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.
