USGS - science for a changing world

Environmental Health - Toxic Substances


U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the Technical Meeting, Colorado Springs, Colorado, September 20-24, 1993, Water-Resources Investigations Report 94-4015

Previous PageTable of ContentsNext Page

Challenges in Detecting Contaminant Effects on an Estuarine Ecosystem Affected by Many Different Disturbances: San Francisco Bay


Samuel N. Luoma (U.S. Geological Survey, Mail Stop 465, Menlo Park, Calif. 94025) and Frederic H. Nichols (U.S. Geological Survey, Mail Stop 465, Menlo Park, Calif. 94025)



The Suisun Bay/Delta at the head of San Francisco Bay is an area where complex factors converge to affect the success of aquatic species. Water diversion and drought have reduced river flows to the bay. The historic elimination of marshes has permanently removed an important source of carbon while river diversion and drought have reduced river-borne inputs of carbon. The invasion of the bay by an exotic clam has affected the abundance of other benthic species and has eliminated previously observed phytoplankton biomass peaks. Coincidentally, populations of important resource species have declined. Persistent contamination in Suisun Bay/Delta accentuates the adverse effects of the above first-order problems. Selenium contamination in benthos is sufficient to affect upper-trophic-level organisms such as birds and fish. Pulse inputs of pesticides occur during high flows. Locations in Suisun Bay were identified that are chronically contaminated with trace organic compounds, cadmium, chromium, and vanadium. At these locations resident bivalves are in poorer condition and have modified reproductive cycles, compared to elsewhere in the estuary. Long-term studies are allowing identification of the relative importance of different factors that disturb biological processes in the estuary. Few multi-disciplinary, long-term field studies are conducted in environments modified by human disturbance. Results from Suisun Bay show how continuity in the study of cause-and-effect may be the only way to separate the influence of the myriad of processes that contribute to ecological characteristics in estuaries.


The array of human activities that have disturbed the San Francisco Bay ecosystem since the gold rush of 1849 are well known (Nichols and others, 1986). However, the effects and relative importance of specific activities are not as well understood.

One focus of the initial phase of the San Francisco Bay toxics program has been the characterization of contamination and its effects in the context of the myriad other disturbances that affect the Suisun Bay and Delta region. In this paper we discuss recent progress in studies of both the natural variability of the Suisun Bay/Delta and effects on aquatic life of human-induced stresses including contaminants.


The upper San Francisco Bay is a complex estuarine system bounded on its landward side by a tidal freshwater Delta, a highly dissected region of channels and islands at the mouths of the Sacramento and San Joaquin Rivers. The rivers converge at the eastern end of Suisun Bay, an important nursery area for estuarine fish populations.

Flow from the Sacramento and San Joaquin river system, draining about 40 percent of the land area of California, reflects both the pattern of precipitation over western North America and the operation of the world's largest man-made water management system (Peterson and others, 1989). More than half of river water flowing toward San Francisco Bay is diverted from the drainage basin through impoundment of snowmelt in reservoirs and pumping of Sacramento and San Joaquin river water from the Delta. The diverted water is consumed in irrigated agriculture and by urban and industrial uses both within and beyond the Bay's watershed (Nichols and others, 1986). The result is greatly reduced flows into the estuary during spring.

Despite the large-scale water diversion, the estuary typically receives large annual winter/spring pulses of freshwater runoff. Since 1984, however, persistent drought combined with the continuing water diversion to virtually eliminate the annual pulses of freshwater except for an exceptional flood during the spring 1986 (fig. 1).

Figure 1. Monthly average discharge of the Sacramento River at Chipps Island in San Francisco Bay.

The reduced flow of freshwater into the estuary has contributed to major changes to the Bay's ecosystem. As an example, striking declines in the abundance of a number of aquatic species were observed over the last several decades (Jassby and others, 1993a). The mechanisms differ, but reduced river flow seems to have affected the success of a native species of zooplankton, the local mysid shrimp, striped bass, smelt, flounder, and mollusks that inhabit Suisun Bay (Jassby and others, 1993a). The freshwater/seawater interface, as indicated by the geographic location of the 20/00 isohaline in bottom water, has moved upstream to the detriment of the freshwater organisms that inhabit the region. The reduced flows and upstream movement of salt also have increased the exposure of fish populations to the diversion pumps in the Delta where huge numbers of fish are lost (Jassby and others, 1993a).

Recent studies have demonstrated that reduced river flow also has caused a reduction of organic carbon inflow into the estuary (Jassby and others, 1993b). This work demonstrated that San Francisco Bay has a low input of organic carbon compared to that of many other estuarine systems (Jassby and others, 1993b). Poor light penetration into the silt-laden waters of the Bay limits in situ carbon production by phytoplankton and vascular plants. The extensive marsh system that once existed was also largely eliminated early in this century, reducing carbon inputs from what was once a major source. Thus the rivers are now the remaining important source of carbon input to Suisun Bay/Delta. As river flow was reduced by drought and water diversion, carbon input was reduced concomitantly. The application of isotopic and molecular tracers has revealed that an important source for the organic matter now supporting benthic organisms in the upper estuary is freshwater algae produced in the rivers and Delta (Canuel and others, in preparation). This contrasts to South San Francisco Bay where in situ production is most important (Jassby and others, 1993a).

Another important change in the estuarine ecosystem since the onset of the drought is the disappearance of the summer phytoplankton biomass maximum that typically appeared in the Suisun Bay region (Alpine and Cloern, 1992). This is likely the result of drought-related increases in the abundance of estuarine benthic suspension-feeding organisms, particularly that of a recently introduced Asian clam.



Historically, the most pronounced change to the benthic biota of San Francisco Bay has come from the accidental and intentional introduction of exotic species. Large numbers of sediment-dwelling invertebrates were first introduced during the latter half of the 19th century with live oysters that were shipped by train from East coast estuaries and transplanted in the bay (Nichols and others, 1986). Exotic invertebrates continue to arrive in the bay in ballast water of cargo ships.

A recent arrival from the estuaries of east Asia, the clam Potamocorbula amurensis, has been remarkable in the rapidity with which it became the numerically dominant species throughout the northern part of the estuary and in its potential to change food-web processes (Carlton and others, 1990).

Potamocorbula arrived in San Francisco Bay immediately after the major flood of 1986 when most of the estuarine benthic invertebrates were eliminated from the upper estuary because of their intolerance to fresh water. Within months of its first detection in October 1986, Potamocorbula became the most abundant benthic organism in Suisun Bay, and has prevented the bottom dwelling species that once dominated during low flow conditions (for example, Mya arenaria) from recolonizing the area (Nichols and others, 1990) (fig. 2). The combination of its great abundance and the efficiency with which it filters food particles from the water column has resulted in the near elimination of phytoplankton (diatoms and other microscopic, single-celled plants that form the base of aquatic food chains) from the water of the Suisun Bay region (fig. 2; see Alpine and Cloern, 1992). Further, there is laboratory evidence that Potamocorbula eats the juvenile stages of some zooplankton, possibly contributing to the reductions in zooplankton abundance noted during the prolonged drought (Obrebski and others, 1992).

Figure 2. Annual discharge of the Sacramento River in cubic meters per second (solid line), concentrations of chlorophyll a in milligrams per cubic meter (line through open squares), and abundance of the clams Mya arenaria (solid bars) and Potamocorbula amurensis (striped bars) in Suisun Bay expressed as number of individuals per meter squared, between the years 1974 and 1992.

The population biology of Potamocorbula has been intensively studied in Suisun Bay, San Pablo Bay and South Bay in monthly samplings between 1989 and the present. Genetic studies (electrophoretic separation of isozymes) indicated Potamocorbula had an unusually high within-population genetic variability, contributing to its ability to survive in a range of estuarine conditions (Duda, 1993). A study of its reproductive activity throughout the Bay, under varying salinity, temperature and food regimes, demonstrated major differences in reproductive seasonality between north and south Bay. The animals from Suisun Bay were reproductively active during shorter periods than elsewhere. This difference coincided with, and thus may be related to, spatial differences in food availability and osmotic stress, or possibly contaminant stress. Age structure and condition index (tissue weight of a bivalve of a given shell length) differed among stations in Suisun Bay, and between Suisun and other parts of the estuary. Clams from the upper end of Suisun Bay were generally of longer shell length, had a lower condition index and demonstrated less seasonal fluctuation in condition index than elsewhere (Brown and Luoma, in preparation). Again it is not yet clear whether this is a response to reduced food availability or higher contaminant exposure.



It is probable that contamination from anthropogenic waste discharges is contributing to some of the ecological changes occurring in the upper San Francisco Bay estuary, and biological differences between Suisun Bay and other regions. Recent results of the analysis of sediment cores from San Francisco Bay indicate sediments and water have been contaminated for decades by potentially toxic trace metals (Hornberger and others, in preparation; Van Geen and others, in preparation) and trace organic contaminants (Pereira and others, in preparation; Hostettler and others, in preparation). Industrial and urban development coincided with increased sedimentation during the last 40 years (Fuller, in preparation) and enriched concentrations of Cu, Ag, Pb and Zn. Sediments contaminated for more than one meter in depth are found from Suisun Bay to Richardson Bay, near the Golden Gate. Pesticides (predominantly DDT) and petroleum by-products are enriched to this depth in Richardson Bay sediments.

The Suisun Bay/Delta was characterized by Biggs and others (1989) as one of the estuaries in the United States most susceptible to pollution impact because the physical characteristics of this system limit its natural resilience. River-transported metals, and wastes form nine of the largest point source dischargers in the Bay area are released directly into Suisun Bay (Luoma and others, 1990).

Recent USGS studies illustrate some characteristics of modern organic and inorganic contamination in Suisun Bay. Water soluble pesticides occur periodically in detectable concentrations in Suisun Bay when runoff from agricultural fields reaches the estuary (Kuivila and others, 1996). These pulse inputs from winter storms are superimposed on chronic contamination with petroleum by-products (Pereira and others, 1992) and trace elements (Luoma and others, 1990; Johns and Luoma, 1988; Luoma and others, 1992; Brown and Luoma, in preparation).

Selenium is an example of a chronic contaminant. Field surveys and mass balance calculations (Johns and Luoma, 1988; Cutter, 1989) demonstrated that the most important sources of Se are industrial discharges located near Carquinez Strait. During the low river flows characteristic of the estuary since 1986, Se enrichment in water, suspended particles and benthic species spread throughout Suisun Bay. Substantial Se contamination is found in large fish and in diving ducks in Suisun Bay. The concentrations of Se in water are well below those that cause toxicity in bioassays, but Se concentrations in clams (the food of diving ducks and some fish) are at the level that causes toxicity to birds and fish in food. The combination of studies showed that the contamination of the upper trophic level organisms, and the concomitant threat to their health, resulted from highly efficient transfer of selenite (the form of Se discharged by industry in the area) from water, to phytoplankton and then to clams via ingestion of phytoplankton (fig. 3).

Figure 3. An illustration of the concentrations of selenite in micrograms per liter, selenium in suspended particles in micrograms per gram, selenium in clams in micrograms per gram, and the toxicity of selenium in the food of ducks typical of Suisun Bay.

Analysis of Potamocorbula tissues has been employed to define chronic trace metal contamination, in addition to selenium. The abundance of this clam across across a broad range of salinities in the system makes it an especially suitable organism for spatially comparative studies of contamination. Laboratory studies also showed that P. amurensis rapidly bioconcentrates metals in its soft tissues from both food and solution (Brown and Luoma, 1995; Decho and Luoma, 1995). Potamocorbula were sampled and analyzed monthly at six stations between January, 1991 and April, 1992, a period of relatively stable river flow. Thus, influences of physical and salinity variability on assessment of source inputs was minimized. A consistent spatial gradient in enrichment with Cd, Cr, Ni, and V was observed in the clam tissues (fig. 4). Concentrations were highest in upper and mid-Suisun Bay and declined through Carquinez Straits into San Pablo Bay. All metals except silver were more enriched in Suisun Bay than in South Bay. The same general gradient in contamination was observed at every sampling time through the 14 month period. Interestingly, the highest concentrations of metals were found in Honker Bay, where no immediate point sources of metal input occur. These data raise the possibility that Honker Bay could be a depositional zone for upper Suisun Bay. Hydrodynamic studies will aid an evaluation of this hypothesis.

Figure 4. Distribution of chromium concentrations in tissues of the clams Potamocorbula amurensis and Corbicula fluminea in the San Joaquin River, Suisun Bay and San Pablo Bay.


The gradient of chronic contamination in Suisun Bay coincides with some of the unique biological characteristics of the area. In P. amurensis these include the gradient of lower condition index in Suisun Bay to higher condition index in San Pablo Bay, the lack of a seasonal cycle of condition index in Suisun Bay, and the spatial differences in the seasonality of reproduction in the species. A decline in the condition of a bivalve and alterations to reproductive capabilities can be symptoms of stress in bivalves. Trace elements can cause these responses by disrupting the energetic balance of the organism and reducing energy available for reproduction and growth (Widdows, 1985). On the other hand, food availability and other natural or anthropogenic disturbances can also cause such changes or interact with contaminants in complex ways to produce responses of communities, populations and individuals (Luoma and Carter, 1991).

Ecologists typically cite natural processes or anthropogenically induced changes in habitat conditions to explain differences in populations or declines in fisheries. Toxicologists often search for effects of contaminants where waste discharges from human activities impinge on an aquatic environment. Sufficiently careful, detailed ecological studies that consider contaminants as one of several variables of influence are rare. The studies of 1989 - 1993 identified and specifically characterized ecological and biological anomalies in Suisun Bay. These studies identified several processes that could cause those anomalies, including reduced river flow, lowered carbon inputs, changes in water column ecology caused by invasion of an exotic species, and persistent contamination. Continuity in collection of data that describe these processes, including time series that extend for decades, have previously provided opportunities to distinguish the relative importance of different processes in complex estuarine environments (Jassby and others, 1993a; Nichols and others, 1986). This same approach is the best approach to distinguishing factors that control ecological and biological processes in Suisun Bay.


Alpine, A.E., and Cloern, J.E., 1992,
Trophic interactions and direct physical effects control phytoplankton biomass and production in an estuary: Limnology and Oceanography, v. 37, p. 946-955.
Biggs, R.B., DeMoss, T.B., Carter, M.M., and Beasley, E.L., 1989,
Susceptibility of U.S. estuaries to pollution: Reviews in Aquatic Science, v. 1, p. 189-208.
Brown, C.L. and Luoma, S.N., 1995,
Use of a euryhaline bivalve to assess trace metal contamination in San Francisco Bay, I-Evaluating the characteristics of Potamocorbula amurensis as a biosentinel species: Marine Ecology Progress Series, in press.
Canuel, E.A., Cloern, J.E., Ringelberg, D., Guckert, J. and Rau, G., 1995,
Application of molecular and isotopic tracers to understand sources of organic matter and tropic relationships in the San Francisco Bay estuary: Marine Ecology Progress Series, in press.
Carlton, J.T., Thompson, J.K. Schemel, L.E., and Nichols, F.H., 1990,
The remarkable invasion of San Francisco Bay (California, USA) by the Asian clam Potamocorbula amurensis, I-Introduction and dispersal: Marine Ecology Progress Series, v. 66, p. 81-94.
Cutter, G.A., 1989,
The estuarine behaviour of selenium in San Francisco Bay: Estuarine, Coastal and Shelf Science, v. 28, p. 13-34.
Decho, A.W. and Luoma, S.N., 1991,
Time-courses in the retention of food material in the bivalves Potamocorbula amurensis and Macoma balthica: Significance to the absorption of carbon and chromium: Marine Ecology Progress Series, v. 78, p. 303-314.
Duda, T.F., 1993,
The genetic population structure of Potamocorbula amurensis in San Francisco Bay: Masters Thesis, California State University, San Francisco CA, p. 120.
Fuller, C., van Geen, A. and Baskaran, M., 1994,
Records of contaminant inputs to San Francisco Bay: 3. Sediment chronology from 210Pb, 137Cs, 239,240Pu and 234Th profiles: Ocean Sciences Meeting, American Geophysical Union, San Diego, CA, Feb., 1994.
Hornberger, M.I., 1994,
Records of contaminant inputs to San Francisco Bay: 4. Downcore concentration of Cr, Cu, Pb, V, and Zn: Ocean Sciences Meeting, American Geophysical Union, San Diego, CA, Feb., 1994.
Hostsettler, F.D., Pereira, W.E., Rapp, J.B., and Kvenvolden, K. A., 1994,
Records of contaminant inputs to San Francisco Bay, 8-Biomarker profiles in sediment cores: Ocean Sciences Meeting, American Geophysical Union, San Diego, CA, Feb., 1994.
Jassby, A.D., Kimmerer, W.J., Monismith, S.G., Armor, C., Cloern, J.E., Powell, T.M., Schubel, J.R., Vendlinski, T.J., 1993a,
Isohaline position as a habitat indicator for estuarine populations: Ecological Applications.
Jassby, A.D., Cloern, J.E. and Powell, T.M., 1993b,
Organic carbon sources and sinks in San Francisco Bay-variability induced by river flow: Marine Ecology Progress Series, v. 95, p. 39-54.
Johns, C. and Luoma, S.N., 1988,
Selenium accumulation in benthic bivalves and fine sediments of San Francisco Bay, The Sacramento-San Joaquin Delta, and selected tirbutaries: Estuarine Coastal and Shelf Science, v. 27, p. 381-396.
Kuivila, K.M. and Copeland D.D., 1996,
Diazinon concentrations and transport in the Sacramento River and San Francisco Bay, California, February 1993, in Morganwalp, D.W., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the technical meeting, Colorado Springs, Colorado, September 20-24, 1993: U.S. Geological Survey Water-Resources Investigations Report 94-4015.
Luoma, S.N. and Carter, J.L., 1991,
Effects of trace metals on aquatic benthos, in Newman, M.C. and McIntosh, A.W., Eds., Metal Ecotoxicology: Concepts and Applications, Chelsea, MI., Lewis Publishers, p. 261-300.
Luoma, S.N., Dagovitz, R., and Axtmann, E., 1990,
Temporally intensive study of trace metals in sediments and bivalves from a large river-estuarine system: Suisun Bay/Delta in San Francisco Bay: Science of the Total Environment, v. 97/98, p. 685- 712.
Luoma, S.N., Johns, C., Fisher, N.S., Steinberg, N.A., Oremland, R.S. and Reinfelder, J.R., 1992,
Determination of selenium bioavailabililty to a benthic bivalve from particulate and solute pathways: Environmental Science and Technology, v. 26, p. 485-491.
Nichols, F.H., Cloern, J.E., Luoma, S.N., and Peterson, D.H., 1986,
The modification of an estuary: Science, v. 231, p. 567-573.
Nichols, F.H., Thompson, J.K., and Schemel, L.E., 1990,
The remarkable invasion of San Francisco Bay (California, USA) by the Asian clam Potamocorbula amurensis, II-Displacement of a former community: Marine Ecology Progress Series, v. 66, p. 95-101.
Obrebski, S., Orsi, J.J., and Kimmerer, W., 1992,
Long-term trends in zooplankton distribution and abundance in the Sacramento-San Joaquin Estuary: Interagency Ecological Studies Program Technical Report no. 32, 42 p.
Pereira, W.E, Hostettler, F.D. and Rapp, J.B., 1992,
Bioaccumulation of hydrocarbons derived from terrestrial and anthropogenic sources in the asian clam, Potamocorbula amurensis, in San Francisco Bay estuary: Marine Pollution Bulletin, v. 24, p. 103-109.
Pereira, W.E. and Hostettler, F.D., 1994,
Records of contaminant inputs to San Francisco Bay, 7-Anthopogenic and biogenic polycyclic aromatic hydrocarbons: Ocean Sciences Meeting, American Geophysical Union, San Diego, CA, Feb., 1994.
Peterson, D.H., Cayan, D.R., Festa, J.F., Nichols, F.H., Walters, R.A., Slack, J.V., Hager, S.E., Schemel, L.E., 1989,
Climate variability in an estuary--effects of riverflow on San Francisco Bay: American Geophysical Union, Geophysical Monograph, v. 55, p. 419-442.
vanGeen, A., 1994,
Records of contaminant inputs to San Francisco Bay: 6. Recent cadmium enrichments in the water column from Cd/Ca ratios in foraminifera: Ocean Sciences Meeting, American Geophysical Union, San Diego, CA, Feb., 1994.
Widdows, J., 1985,
Physiological responses to pollution: Marine Pollution Bulletin, v. 16, p. 129-133.

Previous PageTable of ContentsNext Page

Top of this page

USGS Home Water Climate Change Science Systems Ecosystems Energy and Minerals Environmental Health Hazards

Accessibility FOIA Privacy Policies and Notices

Take Pride in America logo logo U.S. Department of the Interior | U.S. Geological Survey
Page Contact Information:
Page Last Modified: Thursday, 10-Jan-2013 17:12:45 EST