1. What are Zooplankton, and Why are they Important?
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What are Zooplankton, and Why are they Important?
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QUESTIONS ANSWERED
Where are zooplankton in the food web?
How and where are zooplankton measured?
What are SF Estuary zooplankton trends?
What are issues of concern in the SF Estuary?
(content in development)
What is being done to improve the health of zooplankton in the SF Estuary?
What are zooplankton, and why are they important?
Slide show –
SF Estuary zooplankton species
What are zooplankton?
Zooplankton are tiny, drifting or weakly swimming animals found in aquatic environments. The most common ones in the SF Estuary include copepods, cladocerans, rotifers, and mysids. Some zooplankton are native to the Delta, while others have been introduced.
Why are they important?
Zooplankton are important food sources for larval and juvenile salmon, striped bass, and splittail, and small fish including delta smelt. Zooplankton species composition differs between salinity zones, resulting in different zooplankton communities between freshwater to brackish to salty environments. Thus their presence and abundance can indicate water types.
Learn more about how zooplankton abundance is monitored in the SF Estuary. (link to zooplankton monitoring page (next slide)).
Need pictures for blue box (clickable, slideshow like other)

2. How and Where are Zooplankton Monitored in the SF Estuary?
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Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Zooplankton  Measured
How and Where are Zooplankton Monitored in the SF Estuary?
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QUESTIONS ANSWERED
Where are zooplankton in the food web?
How and where are zooplankton measured?
What are SF Estuary zooplankton trends?
What are issues of concern in the SF Estuary?
(content in development)
What is being done to improve the health of zooplankton in the SF Estuary?
What are zooplankton, and why are they important?
Zooplankton Monitoring Stations
Links:
- IEP links to
Environmental Monitoring Program links to and
“Learn more “ links to D1641 report –zooplankton methods content
Meta Data links to
Map:
- Map Reference:
- Click to enlarge
- Future iteration: link to data, include data visualization tools.
Click to enlarge
How and where are zooplankton monitored
Zooplankton are monitored as part of the IEP’s Environmental Monitoring Program (EMP) by the California Department of Fish and Wildlife’s Zooplankton Study. Changes in their composition, abundance, density, and distribution are documented within the SF Estuary, from San Pablo Bay east through the upper Estuary.
19 stations are currently sampled monthly, including 17 fixed stations and 2 floating entrapment zone stations. Three additional stations are sampled in the Carquinez Strait and San Pablo Bay during high outflow periods. Since 1972, 12 of the 19 stations have been sampled. An additional two have been sampled consistently since Three gear types with a range of net mesh sizes are used to capture zooplankton species of different sizes.
Learn more about the methods used to monitor zooplankton.
Where are the data?
More information on zooplankton monitoring can be found in the study Meta Data.

3. What are SF Estuary Zooplankton Trends?
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Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Zooplankton  Trends
What are SF Estuary Zooplankton Trends?
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QUESTIONS ANSWERED
Where are zooplankton in the food web?
How and where are zooplankton measured?
What are SF Estuary zooplankton trends?
What are issues of concern in the SF Estuary?
(content in development)
What is being done to improve the health of zooplankton in the SF Estuary?
What are zooplankton, and why are they important?
Cal/EPA
Natural Resources Agency
About the California Water Quality Monitoring Council
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Stressors
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Zooplankton Trends in the SF Estuary to 2011
Limnoithona abundance trends (log CPUE) 1979 to 2011, spring sampling period.
There was a significant increase in the early 1990’s. Click for the full story and to see other seasons
Eurytemora affinis and Pseudodiaptomus forbesi abundance trends (log CPUE) 1974 to 2011, summer sampling period. Eurytemora saw a significant decrease at the same time that Pseudodiaptomus appeared in the SF Estuary.
Click for the full story and to see other seasons
All of these links go to next page with more details and more graphs.
- Click for the full story and to see other seasons.
- Click for the full story
- More information
Reference for text and graphs:
- IEP Newsletter Zooplankton Monitoring 2011
Notes: Given that we have agreed to avoid discussion of drivers, we probably shouldn’t have an extended discussion about the Asian clam being partly responsible for driving down zooplankton numbers by eating phytoplankton?
The abundance of the most common calanoid copepods (including Eurytemora and Pseudodiaptomus) changes between seasons in the SF Estuary, as shown here for Click for the full story
What are Zooplankton trends?
There have been big changes in zooplankton abundance and species diversity in the SF Estuary. In general, zooplankton abundance and species diversity has changed dramatically, with an overall decline in zooplankton abundance and biomass. This has resulted in less zooplankton available as food for fish. At the same time, native species have decreased and nonnative invasive species have increased in most parts of the Estuary in most seasons and in most years.
More information

4. What are SF Estuary Zooplankton Trends? More information
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What are SF Estuary Zooplankton Trends? More information
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Photo of Limnoithona tetraspina, found in the Low Salinity Zone, a nonnative species that was first detected in 1993
Photo of Limnoithona sinensis, found in the freshwater zone, a nonnative species that was first detected in 1979
Photo of Eurytemora affinis, found in the Low Salinity Zone, a nonnative species that used to be the dominant source of fish food
Photos of Pseudodiaptomus forebsi, found in the Low Salinity Zone, a nonnative species that was first detected in 1987
Figures: if we can re-create, I would like to indicate which species are native (N), and which are invasive (I).
Fig 1 2 & 3: click to enlarge.
Fig 1 & 2 Graphs: Hover over y axes - a pop-up window defining CPUE and log and explaining the reason for using the log abundance:
CPUE: catch per unit effort, indicates the number of organisms per cubic meter of water sampled.
Log:
There are big differences – orders of magnitude differences - in CPUE values. Log values are graphed because they allow differences in small values to be seen more easily.
Other potential facts to add from Emily
Limnoithona inhabit the upper estuary.
L. tetraspina is common in both brackish and freshwater.
L. tetraspina may have benefited from the phytoplankton species composition change (described by Brown 2009) from non-motile diatoms to motile flagellates. De (Bouley and Kimmerer 2006).
Reference for text and graphs: IEP Newsletter Spring Zooplankton Monitoring 2011
There have been big changes in zooplankton abundance and species diversity in the SF Estuary, as shown here with the Department of Fish and Wildlife’s Zooplankton Study of the Delta, Suisun, and San Pablo Bay. In general, there has been a decrease in zooplankton abundance and biomass (that is, a decrease in the availability of zooplankton as food for fish). At the same time, native species have decreased and nonnative invasive species have increased in most parts of the Estuary in most seasons and in most years.
The introduced L. tetraspina has become the most abundant copepod, replacing the slightly larger L. sinensis. Despite high numbers of L. tetraspina in the upper SF Estuary, it may be too small to be a viable food source for visual predators like delta smelt. Other copepods, cladocerans, rotifers, and mysids have generally declined overall.
Figure 1 shows the trends in seasonal (spring, summer and fall) abundance between 1979 and 2011 of two nonnative species of cyclopoid copepods, Limnoithona tetraspina , which first appeared in 1993, and Limnoithona sinsensis, which first appeared in These two species have been increasing since 1979 during all seasons and are now typically two of the most abundant species of zooplankton sampled. They are smaller and are considered lower quality than the native species that were the dominant source of food for native fish in the past (including Eurytemora affinis, Figure 2). The two lines represent sampling results from two different size sampling nets. Abundance is indicated on the Y axis, as catch per unit effort (CPUE) on a log scale. [link to definitions]
Figure 2 shows the trends in seasonal (spring, summer and fall) abundance between 1974 and 2011 of two species of calanoid copepods found in the Low Salinity Zone, Eurytemora affinis, an East Coast species that was introduced before monitoring began, and was historically the dominant source of fish food; and Pseudodiaptomus forbesi, a nonnative species first observed in Since its introduction, Pseudodiaptomus has been 10 to 100 times more abundant than Eurytemora in summer and fall (see also Figure 3).
Figure 3 shows the abundance of the most common calanoid copepods during each month of 2011 (including Eurytemora affinis and Pseudodiaptomus forbesi , Figure 2). In this graph, the native species is Acartia (green); the remainder are nonnatives. Eurytemora affinis, an East Coast species that was introduced before monitoring began and was historically the dominant source of food for fish, and Acartia, the native, were dominant only in winter. The rest of the year was dominated by Pseudodiaptomus (light blue) and Acartiella (dark blue).