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Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home California Estuaries What is an Estuary? …………………. . ………………………………………………………………. . ……… Ø Cal/EPA Reduce Width of questions answered box Ø Natural Resources Agency Ø About the California Water Quality Monitoring Council ESTUARIES Ø Stressors Ø Laws, Regulations & Standards Ø Research QUESTIONS ANSWERED Site Component Ø What is an estuary? Ø Where are California’s estuaries? Ø How healthy is the SF Estuary? Ø What is being done to restore the SF Estuary? Ø How can I be part of the solution? Ø Monitoring Programs, Data Sources & Reports Ø Restoration & Management An estuary is a partly enclosed body of water where fresh water coming down the rivers mixes with salt water from the sea. A range of coastal landforms fit this description, including bays, lagoons, harbors, inlets , and wetlands. Estuaries are among the most productive ecosystems on earth. They provide rich feeding grounds for coastal fish and migratory birds, and spawning areas for fish and shellfish. They are also important in maintaining the quality of coastal waters. Estuaries are amongst the most heavily populated areas throughout the world, with about 60% of the world’s population living along estuaries and the coast. As a result, estuaries are suffering degradation by human impact.

Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home California Estuaries Where are California’s Estuaries? …………………. . ………………………………………………………………. . ……… Ø Cal/EPA Ø Natural Resources Agency There are hundreds of estuaries in California, including Santa Monica Bay, Morro Bay, San Francisco Bay; and Smith, Klamath, Mad, Noyo, Eel, and Russian Rivers. It is the goal of this California Estuaries Portal to include comparable information on each of these estuaries, but initially, this Portal is focused on California’s largest estuary, the San Francisco Bay-Delta. Ø About the California Water Quality Monitoring Council ESTUARIES Ø Stressors Ø Laws, Regulations & Standards Site Component QUESTIONS ANSWERED Ø Research Ø What is an estuary? Ø Monitoring Programs, Data Sources & Reports Ø Where are California’s Ø Restoration & Management estuaries? Ø How healthy is the SF Estuary? Ø What is being done to restore the SF Estuary? Ø How can I be part of the solution?

Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home California Estuaries Where are California’s Estuaries? …………………. . ………………………………………………………………. . ……… Ø Cal/EPA Ø Natural Resources Agency There are hundreds of estuaries in California, including Santa Monica Bay, Morro Bay, San Francisco Bay; and Smith, Klamath, Mad, Noyo, Eel, and Russian Rivers. It is the goal of this California Estuaries Portal to include comparable information on each of these estuaries, but initially, this Portal is focused on California’s largest estuary, the San Francisco Bay-Delta. Ø About the California Water Quality Monitoring Council ESTUARIES Ø Stressors Ø Laws, Regulations & Standards QUESTIONS ANSWERED Ø Research Ø What is an estuary? Ø Monitoring Programs, Data Sources & Reports Ø Where are California’s Ø Restoration & Management estuaries? Site Component Ø How healthy is the SF Estuary? Ø What is being done to restore the SF Estuary? Ø How can I be part of the solution?

Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home California Estuaries Where are California’s Estuaries? …………………. . ………………………………………………………………. . ……… Ø Cal/EPA Ø Natural Resources Agency Ø About the California Water Quality Monitoring Council ESTUARIES Ø Stressors Ø Laws, Regulations & Standards Ø Research Ø Monitoring Programs, Data Sources & Reports Ø Restoration & Management Site Component

Webpage: http: //www. waterboards. ca. gov/mywaterquality/California_Estuaries/where/San_Fra ncisco/ Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home California Estuaries Where San Francisco Bay San Francisco Estuary …………………. . ………………………………………………………………. . ……… Ø Cal/EPA Ø Natural Resources Agency Ø About the California Water Quality Monitoring Council Site Component ESTUARIES Ø Stressors Ø Laws, Regulations & Standards Ø Research Ø Monitoring Programs, Data Sources & Reports Ø Restoration & Management The San Francisco Estuary (SF Estuary) is a valuable ecological and economic resource. It is the largest estuary on the west coasts of North and South America with its watershed draining more than 40% of California’s surface area. Prominent physical features of the estuary include San Francisco, San Pablo, and Suisun Bays and Carquinez Straight to the west, and the Sacramento-San Joaquin River Delta to the east. The SF Estuary provides drinking water for 25 million Californians, irrigation water for 4. 5 million acres of farm land, and habitat for more than 750 species of plants, fish, and wildlife, including several endangered and threatened aquatic and terrestrial species. Two-thirds of the State’s salmon pass through the estuary, and at least half of the Pacific Flyway migratory water birds rely on the wetlands, mudflats, and shoreline areas in the estuary. The SF Estuary is a global tourist destination for aquatic recreation such as boating, fishing, surfing, and swimming from beaches and in bays as well as hiking and

Webpage: http: //www. waterboards. ca. gov/mywaterquality/California_Estuaries/Health/Living_Resources/phytoplankton Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home California Estuaries How healthy is the SF Estuary Living Phytoplankton Ø Cal/EPA Ø Natural Resources Agency What are Phytoplankton and why are they important in the San Francisco Estuary? » What are Phytoplankton & why are they important? Ø About the California Water Quality Monitoring Council » How and where are Phytoplankton measured in SFE? ESTUARIES Ø Stressors Ø Laws, Regulations & Policies QUESTIONS ANSWERED Site Component Ø Research » What are SFE Phytoplankton trends? » What are the issues of concern in SFE? » What is being done to improve the health of Phytoplankton in SFE? Ø Monitoring Programs, Data Sources & Reports Ø Restoration & Management Primary production (carbon fixation through photosynthesis) by phytoplankton is one of the key processes that influence water quality in the estuary. Phytoplankton are small, free-floating

Webpage: http: //www. waterboards. ca. gov/mywaterquality/California_Estuaries/Health/Living_Resources/phytoplankton/wher e Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home California Estuaries How healthy is the SF Estuary Living Phytoplankton Where Ø Cal/EPA Ø Natural Resources Agency Ø About the California Water Quality Monitoring Council ESTUARIES Ø Stressors Where are Phytoplankton & Chlorophyll a measured in the San Francisco Estuary? Phytoplankton Indicator Structural diagram (click to enlarge) Plankton and Chlorophyll a are measured by DWR’s Ecosystem Monitoring Program, part of the Interagency Ecological Program. Site Component Phytoplankton photos Ø Laws, Regulations & Policies Ø Research Ø Monitoring Programs, Data Sources & Reports QUESTIONS ANSWERED Ø Restoration & Management » What are Phytoplankton & why are they important? » How and where are Phytoplankton measured in SFE? Watch how Chlorophyll a changed across the SFE from month to month during 2011. [Click here to start animation with 2011 monthly time series data on map to the left] Phytoplankton / chlorophyll a are dynamic: measurements change » What are SFE Phytoplankton trends? » What are the issues of concern in SFE? » What is being done to improve the health of Phytoplankton in SFE?

Webpage: http: //www. waterboards. ca. gov/mywaterquality/California_Estuaries/Health/Living_Resources/phytoplankton/wher e Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home California Estuaries How healthy is the SF Estuary Living Phytoplankton Where Ø Cal/EPA Ø Natural Resources Agency Ø About the California Water Quality Monitoring Council ESTUARIES Ø Stressors Where are Phytoplankton & Chlorophyll a measured in the San Francisco Estuary? Plankton and Chlorophyll a are measured by DWR’s Ecosystem Monitoring Program, part of the Interagency Ecological Program. Site Component QUESTIONS ANSWERED » What are Phytoplankton & why are they important? » How and where are Phytoplankton measured in SFE? » What are SFE Phytoplankton trends? Ø Laws, Regulations & Policies » What are the issues of concern in SFE? Ø Research » What is being done to improve the health of Phytoplankton in SFE? Ø Monitoring Programs, Data Sources & Reports Ø Restoration & Management Watch how Chlorophyll a changed across the SFE from month to month during 2011. [Click here to start animation with 2011 monthly time series data on map to the left] Phytoplankton / chlorophyll a are dynamic: measurements change

Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home California Estuaries How healthy is the SF Estuary Living Phytoplankton How 2 Ø Cal/EPA Ø Natural Resources Agency Ø About the California Water Quality Monitoring Council ESTUARIES Ø Stressors Ø Laws, Regulations & Policies Ø Research How are Phytoplankton & Chlorophyll a measured in the San Francisco Estuary? (cont. ) Chlorophyll a & Pheophytin Chlorophyll a samples were collected monthly at thirteen monitoring sites throughout the upper estuary (Figure 4 -1) using a submersible pump from one meter below the water’s surface. Approximately 500 m. L of water was passed through a 47 -mm diameter glassfiber filter with a 1. 0 μm pore size at a pressure of 10 inches of mercury. The filters were immediately frozen and transported to Bryte Laboratory for analysis according to the Standard Methods (APHA 1998) spectrophotometric procedure. Samples were processed by mechanically grinding the glass-fiber filters and extracting the phytopigments with acetone. Chlorophyll a and pheophytin a pigment absorptions were measured with a spectrophotometer before and after acidification of the sample. Concentrations were calculated according to the formula in Standard Method (APHA 1998). Ø Monitoring Programs, Data Sources & Reports Ø Restoration & Management Site Component QUESTIONS ANSWERED » What are Phytoplankton & why are they important? » How and where are Phytoplankton measured in SFE? » What are SFE Phytoplankton trends? » What are the issues of concern in SFE? » What is being done to improve the health of Phytoplankton in SFE?

Webpage: http: //www. waterboards. ca. gov/mywaterquality/California_Estuaries/Health/Living_Resources/phytoplankton/trend s Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home California Estuaries How healthy is the SF Estuary Living Phytoplankton Trends Ø Cal/EPA Ø Natural Resources Agency Ø About the California Water Quality Monitoring Council ESTUARIES Ø Stressors Ø Laws, Regulations & Policies Ø Research Ø Monitoring Programs, Data Sources & Reports Ø Restoration & Management How have Phytoplankton & Chlorophyll a changed over time in the San Francisco Estuary? There have been significant changes to the physical structure of the Estuary, extent of wetland habitats, water use within the SFE and upstream, and the surrounding land use in the last few hundred years. These changes in the ecosystem have contributed to changes in phytoplankton density, distribution, and species diversity. Phytoplankton populations and chlorophyll a are dynamic and change seasonally throughout the San Francisco Estuary (click here to go an animation), and change from year to year depending on many factors including climate, freshwater flows, and other facets of water quality. Although there is this variability within and among years, there have been some clear trends over the 40 years of measurement. And in general, the health of phytoplankton indicators (density, distribution, and species composition) has been decreasing. We explore here a few of the relationships between phytoplankton /chlorophyll a and some of the factors that have contributed to long term changes. Invasive Asian Clams vs. Chlorophyll: Where have all the Phytoplankton gone? When Asian clams (Potamocorbula) invaded Suisun Bay around 1985, they started consuming vast proportions of the available phytoplankton, leaving little for the native zooplankton. This had a cascading affect in the food web. Click here for the full story. The graph to right goes here Changes in Phytoplankton Species Composition over time: The Fall of Diatoms and Rise of Toxic Cyanobacteria Larger phytoplankton, including some kinds of diatoms, are an important food source for the zooplankton that are favored by native fishes including delta smelt. In many parts of the SFE, diatoms have decreased, or larger, single-celled species have been replaced by QUESTIONS ANSWERED » What are Phytoplankton & why are they important? » How and where are Phytoplankton measured in SFE? » What are SFE Phytoplankton trends? » What are the issues of concern in SFE? » What is being done to improve the health of Phytoplankton in SFE?