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Modeling and predicting intertidal variations of the salinity field in the Bay/Delta

San Francisco Bay and the Sacramento/San Joaquin Delta have challenged estuarine modelers for some years. Accurate, broad-scale models of this estuary have been in demand by those concerned with its ecological health and the development of sound management policies. A description and better understanding of the dynamics that govern the bay/delta are complicated by the system's complexity, requiring models that are sophisticated enough to capture the subtle physical processes involved. One approach to simulating daily to monthly variability in the bay is the development of intertidal model using tidally-averaged equations and a time step on the order of the day. An intertidal numerical model of the bay's physics, capable of portraying seasonal and inter-annual variability, would have several uses. Observations are limited in time and space, so simulation could help fill the gaps. Also, the ability to simulate multi-year episodes (eg, an extended drought) could provide insight into the response of the ecosystem to such events. Finally, such a model could be used in a forecast mode wherein predicted delta flow is used as model input, and predicted salinity distribution is output with estimates days and months in advance. This note briefly introduces such a tidally-averaged model (Uncles and Peterson, in press) and a corresponding predictive scheme for baywide forecasting.

California

Behind the energetics of the asiatic clam, Potamocorbula amurensis, in San Francisco Bay

The Asian clam (Potamocorbula amurensis) has played a key role in the food web of northern San Francisco Bay since its invasion in the fall of 1986. It has been associated with a dramatic decline in primary production, loss of a zooplankton species and a native mysid shrimp, the probable decline in striped bass, and has introduced alternative pathways for contaminant cycling in the bay food web.

Interagency Ecological Program Newsletter

Exposure of delta smelt to dissolved pesticides in 1998 and 1999

Delta smelt is a threatened species in the San Francisco Bay Estuary. Pesticide toxicity is a possible cause for the need to list this fish (Bennett and Moyle 1996; Moyle and others 1996). Numerous pesticides are transported into the estuary from area rivers (MacCoy and others 1995). However, there are minimal data to document the presence, or absence, of pesticides within delta smelt habitat, especially during their vulnerable early life stages. This study, conducted by the U.S. Geological Survey (USGS), documents the occurrence of pesticides within delta smelt habitat; specifically, the length and variability of their potential exposure to multiple dissolved pesticides. This article reviews delta smelt habitat and early life stages followed by an explanation of the study design for assessing pesticide exposure. Results show the co-occurrence of multiple pesticides and delta smelt in their native habitat; these results are presented within the context of possible toxic effects to delta smelt. Finally, the annual variability of pesticide distributions is discussed.

Interagency Ecological Program Newsletter

USGS supports ecosystem management in the San Francisco bay and delta

In the past several years, the Department of the Interior has ,l?laced particular emphasis on "ecosystem management" - the integration of scientific knowledge of ecological relationships with resource management practices to sustain ecological, cultural, and economic systems in broad habitat areas; eg., forest, desert, and aquatic habitats. The goal of ecosystem management is to understand the habitat requirements of many species and thereby assess the impact of a variety of human activities on regional biodiversity rather than to manage for individual species. In support of the management of the natural resources of San Francisco Bay and the delta, the USGS is augmenting its ongoing research program to provide additional research, monitoring, and assessment information and to improve the availability of that information. Following a workshop with resource and regulatory agency representatives, hosted by the USGS in early 1994, USGS researchers identified specific areas where existing and new scientific information could contribute to resolving some of the critical bay and delta land and aquatic management issues. The "ecosystems initiative" effort now underway addresses questions in three areas: Freshwater flow, including sediment and contaminant transport. Wetlands. Information and data access. Following is a brief description of activities being supported by this initiative.

Interagency Ecological Program Newsletter

Continuous flow measurements using fixed ultrasonic meters

USGS has or soon will be installing four continuous flow-monitoring stations in the delta that will use ultrasonic velocity meters (DVM). Funding for the stations has been provided by USGS, DWR, USBR, and Contra Costa Water District.

Interagency Ecological Program Newsletter

Indirect measurement of Delta outflow using ultrasonic velocity meters and comparison with mass-balance calculated outflow

A measurement of the quantity of water flowing from the Sacramento-San Joaquin Delta into Suisun Bay (Delta outflow) has been desired by those studying and managing the San Francisco Bay/Delta estuary since the 1920s. Historically, Delta outflow has been estimated using a mass-balance calculation that uses measured Delta inflows and exports, and imprecise estimates of consumptive use for the approximately 2,000 small agricultural diversions with the Delta. The DWR has estimated Delta outflow for 1929 to present using the computer program DAYFLOW.

Interagency Ecological Program Newsletter

Measured flow and tracer-dye data for spring 1996 and 1997 for the south Sacramento-San Joaquin Delta, California

During the spring of years when the flow of the San Joaquin River is less than 7,000 cubic feet per second (ft 3 /s) a temporary rock barrier is installed by the California Department of Water Resources (DWR) at the head of Old River (HOR) in the south Sacramento-San Joaquin Delta to prevent out migrating salmon in the San Joaquin River from entering Old River and being drawn to the State and federal pumping facilities (Figure 1). The export rate of the pumping facilities also is reduced during these migration periods to minimize the draw of fish to the export facilities through the other channels connected to the San Joaquin River north of the HOR such as Turner Cut, Columbia Cut, and Middle River.

Interagency Ecological Program Newsletter

Pathway models could aid management of contaminants

Heavy metal and trace organic contaminants are often cited as factors that could affect the riclmess of the biological community of San Francisco Bay as well as the health of resident organisms. Silver (Ag), selenium (Se), mercury (Hg), copper (Cu), nickel (Ni), chromium (Cr), and cadmium (Cd) are among the trace elements of current regulatory interest. All these elements can be toxic to estuarine organisms in minute quantities. However, understanding their toxicity in nature has proven a difficult challenge. In general, it is difficult to prove how pollutants are affecting ecosystems. The undisturbed "baseline" condition in San Francisco Bay is not always well enough understood to identify whether certain processes are affected or unaffected by contamination. Sources of disturbance (flow diversions, drought, invasion of exotic species, etc.) occur in addition to chemical contamination. Responses to contamination in individual organisms, populations, and commumties are seldom pollutant-specific, and the complex responses to moderate levels of contamination are not well known.

California

Pulsey, patchy water quality in the delta: Implications for meaningful monitoring

Valuable water quality and biological datasets have been gathered in the Sacramento-San Joaquin Delta for decades, most notably by the Interagency Ecological Program’s Environmental Monitoring Program (EMP). These extensive data have provided a means of analyzing and detecting long-term trends in water quality and ecosystem function (Jassby and others 2002; Kimmerer and Orsi 1996; Orsi and Mecum 1996) and may shape future restoration actions in the region. EMP water quality data—as well as data generated by the San Francisco Estuary Institute’s (SFEI) Regional Monitoring Program (RMP) and research groups like our own—have often focused on single, monthly or seasonal samples taken at several discrete points in space. Although such discrete data often push the practical limits of our equipment and human resources, higher resolution monitoring approaches can reveal limitations (in some cases severe) of these more coarse sampling schemes.

Interagency Ecological Program Newsletter

Environmental factors influencing the distribution and salvage of young delta smelt: a comparison of factors occurring in 1996 and 1999

The delta smelt (Hypomesus transpacificus) is listed as a threatened species under both the Federal Endangered Species Act (FESA) and the California Endangered Species Act. Through formal consultation under Section 7 of the FESA, USBR and DWR received a Biological Opinion from the USFWS, which allows for the incidental take of delta smelt arising through operation of the Central Valley Project and the State Water Project. The incidental take of delta smelt is estimated as part of the ongoing CVP and SWP fish salvage operations. Salvage levels of young delta smelt have exceeded incidental take levels every spring and summer since 1994, except in the high spring outflow years of 1995 and 1998 (Nobriga and others 1999). These high salvage levels have resulted in changes to project operations, often leading to the curtailment of water exports. An extended period of high salvage and export curtailment in 1999 raised substantial concerns and numerous questions that remain unanswered.

Interagency Ecological Program Newsletter

Fulfilling a paradoxical mandate: can the Environmental Water Account ensure the reliability of freshwater exports from the Sacramento-San Joaquin Delta and simultaneously protect delta smelt (Hypomesus transpacificus) from excessive entrainment?

The San Francisco Estuary (SFE) is often defined by its extremes. It is considered one of the most urbanized estuaries in the world (Conomos 1979, Nichols et al. 1986), and one of the most invaded estuaries in the United States, with hundreds of aquatic nonindigenous species established throughout the system (Cohen and Carlton 1995, Dill and Cordone 1997, Kimmerer and Orsi 1996). It is also one of the most managed estuaries, particularly in relation to freshwater inflow, water circulation, and water quality (Jassby and Powell 1994, CSWRCB 1995, Arthur et al. 1996, Kimmerer 2002). Despite this high level of disturbance, the SFE is one of the most valuable natural resources in the western United States (CALFED 2000). The SFE provides important habitat for numerous native plant and animal species, many of special concern, as well as several species with sport and commercial value (CALFED 2000). Conserving and restoring estuarine habitat and natural resources is a pressing and complex challenge for the responsible government agencies because human water needs continue to increase in concert with continuing urbanization of the watershed.

Interagency Ecological Program Newsletter