of Chinook salmon returning to spawn in the Estuary's tributaries has declined by 70 percent from historical levels. In the SanJoaquin River, there has been a 90 percent reduction. The Sacramento River winter-run salmon has been designated a federal threatened and state endangered species. Water development is the major cause of the decline of this valuable resource.
• The striped bass population is at its lowest level since the species was introduced into the Estuary more than one hundred years ago. The population of adult striped bass has dropped to one-half million, less than 20 pereent of the number in the 1960s. Several factors, including water diversions, pollutants, and habitat alteration, are suspected causes of the decline.
• The U.S. Fish and Wildlife Service listed the Delta smelt as threatened under the federal Endangered Species Act. This once-abundant native species resides in the Delta and Suisun Bay and feeds solely on the diminishing supplies of plankton.
• Many species of bottom-dwelling animals recently introduced to the Bay and Delta have altered the community composition. Unintentional introductions seem to occur at a rate of about one per year.
• The Estuary is one of the most important staging and wintering areas for migratory waterfowl and shorebird populations on the west coasts of North and South America. Nearly one million waterfowl and one million shorebirds use the Estuary's open water and wetland habitats at certain times of the year. As waterfowl habitat has dwindled in other parts of the state, the Estuary has become increasingly important for maintaining bird populations.
• Major factors affecting wildlife in the Estuary basin are habitat loss, disease, introduced predators, and pollution.
• Between 1985 and 2005, some four hundred square miles of range, forest, and agricultural lands in the Estusry basin are expected to be converted to urban uses. This, and additional losses of wetlallds, will further compromse the region's ability to support a thriving community of wildlife.
• Wetlands, one of the Estuary's most valuable resources, are critical for maintaining many of its fish and wildlife species. Of the thirty-two species of wildlife whose populations are declining in the Estuary, twenty-three are associated primarily with wetlands.
• In addition to their value as fish and wildlife habitat, wetlands provide many other important benefits, including flood control, groundwater recharge, shoreline stabilization, open space and recreation, and water quality maintenance.
• Of the 545,375 acres of historical tidal wetlands, only 44,371 acres (8 percent) remain. In the Delta, 92 percent of the original wetlands have been converted to farmland. In San Francisco Bay, 82 percent of the tidal wetlands have been filled or diked.
• More than 100,000 acres of the Estuary's wetlands (about one-sixth of the existing wetland acreage) have been protected in the form of parks, refuges, and preserves. Although wetland degradation and conversion have slowed substantially since the early 1970s, 1oss of valuable habitat still continues.
• Projected urban expansion in the Estuary basin could adversely affect at least 10,000 acres of stream corridor and 3,500 acres of non-riparian wetlands. Mitigation could offset some of the losses.
• Based on expected patterns of urban expansion, seasonal and riparian wetlands are the most threatened wetland types.

The Estuary's biological resources--its habitats, aquatic organisms, and wildlife--have undergone major challges since the Gold Rush. These changes include habitat degradation and conversion, population declines and the extirpation of many native species, and the introduction of hundreds of plant and animal species. Although the estuarine ecosystem relmains diverse and productive, it is highly modified.

In the past 150 years, shoaling caused by hydraulic mining debris and the diking and filling of tidal marshes have decreased the surface area of San Francisco Bay by 37 percent to its present area of 478 square miles. More than half a million acres of the Estuary's historical tidal wetlands have been converted to farms, salt ponds, and urban uses, a reduction of 92 percent. Fewer than 45,000 acres of the Estuary's historical tidal marshes remain intact. Non-tidal wetlands have been converted to farms and other uses, and many of the riparian forests have been removed by flood control projects and urban developmcnt. More than half the natural upland nhabitats in the Estuary's basin have been converted to urban uses.

Whole communities of aquatic resources--phytoplankton, zooplankton, bottom-dwellers, and fish--have undergone extensive change. More than one hundred exotic species of aquatic invertebrates, including clams, oysters, and worms, have been introduced in the past century. Today, most of the large invertebrates of the Bay shallows are introduced species, and the majority of the more than fifty fish species found in the Delta are non-natives.

Much of the Estuary's productivity is dependent upon the growth of phytoplankton, small floating plants that transform sunlight into food. Since the early 1970s, and especially since the 1976-1977 drought, phytoplankton abundance generally has declined in the Estuary's northern reach. Populations of zooplanktoll, which feed on phytoplankton, also have declined and are now at levels much lower than in the 1970s. The causes of these changes are not well understood, but are thought to include, at a minimum, reduced freshwater flows and the introduced Asian clam.

"Of the 545,375 acres of historical tidal wetlands, only 44,371 acres (8%) remain."

The recent arrival of the Asian clam has made it difficult for scientist to understand the causes for alterations of the phytoplanktoll and zooplankton communities. Unintentionally introduced into the Estuary in cargo ship ballast water, the clam was first discovered in the Carquinez Strait area in 1986, following a winter of unusually high river flow. Since then, durring five years of low flows, the Asian clam has spread throughout Suisun and San Pablo Bays and, to a lesser extent, into portions of San Francisco Bay. Growing at densities as high as 25,000 individuals per square meter, the clam population is able to consume vast quantities of phytoplankton. By greatly reducing the availability of phytoplankton to other organisms, this clam may be causing a major shift in the makeup of the aquatic ecosystem in the northern portion of the Estuary.

"The Estuary's salmon stocks have dropped markedly since the turn of the century when an annual average of some 900,000 fish returned to Central Valley streams to spawn."

Several of the Estuary's fish species have undergone changes in population levels in recent years. Although some species have increased in numbers, including the commercially important Pacific herring and many of the native non-game fish that inhabit the South Bay, others have declined. Species with declining populations that are receiving the greatest attention are Chinook salmon, striped bass, and Delta smelt.

The Estuary's salmon stocks have dropped markedly since the turn of the century, when an annual average of some 900,000 fish returned to Central Valley streams to spawn. By the early 1950s, following construction of Shasta Dam on the Sacramento River and Friant Dam on the San Joaquin River, Chinook salmon runs had dropped to about 400,000 fish annually. The construction of Friant Dam completely destroyed the upper San Joaquin River stock of mostly spring-run salmon. Numerous smaller dams are also responsible for the declining salmon populations. Today, an annual average of about 275,000 salmon spawn in the Estuary watershed; most of these are fall-run fish which spawn in the Sacramento River drainage.

Other factors responsible for the decline in salmon populations include reduced spawning habitat, inadequate stream spawning flows, intermittent poor water quality, spawning gravel of unsuitable size, high stream temperatures, and losses of young fish to water diversions. The upper Sacramento River winter-run salmon has declined to such an extent that it has been listed as a federal and a state endangered species. The annual commercial ocean catch of about 400,000 salmon has remained fairly stable, maintained in part by five hatcheries that produce a total of more than thirty million fingerlings and yearlings each year. The natural production of salmon in streams is now inadequate to sustain commercial and sport fisheries.

Striped bass, introduced into the Estuary in the 1880s, supported a large commercial fishery until the 1930s. Today the striped bass is prized as a sport fish. However, at approximately 500,000 fish, the current number of adult striped bass is at the lowest level of this century. Potential causes of the decline include Delta water diversions, reduced Delta outflows, reverse flows, low San Joaquin River flows, pollutants, and wetland filling. Losses to Delta water diversions appear to be a very important factor in the decline. Between 1976 and 1986, tens of millions of young bass and an inestimable number of eggs and larvae were lost to state and federal water project pumps in the southern Delta. Additional losses occurred in the 1,800 unscreened siphons and pumps of Delta farms.

Although the Delta smelt has no commercial or sport value, it is one of the few remaining native species found in the upper reaches of the Estuary. Once common, its numbers have dropped precipitously since the early 1980s. Because this species feeds entirely on plankton, it is not surprising that the changes in the smelt population have occurred at the same time as the decline in plankton production in the Estuary's northern reach. Invasions of exotic invertebrates and phytoplankton, losses to water diversions, and habitat modification have all contributed to its deterioration. The California Fish and Game Commission and the U.S. Fish and Wildlife Service both recently listed the Delta smelt as endangered under their respective Endangered Species Acts. These listings could affect water project operations in thc Delta and upstream.

The Estuary supports more than 380 species of wildlife. About one-third of these species, including most of those with high commercial or recreational value, are associated with open water, wetlands, and adjacent uplands.

Development of the Estuary has drastically altered wildlife habitats, and, as a result, populations of most wildlife species are smaller than in the past. Some ninety species and subspecies, whose populations are dwindling or monitored, are designated by federal or state agencies as being in need of special attention. Of these, sixty-one are affected by the loss of wetlands and riparian areas.

The Bay and Delta comprise one of the most important wintering areas for migratory waterfowl on the west coasts of North and South America. Nearly one million waterfowl use the estuary's open water and wetland habitats. Suisun Marsh and farmed wetlands in the Delta provide valuable habitat for ducks, geese, pelicans, and swans. As wetlands in other parts of California continue to diminish, the Estuary's remaining wetlands are becoming ever more important to waterfowl.

More than thirty-four species of shorebirds occur regularly within the Estuary. Most of these species frequent the Bay and Delta during the spring, en route to northern breeding grounds in Canada and Alaska, and in the fall upon their return. Census figures indicate that shorebird populations peak in the spring months to more than one million birds. In San Francisco Bay, about 60 percent of shorebird use occurs in the South Bay and 20 percent occurs in San Pablo Bay. In the Delta, marshes, mudf1ats, oxidation ponds, and farm fields provide important habitat. Extensive fall and spring flooding of plowed Delta fields can result in large concentrations of shorebirds. In 1990, the San Francisco-San Pablo Bay system was recognized as a site of hemispheric importance by the Western Hemisphere Shorebird Reserve Network. Only three other areas on the west coasts of North and South America have received such high recognition.

Populations of several of the Estuary's wildlife species have recently increased. In the past five years, the breeding population of the double-crested cormorant, a bird that nests on bridges and other constructed structures, increased to more than l,l10 pairs. The breeding population of the western gull has also grown. In 1981, California gulls established a nesting population that s till flourishes in the Bay. Through immigration from other areas and human assistance, the American peregrine falcon, an endangered species, has increased ten-fold in the Bay Area during the past twenty years. However, none of the locally nesting pairs has successfully reproduced recently.

"The Bay and Delta comprise one of the most important wintering areas for migratory waterfowl on the west coasts of North and South America."

Since the l980s, there has been a substantial increase in the red fox population, especially on the eastern shoreline of the South Bay. The fox, introduced to California from the Midwest in the early 1900s, is an efficient predator that has adapted to urbanized areas and now poses a severe threat to ground-nesting birds, waterfowl, and shorebirds in the Estuary. The U.S. Fish and Wildlife Service recently proposed a plan to reduce the threat of fox predation to nesting birds of the San Francisco Bay National Wildlife Refuge.

Although populations of some species have increased in recent years, populations of other species have declined. The endangered California clapper rail, estimated at 1,500 individuals in the mid-l980s, has dropped to below three hundred. The South Bay nesting population of the Caspian tern also has declined from more than one thousand in 1971 to only about two hundred in l990. Predation by the red fox and other introduced predators, as well as habitat changes, are noted causes of these declines. The nest of the least tern, also an endangered species, is subject to predation and human disturbance as well.

Habitat availability for the salt marsh harvest mouse, a state and federal endangered species, has declined markedly in the past twenty years. While about 6,000 acres of habitat remain available to the northern subspecies in Suisun Bay, the southern subspecies inhabits only about 760 acres of South Bay marshes, where diking of tidal marshes, land sinkage, and shoreline erosion have reduced tidal marsh acreage, especially at high tide.

Future land development in the Estuary region is expected to reduce the most valuable habitats and adversely affect populations of many fish and wildlife. Although some species may flourish, many will not. Unless efforts are made to minimize losses of valuable habitat and to improve the way in which the Estuary's land and water are managed, conditions for many of the region's biological resources will continue to deteriorate.

Freshwater Diversions and Altered Flow Regime
Findings:

• The Estuary's freshwater supply strongly influences environmental conditions in the Estuary. It also supports many other beneficial uses, including water for agriculture, municipalities, and industry. Some twenty million Californians, or two-thirds of the state's population, rely on the Estuary's freshwater supply for drinking water.
• Ninety percent of the Estuary's fresh water originates in the Central Valley watershed. The Sacramlento River provides about 80 percent of this flow, and the San Joaquin River and other streams contribute the remainder.
• The total annual volume of fresh water reaching the Estuary is highly variable, primarily as a result of rain, or the lack of it. During the past twenty years, annual inflow has ranged from more than fifty million acre-feet to less than eight million acre-feet and has averaged about twenty-four million acre-feet.
• More than seven thousand diversions for a variety of purposes, such as flood control, storage, and agricultural use, reduce the annual volume of water entering San Francisco Bay by more than one-half in some years. At the current level of development, more than sixteen million acre-feet of fresh water are diverted from the Estuary's supply. Of this volume, more than nine million acre-feet are diverted upstream of the Delta for local use and export, and about seven million acre-feet are diverted from the Delta for local use and export. Reservoirs in the Central Valley are capable of storing about twenty-seven million acre-feet of fresh water, roughly three million acre-feet more than the Estuary's average annual inflow since the 1920s.
• The federal Central Valley Project and the State Water Project are by far the two largest diverters, together removing nearly ten million acre-feet of water from within the Estuary watershed. Eighty-five percent of this water is used by agriculture and 15 percent goes to municipal, industrial, and other uses.
• Storage and diversions affect the seasonal volume of fresh water entering the Bay. Natural Estuary freshwater flow is reduced significantly during late fall, winter, spring, and early summer and is slightly increased during the late summer and early fall. The effects of diversions and storage on seasonal flow are greatest in the spring.
• Diversions and altered flow affect the Estuary's circulation and water quality, habitat conditions for wildlife, production of phytoplankton and zooplankton, and the survival of eggs and young of many fish species, including salmon, striped bass, and others. The effect of these species is magnified during dry and critically dry years.
• Construction of currently planned local water development projects and the completion of the State Water Project are expected to increase annual diversions from the Estuary's water supply by at least 1.1 million acre-feet.

Freshwater flows are among the most important factors influencing physical, chemical, and biological conditions in the Estuary. Many of its biological resources are directly affected by the quantity and timing of these flows, and by the way in which water is diverted for non-estuarine uses. Considering this, and the fact that two-thirds of California's population depend upon the Estuary's fresh water as a supply for drinking and other uses, it is not surprising that the "flows" issue is being discussed avidly by Estuary Project participants and others throughout the state.

The Estuary's freshwater flows originate as precipitation in the Central Valley and in the watershed surroundig the Bay. About 90 percent of the flows are from the Central Valley watershed. The remainder come from the Bay watershed. Because the amount of precipitation varies each year, so does the volume of fresh water that reaches the Estuary.

Development of major flood control and water storage reservoirs began in the latter half of the last century. Today, there are more than one hundred reservoirs in the Central Valley watershed, each with a storage capacity of at least 50,000 acrefeet. Combined, they can store about twenty-seven million acre-feet of water, which exceeds the average annual flow from the Delta into the Bay.

"Currently, development, upstream diversions, in-Delta uses, and Delta exports reduce flows to San Francisco Bay by more than fifteen million acre-feet, a reduction of more than 50% of the average annual flow."

Diversions from the Estuary's tributaries began in the mining regions of the northern Sierra in the mid-1850s as miners diverted water for hydraulic mining operations. At about the same time, farmers began to divert water from streams on the Valley floor. The volume of water diverted upstream of the Delta has grown steadily ever since. As of 1990, upstream diversions reduced the volume of water reaching the Estuary by more than nine million acre-feet. This water is used for agricultural, municipal, and industrial uses in the Central Valley and in the Bay Area. Within the Delta, about one million acre-feet of water are consumed each year to irrigate crops in the rich Delta soils.

Since the 1940s, when the federal Central Valley Project began diverting water into the Contra Costa Canal, the export of fresh water from the Delta has steadily increased. In 1951, the federal Delta-Mendota Canal began to export Delta water southward into the San Joaquin Valley, mostly to farms. In 1968, the State Water Project Delta pumping facility began exporting Delta water into the California Aqueduct, a system that conveys water southward into the San Joaquin Valley and to Southern California.

Currently, development, upstream diversions, in-Delta uses, and Delta exports reduce flows to San Francisco Bay by more than fifteen million acre-feet, a reduction of more than 50 percent of the average annual flow. About 85 percent of the fresh water exported from the Delta goes to farms; the remainder is used by municipalities and industries in the Bay Area, the Central Valley, and Southern California.

Water developmet has changed the patterns of freshwater flow into the Estuary. Water is stored during winter and spring for release later in the year. This greatly reduces flows during April, May, and June, and may increase them slightly during the late summer and early fall. In 1990, Delta outflow during spring and early summer was about one-third of what it would be without water storage and diversions.

Water resources development and associated changes in the timing and volume of freshwater flows have had an enormous impact on the Estuary's biological resources. This impact has been particularly severe on several fish species and results primarily from habitat loss and degradation, altered water temperature regimes, increased mortality of eggs and young from diversions and predators, transport of species into new areas, and alteration or confusion of migration patterns of spawning adults or out-migrating young. The impacts have been most obvious on certain fish species, such as salmon, striped bass, and some resident fishes. The number of naturally reproducing salmon and striped bass has plummeted from historical levels, and populations of other species have declined as well.

Water development is far from complete in the Estuary watershed and in other parts of California. State Water Project planners are currently evaluating ways to incrcase average annual Delta exports by more than one million acre-feet and, at the same time, reduce some of the existing problems associated with Delta diversions. In addition to increasing the export rate at the state's Delta pumping facility, planners are considering modifyillg Delta channels and constructing water storage facilities elsewhere. The federal government is planning to increase its water deliveries from Estuary tributaries and is currently evaluating the environmental impact of various development alternatives.

Given the expected increase in water demand from California's growing population in the coming decades, it is clear that water supplies must be used more efficiently. It is equally clear that the Estuary's freshwater supply must be managed in a scientifically and ecologically sound manner. It is likely that Californians will meet future water needs through a combination of conservation measures, changes in water policy, and new physical facilities.

Increased Pollutants
Findings:

• Each year, an estimated five to forty thousand tons of at least sixty-five pollutants enter the Estuary. Many of the pollutants are carcinogenic, teratogenic, or mutagenic in one type of organism or another.
• The major sources of pollutants to the Estuary are urban runoff, non-urban runoff, municipal wastewater treatment plants, industrial facilities, rivers, dredging, spills, and atmospheric deposition.
• Since the 1950s, improved treatment has lowered the quantity of biodegradable pollutants entering the Estuary from wastewater treatment plants. As a result, effects associated with low oxygen concentrations and high bacteria levels are now rare in the Estuary.
• Improved treatment at municipal wastewater treatment plants and industrial facilities has reduced the discharge of some toxic trace elements, but these substances continue to enter the Estuary in large quantities, especially from uncontrolled sources.
• Pollutants are widespread in the Estuary and reach highest concentrations in harbors, marinas, industrial waterways, and at effluent discharge sites.
• Pollutants that enter the Estuary can concentrate at high levels in animal tissues, even though they may occur at low concentrations in the water and sediments.
• Bioassays of Estuary water, sediments, municipal and industrial effluent, and urban and non-urban runoff have elicited toxic effects in some test organisms.
• Concentrations of silver, copper, and cadmium in South Bay clams vary in response to annual water circulation processes that dilute and transport trace elements.
• Persistent pollutants appear to cause sublethal effects in some species. For example, polychlorinated biphenyls (PCBs) appear to reduce reproductive success in starry flounder in the eastern portion of the Central Bay. PCBs and DDE in black-crowned night heron eggs have been correlated with decreased embryo size and eggshell thickness.
• Concentrations of several pollutants in Estuary waters exceed state water quality objectives. Concentrations of some pollutants in animal tissues exceed international standards and guidelines for the protection of aquatic life.
• While pollutant effects can be demonstrated in laboratory bioassays, effects on animal behavior, population dynamics, or community structure in the Estuary are poorly understood.
• Discontinuing the use of a particular chemical may be more effective in reducing its presence in the Estuary than treating it. After being banned by law, DDT and PCB levels in biota fell dramatically.
• More than twelve million humans will live in the Estuary watershed within the next two decades. Urban runoff and the associated pollutant loading are sure to increase.

Pollutants are substances that adversely affect the physical, chemical, and biological properties of the environment. Some occur naturally and have been components of ecosystems for millions of years. Others are human-produced and introduced only recently.

"Each year, an estimated five to forty thousand tons of at least sixty-five pollutants enter the Estuary."

There are four kinds of pollutants in the Estuary: inorganic chemicals, organic chemicals, biological pollutants, and suspended sediments and other particles. The most important inorganic chemicals are the compounds of phosphorus and nitrogen, and heavy metals, also known as trace elements. Phosphorus and nitrogen, primarily in the form of phosphates and nitrates, are necessary for plant growth. However, in high concentrations, they may cause excessive growth of aquatic vegetation. The trace elements in the Estuary that cause the most concern are arsenic, cadmium, chromium, copper, lead, mercury, nickel, selenium, silver, tin, and zinc.

Organic chemicals of greatest concern are synthetic substances, including plastics, pecsticides, fertilizers, solvents, and pharmaceuticals. PCBs and pesticides, such as DDT and Malathion, are organics that may adversely affect Estuary organisms. Most biological pollutants (bacteria and viruses) that are harmful to human health enter the Estuary in untreated sewage, recreational boat discharge, and runoff from farms, feedlots, and urban areas. Eroding soil and decomposing plant and animal wastes are sources of sediment and other particles that may also degrade water quality.

The kinds of pollutants considered to adversely affect the Estuary have changed markedly over the years. Until the 1940s, the most obvious pollution problems were caused by untreated industrial and sewage wastes. After World War II, increased use of synthetic organic compounds began to pose new, often more subtle, threats.

Pollutants enter the Estuary from many sources, each of which contributes a unique mixture of chemicals. At present, these sources include more than fifty municipal wastewater treatment plants, more than sixty-five industrial facilities, urban runoff, rural runoff, rivers, and dredging and dredged material disposal.

Beginning in the 1950s, some municipal wastewater treatment plants began primary treatment to screen and remove sediment and to digest and disinfect sludge. In the mid-1960s, secondary treatment began to further remove sediment and chemicals. The expenditure of more than $3 billion on enhanced treatment in the 1960s and 1970s led to major improvements of municipal and industrial effluent and of Estuary water quality. For example, between 1955 and 1985, even as the volume of municipal discharges increased from 250 to 550 million gallons per day, improved treatment reduced biochemical oxygen demand by about 80 percent and loadings of suspended solids by about 75 percent.

In the late l970s, advances in pretreatment programs also reduced the load of toxic pollutants entering the Estuary from municipal wastewater treatment plants. Pretreatment programs aim to remove toxic pollutants at their sources rather than at municipal treatment plants. This reduces the volume of pollutants destined for treatment plants, thus helping them operate more effectively.

The treatment of wastewater discharged directly from industrial facilities into the Estuary has also improved. Loading of pollutants from oil refineries, the biggest class of industrial dischargers, has declined dramatica]ly since the early 1960s. For example, in 1961, refineries discharged about two tons of chromium and zinc into the Bay each day. By 1984, daily discharge was about twenty-five pounds. Additional reductions in industrial loadings have been made through pollution prevention and source reduction.

The quantity of conventional pollutants entering the Estuary trom municipal and industrial sources has declined markedly during the past forty years. As a result, the most obvious symptoms of poor water quality--odors, algal blooms, and low oxygen levels--have been eliminated throughout most of the Estuary. Pollutants that continue to be of major concern are the trace elements, organochlorines and other synthetic pesticides, and petrochemical hydrocarbons.

Preliminary estimates indicate that rural and urban runoff contribute the greatest quantities of most trace elements to the Estuary. Urban runoff is the major source of oil and grease. Municipal and industrial effluent contribute sizable proportions of cadmium, mercury, and silver. Agricultural lands contribute large quantities of Pesticides.

Pollutants have been detected in the Estuary's water, sediments, and organisms. Although the concentrations of most pollutants surveyed in water are low, copper, lead, mercury,and nickel have exceeded state water quality objectives establishcd to protect beneficial uses of the Estuary's water.

"Even though pollutant levels for many trace elements from municipal and industrialefluent sources have decreased in recent decades, concentrationsof most pollutants in the Estuary's sediments and animals do not indicate a similar trend."

Compared to background levels attributable to natural sources, pollutant concentrations in sediments are slightly elevated in nearly all parts of the Estuary. Concentrations are highest in harbors, harbor entrances, industrial waterways, and marinas. Trace elements with the highest concentrations in sediments are copper, lead, chromium, and Zinc. Areas with particularly high concentrations of these pollutants include Islais Creek, Alameda Naval Air Station, Channel Creek, Mare Island Strait, and Hunters Point Naval Shipyard. Currently no standards exist for pollutant concentrations in sediments.

Pollutants in the Estuary's water and sediments may ultimately find their way into its animals. Filter feeders, such as clams and oysters, ingest pollutants in the water as they feed on plankton and other microorganisms, snails and worms take in pollutants as they graze on the organic matter in sediments, and so on up the food chain. Eventually, these pollutants can end up in human food. As organisms consume contaminated prey, pollutant concentrations in their tissues may increase. Concentrations of ten trace elements, DDT, and PCB sampled in the Estuary's mussels, clams, fish, and birds are either significantly elevated, compared to samples collected elsewhere in the state, or exceed the State Maximum Allowable Residue Level or the Median International Standard. Concentrations of pollutants in aquatic animals are greatest in organisms inhabiting harbors, harbor entrances, marinas, and industrial waterways.

Even though pollutant loads for many trace elements from municipal and industrial effluent sources have decreased in recent decades, concentrations of most pollutants in the Estuary's sediments and animals do not indicate a similar trend. Based upon available data from repeated analyses of sediments, sediment cores, mussels, and other animals, few reductions in pollutant concentrations have been demonstrated.

While it is fairly easy to measure concentrations of pollutants in water, sediments, and animal tissue, it often is extremely difficult to determine the overall effect of a pollutant on individual animals. Even more difficult to determine are pollutant effects on populations of a single species or on the entire aquatic community. During the past five years, laboratory bioassays (some of which must be considered as preliminary) have indicated that, at times, the Bay's ambient water, some municipal and industrial effluent, and some urban and rural runoff are toxic to test organisms.

The future loading of pollutants to the Estuary will be determined by the number of people living in the watershed, land use patterns, the use and disposal of pollutant-containing products, industrial processes, and treatment technologies In the absence of additional control measures or more widespread and effective pollution prevention, loads from municipal effluent will rise as the population discharging to municipal treatment plants increases. With some 725 square miles of urban land projected to be developed in the watershed by 2005, pollutant loading from urban runoff is expected to increase substantially. Also, unless there are significant changes in farming practices, agriculture will continue to contribute heavily to rural runoff.

Dredging and Waterway Modification
Findings:

• Each year, some six million cubic yards of sediments enter the Estuary, primarily from the Sacramento and San Joaquin River systems. Most of this material is deposited in waterways of the Bay and Delta, where dredging is required to ensure adequate water depths for commercial and recreational vessels.
• Dredging is conducted by the U.S. Army Corps of Engineers, the U.S. Navy, ports, commercial marina operators, local flood control and reclamation districts. and others.
• During 1986-1987, the U.S. Army Corps of Engineers and the U.S. Navy dredged an annual average of 7.3 million cubic yards of material in the Estuary. In combination with other projects, some eight million cubic yards were dredged and disposed of each year.
• Since l975, there have been only three main aquatic disposal sites for dredged materials in the Bay. Of the dredged material disposed of in 1986-1987, 65 percent went to the Alcatraz disposal site. The remainder was disposed of at sites in San Pablo Bay and Carquinez Strait or at upland sites in the region.
• Modeling and field studies indicate that much of the dredged material disposed of at aquatic sites remains in the Bay, with some redepositing in dredged areas.
• Dredging and disposal of dredged material temporarily increases turbidity, influences bottom-feeding communities at and near disposal sites, and may affect the behavior and physiology of fish and other organisms. It also may redistribute toxic pollutants and increase their availability to aquatic organisms.
• The two most hotly debated dredging issues during the past few years have been the effect of dredged material disposal on Central Bay angler success and the redistribution and release of toxic contaminants in dredged sediment.
• In response to dredging-related environmental problems, state, federal, and other interests are developing a Long-Term Management Strategy (LTMS) for dredging and dredged material disposal. This LTMS group seeks to eliminate unnecessary dredging activities, maximize the use of dredged material as a resource, and ensure that dredging activities are conducted in the most environmentally sound fashion possible.
• Between 1995 and 2045, an annual average of about eight million cubic yards of sediments is expected to be dredged in the Estuary. Given the goals of the LTMS, it is likely that the majority of this material will not be dumped in San Francisco Bay. A significant portion will be put to beneficial use, and much of it will be disposed of in the ocean.

Dredging in the Estuary has been an issue of concern for many decades. Although nearly everyone agrees that dredging is necessary to enable safe navigation of commercial, military, and recreational vessels, there are conflicting views regarding the environmental impacts of dredging and how it should be managed.

Dredging is the systematic excavation of bottom sediments. Dredging is conducted to ensure that water depths in navigation channels, turning basins, docking slips, and marinas are deep enough for vessels to maneuver safely. Because rivers carry an average of more than six million cubic yards of sediment into the Estuary each year, and almost fifty times that amount is resuspended in the shallows by currents and waves, dredged areas require periodic maintenance.

"Current projections indicate that between I 995 and 2045, about eight million cubic yards of materials will be dredged annually in the Estuary."

Most of the dredging in the Estuary is undertaken by the U.S. Army Corps of Engineers, which is responsible for nineteen projects in the Bay and Delta. The U.S. Navy dredges to maintain design depths at eight facilities in the Estuary. The fifteen major ports and refineries are also dredged periodically. Flood control districts dredge to maintain channel capacities where tributaries enter the Bay, and reclamation districts dredge periodically as part of levee maintenance. Additional dredging occurs at many of the 223 commercial marinas in the Bay and Delta and at commercial sand mining sites in the Bay. Between 1975 and 1985, the Corps and Navy together dredged an annual average of about 4.9 million cubic yards of material. In 1986 and l987, these agencies dredged an annual average of 7.3 million cubic yards. An unspecified but smaller quantity of materials was dredged by other entities.

Prior to 1972, dredged material was disposed of at more than two dozen sites in the Estuary. In the early l970s, environmental considerations led the Corps to designate six sites in the Bay as acceptable for dredged material disposal. Since 1975, the Corps has limited nearly all aquatic disposal of dredged materials to just three sites--adjacent to Alcatraz Island, in San Pablo Bay, and in Carquinez Strait.

Alcatraz is the major disposal site in the Bay. In recent years, the proportion of dredged material disposed of there has increased considerably. From 1975 to 1984, an average annual volume of less than two million cubic yards of material was disposed of there. From 1985 to 1987, the average annual volume increased to five million cubic yards. In 1986 and 1987, about 65 percent of all dredged material disposed of in the Bay was at the Alcatraz Island site.

When the Corps designated in-Bay disposal sites in the early 1970s, it did so with the belief that currents would disperse dredged material deposited at these sites. By 1982, however, it was discovered that the Alcatraz Island site had accumulated enough material to pose a hazard to navigation. By 1986, the Corps had removed 183,000 cubic yards from the Alcatraz "mound." This event stimulated discussion and re-evaluation regarding disposal practices and the fate of dredged material.

The main impacts of dredging and dredged material disposal include the loss of bottom-dwelling organisms and temporary increases in turbidity. Since dredging disposal occurs with relatively high frequency at the in-Bay sites, bottom-dwellers are prevented from re-colonizing disposal sites. The major effects of increased suspended sediment concentrations at disposal sites probably are on fish behavior, feeding patterns, foraging efficiency, modified prey response, and choice of habitat.

Disposal in the central Bay has been shown to alter the movement of fish schools. In a recent study of striped bass prey species near the Alcatraz Island disposal site, fish schools moved away from the disposal site immediately following disposal, but returned within an hour or two. Considering that materials were disposed of at the site more than ten times each day on nearly two-thirds of the days in l986 and 1987, it is possible that disposal activities kept fish away from the area and reduced angler success.

Current projections indicate that between 1995 and 2045, about eight million cubic yards of materials will be dredged annually in the Estuary. This includes new projects, maintenance of existing projects, and permitted projects. Additional dredging will occur in the Delta to maintain channels, ports, and levees.

In response to the mounding problem at the Alcatraz disposal site and other concerns about dredging impacts on the Bay's water quality and biological resources, a joint effort is underway to prepare a better long-term plan to manage dredging activities. Active participants in this effort include the U.S. Army Corps of Engineers, the U.S. Environmental Protection Agency, the San Francisco Bay Conservation and Development Commission, the San Francisco Bay Regional Water Quality Control Board, and other dredging and environmental interests. The plan is scheduled to be completed by 1995 and will specify where dredged material may be disposed of in the ocean, in the Bay, and at upland sites.

Management of the Estuary
Findings:

• The existing management system has successfully addressed several major problems associated with controlling point source discharges, upgrading publicly owned treatment works, controlling Bay fill, and acquiring and enhancing wetlands and other sensitive ecosystems.
• The McAteer-Petris Act of 1965, the Porter-Cologne Act of 1969, and the Federal Water Pollution Control Act of 1972 (and subsequent amendments in 1977 and 1987) are responsible for many improvements in water quality.
• The success of acquisition activities is largely associated with U.S. Fish and Wildlife Service efforts to establish national wildlife refuges, the establishment of the California Coastal Conservancy, and private funding efforts of groups such as the Nature Conservancy.
• Current environmental laws promote species- and issue-specific resource protection rather than protecting whole ecosystems and biodiversity.
• The number and variety of agencies and entities involved in Estuary management are sometimes confusing to the general public, as well as to other resource managers and decision-makers.
• In some cases, legislation has created overlapping and conflicting agency mandates, making implementation difficult. Additionally, many agencies are operating under outdated missions and mandates.
• In certain instances, agency jurisdiction is ill-defined and does not relate to the resources that are supposed to be protected.
• Goals and strategies for regional coordination of resource management are lacking in a number of areas, such as habitat acquisition, mitigation priorities, growth management, land use, and dredged material disposal.
• There is no legal requirement that local governments coordinate general plans with one another or provide protection to vital natural resources in the Bay-Delta area.
• Lack of sound scientific information hinders effective decision making related to natural resource protection. Often valuable information exists, but is not in a format accessible to those involved.
• Agencies lack adequate financial and human resources to comply fully with mandates to implement programs. The permit review process has become slow and cumbersome due to budget cuts, redirection of resources, and lack of experienced staff to handle the increase in permits.

"Current environmental laws promote species and issue-specific resource protection rather than protecting whole ecosystems and biodiversity."

Managing a natural resource as complex as the San Francisco Estuary is a challenging task. Responsible government bodies, and the private and public interests that influence them, are as diverse as the Estuary itself. While the enactment of significant state and federal laws protecting the nation's waters has led to major improvements in Estuary water quality over the past thirty years, much remains to be done by citizens and government to preserve and restore the Estuary's health and productivity.

Today, a complex array of agencies, plans, regulations, and laws govern activities in the Estuary region. A one-mile stretch of shoreline may be affected by the decisions of up to 412 government bodies with differing mandates and jurisdictions. Some administer municipal responsibilities of a city or County, ranging from social services and infrastructure maintenance to land use and sewage treatment. Some regulate specific activities such as dredging, filling, and wastewater discharge on a state, regional, or nationwide basis. Some manage water, fish, or wildlife resources on state or federal levels. Areas of control often overlap. necessitating inter-governmental communication and coordination.

For example, while existing laws and agencies provide a relatively intricate regulatory framework for wetlands, numerous shortcomings exist. Under the Section 404 program of the Clean Water Act, not all activities that may have detrimental impacts on wetlands are regulated. Also, certain ecologically significant wetland areas are not currently included within Section 404 jurisdiction. Since no single agency has complete or final authority over wetland use, there is a great need for a coordinated framework to protect and manage these valuable areas.

Activities of Estuary resource agencies often overlap. For example, the California Department of Fish and Game manages fish in state waters, while the National Marine Fisheries Service and the U.S. Fish and Wildlife Service oversee the management of fish in state and federal waters. Their overall goals to protect and maintain natural resources are duplicative, although their specific mandates and directions may differ somewhat. The U.S. Army Corps of Engineers has conflicting missions in regard to flood control responsibilities and efforts to protect wetlands. The California Department of Water Resources has a conflicting mandate in terms of planning water resources while also contracting and selling water. Other agencies within the Estuary have similar conflicting or overlapping missions and mandates.

Research is being conducted on a variety of topics related to estuarine systems, but its value to policy development is often limited. Detailed maps of critical natural resources are not available to local governments or the development community to assist in the decision-making process. Information regarding sensitive resource areas, such as wetlands, vernal pools, and riparian habitats, is not available to private developers or landowners. There is no single place or entity where complex regional issues can be considered, decisions made, and policies carried out. There is also a need for information sharing and informal consultation among agency staffs and the private sector.

In many instances, improved coordination may overcome institutional barriers that currently hinder the implementation of essential actions. Such coordination can improve the flow of information, identify possible problems, and minimize delay, cost, and uncertainty for the entity being regulated. Furthermore, establishing common goals may help ensure that all agencies take the appropriate actions to protect and enhance the Estuary's resources.

Some problems facing the Estuary may require a totally new approach. For instance, a new or revised entity may be required to improve research and monitoring. Effective watershed management may require new institutional arrangements to implement best management practices through existing mechanisms. To promote water conservation, specific legal reforms may be necessary to remove barriers to effective water transfers and water marketing. Renewed interest in California concerning growth management and regional planning may lead to new institutions that foster coordination among local governments. 1992, legislation introduced by Senator Pat Johnston was adopted that created a Delta Planning authority to protect important Estuary resources and improve local government coordination.

There are other encouraging signs that public and private interests are undertaking initiatives to improve resource management throughout the Estuary. The California Resources Agency, in coordination with the U.S. EPA, is preparing a State Wetlands Conservation Plan and is working with the State Wetlands Consensus Project. Several agencies concerned with dredging are helping to develop the Long-Term Management Strategy to manage dredging activities. Also, many citizen groups and other private entities are becoming directly involved in habitat restoration projects, monitoring, and pollution prevention.

Comprehensive Approach to Addressing the Issues
Several conclusions emerge from the preceding sections. First, the Estuary Project's five management issues comprise a wide range of environmental problems threatening the Estuary. Although some of these problems are more systemic and serious than others, they all ultimately affect the Estuary's biological resources and water quality.

Second, while management of some of these problems has improved in recent decades, some continue to be untenable. The most notable improvements include a declining rate of wetland loss, reduced pollutant loads of municipal and industrial sources, and improved regulation of dredging. However, urban expansion continues to deplete the stock of valuable upland wildlife habitats, wetlands, and riparian areas and increases the discharge of many point and nonpoint pollutants. Population growth fuels the increasing demand for fresh water. Water projects continue to influence the Estuary's primary productivity and habitat quality and adversely affect populations of valuable commercial and sport fish and other species.

Finally, it is apparent that the problems facing the Estuary are interrelated, linked in a web of interacting chemical, physical, and biological processes. Acknowledging these interactions is critical to developing effective actions to address the issues. It makes little sense, for example, to try to lower the pollutant-related impacts of dredging without also reducing the quantities of pollution that find their way into sediments in effluent and runoff. Similarly, it would be unwise for public entities to spend large sums of money to protect particular wetlands and then to allow incompatible land uses on adjacent uplands.

Given the interrelated nature of the issues confronting the Estuary, a coordinated approach is needed among the groups addressing them. Developing this coordination will be one of the main challenges to the public and private entities that will implement the Comprehensive Conservation and Management Plan.

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