San Franscisco Estuary Project - CCMP - Appendix D: Gaps in Knowledge

Each of the Status and Trends Reports (STRs) contains a chapter on perceived information gaps in scientific knowledge of the Estuary. SFEP staff has compiled in this CCMP a complete list of the Gaps in Knowledge (GIK) chapters of the following Status and Trends Reports :

Aquatic Resources of the San Francisco Estuary;
Wildlife of the San Francisco Estuary;
Pollutants in the San Francisco Estuary;
Dredging and Waterway Modification in the San Francisco Estuary; and
Wetlands and Related Habitats in the San Francisco Estuary.

The original, unedited version of these GIK chapters are available upon request from SFEP staff. Currently, staff is assessing the degree to which research projects funded under the Research Enhancement Program are filling the perceived gaps in knowledge.

Outline of Gaps in Knowledge From The SFEP Status and Trends Reports

Aquatic Resources
In order to attain a useful understanding of the estuarine ecosystem, several steps are needed:

1. Determine patterns of use for the major species of each embayment, regardless of their economic value.

2. Determine the productivity of the various parts of the Estuary and identify food origins for aquatic animals.

3. Determine the trophic connections of the aquatic resources of the Bay. Production of Melosira, Sinocalanus, or Potamocorbula is unlikely to provide the same fish abundances as equivalent densities of Asterionella or Eurytemora. Simply determining the number of trophic levels would provide a much more sound basis for estimating potential fish production.

4. Identify the sources of mortality and the mortality rates for representative species in each habitat.

5. Develop an understanding of how introduced species invade the Estuary and establish populations in order to improve prevention and control of unwanted exotics.

The following section contains information needs by subject area:

6. Phytoplankton productivity: Changes in the array of sampling stations are warranted. First, primary productivity in shoal areas dominates that in deeper areas, especially in Suisun Bay, yet most data are collected from channel stations. Second, almost no long-term series of chlorophyll or productivity measurements are available for Central and San Pablo Bays. Little is known, consequently, about the entrapment zone when it is pushed out of Suisun Bay by high flows. Third, certain areas in South and Suisun Bays appear to be oversampled in space. A commitment needs to be made to a group of "index stations" that will be sampled at a regular frequency.

7. Benthic microalgal productivity: No measurements have yet been made on benthic microalgal productivity, especially in South and Central Bays.

8. Delta discharge: Delta discharge may be the largest source of organic matter for Suisun Bay and a significant one for the northern reach as a whole. The load of organic carbon to San Francisco Bay from the Delta needs to be measured on a regular basis, and the issue of availability needs to be addressed. BOD measurement offers one perspective on this problem. Ongoing studies of multiple stable isotope and lipid markers need to be continued and extended.

9. Tidal marsh export: Tidal marsh sources may be important for Suisun Bay, particularly during drought periods. Direct estimates of tidal marsh export are virtually impossible. The uncertain availability of exported organic carbon is another obstacle.

10. Circulation and mixing: Transport through the Golden Gate requires definition and should be the first objective. A carbon budget for the entire Bay would then be feasible. Further subdivision needs to be done carefully, with due regard to topographical features and existing data.

11. Food web structure: The structure of the food web connecting organic carbon sources to higher organisms is critical in determining the magnitude of their food supply. The number of trophic linkages, for example, is especially important in controlling the efficiency of energy transfer from sources to macroscopic consumers.

The emphasis of research on an introduced fish species has delayed recognition of the status of several native species. Studies based on more sensitive species, on species representing a diversity of habitats within the Estuary, and on species of diverse trophic patterns would allow more accurate monitoring.

12. Sampling procedures and programs: Zooplankton studies of the Estuary have been largely concerned with documenting the food chain affecting striped bass. Consequently, zooplankton data for Central and South Bay are extremely sparse.

13. Life history and habitat requirements: Identification of the critical habitat of threatened and endangered species needs to encompass a large region in order to be sure of adequate protection. Sampling programs are needed to determine specific habitat requirements of native fishes and other organisms and the extent to which Delta species can be managed as a community.

14. Tributary streams: Surveys are needed to identify which streams are still home to heritage resources, how they might be preserved, and their importance as organic carbon contributors or as spawning habitats.

Pollutants
1. Abundance and distribution of pollutants of concern: There exists a substantial data base on metals discharged to the Estuary in municipal and industrial effluent. However, the data describing the extent to which such discharges have affected the concentration of metals in the water column of the Estuary are less reliable. Few data are available on concentrations of organic pollutants, either in discharges or in the water column.

a. Chemical speciation in aquatic toxicology within the Estuary: Studies carried out in the field and in the laboratory make it clear that the toxicity and bioaccumulation of organic and metallic pollutants are affected by chemical state; metals in particular behave differently in the environment depending upon pH, Eh, valence state, association with organic radicals, and salinity. While understanding of the importance of chemical speciation in aquatic toxicology is adequate, knowledge of speciation in the Estuary is lacking for tin, copper, cadmium, mercury, and virtually all organic pollutants.

b. Organic pollutants: The few data available on organic pollutant abundance and distribution from the Estuary suggest that the sources and behavior of organic pollutants should be rather predictable. By gathering specific information on organic pollutants in the water, sediments, and biota of the Estuary it should be possible to apply existing models to the system, thereby making it possible to control and manage the impact of organic pollution.

2. Pollutant Loads

a. Municipal and industrial effluent: Quantitative data for organic pollutants in effluent discharges are virtually non-existent. Very few analyses have been performed to determine the speciation of trace metals and organic pollutants in these discharges.

The data for Estuary metal loading can be improved in several ways: (1) sampling frequently enough to characterize seasonal and annual trends in loads, (2) applying quality assurance testing and reporting, and (3) using analytical methods with lower detection limits relative to concentrations present in effluent.

b. Urban and nonurban runoff: There is almost a complete lack of information on pollutant concentrations in urban runoff to the Estuary. Data on loads of organic pollutants of concern are virtually non-existent. A developing understanding of the importance of urban runoff as a source of organic pollutants also demonstrates that certain critical cognate data are lacking.

Dry season flows of urban runoff appear to be significant. Evidence of the dry-season runoff contribution to urban runoff loads in Sacramento suggests that the magnitude of dry-season flows throughout the Estuary should be investigated. Associated pollutant loads must be better defined before estimates of urban runoff can be considered accurate.

Pollutant concentrations in nonurban runoff have been measured only for agricultural drainage and even these data are limited. Considering the wide spectrum and large mass of pesticides used in the drainage of the Estuary, additional knowledge of pollutant concentrations is critical.

Efforts to model loads of pollutants from nonurban runoff are also hampered by a lack of data, including trace element concentrations in soils, soil moisture, and other parameters. Field verification of these models is needed if they are to be used in support of management activities.

c. Riverine loads: Very few data are available on mass transport of pollutants by the Sacramento River, despite the fact that it is the source of 80 percent of the freshwater inflow to the Estuary and probably carries relatively large loads of pollutants. Loads of pesticides and other organic pollutants of concern have not been assessed in either the San Joaquin or Sacramento Rivers. Ambient toxicity testing of riverine waters should be implemented in conjunction with monitoring and other management activities.

d. Dredging and dredged material disposal: Dredging activities have the potential to mobilize pollutants primarily due to the loss of particulate matter during dredging and due to the transport of slowly settling particles away from disposal sites. Existing information provides an insufficient basis for quantitative analysis of pollutant mobilization. Impacts of the large mass of pollutants associated with disposed, dredged material in the Estuary cannot be evaluated until their distribution and bioavailability are known.

e. Additional inputs: Estimates of loads from other minor inputs, including atmospheric deposition, spills, marine vessel discharges, and waste disposal site leachates, are uncertain. Hydrocarbon loads from atmospheric deposition may be significant, and periodic releases of hydrocarbons in spills are significant on a local, and perhaps regional, scale.

3. Fate of pollutants: A paucity of data regarding the distribution and abundance of pollutants in water, sediment, and biota limits our present understanding of the fate of pollutants in the Estuary. Generic fate models have been developed for pollutants in freshwater, estuarine, and oceanic systems. These models may be applied to the San Francisco Estuary, provided sufficient data have been accumulated.

Understanding the importance of pollutant equilibrium partitioning in aquatic systems is more than adequate for the purpose of applying generalized models. However, there are insufficient data from the Estuary at present even for the application of general models. The extent to which pollutant partitioning is determined by physicochemical and environmental factors specific to the Estuary and biological processes unique to the Estuary is not known and must be determined.

Complex patterns of circulation in the Estuary impede estimation of residence times of pollutants. Residence times are likely to vary significantly within each embayment. Accurate estimates of residence times will depend on an improved understanding of the effects of wind, tides, and freshwater inflows, particularly in broad, shallow reaches of the Estuary.

Since many pollutants of concern partition to particles, the influence of processes such as flocculation, deposition, and erosion on their fate and transport must be determined. The highly dynamic nature of the Estuary and complexity of these processes constrains the development of predictive models of particle transport.

Although several pollutants accumulate in biota of the Estuary (including copper, mercury, nickel, selenium, silver, certain pesticides, and PCBS), few data on tissue concentrations are available. Comprehensive data regarding the abundance and distribution of pollutants in water, sediment, and tissue are sorely needed. Accumulation of pollutants in upper trophic level species and the possible contribution of food web transfer to this phenomenon require further study.

4. Pollutant effects on beneficial uses: Areas of extreme contamination have not been thoroughly studied with respect to sources or effects of the pollutants in place. Studies that have established links between toxic effects and specific pollutants (e.g., between PCBs and reproductive effects in fish and birds) in the Estuary have been correlative in nature. Laboratory studies are needed to demonstrate if such relationships are indeed cause and effect.

The effect of extraneous variables on the results of sediment bioassays, bioassays of water, and benthic community analyses confounds interpretation of results. The influence of such variables needs to be better characterized. High concentrations of silver and copper found in tissues of bivalves in some areas of the South Bay are cause for concern.

Some pollutants, such as PCBs and DDT, have declined rapidly in the Estuary because their use has been restricted; that is, trends in pollutant loading follow trends in their use, rather than trends in treatment level or population growth. It is reasonable to conclude that loads to the Estuary of other pollutants, including some metals, can also be reduced due to declining use. When the use of a pollutant declines it will reduce the potential discharge of the pollutant to the Estuary, independent of population growth.

Wildlife
This section discusses the major informational needs for various species groups and their habitats:

Special Status Species
1. Numerous special status amphibians, reptiles, birds, and mammals that breed within the Estuary study area are known or believed to be currently experiencing population declines. More detailed research is needed on the distribution and status of these species within the Estuary study area, as well as on the migratory routes and wintering grounds outside the study area.

2. Because of recent dramatic population declines in the California clapper rail, special attention to the research needs of this species in San Francisco Bay is warranted. Suspected factors contributing to this population decline include predation, contaminants, and habitat degradation. There is a critical need for information on the effect of contaminants in the food web on which clapper rails rely. Invertebrate foods of the rail should be analyzed for contaminants in all portions of the Bay currently or recently inhabited by rails.

Annual surveys in all tidal habitats in the Estuary should be conducted to determine the clapper rail's distribution and population status. In addition, the quality and extent of rail habitat, including any habitat threats, should be quantified. The extent and characteristics of upland refugia for the clapper rail, as well as the salt marsh harvest mouse, also should be quantified.

3. The existence of the California least tern in the Estuary is also precarious, warranting special attention to research needs for this species. More information is needed on the population dynamics and movements of this species. Banding and marking least tern chicks would provide information on age-class structure, mortality rates, and estimates of longevity. These factors could be used to predict long-range stability of tern populations. Other information needs include the degree of colony fidelity, shifts between colonies, establishment of new colonies, age at first nesting, factors affecting clutch size, and breeding success.

To properly manage the tern, additional research is also needed on: (1) the effects of environmental contaminants; (2) factors affecting the choice of location for roosting, loafing, and feeding areas used during the breeding and post-breeding seasons; (3) the amount of habitat needed (measured in terms of fish density) to maintain the current population size or increase it; (4) what constitutes suitable nesting habitat, including beaches, landfills, salt ponds, and estuarine areas; and (5) factors leading to colony disruption and nest site abandonment.

4. Expansion of the introduced bullfrog has contributed to declines in the California red-legged frog, and the nature of this interaction should be investigated. In addition, the possible effects of contaminants on populations of red-legged frogs and the San Francisco garter snake deserve special attention.

5. For many of the special status wildlife species considered to be State Species of Special Concern, very little information exists on distribution, abundance, or population.

Waterfowl
6. One of the most pressing needs is to determine the effects of contaminants on wintering waterfowl, particularly diving ducks. To assess the effects of contaminants on waterfowl, more information is needed on how the waterfowl community uses habitats within the Estuary. Radio telemetry studies in the Bay and Delta would provide information on where wintering waterfowl concentrate and how long they remain in the Estuary. An estimate of the carrying capacity of the Estuary for waterfowl should be made by assessing available food resources and the use of those resources.

Of particular importance in an assessment of available food resources is quantification of the value of salt ponds and seasonal wetlands to wintering waterfowl. Few data exist on this topic even though these habitat types are often most threatened by development. Further research is also warranted for the western population of the canvasback because of the critically low population levels reached in 1988 and 1989.

7. General waterfowl research topics recommended for the Central Valley and Delta include: (1) an assessment of winter food requirements for certain key species and the ability of major habitats to provide these resources; (2) an evaluation of the influence of weather, agriculture, and hunting on the distribution and abundance of waterfowl; (3) an evaluation of the cause, chronology, and magnitude of non-hunting mortality; and (4) an assessment of the physical condition and reproductive potential of waterfowl relative to winter habitat conditions.

8. Further research on limiting factors of waterfowl wintering in the Estuary is warranted. All waterfowl habitats (wetlands, riparian vegetation, agricultural land, and uplands) need to be quantified according to waterfowl requirements. This would include the amount of available habitat that fulfills waterfowl food, shelter, loafing, nesting, and sanctuary needs during the period of the year when these habitats are available. This information may aid in determining which of the wintering requirements is population limiting.

Shorebirds
9. Unlike waterfowl, yearly inventories of shorebird populations in California have not been conducted on a regular basis. To sustain migratory shorebirds, more information is needed on the seasonal abundance patterns of shorebirds. A long-term monitoring program should be initiated to establish population trend data. Coupled with this, improved techniques should be developed to estimate population sizes. Almost no information is available on shorebird abundance and distribution in Suisun Marsh/Bay and the Delta, and long-term monitoring programs should be initiated for these areas of the Estuary.

10. Research is needed to define precisely the roles that seasonal wetlands and salt ponds play in maintaining the Bay's shorebird population in winter. Research on the availability of roosts and patterns of use in the Central Bay area should be conducted to promote protection of suitable roosts in the future.

11. More information is needed regarding factors limiting shorebird populations in the Estuary. Examples are the effects of power lines on shorebird mortality and the effects of contaminants, especially selenium, on wintering shorebirds. The effect of the introduced Asian clam on benthic invertebrates, the major prey of shorebirds, should also be investigated. Studies should also be conducted to find ways of limiting red fox predation on shorebird nests and young.

Colonial Birds
12. The presence of contaminants in the food web of colonial nesting birds should be investigated throughout the Estuary through sampling of sediments, invertebrates, and fish. This information will shed light on the pathways through which contaminants enter the food web and will better define background contaminant levels and hot spots in the Bay. Telemetry studies of black-crowned night herons and other colonial nesting birds during both the breeding and non-breeding season would help determine where the birds are being exposed to contaminants. Species such as the double-crested cormorant or black-crowned night-heron could serve as biological indicators of background contaminant levels.

13. Studies should also be conducted to determine the impact of predators on nesting colonial birds in the Estuary.

Other Wildlife
14. There is a critical need for studies of populations of mammalian predators in the Estuary. More information is needed on the distribution and abundance of predators, such as the red fox, Norway rat, and black rat. Research is needed on various control techniques, including the feasibility of reintroducing the coyote to control red foxes, where appropriate.

15. Because the harbor seal is a conspicuous mammalian member of the Bay food web, research is needed into the possible effects of environmental contaminants on this species.

16. Research is also warranted on the effects of sea level rise on Bay wildlife.

17. Cowbirds and starlings are well known for their abilities to displace other nesting bird species. The impact that these two species are having on native nesting birds, however, is largely unknown in the Estuary.

Wildlife Habitats
18. Long-term wildlife monitoring studies of several habitat restoration sites are needed to document wildlife recolonization and to determine the true success of each restoration effort.

19. Because tidal marsh erosion is proceeding at an alarming rate in the Bay, particularly in the South Bay, additional research in this subject is warranted. Baywide studies of tidal marshes should be conducted to update where marsh erosion and accretion is taking place and to determine if accelerated rates of erosion are occurring in other locations besides those previously studied. Research is also needed to determine if structural techniques exist to retard erosion and possibly promote marsh expansion.

Contaminants
20. There is a need for basic research at every level to identify significant estuarine processes and to quantify relationships between wildlife and the contaminants present in the Estuary. A first step would be to improve coordination of existing programs.

Certain areas of extreme pollution have not been well studied with respect to sources or effects of pollutants. Further studies are needed regarding forms of arsenic in the Estuary and the biological effects of tin (especially TBT). More congener-specific studies of PCBs are needed, since the toxicological effects of PCBs may be related to only a small number of coplanar forms of these compounds. In the case of correlations of PCBs with reproductive effects in fish and birds, more evidence is needed to determine the significance of observed effects. Additional studies are needed to clarify the role of PCBs that affect economically or biologically important organisms of high trophic levels. Investigations should seek to identify cause-and-effect relationships wherever possible.

21. Clear evidence linking pollution with specific biological effects is lacking in the San Francisco Estuary. Further study needs to be done on the occurrence of chronic or sub-chronic impacts on the biota of the Estuary as the result of exposure to pollutants. In this regard, particular emphasis should be placed upon developing realistic biological indicators of pollutant effects, such as genotoxic effects, physiological effects, or effects on the immune system. Relationships between the accumulation of complex mixtures of pollutants and their effects on the biota of the Estuary should also receive attention.

The effects of many contaminants, including polycyclic aromatic hydrocarbons, industrial chemicals, organotins, current-generation pesticides, and mosquito control agents, on wildlife, and particularly birds, have not been well studied in the San Francisco Estuary. It is important to establish relationships between contaminant concentrations in bird tissues and in those found in their foods to determine sources of contaminants, routes of exposure, and the effects on wildlife.

22. There is a need for field studies and controlled experimental studies that are conceptually related to field observations to determine: (1) acute and chronic toxicity of chemicals for important food-chain organisms and wildlife; (2) the association of contaminant burdens with morphological, histopathological, and biochemical/physiological indices in free-ranging animals; and (3) reproductive success in resident birds and in birds that winter in the Bay but nest elsewhere.

Dredging and Waterway Modification
This section identifies those areas of dredging and dredged material disposal where the lack of knowledge is most critical:

Dredging Activities
1. The precise amounts of dredged material disposed at sites in the Estuary: How much material is disposed of at each site in the Estuary? What types of equipment are used? What is the frequency of disposal at in-water sites and on land?

2. The quantity of sediment dredged in the Delta and used for levee maintenance: Is any of this material contaminated? What are the levels of contamination? What are possible effects?

3. Historical quantities of sediments dredged and disposed of in the Estuary: How well do permitted amounts of dredging coincide with actual quantities dredged and disposed? Is overburden at a site likely to be less or more contaminated than the permitted sediment? Can useful historical trends be constructed by reviewing past dredging permits? How can this information be used to better elucidate the current status of dredging and waterway modification in the Estuary?

Dredged Material Quality: Evaluation and Testing
4. The "background patterns" of sediment contamination in the Estuary: What is the present distribution of contaminants in estuarine sediments? Can any physical characteristics of Bay sediments be correlated with sediment chemical quality? Are there "background" concentrations of contaminants in sediments to which concentrations in dredged material can be compared? Are there regions of the Estuary with "background" concentrations of contamination that can be used for experimental control purposes?

5. The causal mechanisms of toxicity in sediment bioassays: Do sediment bioassays depict chemical toxicity? Are covariant factors in contaminant concentrations actually causing the toxicity observed in sediment bioassays?

6. What bioassays are appropriate for use in examination of contaminated sediments? Are acute, lethal bioassays preferable to chronic bioassays as indicators of potential effects? Are there numerical models adequate for representing potential acute or chronic effects? Which of the many assays currently being tested can be used with confidence? Can any laboratory study adequately represent what results will be in the field? Can data from other parts of the country be transferred directly for use in the Estuary?

7. What sublethal bioassays or endpoints might be suitable for use in evaluating chronic effects? Are chronic bioassays preferable to acute, lethal assays in assessing the effects of dredged material disposal? Do any existing chronic bioassays hold promise for applicability to the Estuary and its dredged material disposal problems? Are there chronic effects for evaluation that may be more useful, or more sensitive, than the bioassays currently used for evaluating dredged material effects? Are there chronic, sublethal assays that allow the identification of effects due to single toxicants, as well as complex mixtures? How can an appropriate suite of chronic assays be developed that will help identify the major contaminants of concern?

8. The ecological significance of test results, including bulk chemistry assays, toxicity bioassays, and bioaccumulation tests: What is the relationship between laboratory tests of contaminated sediment and the actual effects of disposal of this sediment in the Estuary? What is the relationship of contaminant body burden and effects in the Estuary? Can objective standards be developed for determining the types of tests necessary for contaminated sediments and for classifying sediments on the basis of the results of such tests?

The Fate of Disposed Dredged Material
9. The mechanism by which the mound of material formed at the Alcatraz disposal site: How quickly did the mound of material grow? Could the mounding have been slowed or prevented through alternate disposal practices? What is the likelihood of mounding occurring at the other disposal sites?

10. The initial distribution of sediment dispersed from the disposal sites in the Estuary: Where does material dispersed from the disposal sites go initially? What is the rate and magnitude of sediment transport in the Estuary? In sub-sections of the Estuary? How does the equipment used affect the dispersion of the disposed material? How does the method, timing, and frequency of disposal affect transport (or retention) of dredged material at a given site?

11. The ultimate fate of disposed material in the Estuary: What fraction of material is redeposited in quiescent areas of the Estuary? What fraction of material is redeposited in artificially maintained channels, slips etc.? How important are factors not yet modeled, such as wind-driven currents, in determining the ultimate fate of disposed material? What fraction of disposed dredged sediment leaves the Estuary; how much material returns to navigation channels?

12. How well do the complex hydrodynamic and sediment transport models available actually represent the Estuary? How uncertain are the predictions of these models? How sensitive the predictions to changes in the assumptions used to build the models?

The Effects of Dredged Material Disposal
13. The fraction of the contaminants in dredged material that is released to the environment during and after disposal: Can accurate estimates of annual loads of contaminants due to the disposal of dredged material be developed?

14. The bioavailability of the released fraction of contaminants: How does contaminant bioavailability vary with such factors as season, salinity, or species? How much of the observed bioaccumulation of toxic contaminants in the Estuary is due to the disposal of dredged material? Do existing models for chemical equilibrium in the environment hold any promise for application to dredging problems in the Estuary?

15. The contribution of dredged material disposal to suspended sediment concentrations in Central Bay: Does disposal of dredged material at the Alcatraz site significantly increase the suspended sediment concentrations in the Central Bay beyond the short time period after disposal? How does frequent use of the disposal sites affect suspended sediment concentrations in the Estuary?

16. Impacts due to increases in the concentration of suspended solids from dredging operations on estuarine biota: Are egg or larval stages of biota in the Estuary adversely affected by increases in suspended solids concentrations? Are the biota affected by particle-associated contaminants? Is there an interaction (i.e., synergism or antagonism) between suspended solids and contaminants and their effects on organisms? Do such increases result in behavioral changes, such as alterations of migratory patterns or avoidance of historical habitat?

17. How well do we understand the trophic structure ("food chain relationships") in the Estuary? Which predators will be affected by changes in the abundance and distribution of invertebrates? Which predators might particularly be expected to be susceptible to contaminant accumulation from their prey?

Recommended Research
A. The precise amounts of dredged material disposed at sites in the Estuary: It is recommended that more detailed data be collected and routinely analyzed to provide precise information regarding dredging and disposal activities in the Estuary. This is particularly the case with respect to dredging activities carried out under permit from the Army Corps of Engineers (the Corps). The San Francisco District of the Corps has undertaken such efforts in the past few years through the appropriate use of post-dredging bathymetric surveys; these activities should be continued and expanded. It is important to obtain accurate estimates of amounts of material and temporal trends in disposal, particularly with respect to the frequency of disposal events. It is also recommended that the Sacramento District of the the Corps develop estimates of the sediment quantities dredged by Reclamation Districts under their jurisdiction in the Delta and examine the quality of these sediments.

It is also recommended that the frequency of disposal activity should be recorded at all sites. Records should include the date and time of disposal, the volume of material disposed, the source of material that was dredged, the type of equipment, and tidal stage.

B. The ecological significance of test results, including bulk chemistry assays, toxicity bioassays, and bioaccumulation tests: The precise relationship between laboratory tests using contaminated sediment and the actual effects resulting from disposal of this sediment in the Estuary will probably never be determined. This is due to difficulties in conducting controlled field experiments, where numerous factors influence contaminant release, bioavailability, and toxic effects under field conditions. Laboratory studies can, however, provide useful information, particularly for testing "worst case" conditions. It is recommended that regulatory agencies endeavor to develop a more objective method by which the results of sediment testing can be evaluated. This will involve the establishment of criteria that quantitatively define the point at which a sediment must be subjected to biological and chemical tests and that define when test results are to be considered significant in predicting adverse effects upon disposal.

Studies should also be undertaken to investigate the causal mechanism of the toxic responses observed in sediment bioassays. Particular attention must be given to the role of sediment grain size and total organic carbon concentrations, as these factors co-vary with contaminant concentrations and confound the interpretation of bioassay results.

C. The ultimate fate of disposed material in the Estuary: Knowledge of the fate of disposed material is vital in understanding the transport of disposed sediments throughout the Estuary (including back to navigation channels), and the consequent distribution of the contaminants associated with dredged material. This topic can be investigated using both models and tracer studies.

(i) It is recommended that the modeling effort currently underway by the Corps be continued, with a clear focus upon circumventing several key limitations. Field data from the San Francisco Estuary must be made available to verify that the models can accurately represent (over appropriate periods) the complex phenomena that contribute to sediment transport. These include the effects of winds and the vertical stratification of currents. The sensitivity of the models to key parameters (including boundary conditions) should be documented. It is considered essential that estimates of uncertainty be included with model predictions, particularly if modeling data are to be used for assessing effects of alternative management strategies.

(ii) It is also recommended that tracer studies be conducted to define the short- and long-term transport of suspended particles from estuarine disposal sites. These studies could provide information regarding the return of disposed material to navigation channels, the dispersion of disposed material under different hydrological regimes, and the possible contribution of dredged material disposal to "hot spot" formation in the Estuary. New highly sensitive and economical tracing techniques using biological tracers (bacteriophages) are now available and could provide information regarding estuarine sediment transport.

D. The bioavailability of contaminants released by disposal of dredged material: Data regarding the bioavailability of contaminants released from dredged material is essential to determine the potential for toxicological effects due to the bioaccumulation of contaminants. It is recommended that a routine biomonitoring program be established at aquatic disposal sites in the Estuary. This program should use the California mussel (Mytilus californianus) and follow the established procedures for the use of biomonitors. This program should also be coordinated with the implementation of a local and regional biomonitoring program.

E. The spatial and temporal trends in suspended solid concentrations at disposal sites: It is recommended that the concentration of suspended solids be monitored throughout the water column at the disposal sites in the Estuary, with an emphasis on understanding the contribution of dredged material disposal to suspended sediment concentrations. In particular, suspended sediment concentrations should be documented in the Central Bay during periods of frequent use of the Alcatraz disposal site.

F. The impact of suspended solids from dredging operations on life-stages of estuarine biota: It is recommended that additional laboratory studies be conducted to improve predictions of the impact of suspended sediments upon sensitive life stages of resident species that could be exposed to sediment plumes from dredging and disposal operations. Commercially important species should be emphasized in such studies, and experiments should be designed to simulate field conditions to the maximum possible extent. Such studies should concentrate not only on lethality, but also on the development of sensitive assays useful in estimating the potential for organisms to survive, grow, and reproduce under prevailing conditions in the test aquarium.

Waterway Modification
Gaps in Knowledge
This section briefly summarizes areas of inadequate technical knowledge, or "data gaps," providing examples of management questions raised by these gaps in understanding:

1. Coastal flooding: What are the most recent 100-year high water level estimates for the Estuary? How can they be adjusted to account for the probabilities of flood flows and storm surges? What are the consequences of Delta Island failure on San Francisco Bay morphology, hydrodynamics, and salinity? What is the present condition of the perimeter levees surrounding the Bay and the Delta?

2. Shoreline erosion: What are the long-term trends in shoreline erosion? What are the causative factors? Can a current sediment budget be produced for the Estuary? How can sediment transport data be analyzed to update the sediment budget for the Estuary?

3. The extent (both historical and current) of stream channelization for flood control and stormwater management purposes: How much material has been dredged for this purpose? Over what distances have streams been modified? What effects do these activities have upon local biota, including fisheries and riparian vegetation? What effects do these activities have upon local sedimentation rates and other aspects of habitat viability? Is channelization a significant factor in the loss of fish and other wildlife habitats?

Recommended Research
A. It is recommended that estimates of 100-year high water levels around the Estuary be updated and revised to systematically account for the joint probability of flood flows and storm surges. Consistent flood protection design standards should be developed for different land uses around the Estuary, and analyses should be performed to allow future planning for coastal flood protection to account for projections of sea-level rise. The consequences of failure of the Delta islands upon the morphology, hydrodynamics, and salinity distribution of the Estuary need to be analyzed to determine management strategies. In addition, it is recommended that a comprehensive survey of the condition and elevation of all perimeter levees surrounding the Estuary be undertaken. There is a also a need for a detailed topographic survey of low-lying areas around the Estuary in order to determine areas of risk under future hazard scenarios.

B. Existing bathymetric surveys and sediment transport data should be analyzed to update the sediment budget for the Estuary. Periodic bathymetric surveys need to be made of mudflat and shallow inter-tidal areas to monitor long-term changes in Estuary morphology that might affect shoreline erosion. There is also a need for a coordinated, long-term plan for the future of the Delta.

Wetlands Status and Trends Report
Ecological and Biological Questions
1. What are the food web interactions in the Estuary, including species represented, food habits, predator-prey relationships, etc.? What are the fish and invertebrate communities associated with Delta wetlands, especially intertidal zones? What are the invertebrate communities of seasonal wetlands and of riparian communities of the Bay and Delta wetlands? What are the invertebrate, fish, and wildlife communities of perennial and intermittent streams of the Bay-Delta Estuary?

2. What is wetland-associated wildlife's use of farmed wetlands and grazing lands in the Suisun Marsh and diked historic baylands?

3. How would changes in freshwater inflow into the Estuary affect vegetation and wildlife resources in the Suisun Marsh, Suisun Bay, and San Pablo Bay?

4. What specific functions and values are provided by the major wetland habitat types, and what combinations of these wetland types are necessary to maintain and enhance viable fish and wildlife populations in the Delta and in North and South San Francisco Bays? What factors account for the apparent difference in the productivity, diversity, and composition of plant and animal populations found in the North and South Bays?

5. How do tidal hydrodynamics affect the evolution of tidal marshes? What are the relationships between stored marsh and slough channel geometry?

6. Is there evidence that tidal marshes help to control erosion, and, if so, how effectively?

7. What are the best strategies or methods for creating or restoring existing wetlands, and what particular aspects of wetland restoration projects have proven most successful?

8. To what extent do contaminants bioaccumulate or bioconcentrate in plants, invertebrates, fish, and birds using wetlands? Do contaminants from applying treated wastewater to wetlands bioaccumulate in plants and animals?

9. What wetland species, particularly endangered species such as the salt marsh harvest mouse and the clapper rail, require contiguous upland habitat? How wide an area of non-wetland habitat is needed? What habitat characteristics are necessary?

10. What is the habitat preference of the Suisun song sparrow?

11. Would the creation and/or enhancement of North Bay wetlands habitat adequately offset South Bay wetland losses due to development projects?

12. What are the reasons for the recent drastic decline of the California clapper rails in Bay wetland habitats? This inquiry should investigate: (1) the possible effect of contaminants on populations and the food chain, including a sampling of invertebrate populations within rail habitat and rail eggs; (2) laboratory toxicitation.

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