The San Francisco Bay and Sacramento-San Joaquin Delta together form a biologic resource of enormous importance. Thirty species of threatened or endangered plants and animals use the estuary during at least a part of the their lives. Two-thirds of the state's salmon and over a million waterfowl and shorebirds migrating on the Pacific Flyway pass through the estuary each year.

The Bay-Delta system drains an area nearly 60,000 square miles that covers 40% of California and extends north into Oregon. It includes the largest inland delta, the largest brackish water marsh, and the largest estuary on the West Coast.

Before humans began to alter the Bay-Delta, the central part of the system was covered by a vast, freshwater marsh that was inundated with each high tide. Natural channels and sloughs separated the tidal marshlands, forming "tule islands." Rivers and streams entering the Delta from the north, east and south created waterways bordered by large stands of riparian forest.

Since Western settlers began to populate the area in the 1840s and '50s, however, the Bay-Delta has seen dramatic change. Channels and levees constructed to protect islands used for agriculture have altered the hydrology and eliminated many marshes. Roughly half of the freshwater in the watershed is now diverted to nourish cities and crops both upstream and downstream of the Delta. Bird and fish populations are a fraction of their former size, and in many parts of the ecosystem, introduced species far outnumber native ones.

The Bay-Delta today supports 28 species of native fish, including resident and anadromous species. Resident fish include Delta smelt, longfin smelt, and the Sacramento splittail. Native anadromous fish include steelhead, four different runs of Chinook salmon, and two species of sturgeon.

The Delta smelt and winter-run Chinook are listed as threatened and endangered, respectively, under the federal Endangered Species Act. Federal agencies have proposed listing the steelhead as endangered, and a listing for spring-run salmon is being considered.

What is an Estuary_

Estuaries are among the word's richest and most productive ecosystems. Scientists define an estuary as a partially enclosed body of water where fresh river water meets and mixes with the salty ocean. In estuaries, sunlight in warm shallow waters and nutrients from rivers and the ocean encourage the growth of phytoplankton, algae and marsh vegetation. Plants and other types of vegetation provide cover for fish, birds and mammals. This primary productivity supports small animal life known as zooplankton, other invertebrates and fish, birds and mammals.

Freshwater and ocean water meet in what is called the mixing zone. The location of the mixing zone in the Delta is highly variable, moving two to six miles twice each day in response to the tides. The mixing zone can also move great distances upstream and downstream as a result of changes in river inflow. In the great flood of 1862, for example, the mixing zone was beyond the Golden Gate for several weeks. After the dry summer and fall of 1931, by contrast, the zone's upstream border moved inland as far as Courtland on the Sacramento River and Stockton on the San Joaquin.

The mixing zone is critical to biological activity in the estuary. It is the location of the all-important "entrapment zone," where suspended nutrients, phytoplankton, zooplankton, and eggs and larvae of many fish tend to accumulate.

With very high flows, the entrapment zone is in San Pablo Bay or Carquinez Straits. With moderate flows it is generally in Suisun Bay, and with low flows it moves upstream into the lower Sacramento River.

Conditions appear to be most favorable for many species of fish when the entrapment zone is located in the warm, shallow waters of Suisun Bay during spring, summer and fall. This knowledge is the foundation of the so-called X-2 standard used to regulate water quality in the Bay-Delta.

The standard, which is part of the Water Quality Control Plan adopted by the State Water Resources Control Board in 1995, establishes salinity criteria for the Bay-Day estuary. The criteria are designed to ensure that the entrapment zone is located in Suisun Bay at critical times to provide more favorable conditions for Delta smelt and other larvae.