San Franscisco Estuary Project - SOE: Ch 7

Pollutants may be found in soil, air, rivers, lakes, and ground water--in short, just about everywhere. Some pollutants occur naturally and have been components of natural ecosystems for millions of years. They have their greatest impact when highly concentrated, often by human activities. Other pollutants are synthetic and have been introduced into the environment only recently. Even at low concentrations, synthetic pollutants may severely affect plants and animals that have no natural defenses against them.

Measurement of Pollutants
Pollution is usually expressed in terms of concentration, the quantity of a pollutant in a given amount of water, sediment, or animal tissue. The quantity of a pollutant in a sample is described as a fraction of the sample's total weight or volume. Because pollutants often occur in the environment and biota at very low concentrations, the units of measurement for describing pollutant concentrations are correspondingly low. Units commonly used are parts per thousand (ppt), parts per million (ppm), and parts per billion (ppb).

Although concentrations in the parts per million or parts per billion range may seem insignificant, some chemicals (especially some organic chemicals) can be harmful to animals even at these low concentrations. American oyster embryos, for example, will be killed if exposed to water containing silver at a concentration of less than 6 parts per billion.

Kinds of Pollutants
There are four kinds of pollutants in the estuary: inorganic chemicals, natural and synthetic organic chemicals, biological contaminants, and suspended sediments and other particles.

Inorganic Chemicals
Inorganic chemicals, except for carbonates and carbon dioxide, are those that do not contain carbon. From a pollutant perspective, the most important inorganic chemicals are the trace elements (also known as trace metals or heavy metals) and compounds of phosphorus and nitrogen.

Trace elements occur naturally in low concentrations in the estuary's waters, carried there from the ocean and from soil. Most are necessary in small amounts to support plant and animal life. Refined into useful metals, enriched in many commercial products, or contained in fossil fuels, they also enter the estuary in sewage and industrial effluent and in urban and nonurban runoff at concentrations above background and in forms that are quite toxic. The trace elements in the estuary for which there is most concern are arsenic, cadmium, chromium, copper, lead, mercury, nickel, selenium, silver, and zinc (Phillips, 1987).

Nitrogen and phosphorus, primarily in the form of nitrates and phosphates, are nutrients necessary for plant growth. Occurring naturally at low concentrations in estuarine waters, these compounds enable the growth of algae and phytoplankton, plants at the base of the aquatic food web. The introduction of high levels of nitrates and phosphates in incompletely treated municipal effluent or in agricultural runoff may stimulate excessive growth of aquatic plants. After the plants die, their decomposition may reduce the amount of dissolved oxygen available for fish and other organisms.

Organic Chemicals
The term "organic," first used in 1808, originally pertained to the study of the substances in living cells. Since then, it has been broadened to include all natural and synthetic compounds that contain carbon. Many of the natural organic compounds are familiar. They are the stuff (fats, proteins, and carbohydrates) of which animals and plants are made. Natural products such as wood, leather, cotton, and wool all contain organic compounds. Organic materials, altered over millions of years, form the fossil fuels on which humans are currently so dependent.

Synthetic organic chemicals are organic compounds made by humans. Since 1828, when the first synthetic compound was made, the list of these chemicals has grown enormously. Today, tens of thousands of synthetic substances are produced each year. These plastics, pesticides, fertilizers, solvents, pharmaceuticals, detergents, and other products are as much a part of modern life as are wood and cotton.

Synthetic chemicals have changed our lives in remarkable ways, but they also can pose severe threats to the natural systems on which we depend. Many synthetic compounds are resistant to decomposition and are toxic to living organisms. Some, especially pesticides developed during the past several decades, are designed specifically to have these properties. Compounds containing chlorine or bromine, members of a group of elements known as halogens, are among the most persistent and toxic of organic chemicals. Familiar halogenated compounds include PCBs and pesticides such as DDT. Once these chemicals enter the environment, their detrimental effects may continue for decades. Recognition of the long-term environmental effects of these persistent compounds has gradually brought into production replacement formulations that are more short-lived yet still effective. The widespread pollution of the estuary with PCBs and DDT is a result of the former use and improper handling of these persistent compounds.

Biological Pollutants
Organisms harmful to human health can enter the estuary from septic systems; in untreated municipal sewage and recreational boat discharges; and in runoff from farms, feedlots, and urban areas. Bacteria and viruses are the main agents of concern, particularly those organisms that cause cholera, hepatitis, salmonella, and typhoid.

Of the many species of microbes that human activities introduce into the estuary, only fecal coliform bacteria are monitored (since 1978, all municipal wastewater treatment plants test for coliform bacteria). Although these bacteria do not cause disease in humans, their occurrence in the estuary indicates that other harmful organisms may be present. To protect human health, when coliform levels in the water are too high, officials close beaches or prohibit the harvest of shellfish.

Sediments and Other Particles
Particles of organic and inorganic matter enter the estuary from shorelines and rivers. They are generated by natural sources such as eroding soil and decomposing plant and animal wastes. Disturbance of the land surface, as in farming, residential construction, and road-building, can increase the influx of particulate material to receiving waters. Municipal wastewater also carries particulates. Once in the estuary, particulates are transported by currents until they settle to the bottom as sediment or are carried to the ocean. Dredging disturbs sediments, releasing particles and adhered pollutants into the water column.

Particulates may affect estuarine waters in several ways. At high concentrations they may clog the gills of fish and reduce the penetration of sunlight, thereby lowering the production of phytoplankton. The settling of suspended material may smother benthic animals and modify the behavior of other aquatic organisms. Depending on grain size and organic carbon content, particulates can influence the bioavailability and toxicity of chemical pollutants. As a benefit, suspended material may bind some pollutants, reducing their availability to animals.

Mixtures of Pollutants
Many pollutants enter the estuary in complex mixtures. A freshwater stream entering the Bay, for example, may carry particles of asbestos from worn automobile brake shoes, petroleum hydrocarbons from a leaking engine crankcase, bits of synthetic rubber from worn tires, fertilizer from the lawn of a business park, organic pesticides from back yard gardens, bacteria from pet droppings, and arsenic and clay particles from eroded soil. Likewise, the effluent from wastewater treatment plants and industrial facilities may contain hundreds of separate compounds, from viruses to persistent pesticides.

Conventional Pollutants
Conventional pollutants are defined in the federal Clean Water Act as total suspended solids, fecal coliform bacteria, biochemical oxygen demand, pH, and oil and grease. They are most often associated with effluent discharged from municipal wastewater treatment plants, but they also may be components of industrial effluent. Conventional pollutants were the first water pollutants to be regulated by state and federal laws.
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The Behavior of Pollutants in the Estuary
Pollutants entering the estuary become part of a very complex environment. A pollutant's behavior in this environment is determined largely by its own physical characteristics. As a pollutant moves through the ecosystem, en route to its ultimate fate--incorporation in sediments, transfer to the ocean, or removal from the system in some other way--it is influenced by environmental conditions and may be involved in numerous physical, chemical, and biological processes (Figure 58:Generalized Transport and Fates of Pollutants in a Typical Estuary).

Physical Characteristics
A pollutant has several physical characteristics which determine its behavior in the environment. Two of the most important are solubility and volatility. Solubility is a measure of how readily a pollutant dissolves in water. Organic pollutants, especially halogenated and aromatic hydrocarbons, have low solubility in water and may essentially be non-detectable in the estuary's waters, but highly concentrated in the sediments. Trace elements, on the other hand, are much more soluble in water and tend to stay there longer. Highly volatile pollutants, such as organic solvents, remain in water for only a short time before entering the air.

Environmental Conditions
Environmental conditions may affect the distribution of a pollutant or its availability to estuarine animals. Currents are one of the most important environmental factors that determine the distribution of pollutants. Pollutants that enter the estuary where there are strong currents may be carried far from their point of introduction. Pollutants reaching portions of the estuary where currents are slow, as in marinas and quiet sloughs, may accumulate there in the sediments. In this respect, winds, tides, and freshwater flows play important roles in distributing pollutants.

Salinity affects the availability of many pollutants to estuarine organisms. As pollutants move from fresh to saline water, for example, they may change their chemical state. A trace metal, such as cadmium, adhered to sediment particles in a river will dissolve when it reaches more saline water. In its dissolved state, it is more available for uptake by animals.

Transformation
Transformation occurs when a pollutant is changed from one form into another. This may occur as a chemical reaction (as described for cadmium in the preceding section) or may be mediated by organisms such as bacteria, invertebrates, and fish. Chemical reactions are the primary transformers of trace elements, while bacteria are the most important agents in the transformation of organic pollutants. Transformation may reduce the toxicity of some compounds, as when bacteria remove chlorine from some forms of PCB, or it may increase toxicity, as when bacteria increase the toxicity and mobility of mercury.

Bioaccumulation
As animals ingest food or pass water over their gills, they also may take in pollutants. These pollutants may be stored in the body, especially in fats and oils. Over time, pollutant concentrations in the body may increase (bioaccumulate), even though they are low in water and sediments. Such concentrations might not affect the organism itself, but may adversely affect the health of an animal that consumes it.

Bioaccumulation also occurs when organisms eat contaminated prey. In this way, pollutants move through the food web and eventually may reach harmful levels in predators at the top, including fish-eating birds, seals, and humans.
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Pollutants in the Estuary--A Chronicle of Change
To appreciate the current status of pollutants in the estuary, it helps to understand how the very nature of pollution has changed since the last century. This section traces this change and describes some of the progress made in reducing pollutant loads.

Before the arrival of Europeans, the few pollutants that entered the estuary came from natural sources such as the weathering of rocks, from oil seeps, and from the settlements of Native Americans along the shoreline. The effects of these pollutants were probably small and localized. The first major anthropogenic, or human-caused, pollutant effect on the estuary probably occurred during the gold mining period between 1853 and 1884, when an estimated 3,500 tons of highly toxic mercury were used to extract gold. Undoubtedly, some of this mercury, along with millions of cubic yards of sediments, reached the estuary (Phillips, 1987).

By the end of the 1800s, untreated industrial and sewage wastes adversely affected water quality in many portions of the Bay. Oily discharges from bilge pumping and the flushing of storage and process tanks were common sights. Oil tankers frequently deposited oil on the shoreline in Marin and San Mateo counties. Discharges of untreated domestic sewage reduced oxygen concentrations near sewage outfalls. This led to the growth of bacteria that caused avian botulism and cholera and made the Bay a focal point for these devastating waterfowl diseases (Skinner, 1962).

By the early 1900s, many of the estuary's premier commercial fisheries-- salmon, sturgeon, and striped bass--were in decline. The discharge of untreated municipal and industrial wastes (along with overfishing and water and land development) contributed to this (Skinner, 1962; Miller, 1986). Later, automobiles became an additional source of pollutants; in 1925, for example, car repair shops in Berkeley and Oakland disposed some 3,000 gallons of waste oil daily into wastewater systems that discharged directly to the Bay.

After the Second World War, with industry and agriculture thriving and more people moving into the region each year, the estuary was receiving large and mostly uncontrolled amounts of inadequately treated sewage, industrial effluent, urban runoff, and agricultural wastes. The increased use of synthetic organic pesticides, in particular, began to pose new threats. Using water of the federal Central Valley Project, farmers brought thousands of acres of land into cultivation. As farm output grew to record levels--enhanced with scores of new insecticides, herbicides, and fungicides--so did the quantity of pesticides in the estuary and its tributaries.

In the 1950s, it was apparent to even casual observers that parts of the Bay and Delta had poor water quality. Decomposing mats of algae, the growth of which had been fueled by nutrients in wastewater effluent, commonly led to reports of "rotten egg" odors along the shoreline. Field studies in the East Bay showed evidence of pollutant impacts to the aquatic communities there. For example, where Castro Creek flowed into San Pablo Bay, the water was described as having "... a low pH, toxic chemical waste, a rich bacterial and detrital content, and practically no oxygen" (Filice, 1954). In the Delta, cannery effluent caused low oxygen levels in the San Joaquin River near Stockton, often blocking the upstream migration of anadromous fishes. Throughout the estuary, there were indications that pollutants were adversely affecting water quality and biological resources.

The beginning of the effort to control the effects of sewage in the estuary started in the early 1950s, when some publicly owned wastewater treatment plants began primary treatment of municipal wastewater. Primary treatment consists of screening, primary sedimentation, sludge digestion, and disinfection. It removes about half of the conventional pollutants and half of the trace elements from wastewater (Galvin et al., 1984).

Construction of facilities to enable secondary treatment--microbial degradation and secondary sedimentation--began in the mid-1960s. Secondary treatment removes about 85 to 95 percent of conventional pollutants, three-quarters of the trace elements, and a variable percentage of other toxic pollutants from wastewater (Figure 59:Effectiveness of Primary and Secondary Treatment). Since 1960, more than $3 billion have been spent on wastewater treatment facility upgrades, outfall consolidation, and outfall relocation in the estuary (Condit, 1987).

Implementation of the state Porter-Cologne Water Quality Act of 1969 and the federal Clean Water Act of 1972 led to rapid improvements in the quality of municipal and industrial effluent and of the Bay's waters in the 1970s. Even with an increase in the human population and the volume of sewage effluent it produced, wastewater treatment facilities decreased their loads of conventional pollutants (Figure 60:Flow and Pollutant Loadings from Municipal Dischargers in the San Francisco Bay Region, 1955-1985).

Reducing the discharge of conventional pollutants into the estuary during the past four decades has resulted in significant improvements in water quality. Foul odors and unsightly evidence of raw sewage discharges that were once prevalent in the Bay no longer occur. Levels of bacteria in Bay waters also have dropped (Luoma and Cloern, 1982). As a result, the 50-year-long ban on shellfish harvesting in the waters of San Mateo County was partially relaxed in 1982.

In the late 1970s, advances in municipal wastewater treatment and pretreatment programs also reduced the load of toxic pollutants entering the estuary from municipal treatment plants. Pretreatment programs are aimed at reducing the amount of industrial waste discharged into municipal wastewater treatment plants. By removing toxic pollutants at their sources rather than at municipal treatment plants, pretreatment reduces the stream of pollutants that may pass through the plants to contaminate the water, sludge, or air. It also may help treatment plants operate more effectively. Between 1975 and 1985, pretreatment programs and other advances reduced the amounts of trace elements discharged from municipal treatment plants by 37 to 92 percent (SFBRWQCB, 1988).

The treatment of waste water discharged directly from industrial facilities into the estuary also has improved. As indicated in Figure 61(Bod, Suspended Solids, Oil & Grease, Chromium and Zinc Loadings from Bay Area Refineries1961- 1984), loads of some pollutants from the biggest class of industrial dischargers, petroleum refineries, have declined dramatically since the early 1960s. Additional reductions also have been made through pollution prevention and source reduction. For example, Chevron (the largest refinery) has reduced discharges of chromium, lead, and nickel by substituting less toxic raw materials, reformulating products to contain or require fewer toxic materials, improving plant operating efficiency, and recycling wastes. Compared to its discharges for 1982 and 1983, the Chevron refinery has reduced chromium by 67 percent, nickel by 86 percent, and lead by 97 percent (CBE, 1989).

The quantity of conventional pollutants entering the estuary from municipal and industrial sources has been reduced markedly over the past 40 years. As a result, the most obvious symptoms of poor water quality--odors, algal blooms, and low oxygen levels--have been nearly eliminated throughout most of the estuary.

Although the loadings of toxic pollutants from municipal treatment works and industrial plants also have declined, repeated analyses of sediments, sediment cores, mussels, and other biota have been unable to show very many significant reductions in toxicant concentrations in the estuary (Long et al., 1988). Toxic pollutants continue to enter the estuary from many sources and in amounts that may threaten the well-being of populations of shellfish, fish, and wildlife (Luoma and Cloern, 1982; Luoma and Phillips, 1988; Phillips and Spies, 1988). In the coming decade, toxic loadings will need to be reduced even further.

More than 50 municipal wastewater treatment plants, like this one operated by the East Bay Municipal Utility District, discharge to the estuary a combined daily average of 855 million gallons of treated effluent. (Photo: courtesy , EBMUD)
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Current Status of Pollutants in the Estuary
Pollutants of Concern
In terms of pollutants, toxic chemicals now pose the greatest threat to the estuary. Although there are hundreds of individual toxicants that enter the estuary's waters daily, there is greatest concern for those listed in Table 18. These pollutants were selected by the Estuary Project's Pollutants Subcommittee, based on five criteria: 1) the potential to cause toxicity or to affect beneficial uses of the estuary; 2) the extent of the database for each pollutant within the estuary; 3) whether the pollutant is found at high levels throughout the estuary; 4) whether the pollutant is found at high levels locally; and 5) whether the pollutant exerts or has the potential to exert detrimental effects on the estuary's biological resources. For further information on the process used for selecting the pollutants of concern, refer to Appendix I in Davis et al., 1991.

To a large extent, the pollutants listed in Table 18 are the ones that have been detectable and quantifiable in the estuary's waters, sediments, and biota. Many other chemicals are discharged to the estuary and possibly have similar detrimental effects. There is a need to continue to investigate the effects of all of these chemicals on the beneficial uses of the estuary's waters.

Sources of the Estuary's Pollutants
The estuary's pollutants come from many different sources, and each source contributes a unique mixture of chemicals. For example, nonurban runoff from agricultural fields may carry large loads of organic pesticides, while urban runoff carries large quantities of trace elements generated by motor vehicles. This section briefly describes the main sources and their characteristic pollutants.

Municipal Wastewater Treatment Plants
Municipal wastewater treatment plants process a variety of substances including human wastes, trace elements, synthetic organic chemicals (including pesticides, solvents, and plastics), and solid materials. Although most of the pollutants are removed to some degree by the treatment process, significant amounts pass through the plants and are discharged into the estuary (Gunther et al., 1987). Considering the diversity and quantity of waste treated, it is quite remarkable that treatment plants function as well as they do.

More than 50 publicly-owned wastewater treatment plants discharge enormous volumes of effuent into the Bay and Delta. From 1984 through 1986, the combined daily flow from these facilities averaged 855 million gallons, a flow rate that is about one-quarter of the Central Valley Project's Tracy Pumping Plant capacity. Of the total volume of effluent discharged by the plants, nearly one-half was contributed by four facilities: the Sacramento Regional Water Treatment Plant, East Bay Municipal Utility District facility in Oakland, San Francisco Southeast Treatment Plant, and San Jose/Santa Clara Regional Water Treatment Plant. Figure 62(Municipal Dischargers and Mean Discharge Volumes to the Bay/Delta Estuary, 1984-1986) shows the distribution of some of the larger municipal dischargers in the estuary basin and the relative contribution of each. The segments of the estuary which receive the largest quantities of municipal effluent are the North Delta and South Bay.

Industrial Facilities
Industrial facilities generate a wide array of pollutants. Some of these pollutants are conveyed to municipal wastewater treatment plants; others are treated on-site and then discharged to the estuary. Activities that produce large quantities of pollutants include petroleum refining and the manufacture of agricultural pesticides and fertilizers, solvents, steel, paper, sugar, and many other products (Phillips, 1987). More than 65 industrial dischargers dispose of wastes to the estuary.

Petroleum refineries are the largest single class of industrial dischargers. During 1984-1986, six refineries disposed of more than 30 million gallons of process water into the estuary each day. Figure 63(Industrial Facilities and Mean Discharge Volumes to theBay/Delta Estuary, 1984-1986) shows the location and volume of these discharges. Of the total combined volume discharged by all six refineries, the Chevron facility in Richmond accounted for more than one-half.

Another large class of industrial dischargers are those which generate at least 100,000 gallons of effluent per day. From 1984 through 1986, a dozen of these facilities accounted for a total volume of effuent about equal to that of the petroleum refineries. Located primarily in the estuary's northern reach, these facilities discharged a total average flow of nearly 29 million gallons per day. One discharger, U.S. Steel, accounted for nearly 70 percent of the total volume.

There are more than 50 industrial facilities that discharge less than 100,000 gallons per day. These facilities include power plants; oil terminals; chemical, metal, and paper facilities; and others. Unlike the larger industrial dischargers that tend to be located in the estuary's northern reach, small facilities are more widespread.

From 1984 through 1986, industrial facilities discharged an average daily volume of about 60 million gallons of effluent to the estuary. This volume is substantial, but it accounts for less than 10 percent of the flow discharged by municipal wastewater treatment plants. Even though industrial sources discharged less effluent than did municipal wastewater treatment plants, they contributed greater quantities of certain pollutants such as selenium and polyaromatic hydrocarbons.

Urban Runoff
Urban runoff is the water from urban areas that flows into the estuary in streams and storm drains. It includes rainwater, excess irrigation flows, and water used for washing down sidewalks and parking lots.

Sources of pollutants in urban runoff are extremely varied and include commercial, industrial, and residential land uses, as well as managed open space areas such as parks, cemeteries, planted road dividers, and construction sites. Everyday human activities in these areas--the application of pesticides and fertilizers to gardens and landscaping, operation of motor vehicles, and construction of roads and buildings-- all contribute pollutants to urban runoff.

More than ten studies in the estuary basin and elsewhere during the past decade indicate the kinds of pollutants that occur in urban runoff. One national study, conducted over several years in 22 cities (including sites on Castro Creek in Alameda County, and in Fresno), showed that runoff commonly carries many trace elements and organic toxic materials (USEPA, 1983). Recent studies in Sacramento and Santa Clara counties confirmed the presence in runoff of trace elements such as arsenic, cadmium, chromium, copper, lead, nickel, and zinc, as well as nutrients and sediments (Montoya et al., 1988; Woodward-Clyde Consultants, 1991).

Although fecal bacteria are not on the Estuary Project's list of pollutants of concern, they are common constituents of urban runoff and may present health hazards at high concentrations. Following storms, bacteria counts in portions of the East Bay shoreline waters have increased one thousandfold (EBMUD, 1986).

For many pollutants, urban runoff contributes much larger quantities than do municipal and industrial sources. In the Sacramento Valley, for example, urban runoff contributes greater loads of six trace elements to receiving waters than do municipal and industrial discharges combined. More than 20 times as much lead enters receiving waters in urban runoff than in effluent discharges (Montoya et al., 1988). Studies in Santa Clara County show that, except for nutrients, urban runoff is the major source of many trace elements, biochemical oxygen demand, and total suspended solids in South Bay tributaries (Woodward-Clyde Consultants, 1991).

Rainfall patterns have a strong influence on the quantity and quality of urban runoff. Pollutants build up on streets, lawns, and soil between rainy seasons and between storms. Much of this build-up may be flushed out by the first rain. Because of this "first flush" effect, concentrations of pollutants in runoff often are much higher during the first storms of the season.

Although the concentrations of pollutants in runoff are highest during the winter, dry-weather runoff represents a significant source of pollutants to the estuary. Domestic and commercial landscape irrigation, car washing, and construction sites are prime sources of runoff during the summer months (Montoya et al., 1988). Illegal dumping also is a prime source of pollution in urban runoff during summer months (R. James, pers. comm.).

Nonurban Runoff
Nonurban runoff refers to runoff from agricultural lands, forests, pasture, and natural range. It includes rainfall runoff, excess irrigation return flows, and subsurface agricultural drainage. Pollutants of concern in nonurban runoff include trace elements, synthetic organic pollutants (particularly pesticides), and solvents used for pesticide application.

There is growing concern about nonurban runoff in the estuary watershed, especially its agricultural component. This results from the detection of agricultural chemicals in water, sediment, and animals; the toxic effects of agricultural drainage at the Kesterson National Wildlife Refuge; and acute toxicity demonstrated in bioassays of water from or near agricultural drains. Although nonurban runoff enters the estuary from many areas, actual data on pollutant concentrations exist only for agricultural runoff that enters the estuary's tributaries upstream of the Delta. Most of the available information pertains to pesticides.

Pesticides are one of the most important components of agricultural runoff. In 1982, nearly 50 million pounds of about 500 different pesticides were applied in the San Joaquin Valley alone. This was about 10 percent of the total annual pesticide application in the United States (Clifton and Gilliom, 1986). As a result of this extensive pesticide use, pesticide concentrations in some of the estuary's tributaries are significantly elevated. Studies of San Joaquin River water indicate that, in February 1990, the organophosphorous pesticides diazanon and parathion occurred at the confluence of the Merced and San Joaquin rivers at concentrations of 0.28 ppb and 0.25 ppb, respectively. At these concentrations, diazanon exceeded EPA-recommended water quality criteria to protect aquatic life by 31 times; parathion exceeded the criteria by 19 times (CVRWQCB, 1990). Studies in the Sacramento River basin have also indicated elevated concentrations of pesticides in estuary tributaries that receive agricultural drain water (CVRWQCB, 1987).

Agricultural drainage is a major source of trace elements and pesticides to the estuary. This drainage has made many miles of streams in the Central Valley toxic to aquatic organisms. (Photo:USBR)

The extent to which agriculture is a source of nonpoint pollutants other than pesticides is exemplified by small streams that carry excess irrigation water and subsurface drainage from farm fields. For example, in 1985, two channels in the San Joaquin Valley--Mud and Salt sloughs--contributed 12 percent of the flow in the San Joaquin River at Vernalis. However, these sloughs contributed 81 percent of the selenium, 69 percent of the boron, 46 percent of the dissolved solids, and 44 percent of the molybdenum entering the river (CVRWQCB, 1988). These sloughs drain intensively cultivated agricultural lands on the west side of the Valley where runoff from soils high in selenium led to the serious ecological problems at the Kesterson National Wildlife Refuge in the early 1980s. Farming operations in the Delta also contribute substantial amounts of pollutants, particularly organic materials, that may adversely affect estuarine water quality (SWRCB, 1991).

Riverine Inputs
The rivers of the Central Valley carry large quantities of water and pollutants into the estuary. Although riverine pollutants originate in municipal and industrial effluent discharges and in urban runoff and nonurban runoff, once carried past Sacramento or Vernalis, they are considered to have entered the estuary as riverine input. Although this aspect of pollutant loading to the estuary has not been well characterized, the best existing information indicates that riverine input is substantial.

Agricultural drainage is a major component of riverine inputs, particularly during the early summer. Agricultural drainage may contribute over 30 percent of the total flow of the Sacramento River in May and June (Comacchia et al., 1984). It is estimated that agricultural drainage contributes more than 20 percent of the total time-averaged flow in the San Joaquin River and most of the flow during the summer (DWR, 1986b; Nichols et al., 1986).

Dredging and Dredged Material Disposal
Considerable attention has been focused lately on the pollutant-related effects of dredging and dredged material disposal in the estuary. Dredging and the disposal of dredged sediment redistributes pollutants and may increase their availability to aquatic organisms. Studies indicate that sediments in many parts of the estuary have elevated concentrations of trace elements and organic pollutants. Pollutant concentrations are highest in sediments from harbors, harbor entrances, marinas, and industrial waterways (Long et al., 1988).

Given the complex way in which sediments and pollutants interact, it is difficult to determine the quantities of pollutants that are released when sediments are dredged. Estimates vary widely (Gunther et al., 1987; Segar, 1988). Also, it is important to remember that, in most instances, the release of pollutants during dredging does not represent a new source of pollutants, but the remobilization of pollutants previously discharged into the estuary from various sources.

Atmospheric Deposition
Some pollutants enter the estuary directly from the air. These pollutants are generated by industrial plants, oil refineries, motor vehicles, and many other sources within the watershed.

Pollutants in the atmosphere exist in several forms--as vapor, as vapor adhered to particulate matter, and as aerosols. Through a variety of chemical and physical processes, a portion of these airborne pollutants reaches the estuary's water surface.

There have been very few estimates of the role of atmospheric deposition as a source of toxic pollutants to the estuary. The most recent estimates by Gunther et al. (1987) are based on deposition rates in other parts of the United States. Given the uncertainty of these estimates, they should be viewed only as indicators of the possible role of airborne pollutants in the estuary's total loading of pollutants.

With the possible exception of PCBs and PAHs, the contribution of airborne pollutants to the estuary's total pollutant loading seems to be relatively small compared to point and nonpoint pollutant sources. However, as noted below, these air pollutants may have significant adverse effects on organisms.

Marine Vessel Discharges
Commercial and recreational vessels discharge sewage and gray water (waste water from kitchens and baths) into the Bay and Delta. This effluent can be a source of coliform bacteria, toxic soap residues, biochemical oxygen-demanding substances, suspended solids, oil and grease, and nutrients. Although houseboat operators are required to pump out wastes at approved facilities, they and the operators of other recreational vessels continue to discharge an unknown amount of waste directly into the estuary's waters. The discharge of untreated wastes has caused concern in several portions of the estuary including Richardson Bay, Alviso Slough, Redwood Creek, and parts of the Delta (BCDC, 1987).

Large commercial vessels also discharge ballast water within the estuary. This may introduce exotic species of aquatic organisms, with profound effects to the estuarine ecosystem, as noted in Chapter 4.

Accidental Spills
Accidental spills contribute a significant load of pollutants to the estuary. Spills of petroleum products occur frequently and are of particular concern. Such spills can cause direct toxicity to fish and wildlife, disrupt food chains, damage habitat, and affect public health. They also are unsightly.

Most spills are small and unpredictable and result from damaged ships, operator errors, handling accidents at terminals, and accidents involving material carried on shoreline highways. According to the Coast Guard, during 1984 through 1986, an average of some 31,000 gallons of petroleum products was accidentally spilled into the estuary each year.

Although most spills are small, some are huge. Two major spills have occurred in the past 20 years: in 1971, two oil tankers collided just outside the Golden Gate, spilling 845,000 gallons of fuel oil. In 1988, more than 370,000 gallons of crude oil were accidentally discharged into the Carquinez Strait from the Shell oil refinery in Martinez. Although the tanker spill was larger, the Shell spill resulted in more obvious impacts to the estuary, as some 50 miles of shoreline from San Pablo Bay to the Delta were affected. In a costly but effective cleanup effort, more than 80 percent of the oil was recovered.

Leakage from Waste Disposal Sites
Hazardous wastes and municipal solid wastes have been disposed at some 2,000 sites in the Bay area. Some 90 percent of these sites contain hazardous wastes. It is generally recognized that all older disposal sites leak and that those near the estuary or its tributaries may contribute loads of toxic leachate. Additional sites exist throughout the estuary watershed.

There are nearly 50 active municipal landfills and 60 closed facilities in the 12 counties surrounding the estuary. Some of these undoubtedly pose threats to surface and ground water. Although only about one percent of the material in municipal landfills is toxic, much of it is in household wastes including paints, insecticides, cleaners, and solvents (ABAG, 1989b). Toxic pollutants commonly found in landfills include hydrocarbon solvents, nickel, copper, chromium, arsenic, and also lead from gasoline and old paint (CH2M Hill, 1988).

Floatable Debris
Most pollutants reach the estuary's waters in liquid form, either in discharge effluent or in runoff. A significant number of larger solid items also enter, primarily from storm drains, in combined sewer overflows, and in runoff. This material, known as floatable debris, not only degrades the environment, but it may also endanger marine life and pose serious risks to public health.

Floatable debris comprises a wide array of items such as wood, plastic plates, food containers, cigarette butts, diapers, and many others. Items of greatest concern are those that pose a risk to human health or marine life or cause aesthetic or economic damage to an area. According to the EPA, such items include plastic and polystyrene pellets used as raw materials for molded products, condoms, tampons, syringes, nets and traps, line and rope, six-pack yokes, and plastic bags and sheeting.

In a recent survey of Central Bay, researchers collected more than 4,800 pieces of 124 different kinds of floatable debris (USEPA, 1990b). The categories of materials represented by the samples are shown in (Figure 64: Floatable Debris Found in San Francisco and Oakland Harbor Areas, 1989) In most respects, the make-up of the debris was similar to that found in other U.S. harbors. Compared to the East Coast harbors, however, samples in the Bay contained very few medical wastes, probably because there are only two combined sewer systems that discharge into Bay waters (a combined sewer system receives residential and industrial sewage as well as runoff from streets).
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