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What is an Estuary?
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 What is an estuary?
 Where are California’s
estuaries?
ESTUARIES
 How healthy is the SF Estuary?
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 What is being done to restore
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the SF Estuary?
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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 .
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Home  California Estuaries  Where
Where are California’s Estuaries?
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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.
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QUESTIONS ANSWERED
 What is an estuary?
 Where are California’s
estuaries?
 How healthy is the SF Estuary?
 What is being done to restore
the SF Estuary?
 How can I be part of the
solution?
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Home  California Estuaries  Where
Where are California’s Estuaries?
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 Cal/EPA
 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.
 About the
California Water
Quality Monitoring
Council
ESTUARIES
 Stressors
 Laws,
Regulations &
Standards
QUESTIONS ANSWERED
 What is an estuary?
 Research
 Monitoring
Programs, Data
Sources &
Reports
 Restoration &
Management
 Where are California’s
estuaries?
Site Component
 How healthy is the SF Estuary?
 What is being done to restore
the SF Estuary?
 How can I be part of the
solution?
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Home  California Estuaries  Where
Where are California’s Estuaries?
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Webpage:http://www.waterboards.ca.gov/mywaterquality/California_Estuaries/where/San_Fra
ncisco/
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Home  California Estuaries  Where  San Francisco Bay
San Francisco Estuary
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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
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Home  California Estuaries  How healthy is the SF Estuary  Living  Phytoplankton
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What are Phytoplankton and why are they important in the
San Francisco Estuary?
» What are Phytoplankton &
why are they important?
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in SFE?
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» What are SFE
Phytoplankton trends?
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Phytoplankton in SFE?
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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
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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.
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Phytoplankton photos
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» How and where are
Phytoplankton measured
in SFE?
» What are SFE
Phytoplankton trends?
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 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
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Home  California Estuaries  How healthy is the SF Estuary  Living  Phytoplankton 
Where
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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.
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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?
 Laws, Regulations
& Policies
» What is being done to
improve the health of
Phytoplankton in SFE?
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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
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How2
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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 mL 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).
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» 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
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Trends
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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 has 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?