What are Estuaries, and Why are They Important?

What are Estuaries, and Why are They Important?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries What are Estuaries, and Why are They Important? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED What are estuaries, and why are they important? Where are California’s estuaries? How healthy are California’s estuaries? What’s being done to restore California’s estuaries? What laws, regulations, and policies protect California’s estuaries? How can I be part of the solution? Main image/video would be of SF Estuary (only one we’re working on now and people could click to SF pages from that image) Each of these questions will link to intro pages on each of these topics. Are we building pages for bar-built, open river mouths, perennially tidal? What are estuaries? Estuaries are partly enclosed bodies of water where fresh water coming down the rivers mixes with salt water from the sea. A range of coastal landforms fits this description, including bays, lagoons, harbors, inlets , and some wetlands. There are many types of estuaries in California including bar-built, open river mouths, and perennially tidal estuaries. Why are they important? Estuaries and Ecosystems Estuaries are among the most ecologically productive environments 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 and Humans Estuaries are some of 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 face degradation from human impacts.

Where are California’s Estuaries?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where Where are California’s Estuaries? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED Where are California’s estuaries? SF Estuary ? Estuary Hundreds of estuaries are found in California, including Santa Monica Bay, Morro Bay, and San Francisco Bay among others. It is the goal of this California Estuaries Portal to include comparable information on each of these estuaries. Initially, however, this Portal is focused on California’s largest estuary, the San Francisco Bay-Delta. - These question links would take you to intro pages on each of the estuaries that the site will focus on. - Right now, the only one that would work will be SF Estuary, others will say content in development. Clicking on SF Estuary will take you to the “What is the SF Estuary and why is it important page”. - Need to discuss if we like setting up the question like that.

Water Habitat Living Resources Ecological Processes Stewardship
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health How Healthy are California’s Estuaries? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Water Habitat Living Resources Ecological Processes Stewardship QUESTIONS ANSWERED How healthy are California’s estuaries? SF Estuary Health How do we determine the health of each attribute? Water Habitat Living Resources Ecological Processes Stewardship This is the intro slide to how healthy are CA’s estuaries. You wouldn’t get to this slide from the previous one. You would get here by clicking on the question link “How healthy are CA’s estuaries” on the first page. Each estuary would have their own health page. The only link that will work for now is the SF Estuary Health link and the water and living resources concept links. The water link would go to the concept for assessing water health (need to develop this) and the living resources link would go to the concept for assessing living resources health (next slide). Image: It would be clickable too, and need pictures for it. BIGGER QUESTION: Can we keep this attribute thing for the other estuaries in California, i.e. is it specific to the Bay-Delta? How healthy are California’s estuaries? Just as the health of the human body is dependent upon the health of its parts – the brain, the bones, the heart -- the health of California’s estuaries depends on the well-being of their parts. Those parts, also known as attributes, are defined by the authors of The State of the San Francisco Bay Report as water, habitat, living resources, ecological processes, and stewardship. How do we assess health? The initial focus of this Portal is on a robust evaluation of the health of Living Resources and Water for the SF Estuary. The remaining key attributes for the SF Estuary and all of the attributes for other California estuaries are under development.

How do We Determine the Health of Living Resources?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Concept  Living Resources How do We Determine the Health of Living Resources? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED How do we determine the health of each attribute? Water Habitat Living Resources Ecological Processes Stewardship Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Identify Key Attributes Water Habitat Living Resources Ecological Processes Stewardship Describe Health Indicators Species Composition (e.g. native v. exotic) Species Distribution Species Abundance STEP 1 STEP 2 Food Web Base Fish Birds Define Focal Categories Phytoplankton Zooplankton Resident Migrant Group #1 Group #2 STEP 3 STEP 4 Visualize Trends Native Richness over time Area occupied over time Abundance over time Identify & Evaluate Drivers STEP 5 Water (Quantity) Habitat loss Predation Water (Quality) Food Web Entrainment - Need to think this diagram through more. Grayed out boxes – mammals, bacteria, plants, etc. only links in the questions answered box that would work would be living resources, water, and stewardship where are benthic organisms? What about bay/marine fish? What are the groups of birds? And do these indicators stay the same for each? (don’t think that they do, based on SOTB 2011 report (pg. 7)) Kris Jones’s Comment: “As the notes mention in this slide, is there going to be portions of this diagram dealing with mammals, plants, benthic organisms etc. If not currently, should there be place holders? This page should have some text to describe what’s going on in the diagram; for example, going through Steps It might be worth considering having separate pages for each of the steps (rather than including it all in a single crowded page).” So in response to Kris’s comment, I mocked up the next 3 slides, just so we can visualize how it might look like. Next step: identify someone who is responsible for fixing this issue. How do we determine the health of each attribute? Assessing the health of any one attribute can be a complicated process. Conceptual models, such as the one depicted above, can help us assess the health of each attribute by allowing us to identify important health indicators, their trends over time, and the types of drivers that cause changes in the health of the estuary.

Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Concept  Living Resources How do We Determine the Health of Living Resources? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED How do we determine the health of each attribute? Water Habitat Living Resources Ecological Processes Stewardship Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Identify Key Attributes Water Habitat Living Resources Ecological Processes Stewardship STEP 1 STEP 2 Food Web Base Fish Birds Define Focal Categories Phytoplankton Zooplankton Resident Bay Group #1 Group #2 Mammals Bacteria Submerged Plants Migratory Benthic Invertebrates - fix this. Grayed out boxes – mammals, bacteria, plants, etc. How do we determine the health of each attribute? Step 1: Identify Key Attributes Identify attributes that comprise the Bay’s integrity and reflect its health. Here, living resources is the attribute that is discussed. Step 2: Define Focal Categories Identify and define important, distinctive categories within each attribute. Here, those are identified as the food web base, fish, birds, mammals, bacteria, and submerged plants.

Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Concept  Living Resources How do We Determine the Health of Living Resources? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED How do we determine the health of each attribute? Water Habitat Living Resources Ecological Processes Stewardship Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Describe Health Indicators Species Composition (e.g. native v. exotic) Species Distribution Species Abundance STEP 3 STEP 4 Visualize Trends Native Richness over time Area occupied over time Abundance over time How do we determine the health of each attribute? Step 3: Describe Health Indicators Identify measurable health indicators that are meaningful to the public, consistent with scientific understanding of the ecosystem, and can be measured with existing, reliable data. Step 4: Visualize Trends Identify and depict trends over time.

Identify & Evaluate Drivers
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Concept  Living Resources How do We Determine the Health of Living Resources? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED How do we determine the health of each attribute? Water Habitat Living Resources Ecological Processes Stewardship STEP 5 Water (Quantity) Habitat loss Predation Water (Quality) Food Web Entrainment Identify & Evaluate Drivers How do we determine the health of each attribute? Step 5: Identify and Evaluate Drivers Identify and evaluate the causes of changes in the health of living resources in the estuary. This Portal will not initially identify and evaluate drivers.

What is Being Done to Restore California’s Estuaries?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Restoration What is Being Done to Restore California’s Estuaries? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED What’s being done to restore California’s estuaries?? SF Estuary Restoration Other Estuaries Intro slide for this question. You would get here by clicking on the same question on the main page. Only link that would work would be SF Estuary link. For the moment, this page would link to Erin’s stewardship work. What’s being done to restore them? The initial focus of the Portal is on an evaluation of the restoration activities for the SF Estuary. Information on restoration activities in other California estuaries is under development.

What Laws, Regulations, and Policies Protect California’s Estuaries?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Protection What Laws, Regulations, and Policies Protect California’s Estuaries? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED What laws, regulations, and policies protect California’s estuaries? SF Estuary Protection Other Estuaries Intro slide for this question. You would get here by clicking on the same question on the main page. Only link that would work would be SF Estuary link. For the moment, this page would link to Erin’s stewardship work. What’s being done to protect them? [Erin Aquino-Carhart’s information]

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  Eco Health  Estuaries  Solution How Can I Be Part of the Solution? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED How can I be part of the solution? SF Estuary Solutions Other Estuaries Intro slide for this question. You would get here by clicking on the same question on the main page. For the moment, this page would like to “Friends of ….” page How can I be part of the solution? Information about how you can get involved with restoring and protecting the SF Estuary is currently available. Information on activities in other California estuaries is under development.

Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco What is the San Francisco Bay Estuary, and Why is it Important? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED How can I be part of the solution? (content in development) How healthy is the SF Estuary? What’s being done to protect the SF Estuary? What are issues of concern in the SF Estuary? (content in development) What is being done to improve the health of the SF Estuary? What is the SF Estuary, and why is it important? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED What is the SF Estuary, and why is it important? How healthy is the SF Estuary? What’s being done to protect the SF Estuary? How can I be part of the solution? < > What is the San Francisco Bay Estuary? Like all estuaries, the San Francisco Bay Estuary (SF Estuary) is a wide river mouth flooded by the sea. Salty water brought in by the tides through the Golden Gate mixes with fresh water carried into the estuary from the surrounding rivers. The estuary is fed by two of California’s largest rivers, the Sacramento River and the San Joaquin River. The two rivers meet in the Delta, about 40 miles northeast of San Francisco. The water then flows into Suisun Bay, through the Carquinez Strait into San Pablo Bay, and finally into San Francisco Bay itself. These three bays and five others--Honker, Richardson, San Rafael, San Leandro, and Grizzly--make up the rest of the estuary. Why is it important? Ecology The continual mixture of salt and fresh water provides the foundation of the ecological richness of the estuary, which provides food and shelter for more than 750 species of plants, fish, and other wildlife including several endangered or threatened ones. Two-thirds of the State’s salmon pass through the estuary on their way upstream to lay their eggs. Hundreds of thousands of birds migrating between the Arctic and South America, about half of the Pacific Flyway migratory water birds, use the wetlands, mudflats, and shoreline areas in the estuary to rest and feed. Over a million birds visit the area each year. Other mammals such as harbor seals and various reptiles make their home in the estuary too. Economics The region attracts and supports a vibrant economy. The visually striking shorelines and beautiful bays and beaches make it one of the country’s most desirable places to live as well as a global tourist destination for both water and land recreation including boating, fishing, surfing, swimming, hiking, and biking. The estuary also supports other parts of the regional economy including commercial and recreational fisheries, diverse agricultural production that helps feed California and the rest of the world, three large commercial ports, and important water supply infrastructure. The SF Estuary provides drinking water to upwards of 30 million Californians and irrigation water to 4.5 million acres of farm land. Even though the SF Estuary is such a valuable resource, it is confronted with a broad range of challenges. Knowledge about the SF Estuary is developing at a rapid pace to confront those challenges, and a list of critical documents is available for interested readers. [links to what?] EPA flyovers and special sites – use progression starting at headwaters and move through the estuary to show both the scenic and man-made, Cache Slough, Suisun Marsh, Yolo Bypass, Yosemite (tulomne), Hetch Hetchy, Aquaduct… You would get to this slide from clicking on the SF Estuary from the “Where are CA’s estuaries slide?” Text Reference: In response to Kris’s comment, I was thinking that the very first slide would be the general what are estuaries and why are they important? slide, and then this one would be specific to SF. Each estuary the portal eventually covers would have their own intro page like this.

How healthy is the SF Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health How Healthy is the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED Ecological Processes Water How healthy is the SF Estuary? Living Resources Habitat Stewardship Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED How healthy is the SF Estuary? Water Habitat Living Resources Ecological Processes Stewardship Water Habitat Living Resources Ecological Processes Stewardship Sliding thing would be clickable too. Need photos here. Links: living resources would take you to the next slide. Clicking on water would take you to slide 33. “The State of the Bay report” link would take you to How healthy is the SF Estuary? Just as the health of the human body is dependent upon the health of its parts – the brain, the bones, the heart – so too does the health of the SF Estuary depend on the well-being of its parts. Those parts, as defined by the authors of The State of the San Francisco Bay Report, are water, habitat, living resources, ecological processes, and stewardship. The initial focus of this Portal is on a robust evaluation of Living Resources and Water. The remaining key attributes are under development.

What are SF Estuary living resources?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources What are SF Estuary Living Resources? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED Fish Phytoplankton What are SF Estuary living resources? Zooplankton Benthic Organisms Birds Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management < > QUESTIONS ANSWERED What are SF Estuary living resources? Phytoplankton Zooplankton Benthic Organisms Fish Birds Pictures of living resources that you can click on to get to details - You would get to this slide by clicking on living resources from previous slide - Pictures in box would be links to phytoplankton, zooplankton, etc. pages too (the questions from the box are links too). - need these photos. What are SF Estuary living resources? Healthy estuaries support diverse and resilient populations of living resources, dominated by native species and broadly distributed across different habitats. These living resources include birds, fish, benthic organisms, and the base of the food web — phytoplankton, and zooplankton. How do you evaluate the health of living resources? To evaluate the health of living resources, scientists have identified health indicators for the SF Estuary. Learn more about the most recent evaluation of the state of the SF Bay. (link to SOTB Report 2011)

What are Phytoplankton, and Why are They Important?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Phytoplankton What are Phytoplankton, and Why are They Important? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED Where are phytoplankton in the food web? How and where are phytoplankton sampled? What are SF Estuary phytoplankton trends? What are issues of concern in the SF Estuary? (content in development) What is being done to improve the health of phytoplankton in the SF Estuary? What are phytoplankton, and why are they important? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED What are phytoplankton, and why are they important? How and where are they monitored in the SF Estuary? What are their trends in the SF Estuary? What’s being done about it? What are phytoplankton? Phytoplankton are small organisms that can be found floating in most water bodies. Like plants, they are primary producers, meaning that they convert light energy from the sun and carbon dioxide into the living matter of their bodies through photosynthesis. Phytoplankton from the SF Estuary fall into four broad categories: cyanobacteria, diatoms, green algae, and various flagellate groups. Why are they important? Phytoplankton are the foundation of the aquatic food web. They feed everything from microscopic, animal-like zooplankton to multi-ton whales. Small fish and benthic organisms also graze on these creatures, and then those smaller animals are eaten by bigger ones. Changes in phytoplankton populations in the SF Estuary can have reverberations that are felt throughout the food web. Phytoplankton can also affect elements of water quality, including pH, Dissolved oxygen, Color, taste, and odor, and Algal blooms (toxic and non-toxic). Monitoring changes in phytoplankton can be useful in assessing water quality trends. It is important to note, however, that because of the transient and free-ranging nature of phytoplankton, their use as water quality indicators is limited and should be interpreted in conjunction with physiochemical and other biological data. Learn more about how phytoplankton are measured in the SF Estuary. - For links in blue, either need to create these pages as part of the water quality slides and these would link to them or say “Content in Development” “Learn more “ links to phytoplankton measuring page (next slide) Tiffany’s Notes: - For what it’s worth, prefers smaller questions answered box. Will find phytoplankton photos for us. (next week)

How and Where are Phytoplankton Monitored in the SF Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Phytoplankton  Monitored How and Where are Phytoplankton Monitored in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What are phytoplankton, and why are they important? How and where are they monitored in the SF Estuary? What are their trends in the SF Estuary? What’s being done about it? QUESTIONS ANSWERED Where are phytoplankton in the food web? How and where are phytoplankton sampled? What are SF Estuary phytoplankton trends? What are issues of concern in the SF Estuary? (content in development) What is being done to improve the health of phytoplankton in the SF Estuary? What are phytoplankton, and why are they important? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Phytoplankton Monitoring Stations How and where are phytoplankton monitored? Phytoplankton are monitored as part of the IEP’s Environmental Monitoring Program (EMP) by the California DWR’s Phytoplankton Study. Changes in their densities and distribution are documented in the SF Estuary, from San Pablo Bay east through the upper Estuary. 22 sites are currently sampled monthly. They represent a wide range of habitats of varying sizes and physical conditions, including different types of water quality. Sites range from narrow, freshwater channels in the Delta to broad, estuarine bays. Phytoplankton density estimates are calculated in two ways, either by counting phytoplankton cells under a microscope or by measuring concentrations of chlorophyll a in the water. Scientists can use chlorophyll a, the most common green pigment in all photosynthetic organisms, as a proxy measure of phytoplankton biomass. Chlorophyll a is relatively easy to measure and is a fairly accurate estimate of phytoplankton volume. In the animation above, the size of the monthly mean chlorophyll measurements is represented by the relative size of the circles. Learn more about the methods used to measure phytoplankton. Where are the data? More information on phytoplankton monitoring can be found in the Phytoplankton Study Meta Data. Tiffany’s Notes: - Nothing to change about this slide. Links: - IEP links to - Environmental Monitoring Program links to “Learn more . . “ links to the D1641 report – phytoplankton methods content (34 North already has this document.) Meta Data links to Other notes: - Don’t say “click here” underneath the animation. Just have the “Start Animation” be a link or button.

What are SF Estuary Phytoplankton Trends?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Phytoplankton  Trends What are SF Estuary Phytoplankton Trends? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What are phytoplankton, and why are they important? How and where are they monitored in the SF Estuary? What are their trends in the SF Estuary? What’s being done about it? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management What are SF Estuary phytoplankton trends? Phytoplankton populations in the SF Estuary have been decreasing since 1985, particularly in Suisun Bay and in parts of the Central Delta. Larger phytoplankton, including some kinds of diatoms, are an important food source for the zooplankton that are favored by native fish, including delta smelt. In many parts of the SF Estuary, diatoms have either decreased or larger, single-celled phytoplankton have been replaced by smaller, chain-forming species that are not as nutritious for fish. Cyanobacteria, some of which can produce toxins that make humans and pets sick, have been increasing in portions of the SF Estuary. Learn more about phytoplankton trends in the SF Estuary. Chlorophyll a Trends ( ) This graph depicts the downward trend in chlorophyll a concentrations from 1975 to 2011 in 10 regions of the SF Estuary averaged by year. Text for this chart. Text for this chart Text for this chart, Phytoplankton Species Composition Trends Tiffany’s additional notes: She divided the sampled stations into regions (see left graph) and said, “I haven’t figured out a way to really weight the regions by number of stations sampled, but in most regions, not more than 4 stations are sampled, and most are just one or two in recent years, so I’m not too concerned about it. The first graph has all the data graphed by region (all data from all stations grouped into their respective regions and averaged by year). I thought it still looked kind of cluttered, and the high values from the South Delta sites were masking the trends in other regions. So the remaining graphs are parsed by broader categories for each region (see next slide). I think these graphs would be more useful; since there are only 2 or 3 data lines per graph, the overall trends are easier to see.” (Emily’s note: I have the Excel file with this data and these graphs.) “I think the pie charts are good on an annual basis, but only when coupled with a monthly/seasonal bar graph for that year so that trends in the phytoplankton community are clearly visible. For example, you could have two regions with similar percentages of diatoms (say, 60%), but in one region, that percentage is driven by similar numbers of diatoms spread out over several months, whereas the other region the percentage is driven by a single large bloom. Pie charts won’t reveal this but the bar graphs will. I don’t have time to put these graphs together until next week.” Idea is that clicking on the left most graph would take you to the next slide. Clicking on the pie charts would take you to a slide that shows them in more detail with the bar graphs that Tiffany suggest. Questions to Discuss: Which graphs do we want to use? All of the ones she’s made up, plus the additional pie charts? Emily’s Notes: If we keep the pie charts, each one should have a sentence or two clarifying what is depicted. Even if we go with stacked bar graphs, we’ll still need the text clarifying what they depict. I also think that Hildie’s notes about the graphs below are helpful, and we should go over them with the rest of the group and 34 North. Hildie’s Notes: Instructions for graphs. Chlorophyll a trends – line graph – do not include separate lines for each station. Instead, group data by regions: Suisun, South Delta, North Delta, Central Delta so there will be FOUR lines on the graph (May – Nov – monthly chl a data); Add 10 ug/L line ( label: “zooplankton growth limitation”). Source: Kimmerer et al 2012 Species composition: Need to get vote on whether to display pie charts (as created by 34 North) or stacked bar graphs. Two stacked bar graphs. Phytoplankton abundance over time for 1) Suisun and 2) Delta [data points are annual means for all stations surveyed in each region]. Begin Stacked bar graphs with phytoplankton classes, including the top 6 or 7 categories and lumping everything else: Cyanobacteria, centric diatoms, pennate diatoms, cryptophyceae, haptophytes, unknown and Other (everything else)] Source: Lehman 1996, Lehman 2000, Glibert 2010 [If there is time, also graph seasonal species composition over time for each region – Suisun, Sac R & SJ River. These graphs will be available by clicking on a link: for more detailed information] Pie chart – if we go with this, can we go back further? Note: need to keep % to no more than 2 significant places. Need to specify region – do these graphs use all stations? Can we do separate for Suisun and Delta? Also: - In graphs, think you should keep the same colors for each species in each graph (the same shade of green or whatever for cyanobacteria, etc.)

What are SF Estuary Phytoplankton Trends?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Phytoplankton  Trends What are SF Estuary Phytoplankton Trends? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What are phytoplankton, and why are they important? How and where are they monitored in the SF Estuary? What are their trends in the SF Estuary? What’s being done about it? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Chlorophyll a Trends ( ) This graph depicts the downward trend in chlorophyll a concentrations from 1975 to 2011 in 10 regions of the SF Estuary averaged by year. Decreasing chlorophyll a concentrations means less phytoplankton available for zooplankton, benthic organisms, and fish to eat. Chlorophyll a Trends ( ) - Upstream Chlorophyll a Trends ( ) – Mid-Delta Chlorophyll a Trends ( ) – Rivers Chlorophyll a Trends ( ) - Downstream Chlorophyll a Trends ( ) – Low Salinity Zone This graph depicts the downward trend in chlorophyll a concentrations averaged by year over time in the South Delta and the stable trend in concentrations in the North Delta. This graph depicts the downward trend in chlorophyll a concentrations over time in the central Delta averaged by year and the fluctuations in concentrations in the eastern Delta This graph depicts the downward trend in chlorophyll a concentrations over time in the lower Sacramento and San Joaquin Rivers averaged by year. There has been a recent upward trend since 2011. This graph depicts the downward trend in chlorophyll a concentrations averaged by year over time in areas downstream of the Delta. This graph depicts the recent upward trend in chlorophyll a concentrations in the low salinity zone. Data are averaged by year over time. Tiffany’s additional notes: She divided the sampled stations into regions (see top graph) and said, “I haven’t figured out a way to really weight the regions by number of stations sampled, but in most regions, not more than 4 stations are sampled, and most are just one or two in recent years, so I’m not too concerned about it. The first graph has all the data graphed by region (all data from all stations grouped into their respective regions and averaged by year). I thought it still looked kind of cluttered, and the high values from the South Delta sites were masking the trends in other regions. So the remaining graphs are parsed by broader categories for each region. I think these graphs would be more useful; since there are only 2 or 3 data lines per graph, the overall trends are easier to see.” (Emily’s note: I have the Excel file with this data and these graphs.) “I think the pie charts are good on an annual basis, but only when coupled with a monthly/seasonal bar graph for that year so that trends in the phytoplankton community are clearly visible. For example, you could have two regions with similar percentages of diatoms (say, 60%), but in one region, that percentage is driven by similar numbers of diatoms spread out over several months, whereas the other region the percentage is driven by a single large bloom. Pie charts won’t reveal this but the bar graphs will. I don’t have time to put these graphs together until next week.” Questions to Discuss: Which graphs do we want to use? All of the ones she’s made up, plus the additional pie charts? How to arrange these on the page? Emily’s Notes: If we keep the pie charts, each one should have a sentence or two clarifying what is depicted. Even if we go with stacked bar graphs, we’ll still need the text clarifying what they depict. I also think that Hildie’s notes about the graphs below are helpful, and we should go over them with the rest of the group and 34 North. Hildie’s Notes: Instructions for graphs. Chlorophyll a trends – line graph – do not include separate lines for each station. Instead, group data by regions: Suisun, South Delta, North Delta, Central Delta so there will be FOUR lines on the graph (May – Nov – monthly chl a data); Add 10 ug/L line ( label: “zooplankton growth limitation”). Source: Kimmerer et al 2012 Species composition: Need to get vote on whether to display pie charts (as created by 34 North) or stacked bar graphs. Two stacked bar graphs. Phytoplankton abundance over time for 1) Suisun and 2) Delta [data points are annual means for all stations surveyed in each region]. Begin Stacked bar graphs with phytoplankton classes, including the top 6 or 7 categories and lumping everything else: Cyanobacteria, centric diatoms, pennate diatoms, cryptophyceae, haptophytes, unknown and Other (everything else)] Source: Lehman 1996, Lehman 2000, Glibert 2010 [If there is time, also graph seasonal species composition over time for each region – Suisun, Sac R & SJ River. These graphs will be available by clicking on a link: for more detailed information] Pie chart – if we go with this, can we go back further? Note: need to keep % to no more than 2 significant places. Need to specify region – do these graphs use all stations? Can we do separate for Suisun and Delta? Also: - In graphs, think you should keep the same colors for each species in each graph (the same shade of green or whatever for cyanobacteria, etc.)

Phytoplankton Species Composition Trends
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Phytoplankton  Trends What are SF Estuary Phytoplankton Trends? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What are phytoplankton, and why are they important? How and where are they monitored in the SF Estuary? What are their trends in the SF Estuary? What’s being done about it? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Text for this chart. Text for this chart Text for this chart, Phytoplankton Species Composition Trends Tiffany’s additional notes: She divided the sampled stations into regions (see top graph) and said, “I haven’t figured out a way to really weight the regions by number of stations sampled, but in most regions, not more than 4 stations are sampled, and most are just one or two in recent years, so I’m not too concerned about it. The first graph has all the data graphed by region (all data from all stations grouped into their respective regions and averaged by year). I thought it still looked kind of cluttered, and the high values from the South Delta sites were masking the trends in other regions. So the remaining graphs are parsed by broader categories for each region. I think these graphs would be more useful; since there are only 2 or 3 data lines per graph, the overall trends are easier to see.” (Emily’s note: I have the Excel file with this data and these graphs.) “I think the pie charts are good on an annual basis, but only when coupled with a monthly/seasonal bar graph for that year so that trends in the phytoplankton community are clearly visible. For example, you could have two regions with similar percentages of diatoms (say, 60%), but in one region, that percentage is driven by similar numbers of diatoms spread out over several months, whereas the other region the percentage is driven by a single large bloom. Pie charts won’t reveal this but the bar graphs will. I don’t have time to put these graphs together until next week.” Questions to Discuss: Which graphs do we want to use? All of the ones she’s made up, plus the additional pie charts? How to arrange these on the page? Emily’s Notes: If we keep the pie charts, each one should have a sentence or two clarifying what is depicted. Even if we go with stacked bar graphs, we’ll still need the text clarifying what they depict. I also think that Hildie’s notes about the graphs below are helpful, and we should go over them with the rest of the group and 34 North. Hildie’s Notes: Instructions for graphs. Chlorophyll a trends – line graph – do not include separate lines for each station. Instead, group data by regions: Suisun, South Delta, North Delta, Central Delta so there will be FOUR lines on the graph (May – Nov – monthly chl a data); Add 10 ug/L line ( label: “zooplankton growth limitation”). Source: Kimmerer et al 2012 Species composition: Need to get vote on whether to display pie charts (as created by 34 North) or stacked bar graphs. Two stacked bar graphs. Phytoplankton abundance over time for 1) Suisun and 2) Delta [data points are annual means for all stations surveyed in each region]. Begin Stacked bar graphs with phytoplankton classes, including the top 6 or 7 categories and lumping everything else: Cyanobacteria, centric diatoms, pennate diatoms, cryptophyceae, haptophytes, unknown and Other (everything else)] Source: Lehman 1996, Lehman 2000, Glibert 2010 [If there is time, also graph seasonal species composition over time for each region – Suisun, Sac R & SJ River. These graphs will be available by clicking on a link: for more detailed information] Pie chart – if we go with this, can we go back further? Note: need to keep % to no more than 2 significant places. Need to specify region – do these graphs use all stations? Can we do separate for Suisun and Delta? Also: - In graphs, think you should keep the same colors for each species in each graph (the same shade of green or whatever for cyanobacteria, etc.) Pie charts showing annual species composition change with bar graphs that show seasonal change (Tiffany Brown’s idea, see note section below) would go here.

What are Zooplankton, and Why are they Important?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Zooplankton What are Zooplankton, and Why are they Important? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management 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) - Insert a page for copepods and rest (?)

How and Where are Zooplankton Monitored in the SF Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Zooplankton  Monitored How and Where are Zooplankton Monitored in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management 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.

What are SF Estuary Zooplankton Trends?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Zooplankton  Trends What are SF Estuary Zooplankton Trends? …………………………………..………………………………………………………………………………………………………………………………..……… 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 ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management 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? 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

What are SF Estuary Zooplankton Trends? More information
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Zooplankton  Trends  More What are SF Estuary Zooplankton Trends? More information …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management 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).

< > What are Benthic Organisms, and Why are They Important?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Benthics What are Benthic Organisms, and Why are They Important? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED Where are benthics in the food web? How and where are benthics measured? What are SF Estuary benthic trends? What are issues of concern in the SF Estuary? (content in development) What is being done to improve the health of benthics in the SF Estuary? What are benthic organisms, and why are they important? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED What are benthic organisms, and why are they important? How and where are they monitored? What are their trends in the SF Estuary? What’s being done about it? < > Pictures of benthic organisms that you can click on to get to details Links: - Phytoplankton – link to “what are phytoplankton page” - zooplankton – link to “What are zooplankton page” - “Learn more “ – link to benthic measuring page (next slide) Photo References: Photos are from – Benthic BioGuide SOTB 2011 Living Resources – Invertebrate Section– information reference What are benthic organisms? Benthic organisms are small animals that live in or on the bottom of water bodies. They include a number of familiar species such as clams, shrimp, and crabs and other less recognized ones including segmented and unsegmented worms, various crustaceans, and aquatic insects. Some of these invertebrates — they have no backbone — live in or on the soft mud of the Estuary, while others attach themselves to rocks and other hard surfaces. Many benthic organisms are filter feeders. They pump immense volumes of water through their bodies or through holes they have burrowed in the mud in order to catch food suspended in the water. Others graze on food they find in and on the surface of the bottom. Both types of benthics eat plankton, phytoplankton and zooplankton, other benthic organisms, and/or decaying organic debris washed in from the surrounding watershed. Why are they important? Benthic organisms are important part of the estuarine food web. They consume and are consumed by other creatures. Every winter during low-tides, thousands of migrating shorebirds feast themselves upon uncovered clams, crabs, and worms found in the mudflats. Humans, as well, take advantage of the low-tides to harvest their own feast. Historically, bay shrimp supported a large commercial fishery in the Bay, and California’s commercial crab fishery still depends upon crabs that spend the first two years of their life growing in the SF Estuary. Changes in benthic organisms’ populations also can be indications of larger changes in the physical conditions of the SF Estuary, including alterations in freshwater inflows, salinity, and sediment composition. These changes can then affect other living things and general water quality. More research is needed to better understand the role of these bottom dwellers in the larger estuarine ecosystem. Learn more about how benthic organisms are measured in the SF Estuary.

How and Where are Benthic Organisms Measured in the SF Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Benthics  Monitored How and Where are Benthic Organisms Measured in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED Where are benthics in the food web? How and where are benthics measured? What are SF Estuary benthic trends? What are issues of concern in the SF Estuary? (content in development) What is being done to improve the health of benthics in the SF Estuary? What are benthic organisms, and why are they important? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Benthic Organism Monitoring Stations QUESTIONS ANSWERED What are benthic organisms? How and where are they monitored? What are their trends in the SF Estuary? What’s being done about it? How and where are benthic organisms monitored? Benthic organisms are monitored as part of the IEP’s Environmental Monitoring Program (EMP) by the California DWR’s Benthic Organisms Study. Changes in their composition, abundance, density, and distribution are documented within the SF Estuary, from San Pablo Bay east through the upper Estuary to the mouths of the Sacramento, Mokelumne, and San Joaquin Rivers. Ten sites are currently sampled. Because different benthic species live in different parts of the Estuary, the sites represent a wide range of habitats of varying sizes and physical conditions, including different types of salinity and sediment composition. Sites range from narrow, freshwater channels in the Delta to broad, estuarine bays. Samples are collected monthly using a hydraulic winch and Ponar dredge. From 1975 to 1979, biannual sampling was conducted in late spring and fall. Monthly sampling started in June 1980 and ended in October Samples were collected quarterly from October 2003 through October 2005, after which monthly sampling was resumed. Sediment samples are also collected at each site for sediment analysis. Learn more about the methods used to measure benthic organisms. Where are the data? Benthic Dictionary - list of all species of macro-benthic organisms identified and the total number of individuals counted Sediment composition data is provided to the program by the DWR Soils Laboratory in the form of monthly written reports. These data are then entered monthly by DWR Personnel into EMP’s benthic database. For more information regarding the sediment data please contact Heather Fuller. More information on benthic organism monitoring can be found in the study Meta Data and the Benthic BioGuide. Links: - IEP links to Environmental Monitoring Program links to “Learn more “ links to D1641 report –benthic methods content Benthic Dictionary links to Heather Fuller links to Meta Data links to Benthic BioGuide links to

Graph from monitoring data. Show Asian clam, other crabs, etc.?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Benthics  Trends What are Benthic Organism Trends in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED Where are benthics in the food web? How and where are benthics measured? What are SF Estuary benthic trends? What are issues of concern in the SF Estuary? (content in development) What is being done to improve the health of benthics in the SF Estuary? What are benthic organisms, and why are they important? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Where are their trends? There have been important changes in benthic organism abundance (how many?) and species diversity (what types?) in the SF Estuary since monitoring began in Both shrimp and crab abundances have increased during the last 15 years, and over 85 percent of those populations are native species. Several invasive benthic species have also been introduced to the Estuary. Most notably is the Asian clam that was introduced to the environment in the eighties, probably as larvae in ballast water used to keep ships balanced in the ocean. In any estuary, environmental conditions have to be right in order for an introduced species to become an invasive one, and the conditions in the SF Estuary have been ideal for the clams. Since their introduction, they have covered large swaths of the bay’s bottoms, displacing other benthic organisms and feeding on phytoplankton and zooplankton. Their effects on the estuarine food web are still being studied, but phytoplankton abundances have declined since the mid-eighties. Such declines may have negative impacts on the zooplankton that eat these phytoplankton and the fish that feed on the zooplankton. QUESTIONS ANSWERED What are benthic organisms, and why are they important? How and where are they monitored? What are their trends in the SF Estuary? What’s being done about it? Benthic Organism Trends ( ) Graph from monitoring data. Show Asian clam, other crabs, etc.? Particularly important years: Before mid-eighties (1977 or so), Around mid-eighties (1986 or 87), Mid-nineties (1995 or so) More recently (2010 or 2011) Abundance of Shrimp in the SF Bay ( ) Abundance of Crabs in the SF Bay ( ) Notes: For making our own graphs, focus on the decline in Diatoms, chlorophyll a, and Eurytemora and the increases in Clams, Limnoithona, Toxic Algae, submerged plants… from 1980 to current too. References: - shrimp and crab graphs from SOTB - Cohen and Carlton 1995 - Peterson, H.A. and M. Vayssières Benthic assemblage variability in the upper San Francisco Estuary: A 27-year retrospective. San Francisco Estuary and Watershed Science 8(1). Overall crab abundance has generally increased over time in the SF Bay. Overall shrimp abundance has increased over time in the SF Bay.

Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Living Resources  Fish What are Types of Fish in the SF Estuary, and Why are They Important? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED What are the types of fish in the SF Estuary, and why are they important? How and where are fish surveyed in the SF Estuary? What are SF Estuary fish trends? Or How healthy are fish in the SF Estuary? What’s being done to protect them ? How can I be a part of the solution? QUESTIONS ANSWERED How healthy are fish in the SF Estuary? How do we measure fish health? How are we improving fish health? How do we track improvements of fish health? What are the drivers of fish health? How can I be part of the solution? < > Insert slide show with clickable images of the different types of fish. Non-native What are the types of fish in the SF Estuary? The diverse habitats of the SF Estuary support over 100 native and non-native fish. The region is home to resident fish, Fish that, for the most part, complete (or can complete) their entire life cycle in or very close to the estuary. marine fish that lay their eggs (spawn) and/or rear in bay habitats, and migratory fish that must transition between freshwater and marine habitats beyond the Estuary to complete their life cycle. (link: resident species, link: bay species, link: migratory species, respectively) Pressures on California’s native fish are typified in the Estuary, including diversion of freshwater for human uses, deterioration of water quality, extensive habitat alteration and degradation, introduced species, and climate change. Some of the area’s most abundant fisheries have either been driven to extinction or are threatened or endangered. Why are they important? Fish in the SF Estuary are important for economic, recreational, and ecological reasons. Economically important fish include Chinook salmon and Pacific herring. Sport fish like striped bass and sturgeon are popular among local and tourist fishermen. Other ecologically important fish such as delta smelt are also present. Because fish populations are responsive to environmental conditions in the Estuary, measuring their populations can be useful for monitoring changes within the Estuaryin these conditions. Also, a large, diverse fish community that is distributed broadly throughout the Estuary and dominated by native species is a good sign of a healthy estuary. Is rear jargon? Kinda. Need consistency with names (resident vs pelagic, marine vs bay) AWS - NEED to resolve the categories, sending with this

Insert map with distribution
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Living Resources  Fish  Resident What are the Types of Fish in the SF Estuary, and Why are They Important? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What are types of fish in the SF Estuary, and why are they important? (this top question link would take you back to the main fish summary page. The rest link you to their specific pages.) What are resident fish? What are bay fish? What are migratory fish? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management What are resident fish? Many fish use the SF Estuary for only particular parts of their life cycle — as juvenile rearing ground or as migratory corridors. Some species, however, reside here for all or most of their lives. These fish includes endemic species (those found nowhere else in the world) like Delta smelt and Sacramento splittail. Because they spend most of their lives within the Estuary, these species are particularly susceptible to changes in estuarine environment. The following species were chosen as indicator species of resident fish health. Delta Smelt Indicator: estuarine dependent, short-lived, open water resident Delta smelt (Hypomesus transpacificus) are found only in the SF Estuary’s Delta and northern bays. They are protected as an endangered species under state and federal law. Delta smelt typically live one year, spawning in freshwater and rearing for several months in brackish waters.. They are found primarily in brackish, tidal and open water habitats of the Estuary. [link to appropriate habitat] [Picture: need link. All of these pictures would be clickable] Longfin Smelt Indicator: short lived, deep water? Longfin smelt (Spirinchus thaleichthys) are distantly related to Delta smelt. They are found in estuaries and coastal lakes from the SF Estuary up the Pacific Coast to Alaska. The species is listed as threatened under the California Endangered Species Act. They enter freshwater briefly to spawn and migrate to brackish or marine environments to rear [link to brackish open water habitat]. They are found primarily in deep open water environments, where they feed on zooplankton. These fish are presented as indicators of resident fish health because they represent a short-lived species dependent completely on the estuary for their survival. [Picture: need link] Sacramento Splittail Indicator: floodplain indicator? Sacramento splittail (Pogonichthys macrolepidotus) are an endemic minnow species that spawn and rear in floodplains and shallow freshwater marsh environments [link to habitat] before migrating to shallow freshwater and brackish environments as juveniles. Splittail are a popular sport fishery and are important prey for fish and bird predators in the shallow waters of the marshes [link to habitat]. [Picture: need link] Young Striped Bass (Non-native) (Migratory) Indicator: estuarine dependent juveniles Striped bass (Morone saxatilis) were introduced to the SF Estuary from the Atlantic in A sought after sportfish, these predators are an important indicator of estuarine conditions. Although adults migrate between fresh and saltwater habitats, juvenile striped bass (age 0) are estuarine dependent so have been included in the resident fish section. A sought after sportfish, these predators are an important indicator of estuarine conditions. “Declines in the striped bass population were the driving force for changes in water management operations in Sacramento and San Joaquin Rivers and the Delta in the 1980s. Until the mid-1990s, State Water Resources Control Board-mandated standards for the estuary were aimed at protecting larval and juvenile striped bass.” (Ecological Scorecard reasoning for including striped bass) [link to open-water brackish habitat] [Picture: need link] Learn more about how resident fish are surveyed. (link to resident fish monitoring page) Images of species Insert map with distribution for each species? Notes: - You would get to this page by clicking on the blue resident fish words on the previous slide. Same thing for the others. Then once you are on this page, you can either click on the bold first sentence of the “Questions Answered” box and go back to the main summary page (the first page of this powerpoint) or you can click on the other questions and go to their pages. Add images. Images would be clickable. May need some sort of image at top? Although I like it like this. May need to add threadfin shad to this b/c we display information about its trends on the resident trend page. Let’s get a photo of YOY if keeping in this section

Distribution map of species?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Living Resources  Fish  Marine/Bay What are the Types of Fish in the SF Estuary, and Why are They Important? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What are types of fish in the SF Estuary, and why are they important? What are resident fish? What are bay fish? What are migratory fish? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management What are bay/marine fish? Fish in the SF Estuary represent a mixture of marine, brackish, and freshwater species. They are found along a salinity gradient from the Delta (largely freshwater) to the Central and South Bays (marine habitats). Here we consider marine fish to be those that are ocean going fish that use the estuary (either obligately or non-obligately) as an important rearing habitat. There are more than 100 species living in the San Francisco Bay. The Estuaries Portal initially presents four species that capture a broad assemblage of ecological diversity and life history traits as representatives of bay fishes. Pacific Herring Indicator: marine open water, (winter/spring?or flatfish?) Pacific herring (Clupea pallasii) spawn in San Francisco (Central) and Richardson Bays from October through April. They live in shallow estuarine substrates and gradually migrate to deeper estuarine waters and finally to the ocean as they mature. Their populations support a commercial roe fishery, and they are important prey for marine fish and bird predators. [Picture here Northern Anchovy Northern anchovy (Engraulis mordax nanus ) are an important forage fish for bird and fish predators in the SF Estuary and along the California coast. They historically migrated into the brackish waters of Suisun Bay, but their range within the estuary appears to have shifted (Kimmerer 2006). [Picture here: Starry Flounder Indicator: Upper estuary fish Starry flounder (Platichthys stellatus) are bottom dwelling predatory fish that are dependent on estuarine environments for rearing. Young flounder rear in the Estuary before migrating back into the ocean. Starry flounder are a sport fishery in California. [pictures here: English Sole Pacific Halibut Shiner Perch Indicator: marine open water, (spring/summer? Or surfperches?) Learn more about how bay fish are surveyed. (link to bay fish monitoring page) Kimmerer, W.J Response of anchovies dampens effects of the invasive bivalve Corbula amurensis on the San Francisco Estuary foodweb. Marine Ecology Progress Series 324: 207–218. [where to put this reference?] Images of species Distribution map of species? Notes: Add images Fix text at top. Where are we putting references? Resolve marine/bay issue. Reference: Kimmerer, W.J Response of anchovies dampens effects of the invasive bivalve Corbula amurensis on the San Francisco Estuary foodweb. Marine Ecology Progress Series 324: 207–218. AWS – problems with mentioning delta if we are in the bay/marine fish section.

Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Living Resources  Fish Migratory What are the Types of Fish in the SF Estuary, and Why are They Important? …………………………………..………………………………………………………………………………………………………………………………..……… What are migratory fish? Many estuarine fish migrate to habitats with different depths or salinities during their life cycles. Some fish must migrate between fresh and saltwater to complete their life cycle. Anadromous fish spawn in freshwater and rear in marine environments and must ,”Species that undergo their greatest growth at sea and which, prior to the attainment of maturity, migrate into rivers where spawning subsequently occurs.” Elliot et al whereas catadromous species spawn in marine environments and rear in freshwater. Both native and introduced fish are present in the Estuary. Many of the native and non-native anadromous fish abundance indices have declined precipitously in the latter part of the 20th century. For example, among the four formerly robust runs of Chinook salmon spawning in the Central Valley, all are classified as endangered, threatened, or species of concern. However, tThe Sacramento fall-run Chinook is still abundant enough to support sport and commercial fisheries in most years. Anadromous Fish (more info on each of these, like with the residence and bay fish sections) Chinook Salmon Chinook salmon – rest of text Steelhead Steelhead – rest of text Green and White Sturgeon Green and white sturgeon – rest of text Pacific Lamprey Pacific lamprey – rest of text Striped Bass Striped bass Bass (Non-native) (Migratory) have been important fisheries since their introductions in the late 1800s. Rest of text. Striped bass on this page and on bay page? American Shad American shad Bass (Non-native) (Migratory) have been important fisheries since their introductions in the late 1800s. Rest of text Catadromous Fish Learn more about how migratory fish are surveyed. (link to migratory fish monitoring page, also need to pick whether we’re calling it fish monitoring or fish surveying) Images of species QUESTIONS ANSWERED What are types of fish in the SF Estuary, and why are they important? What are resident fish? What are bay fish? What are migratory fish? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management EPD Notes: -Put the right images - Add text for each species. AWS- would it be a good idea to have a way of indicating native/non-natives in this list? Wait, are lamprey “catadromous”? Did I write that? Anyway, re: native/naon-native yes. Re: using Striped bass as an indicator, I think they’re better as an indicator of delta (resident) species health. Elliott, M. et al. The guild approach to categorizing estuarine fish assemblages: A global review. Fish and Fisheries, 8(3):

How and Where are Fish Surveyed in the SF Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Living Resources  Fish  Surveyed How and Where are Fish Surveyed in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED How and where are fish surveyed in the SF Estuary? (this top question link would take you back to the main fish summary page. The rest link you to their specific pages.) How are resident fish surveyed? How are bay fish surveyed? How are migratory fish surveyed? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management This would be the intro surveying/monitoring page. If you click on “How and where are fish surveyed in the SF Estuary?” on the very first slide, this is the page that link would take you to. Then you can click within this page (either on the blue in the text or in the questions on the box at the side) to get to each monitoring page (for resident, for bay, for migratory). Clicking on the bold question in the questions answered box would take you back to the summary page (the first slide in this powerpoint). Notes: What main image at top would this be? – map of all? AWS – Is there a map of all? There are so many sampling programs. Perhaps rotating maps of several? Or would we want to have link or imported info from various programs? IEP - And/or for Salmon - And/or Suisun Marsh... There are a variety of sampling programs, here are some, differences in where they sample, why they sample, and how long they’ve been operating. How and where are fish surveyed? Add generic info that applies to all three. Learn more about how resident, bay, and migratory fish are surveyed in the SF Estuary. (link to resident surveying page, bay fish surveying page, and migratory fish surveying page respectively)

Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Living Resources  Fish  Surveyed Resident How and Where are Fish Surveyed in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED How and where are fish surveyed in the SF Estuary? How are resident fish surveyed? How are bay fish surveyed? How are migratory fish surveyed? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management - Need to add Resident fish survey image at top AWS – I don’t think we should we be using Peter Moyle and Teejay’s addresses. These data (I think) are technically DWRs and supposed to be available on CDEC. It’s a bit like putting Kathy Hieb’s for the Bay Study data… Mention other sampling programs? There are so many, not just the FMWT How and where are resident fish surveyed? Resident, open-water (pelagic) fish are monitored in the Delta and Bays by the California Department of Fish and Wildlife as part of the IEP. The Fall Midwater Trawl Survey (FMWT) has sampled annually from September to December since 1967, with the exceptions of 1974 and The FMWT initially determined the relative abundance and distribution of age-0 striped bass in the estuary, but the sample data have also been used for other upper estuary open-water species, including Delta smelt, longfin smelt, threadfin shad, American shad, and Sacramento splittail. (IEP links to Many estuarine resident fish historically made use of the SF Estuary’s extensive inter-tidal and sub-tidal marshes [link to habitat]. The largest fragments of those habitats that still remain are found in Suisun Marsh, north of Suisun Bay. The aquatic community of the Marsh, the largest freshwater-brackish marsh in western North America, has been sampled monthly since 1980 by researchers at the University of California Davis. The Suisun Marsh sampling program thus provides one of the longest continuous sampling records available for any estuarine marsh system in the world. Learn more about resident fish trends. (link to resident fish trends page) Where are the data? Fall Midwater Trawl Survey (FMWT) Summary (link to FMWT Abundace Indices (link to UC Davis data available upon request. Contact TeeJay O’Rear (link to or Peter B. Moyle (link to State of San Francisco Bay Appendix F LIVING RESOURCES - Fish Indicators and Index - Technical Appendix ( link to (keep this link?)

Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Living Resources  Fish  Surveyed Bay How and Where are Fish Surveyed in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED How and where are fish surveyed in the SF Estuary? How are resident fish surveyed? How are bay fish surveyed? How are migratory fish surveyed? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Add Bay fish survey image at top – Add other data links How and where are bay fish surveyed? Since1980, the California Department of Fish and Wildlife has conducted a year-round, estuary-wide fish and mobile crustacean (shrimp and crabs) sampling program known as The Bay Study. 52 fixed sampling locations are in each of the Estuary’s main bays (South, San Francisco, San Pablo, and Suisun Bays) and the Delta. Stations are sampled monthly with two types of gear — a midwater trawl and an otter (bottom) trawl. The otter trawl collects bottom-feeding fish, shrimp, and crabs. The mid-water trawl collects open-water (pelagic) fish. Fish and mobile crustaceans are identified and counted for each net trawl. These data are reported as catch-per-unit effort based on the estimated or measured volume of water sampled in each net tow. Learn more about bay fish trends. (link to bay fish trends page) Where are the data? San Francisco Bay Study (link to State of San Francisco Bay Appendix F LIVING RESOURCES - Fish Indicators and Index - Technical Appendix ( link to (keep this link?)

Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Living Resources  Fish  Surveyed Migratory How and Where are Fish Surveyed in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED How and where are fish surveyed in the SF Estuary? How are resident fish surveyed? How are bay fish surveyed? How are migratory fish surveyed? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Migratory fish survey image at top – need to add this Add other data links How and where are migratory fish surveyed? The California Department of Fish and Wildlife (CDFW) and U.S. Fish and Wildlife Service (USFWS) have a role in monitoring salmon populations in the Central Valley. The National Marine Fisheries Service (NMFS) also has management responsibility for the fish in their marine environment. Throughout their range, salmon are protected under the Endangered Species Act. Salmon surveys are performed at various points in their life cycles including juvenile monitoring in rivers and throughout the Delta, marine harvest monitoring, and carcass and weir surveys of adults returning to spawn. Learn more about migratory fish trends. (link to migratory fish trends page) Where are the data? U.S. Fish and Wildlife Service (Stockton) - Anadromous Fish Restoration Program (link to Link to the CDFW data (spent a few minutes looking for it and couldn’t find it, add in later) State of San Francisco Bay Appendix F LIVING RESOURCES - Fish Indicators and Index - Technical Appendix ( link to (keep this link?)

What are SF Estuary Fish Trends?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Living Resources  Fish  Trends What are SF Estuary Fish Trends? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What are SF Estuary fish trends? (this top question link would take you back to the main fish summary page. The rest link you to their specific pages.) What are resident fish trends? What are bay fish trends? What are migratory fish trends? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management This would be the intro trend page. If you click on “What are SF Estuary Fish trends?” on the very first slide, this is the page that link would take you to. Then you can click within this page (either on the blue in the text or in the questions on the box at the side) to get to each trend page (for resident, for bay, for migratory). What would be the image here? What are SF Estuary Fish Trends? Add generic info that applies to all three. Learn more about resident, bay, and migratory fish trends in the SF Estuary. (link to resident trend page, bay fish trend page, and migratory fish trend page respectively)

Trend Graph What are SF Estuary Fish Trends?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Living Resources  Fish  Trends  Resident What are SF Estuary Fish Trends? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What are SF Estuary fish trends? What are resident fish trends? What are bay fish trends? What are migratory fish trends? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management The FMWT abundance indices for Delta smelt, longfin smelt, age-0 striped bass, and threadfin splittail shad are presented below. Abundance trends vary among these species; however, the abundance indices for all four species rapidly declined to record low levels around In 2005, the IEP formed a Pelagic Organism Decline (POD) Management Team to evaluate the potential causes of the declines. Learn more about the POD. (link to What are Resident/Pelagic Fish Trends? Delta Smelt A substantial decline in this fish led to its listing under the federal Endangered Species Act in Since that time, declines have continued to levels that are barely detectable in long-term community sampling programs. Longfin Smelt Once among the most abundant fish in the estuary, longfin smelt have experienced one of the most severe population declines of any species in the estuary. Population abundance is strongly correlated over the long and short term with springtime flows of freshwater out of the Delta (Jassby et l. 1995; Kimmerer 2002; Kimmerer et al. 2009; Mac Nally et al. 2010; Thompson et al. 2010). Sacramento Splittail Extreme fluctuations in abundance characterize this species and make long-term trends difficult to detect. Populations increase explosively following years with extensive floodplain inundation in the spring. Populations decline precipitously during long dry spells when reproductive opportunities are rare and as older fish reach their maximum life spans Age-0 Striped Bass (Non-native) (Migratory) Despite its long success in the Estuary, production of juvenile striped bass has declined substantially over the past two decades. Threadfin Shad Need text here. - I don’t really like that black line separating native from non-native like that, but need something like that there. (maybe a greyed out box like on other slides.) Graphs would be clickable and expand. Missing sacramento splittail graph. Also should probably cover threadfin shad in “What are resident fish section?” if we are going to include information about their trends here. AWS – I don’t think we should have pelagic in the title. We can put in descriptions. Did we decide to include threadfin? JR - I was thinking we should skip threadfin. I agree about not including “pelagic” since splittail are not. AWS – we should also put notation on where we are getting the data for each graph and any important info… (e.g. bay study includes the months or index period for annual indices and the age class) Trend Graph

Trend Graph Trend Graph Trend Graph What are SF Estuary Fish Trends?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Living Resources  Fish  Trends  Bay What are SF Estuary Fish Trends? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What are SF Estuary fish trends? What are resident fish trends? What are bay fish trends? What are migratory fish trends? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management What are Marine/Bay Fish Trends? The State of the San Francisco Bay Report (2011) summarized fish indicators associated with the health of the San Francisco Bay and said the following: “Based on the Fish Index and its component indicators, the health of the San Francisco Bay has declined since the 1980s in all regions except Central Bay, near the Golden Gate. The decline is most severe in Suisun Bay, the upstream region of the Estuary heavily influenced by the amounts, timing and quality of freshwater inflows from the Bay’s Sacramento-San Joaquin watershed. Since 1993, when the CCMP (Comprehensive Conservation and Management Plan) called for recovery of and reversing the declines of estuarine fish and wildlife species, none of the Bay fish communities in any part of the Bay have improved. Instead six native fish species that rely on the Bay have been listed under the federal and/or state Endangered Species Acts. Native/Non-native Fish? Northern Anchovy Northern anchovy populations have declined in each SF Estuary bay since at least the mid-1990’s (SOTB 2011). Kimmerer (2006) attributed the decline in the upper (less saline) portions of the estuary to a decline in available prey. (this is a driver. Keep?) Pacific Herring Though the commercial catch of Pacific herring has dropped substantially since early in the last century, trends over the last several decades are not statistically significant. A long-term decline in the median age of herring is of concern and has been attributed to intensive fishing (Pew 2013 ). Starry Flounder Population trend is variable through time but significantly correlated with freshwater flow out of the Delta in late spring (Kimmerer 2002). - graphs would be clickable AWS – maybe rather than “native/non-native” we could have a title of “Representative Fish”? As mentioned previously, there are so many fish to choose from, but these species were chosen as key representatives of this part of the estuary. YES. I think the “native/non-native” issue is part of a a different story line of fish health. Let’s have native non-native in parentheses Endemic could be cool Trend Graph Trend Graph Trend Graph

What are SF Estuary Fish Trends ?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Living Resources  Fish  Trends  Migratory What are SF Estuary Fish Trends ? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What are SF Estuary fish trends? What are resident fish trends? What are bay fish trends? What are migratory fish trends? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management What are Migratory/Anadromous Fish Trends? Migratory fish, particularly anadromous species, of interest in the SF Estuary include commercial, sport and regulated fish. Many of these native and non-native anadromous species populations abundance indices have declined precipitously in the latter part of the 20th century. Among the four runs of Chinook salmon spawning in the Sacramento-San Joaquin River system, all are classified as endangered, threatened, or species of concern. Estimated yearly natural production and in river escapement are presented below for fall-run, spring-run, and winter-run Chinook salmon (source: CDFW Grand Tab; Mills and Fisher [CDFW 1994]). Learn more about migratory fish trends. (link to Right link?) Native/Non-native Fish? Sacramento River Fall Run Chinook Indicator: ______ Major long-term declines are obscured because official counts began after construction of major dams that had already eliminated much of this fish’s historical habitats. Estimates suggest that this run regularly produced hundreds of thousands to over a million fish each year. Recent major declines led to the unprecedented closing of California’s commercial salmon fishery in 2008, 2009 and most of 2010. Sacramento River Winter Run Chinook Completion of Shasta dam in 1945 blocked access to this endemic and genetically unique population’s historic spawning grounds in the far northern watersheds of the Sacramento River. Habitat created by cold-water releases from Shasta Reservoir has declined over time, and the population has experienced another catastrophic decline over the past several decades. This species is listed as endangered under state and federal Endangered Species Acts. Central Valley Spring Run Chinook Believed to be the most abundant Chinook salmon population historically, spring run populations have declined by 99%-99.9%. This once widespread fish is now hardly found in the San Joaquin Drainage where it used to flourish. Spring run are now found predominantly in the small tributaries to the Sacramento River that originate on the slopes of Mt. Lassen. San Joaquin River Fall Run Chinook Friant Dam blocks this fish from reaching the cool, upstream environment of the San Joaquin River. This population has continued to decline as habitat and necessary, fresh, cold water flows have declined on the San Joaquin’s three major tributaries (the Merced, Tuolumne, and Stanislaus). Graphs would be clickable. What about steelhead and sturgeon? Nothing in the word document about these. AWS – didn’t include as per long discussions, data availability Selected fish as an abundance category, don’t need

< > Why is Water a Key Attribute?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Water Why is Water a Key Attribute? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED Why is water a key attribute? What is water quantity, and why is it important? What is water quality, and why is it important? < > Water related pictures that you can click on to get to details (?) You get to this slide by clicking on the water tab on slide 9. Links: water quantity links to next slide (34) and water quality links to slide ? Why is water a key attribute? Water is a key attribute for any aquatic ecosystem, especially estuaries. The quantity, timing of flows, and the quality of the water have direct affects on the health of an estuary. The SF Estuary is dependent on: Freshwater inflow from rivers that drain the western slope of the Sierra Nevadas Salt water inflow from the Pacific Ocean The variation in these inflows and their interaction has resulted in the formation of a unique and diverse ecosystem. How do you evaluate the health of water? Learn more about the most recent evaluation of the state of the SF Bay. (link to SOTB Report 2011)

< > What is Water Quantity, and Why is it Important?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Water  Quantity What is Water Quantity, and Why is it Important? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED What is water quantity, and why is it important? How and where is water quantity measured in the SF Estuary? What are trends in water quantity in the SF Estuary? < > Water quantity related pictures that you can click on to get to details (?) – dams, diversions, snow pack, etc. “Water year. . . Index” links to slide 35 “Unimpaired” links to slide 36 “Net . . Index” links to slide 37 What is water quantity? Water quantity is impacted by natural, seasonal, and annual climatic variations as well as by diversions and discharges by water users. [need more text here] Why is it important? [need text here]

< > How and Where is Water Quantity Monitored in the SF Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Water  Quantity  Monitored How and Where is Water Quantity Monitored in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED What is water quantity, and why is it important? How do we determine the health of water quantity? How and where is water quantity monitored in the SF Estuary? What are trends in water quantity in the SF Estuary? < > Water quantity related pictures that you can click on to get to details (?) – dams, diversions, snow pack, etc. “Water year. . . Index” links to slide 35 “Unimpaired” links to slide 36 “Net . . Index” links to slide 37 How and where is water quantity monitored in the SF Estuary? Water quantity is impacted by natural, seasonal, and annual climatic variations as well as by diversions and discharges by water users. Water quantity is measured with a series of tools including A Water Year Hydrologic Classification Index has been created for both the Sacramento Valley and for the San Joaquin Valley to help us determine water year classifications, based off current hydrologic conditions, and forecast future runoff assuming normal precipitation for the remainder of the water year. Unimpaired Runoff and the Net Delta Outflow Index help us understand the impacts of dams and diversions on the SF Estuary.

How do We Determine the Health of Water Quantity?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Concept  Water  Quantity How do We Determine the Health of Water Quantity? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Identify Key Attributes Habitat Water Ecological Processes Stewardship Describe Health Indicators Amount ? Patterns STEP 1 STEP 2 Quality Quantity Define Focal Categories Freshwater Inflow STEP 3 STEP 4 Visualize Trends Identify & Evaluate Drivers STEP 5 Living Resources ? Timing - This is just an initial mock up to see if this sort of diagram would work for the water quantity section. How do we determine the health of water quantity? [text]

How and Where is Water Quantity Measured in the SF Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Water  Quantity  Measured  Water Year How and Where is Water Quantity Measured in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED How and where is water quantity measured in the SF Estuary? What is the Water Year Hydrologic Classification Index? What is Unimpaired Runoff? What is the Net Delta Outflow Index? Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management What is the Water Year Hydrologic Classification Index? 2011 Sacramento River Water Year Classification The Sacramento Valley Index is used to characterize WY type for the current water year (October 1 of the proceeding calendar year through September 30 of the current water year) for the sum of the following locations: Sacramento River above Bend Bridge, near Red Bluff; Feather River, total inflow to Oroville Reservoir; Yuba River at Smartville; American River, total inflow to Folsom Reservoir. The San Joaquin Valley Index is used to characterize WY type for the current water year (October 1 of the proceeding calendar year through September 30 of the current water year) for the sum of the following locations: Stanislaus River, total flow to New Melones Reservoir; Tuolumne River, total inflow to Don Pedro Reservoir; San Joaquin River, total inflow to Millerton Lake. Images would be clickable and expandable? Maybe not necessary. Kari’s additional notes: Slide originally said: “The Sacramento Valley Index is used to characterize water years statewide because the majority of California’s precipitation falls within the northern half of the state and flows down the Sacramento River to the SF Estuary.” She revised it to what is above and made the following comments. “Is this an accurate statement? I’m not sure myself here so just asking. I would think that the 8 river index (sac+sjr) would be a more accurate predictor of the entire states WY type. I would make this more clear. To be technically correct, I believe that WYs are determined only for each individual region, and that although the Sacramento region/basin is the largest, I am not sure that you can say it depicts the WY classification for the entire state of CA.” 2011 San Joaquin River Water Year Classification

Yearly Average Unimpaired Runoff
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Water  Quantity  Measured  Unimpaired How and Where is Water Quantity Measured in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED How and where is water quantity measured in the SF Estuary? What is the Water Year Hydrologic Classification Index? What is Unimpaired Runoff? What is the Net Delta Outflow Index? What is Unimpaired Runoff? Unimpaired Runoff represents the natural water production of a river basin, unaltered by upstream diversions, storage, and the export of water to, or the import of water from, other basins. It is measured in Million Acre Feet per year (Dayflow 2011). Yearly Average Unimpaired Runoff ( ) Image would be clickable and expandable? Maybe not necessary.

Replace this one with one showing 5 or 10 years of record
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Water  Quantity  Measured  Net Delta How and Where is Water Quantity Measured in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED How and where is water quantity measured in the SF Estuary? What is the Water Year Hydrologic Classification Index? What is Unimpaired Runoff? What is the Net Delta Outflow Index? What is the Net Delta Outflow Index? The Net Delta Outflow Index is determined by subtracting net delta consumptive use and delta exports from delta inflow. Much of this outflow occurs during late winter and early spring. Currently, the location of X2 is used as the primary indicator in managing Delta outflows. Replace this one with one showing 5 or 10 years of record - Links: X2 links to the next slide (slide 38)

How and Where is Water Quantity Measured in the SF Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Water  Quantity  Measured  X2 How and Where is Water Quantity Measured in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED How and where is water quantity measured in the SF Estuary? What is the Water Year Hydrologic Classification Index? What is Unimpaired Runoff? What is the Net Delta Outflow Index? What is X2, and why is it important? The meeting of the ocean and the rivers creates a dynamic balance between freshwater and saltwater in the estuary. This creates a biologically rich “mixing zone” referred to as X2 in the Delta. The location of X2 is the calculated distance in kilometers from the Golden Gate Bridge to the place in the estuary that has a defined mix of saltwater and freshwater (called the 2 psu isohaline). Upstream of the X2, water becomes fresher and downstream of the X2 water becomes more brackish until it reaches the ocean. X2 is important because phytoplankton, zooplankton, benthic organisms, larval fish, and many of the Delta’s fish have direct relationships with Delta outflows. Clean up this text. Links in blue connect to each of these pages, e.g. phytoplankton links to “What are phytoplankton, and why are they important?” Other images/maps here?

What are Water Quantity Trends in the SF Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Water  Quantity  Trends What are Water Quantity Trends in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management What are water quantity trends in the SF Estuary? QUESTIONS ANSWERED What is water quantity, and why is it important? How and where is water quantity measured in the SF Estuary? What are trends in water quantity in the SF Estuary? Few sentences of text here? Freshwater flows into the Bay are reduced by about 50% on average, dramatically increasing the number of years in which native species experience extreme droughts (FIGURE 1 or 5). Figure 1. Trends in the mean, minimum, and maximum percentage of unimpaired flow that becomes actual delta outflow across 8 decades Fix figure caption text and bullets text … Discuss other info and graphs from the water quantity word doc. Spring flows in the San Joaquin Valley are reduced by approximately 70% on average and more than 90% in some years (FIGURE 2). Figure 2. Horizontal lines indicate average for each period. Over time percentage of winter-spring runoff available in the SJ basin that has reached the delta has declined. Have a similar graph for Sac River at Verona. [shorten this] Spring flows in the Sacramento Valley are …… Figure 3. Trends in the mean, minimum, and maximum percentage of unimpaired flow that becomes actual delta outflow across 8 decades With increasing frequency, the net flow of water in some Delta waterways is away from the Bay and towards export pumps (FIGURE 4). Figure 4. Days of reverse flow at OMR

< > What is Water Quality, and Why is it Important?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Water  Quality What is Water Quality, and Why is it Important? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED What is water quality, and why is it important? How do we determine the health of water quality? Where is water quality monitored in the SF Estuary? What are water quality trends in the SF Estuary? < > Water quality related pictures that you can click on to get to details (?) – pH, algal blooms, etc. Work on this text. May need to break all this down into pH, temperature, dissolved oxygen, etc. (especially to get at trends) What is water quality? Water quality is impacted by natural seasonal and annual climatic variations, land uses, as well as diversions and discharges by water users. Water quality parameters can include “Vital Sign” indicators such as temperature, conductance, pH, dissolved oxygen, and contaminants, such as nutrients, pesticides (e.g. DDT, dieldrin, chlordane & pyrethroids) and heavy metals (e.g. mercury and selenium). Why is it important? [text]

How do We Determine the Health of Water Quality
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Concept  Water  Quality How do We Determine the Health of Water Quality …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Identify Key Attributes Habitat Water Ecological Processes Stewardship Describe Health Indicators Dissolved Oxygen Contaminants Silver STEP 1 STEP 2 Quality Quantity Define Focal Categories Fish Sediment STEP 3 STEP 4 Visualize Trends ? Identify & Evaluate Drivers STEP 5 Living Resources Copper Bacteria Toxicity - This is just an initial mock up to see if this sort of diagram would work for the water quality section. How do we determine the health of each attribute? Assessing the health of any one attribute can be a complicated process. Conceptual models, such as the one depicted above, can help us assess the health of each attribute by allowing us to identify important health indicators, their trends over time, and the types of drivers that cause changes in the health of the estuary.

Where is Water Quality Monitored?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Water  Quality Monitored Where is Water Quality Monitored? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED What is water quality, and why is it important? How and where is water quality monitored in the SF Estuary? What are water quality trends in SF Estuary? Map of where water quality is monitored? How and where is water quality monitored? Monitoring of water quality can include discrete (grab) sampling (fixed locations with no permanent gage house), or continuous sampling (fixed locations with a gage structure housing instruments that automatically record specific indicator parameters) Discrete water quality monitoring happens at 24 active locations in the Delta for the D-1641 mandated sites. Continuous monitoring happens at 13 fixed locations with a gage structure housing instruments that automatically record specific indicator parameters. Overall, DWR operates 10 monitoring programs, 171 monitoring stations and compiles up to 21 physical and chemical parameters in addition to weather and biological constituents that effect water quality throughout the SF Estuary. This monitoring by DWR is only a part of the entire set of monitoring networks that in the SF Estuary (insert Regional Monitoring map, (the one used above). “Discrete Monitoring” links to “Continuous Monitoring” links to (looks like these are images) Clean up this text more.

How Can You Determine the Status of Habitats?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Habitats How Can You Determine the Status of Habitats? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED Why are ecological processes important? What ecological processes are being measured in the SF Estuary? How are SF Estuary ecological processes trending? What are the issues of concern in the SF Estuary? What is being done to improve ecological processes in the SF Estuary?

How Can You Determine the Status of Ecological Processes?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  EcoProcesses How Can You Determine the Status of Ecological Processes? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED Why are ecological processes important? What ecological processes are being measured in the SF Estuary? How are SF Estuary ecological processes trending? What are the issues of concern in the SF Estuary? What is being done to improve ecological processes in the SF Estuary?

What is the Base of the Food Web, and Why is It Important?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Where  San Francisco  Health  Living Resources  Food Web What is the Base of the Food Web, and Why is It Important? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Insert slide show with clickable images of examples of phytoplankton, zooplankton and benthic invertebrates. Insert clickable cartoon diagram of food web – To be developed The base of the SF Estuary food web includes the microscopic organisms, plants, and invertebrates that are food for fish, birds, and other wildlife. The diagram at the left shows a simplified version of the relationships between these organisms – in reality it is much more complex. The base of the food web is made up of organisms called primary producers, a group of organisms that includes microscopic aquatic plants (phytoplankton) and larger terrestrial and aquatic vegetation. Phytoplankton is consumed by microscopic aquatic animals (zooplankton) and larger terrestrial and aquatic invertebrates. The condition of the base of the food web is critical to the rest of the organisms in the food web. Changes in the abundance, distribution, or quality of key organisms at the base of the food web can affect those at the top, and changes in organisms at the top of the food web can in turn affect the abundance of organisms at the base. - Food Web goes as part of Ecological Processes right? Are we holding off on that section for now? So where should this slide go? Erin F.’s notes: Is it possible to change the SF Estuary Aquatic Food Web diagram? I was hoping we could use simpler words than “ecosystem processes” and “piscivores” – though “fish-eating fish” isn’t great either. Can we work with the words used in the boxes? Food web conceptual model. [Click to navigate to other portal pages].

What Types of Stewardship Support a Healthy Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Health  Stewardship What Types of Stewardship Support a Healthy Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED Why are habitat location, type, quality, and quantity important? How can habitat be measured in the SF Estuary? What are SF Estuary habitat trends? What is being done to improve habitats in the SF Estuary?

What Laws, Regulations, and Standards Protect the SF Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Laws Regulations & Standards What Laws, Regulations, and Standards Protect the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management 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? Laws regulations and policies that protect estuaries include those that are associated with freshwater (click to connect to Streams Rivers & Lakes portal [ surrounding land, including tidal wetlands, managed and seasonal wetlands, and riparian habitat (click to connect with Wetlands Portal: [ shtml]), coasts and oceans (click to connect with Oceans portal). California’s estuaries, and the organisms that live in them, are protected by many federal and state laws, regulations, and policies designed to prevent further degradation and destruction. Regulations protect ecological services and benefits derived from estuaries as well as protecting special status fish, wildlife and plants and their habitats, vegetation communities, wetland extent, water quality, and beneficial uses. Each law and regulation has been put into place over many decades to address different resource and habitat protection needs, with responsibility for enforcement assigned the appropriate government agencies. Understanding the different laws and the agencies that enforce them is necessary for a complete picture of estuary protection in California and the United States. Water quality standards are an effective tool available to protect the overall health of estuaries in California and the functions they provide, including shoreline stabilization, nonpoint source runoff filtration, wildlife habitat, and erosion control, which directly benefit adjacent and downstream waters. Water quality standards, including designated uses, criteria, and anti- degradation policies can provide a sound legal basis for protecting estuarine resources through State water quality management programs. Other regulations protect wetlands within the estuaries from damage, filling, or destruction through planned construction activities. Several additional programs safeguard estuarine integrity, whether directly and indirectly, by preventing changes to important populations of plant and animal species and their habitats. In addition to enforcing regulations, the United States and California have set an overarching goal to prevent further decline of wetlands through a “no net loss” approach, a goal recommended by the National Wetlands Policy Forum in 1987 and adopted in 1989. Other mechanisms for wetland protection include acquiring land in high priority areas, integrating knowledge of wetland resources into land use planning, mitigating the effects of construction activities (wetland creation or restoration in one area to account for destruction in another area), and creating disincentives for conversion of wetlands to other land uses. For example, state transportation agencies, such as Caltrans, are required to be in compliance with regulations pertaining to wetlands and to implement the state and federal policies of "no net loss" of wetlands. As a result of these policies, disturbances or impacts to wetlands due to transportation projects are compensated through the creation, restoration, enhancement, and/or preservation of wetlands. While government regulatory efforts are important, they cannot protect the majority of California’s remaining wetlands alone. Partnerships have developed among nonprofit organizations, private landowners, and federal, state, tribal, and local governments to manage whole watersheds (large land areas where water drains to a common point). The goal of these partnerships is to comprehensively protect all of the connected waterways in a given watershed, including wetlands. Education and volunteer wetland restoration efforts are also helping to speed wetland recovery and increase appreciation of wetland functions and values among the public. Click for information on San Francisco Estuary – specific laws regulations and policies - These slides have been altered by Erin Aquino-Carhart. I have not turned her word doc into a powerpoint slide yet.

Click here for more detailed information on these Federal Programs
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Laws Regulations & Standards  Federal What Federal Laws, Regulations, and Standards Protect the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Federal Endangered Species Act Clean Water Act Clean Water Act, Section 404 Farm Bill Rivers and Harbors Act, Section 10 Coastal Zone Management Act Other Federal Agency Programs Executive Order 11990, "Protection of Wetlands" Executive Order 11988, "Floodplain Management" Click for information on San Francisco Estuary – specific laws regulations and policies Click here for more detailed information on these Federal Programs QUICK LINKS California State Laws, Regulations, and Policies to Protect Estuaries San Francisco Estuary – specific Laws, Regulations, and Policies

What Federal Laws, Regulations, and Standards Protect the SF Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Laws Regulations & Standards  Federal  More What Federal Laws, Regulations, and Standards Protect the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Endangered Species Act Federal Endangered Species Act [link to The purpose of the Endangered Species Act (ESA), which was passed in 1974, is to protect and recover imperiled species and the ecosystems upon which they depend. It is administered by the U.S. Fish and Wildlife Service (USFWS) [link to and the National Marine Fisheries Service (NMFS) [link to: Under the ESA, species may be listed as either endangered or threatened. “Endangered” means a species is in danger of extinction throughout all or a significant portion of its range. “Threatened” means a species is likely to become endangered within the foreseeable future. All species of plants and animals, except pest insects, are eligible for listing as endangered or threatened. For the purposes of the ESA, Congress defined species to include subspecies, varieties, and, for vertebrates, distinct population segments. The USFWS [link to has primary responsibility for enforcing the ESA in relation to protecting terrestrial and freshwater organisms. In California’s estuaries, federally listed endangered and threatened species include Delta smelt, salt marsh harvest mouse, giant garter snake, light-footed clapper rail, California least tern, Western snowy plover, salt marsh bird’s- beak, and California seablite. NMFS [link to a division of the National Oceanic and Atmospheric Administration (NOAA), has the primary Federal responsibility for the conservation, management, and development of living marine resources and for the protection of certain marine mammals and endangered species on all public and private lands, under numerous federal laws. NMFS is responsible for the protection of anadromous fish [link to definition] listed under the Endangered Species Act, including Chinook and coho salmon, steelhead trout, and green sturgeon species that use California’s estuaries [link to: Clean Water Act The Clean Water Act (CWA) is the primary federal law in the United States governing water pollution and regulating water quality standards for surface waters. The basis of the CWA was enacted in 1948 and was called the Federal Water Pollution Control Act, but the Act was significantly reorganized and expanded in "Clean Water Act" became the Act's common name with amendments in Two agencies have primary responsibility for enforcement of the Clean Water Act: The U.S. Army Corps of Engineers (the Corps) and the U.S. Environmental Protection Agency (USEPA). One of the primary civilian missions of the U.S. Army Corps of Engineers is to manage the nation's waterways and wetlands. USACE activities include regulating activities in wetlands including issuing dredge and fill permits and authorizing the establishment of wetland areas. The Corps’ also builds and manages civil projects such as e, constructing projects approved by Congress for flood control, commercial navigation, or shipping channel maintenance; operating and maintaining flood control reservoirs and public reclamation facilities; and many other public works. The U.S. Environmental Protection Agency (USEPA) is responsible for implementing federal laws designed to protect air, water, and land. While this is done primarily through regulation, the USEPA has also developed a wide variety of funding, planning, and education programs. USEPA responsibilities which affect wetlands include, but are not limited to, developing rules to regulate municipal and industrial wastewater discharge, and stormwater discharge; overseeing drinking water quality; and overseeing USACE regulatory activities pertaining to wetlands protection, and dredge and fill activities. Clean Water Act, Section 404 In 1972, Section 404 of the federal Clean Water Act (CWA) established a program to regulate the “discharge of dredged or fill material (such as soil or sediments) into water waters of the U.S.,” including wetlands. Dredged or fill materials can be almost any substance or pollutant that can adversely affect water quality or navigation. Section 404 permits are issued by the U.S. Army Corps of Engineers (Corps) for a range of activities such as construction, mining, and levee installation. Typically, the permit review process seeks to avoid or minimize impacts on aquatic ecosystems. If avoiding impacts is not possible, actions to offset the impacts by improvement or restoration of other sites (called “compensatory mitigation”) are needed. Section 404 Permits may be individual or general. General permits are given for up to 5 years for broad classes activities that are similar in nature and have minimal impacts. Activities that do not qualify for a general permit must be authorized individually through the Corps, requiring a public notice and comment period as well as specific environmental analyses. The U.S. Environmental Protection Agency (USEPA) examines proposed individual permits during the public review period and can elevate projects for closer scrutiny if needed. Corps and USEPA regulators also partner to conduct enforcement activities if discharges of dredged or fill material violations occur. Section 404 has evolved over the years, with the introduction of the latest Mitigation Rule which revised CWA Section 404(b)(1) which provides much detailed guidance on compensatory mitigation for impacts to wetlands. Farm Bill The farm bill is the primary agricultural and food policy tool of the federal government. This comprehensive “omnibus bill” is passed every 5 years or so by the United States Congress. It deals with both agriculture and all other affairs under the purview of the United States Department of Agriculture. The Farm Bill provides regulations and guidance for wetland management and protection on agricultural lands that are enrolled in Farm Bill programs. Farm Bill programs are administered primarily by the U.S. Department of Agriculture (USDA) Farm Service Agency (FSA) and the Natural Resources Conservation Service (NRCS). (Wetlands on agricultural lands not enrolled in Farm Bill programs are regulated under the Clean Water Act section 404 just like any other wetlands). • FSA directly administers programs such as the Conservation Reserve Program. • NRCS makes wetlands determinations and delineations in agricultural lands for the U.S. Army Corps of Engineers and for Farm Bill purposes, but does not issue permits pertaining to wetlands. As part of the NRCS's Wetlands Protection Policy, landowners have the option of mitigating wetland impacts in order to continue receiving NRCS assistance. • The NRCS has long provided technical assistance to those involved in land conservation and planning, and wetlands restoration and enhancement. The agency has assisted in wetlands restoration and enhancement through programs such as, the Water Bank Program, the Wetland Reserve Program, the Environmental Quality Incentives Program (EQIP) and the Small Watersheds Program (PL-566). • The NRCS also provides substantial support and leadership for the Resource Conservation and Development Councils(RC&D), and local Resource Conservation Districts (RCDs) which are often active in wetland, stream and watershed restoration. Rivers and Harbors Act, Section 10 The Rivers and Harbors Act of 1899, administered by the U.S. Army Corps of Engineers (Corps) is the oldest federal environmental law in the United States. Although many activities covered by the Rivers and Harbors Act are regulated under the Clean Water Act, the 1899 Act retains independent vitality. Section 10 of the River and Harbors Act prevents unauthorized obstruction or alteration of US waterways, including wetlands. As such, the Corps oversees and regulates any work activities (such as dredging, beach nourishment, and geotechnical surveys) or construction of structural features (such as piers, boat docks or ramps, wharfs, weirs, booms, breakwaters, bulkheads, and jetties) that would affect a wetland’s location, condition, or support capacities. Coastal Zone Management Act The U.S. Congress recognized the importance of meeting the challenge of continued growth in the coastal zone by passing the Coastal Zone Management Act in The Act, administered by the National Oceanic and Atmospheric Administration’s (NOAA) Office of Ocean and Coastal Resource Management, (OCRM) provides for management of the nation's coastal resources and balances economic development with environmental conservation. The CZMA outlines two national programs, the National Coastal Zone Management Program and the National Estuarine Research Reserve System. The coastal programs aim to balance competing land and water issues in the coastal zone, while estuarine reserves serve as field laboratories to provide a greater understanding of estuaries and how humans impact them. The overall program objectives of CZMA remain balanced to "preserve, protect, develop, and where possible, to restore or enhance the resources of the nation's coastal zone.“ Other Federal Agency Programs The USFWS is also involved in many responsibilities and services related to wetland protection and restoration: acquiring wetlands, fishery habitats, and other lands for restoration and preservation; managing National Wildlife Refuges; and reviewing and commenting on water resource projects. USFWS also manages many private-public partnerships for habitat conservation, notably through the Partners for Fish and Wildlife Program which supports thousands of wetland conservation sites nationwide. USFWS plays a key role as administrator of the North American Waterfowl Management Plan, under which extensive wetland projects in California are managed through the San Francisco Bay Joint Venture and the Central Valley Habitat Joint Venture. The National Park Service (NPS) has a multi-faceted program for protecting and managing wetland resources within the National Park System, which includes: protecting park wetlands from pollution; providing technical expertise and funding to parks for wetland inventory and restoration projects; providing up-to-date management techniques to preserve wetland functions and values; and protection or acquisition of water rights. Also, the NPS plays key roles in other local, state, and federal government wetlands-related programs including the Rivers and Trails Conservation Assistance Program, the Wild and Scenic Rivers Program, and the preparation of State Comprehensive Outdoor Recreation Plans. The U.S.D.A. Forest Service and the Department of Interior Bureau of Land Management also play key roles in Wild and Scenic River management, and are responsible for wetland protection on federal lands. Executive Order 11990, "Protection of Wetlands" In 1977, Executive Order 11990 was signed by President Carter to ensure protection and proper management of wetlands by federal agencies. It requires federal agencies to avoid undertaking or providing financial assistance for new construction projects located within wetlands unless no practical alternative is available. Executive Order 11988, "Floodplain Management" Executive Order 11988, also issued in 1977 by President Carter, ensures federal agency activities reduce the risk of flood impacts and restore or preserve the natural beneficial values of floodplains. This guidance helps protect wetlands because they play an important role in buffering flood impacts and are often located in floodplains. Click for information on San Francisco Estuary – specific laws regulations and policies

What Research is Being Performed in the SF Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Research What Research is Being Performed in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Many groups are conducting and funding original research in the San Francisco Estuary, including those listed below. Interagency Ecological Program San Francisco Estuary Institute State and Federal Contractors Water Agency SWAMP DSP - Fellows Ecosystem Restoration Program NSF NCEAS USGS (e.g., San Francisco National Estuarine Research Reserve System and San Francisco Bay Joint Venture PRBO Conservation Science – San Francisco Bay Program San Francisco Invasive Spartina Project University of California, Davis (many labs to link to) University of California, Berkeley Maggi Kelly lab -

Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  Monitoring What Monitoring Programs, Data Sources, & Reports are there for the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Many groups are performing ecosystem monitoring in the San Francisco Estuary, including those listed below. The Central Valley Monitoring Directory is a good source of metadata for much of the monitoring being performed in the Central Valley. Interagency Ecological Program San Francisco Bay Regional Monitoring Program Surface Water Ambient Monitoring Program Irrigated Lands Regulatory Program USGS (e.g., DPR CDFW USFWS DWR salvage and Suisun BoR? San Francisco Bay Joint Venture PRBO Conservation Science – San Francisco Bay Program San Francisco Invasive Spartina Project

Where Did we Find the Information Used for the SF Estuary Assessments?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries  References Where Did we Find the Information Used for the SF Estuary Assessments? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management For readers interested in more detail, you can find more from the links below. (summaries and plans-link to EPA’s page specifically for document repository) Delta Delta Historical Ecology The State of Delta Science PPIC Reports ERP Conservation Strategy Delta Plan Delta Vision Foundation EPA’s SF Delta watershed map – Erin check for other WS docs Delta Atlas Delta Science Plan Pulse of the Delta Suisun Marsh Plan Creating an Adaptive Management Decision-Making Framework to Address Uncertainties in Delta Habitat Restoration: Tidal Marsh Productivity Exports, Aquatic Food Webs, and Delta Smelt (move to PMs page) POD Report San Francisco Bay SFEP CCAMP Check-ups CCMP NEP (Erin) Nat’l Est Coastal Conditions Report State of The Bay Report State of the Birds Report Pulse of the Estuary State of the Estuary Report SF Habitat Goals Project References used on this Estuaries website [APHA] American Public Health Association, American Waterworks, and Water Environmental Federation Standard Methods for the Examination of Water and Wastewater. 20th edition. Washington, D.C.: American Public Health Association. Gannon, J. E. and R. S. Stemberger Zooplankton (especially crustaceans and rotifers) as indicators of water quality. Trans. Amer. Microsc. 97:16. Glibert, P.M Long-term changes in nutrient loading and stoichiometry and their relationships with changes in the food web and dominant pelagic fish species in the San Francisco Estuary, California. Reviews in Fisheries Science 18: 211– 232. Horne, A. and Goldman, C Limnology. 2nd edition. New York, New York, McGraw-Hill, Inc. Lehman, P.W Changes in chlorophyll a concentration and phytoplankton community composition with water-year type in the upper San Francisco Estuary. In San Francisco Bay: The ecosystem, ed. J.T. Hollibaugh, 351–374. San Francisco: AAAS. Lehman, P.W The influence of climate on phytoplankton community biomass in San Francisco Bay Estuary. Limnology and Oceanography 45(3): Kimmerer, W.J., A.E. Parker, U.E. Lidstrom, and E.J. Carpenter Short-term and interannual variability in primary production in the low salinity zone of the San Francisco Estuary. Estuaries and Coasts 35: Müller-Solger, A.B., A.D. Jassby, and D.C. Müller-Navarra Nutritional quality of food resources for zooplankton (Daphnia) in a tidal freshwater system (Sacramento–San Joaquin River Delta). Limnology and Oceanography 47(5): Utermöhl, H Zur Vervollkommnung der quantitativen Phytoplankton Methodik. Mitt. Int. Verh. Limnol. 9: 38. van den Hoek, C., D.G. Mann, and H.M. Jahns Algae: an introduction to Phycology. Cambridge University Press, United Kingdom. Water Quality Conditions in the Sacramento-San Joaquin Delta and Suisun and San Pablo Bays during Chapter 4 Phytoplankton and Chlorophyll a.

What are Estuaries, and Why are They Important?

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What are Estuaries, and Why are They Important?

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