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42 STATE OF THE ESTUARY FISH CONTEXT Sports fishers appreciate the Estuary for its tasty striped bass and white sturgeon, but its sparkling blue-grey waters are also habitat for more than 100 fish species, both resident and migratory, including commer- cially important Chinook salmon and Pacific herring. The Estuary is also home to the threat- ened Delta smelt. These fishes variously use the Estuary to spawn in and raise their young, and to migrate between the Pacific Ocean and the rivers of the watershed. Amounts and timing of freshwater inflows, extent of rich tidal marsh and floodplain habitats, pollution, and the prevalence of non-native species all affect the numbers and types of fish that the Estuary can support. Measures of fish abundance, diversity, species composition and distribution are useful biological gauges for environmental conditions in the Estuary. A large, diverse fish community distributed broadly throughout 2015 were then aggregated into a regional Fish Index, a single metric for each sub-region. Except for the species composition indicators and the sensitive species abundance indicator, all indicators measure only fish species that are native to the San Francisco Estuary and local coastal waters. Sturgeon migrate through the Estuary all the way up to Shasta Dam near Redding. Photo courtesy SJWTP To provide a geographically comprehensive view of trends among fishes in the San Fran- cisco Estuary, a smaller set of indicators was developed to reveal conditions in Suisun Marsh, Suisun Bay, and the Sacramento-San Joaquin River Delta (collectively, the upper Estuary). The upper Estuary’s aquatic habitat and fish fauna differ from those found in the open waters of the Estuary’s main bays. Data for indicators in the upper Estuary comes from three long-term sampling programs and the approach mirrors that used in the Bay Fish Index. An additional indicator, portraying the fish assemblage’s role in the Estuary’s food web, their habitat and dominated by native species is an indicator of a healthy Estuary. INDICATORS The Bay Fish Index uses ten indicators to measure and evaluate the status and trends of the Estuary’s fish community in four sub-regions: South, Central, North and Suisun Bays. The indicators evaluate different attributes of the fish community: abundance, diversity, species composition and distribution. Indicator results for each of these attributes DETAILS B AY F I S H I N D E X B A S E D O N T E N I N D I C AT O R S 4 0 Poor 1 Fair 2 Good 3 SUISUN BAY 2013 2012 2008 2004 2000 1996 1992 1988 1984 1980 0 Poor 1 Fair 2 4 Good 3 SAN PABLO BAY 2013 2012 2008 2004 2000 1996 1992 1988 1984 1980 0 Poor 1 Fair 2 4 2013 2012 2008 2004 2000 1996 1992 1988 1984 1980 2013 2012 2008 2004 2000 1996 1992 1988 1984 1980 0 Poor 1 3 CENTRAL BAY Good 2 Fair INDEX 4 Good 3 SOUTH BAY