and biological properties. More than 95 percent of the historic tidal marshes have been leveed and filled. These alterations have significantly reduced most native fish and wildlife populations. Most of the major rivers and streams that flow into the estuary have been dammed for flood control, power generation, and water supply. These structures, plus diversion canals, have reduced the inflow into the estuary by 40 percent, thereby altering flow and sedimentation patterns and water temperatures and blocking migration pathways for salmon and steelhead and altering their spawning habitats (Nichols et al. 1986).
Hydraulic mining in the foothills of the Sierra Nevada during the gold rush, especially between 1856 and 1887, resulted in massive inputs of sediments to San Francisco Bay. Starting in about 1950 with dam construction, some of these sediments were gradually lost, but there has still been a net sediment gain over the last century in the northern portions of the bay (San Pablo Bay) of nearly 400 million m3. New input of sediments is now quite reduced because of upstream dams, and the waters are clearer than before (USGS 1998).
There continue to be large inputs of organic and inorganic chemicals into the bay. Toxic trace-metal accumulations accelerated during the 1950s. Some high accumulations of silver, cadmium, lead, and selenium are found at certain sites in the bay, which receives effluents from 46 wastewater-treatment plants and the discharges of 65 large industries. Approximately 40,000 tons of at least 65 contaminants accumulate in the bay each year. The sediments have been the repository of many organochlorine compounds, some of which bioaccumulate in the livers of striped bass and may be one cause of their declining populations (Pereira et al. 1994).
Sewage treatment plants discharge about 60 tons of nitrogen into the bay every day. Despite this input of fertilizer, the bay has not become more eutrophic because the very large populations of filter-feeding invertebrates keep phytoplankton from building up. Formerly, when ammonium nitrogen was not removed from treated sewage water, the south bay, with its poor circulation, became anoxic and fish died. Advanced sewage treatment has alleviated this problem and reduced the input of toxic metals (Cloern and Jassby 1995, Cloern 1996). Superimposed on this massive alteration of the San Francisco Bay estuary by human action are patterns of periodic major perturbations of the operation of the bay ecosystem in response to wide interannual variations in rainfall that affect salinity gradients. These perturbations are particularly evident during El Niño events (Peterson et al. 1995).
San Francisco Bay has been, and continues to be, considerably altered by invasive species. In recent years a new marine introduction has occurred about every 14 weeks. Many of these introductions have large impacts on the bay ecosystem. The Asian clam Potamocorbula amurensis first became established