Many physical processes affect how constituents within San Francisco Bay vary. Processes and their associated time scales include turbulence (seconds), semidiurnal and diurnal tides (hours), the spring-neap tidal cycle (days), freshwater flow (weeks), seasonal winds (months), ecological and climatic changes (years), and geologic changes (thousands of years). Continuous time series of data on basic state variables of the bay, such as suspended-solids concentration (SSC), salinity, and water temperature, provide insight on the effect and relative importance of physical processes on the bay. SSC time series and Regional Monitoring Program (RMP) water-quality data can be used to calculate time series of some traceelement concentrations (Schoellhamer, 1997a, 1997b). The purpose of this chapter is to describe qualitatively time series of SSC, salinity, water temperature, and mercury during water year 1998 (October 1997 through September 1998).

Salinity, temperature, and sediment are important components of the San Francisco Bay estuarine system. Salinity and temperature affect the hydrodynamics (Monismith et al., 1996; Schoellhamer and Burau, 1998), geochemistry (Kuwabara et al., 1989), and ecology (Cloern, 1984; Nichols et al., 1986; Jassby et al., 1995) of the bay. Suspended sediments limit light availability in the bay, which, in turn, limits primary production (Cloern, 1987; Cole and Cloern, 1987), and thus food for higher trophic levels. Sediments deposit in ports and shipping channels, which must be dredged to maintain navigation (U.S. Environmental Protection Agency, 1992). Potentially toxic substances, such as metals and pesticides, adsorb to sediment particles (Kuwabara et al., 1989; Domagalski and Kuivila, 1993; Flegal et al., 1996; Schoellhamer, 1997a, 1997b).

The transport and fate of suspended sediments are important factors in determining the transport and fate of constituents adsorbed on the sediments. For example, the concentration of suspended particulate chromium in the bay appears to be controlled primarily by sediment resuspension (Abu-Saba and Flegal, 1995). Concentrations of dissolved trace elements are greater in South Bay than elsewhere in San Francisco Bay, and bottom sediments are believed to be a significant source (Flegal et al., 1991). The sediments on the bay bottom provide habitat for benthic communities that can ingest these substances and introduce them into the food web (Luoma et al., 1985; Brown and Luoma, 1995, Luoma 1996). Bottom sediments also are a reservoir of nutrients that contribute to the maintenance of estuarine productivity (Hammond et al., 1985).