California Estuary Monitoring Workgroup’s Estuary Portal Instructions for Comments Please send all comments to Stephanie Fong (State and Federal Contractors.

California Estuary Monitoring Workgroup’s Estuary Portal Instructions for Comments
Please send all comments to Stephanie Fong (State and Federal Contractors Water Agency) at by July 19. Comments about overarching issues and specific issues are requested. aaaa Please be sure to include the page number of the slide you are commenting on with your comments. Thank you

Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home  Eco Health  Estuaries California 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 are estuaries, and why are they important? Where are California’s estuaries? How healthy are California’s estuaries? What’s being done to protect them? How can I be part of the solution? Main image/map would be of SF Estuary. People will be able to click directly to the SF Estuary pages (slide 7 and following) from that image. Other images will be other California estuaries that when clicked upon will have a short, introduction page on each of them. In the future, these pages will be developed further. Each of the questions in the “Questions Answered” box will link to introduction pages on each of those questions. Clicking on the blue text will open a viewer window with basic information on those topics. 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? San Francisco Estuary Santa Monica Bay Morro Bay Estuary Smith River Estuary Klamath River Estuary Mad River Estuary Noyo River Estuary Eel River Estuary Russian River 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. - Clicking on “San Francisco Estuary” will take you to the “What is the San Francisco Estuary, and why is it important page? (slide 7)” - Clicking on the other estuaries takes to you a viewer window with basic information on each of them. These pages will be developed further in the future.

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 - This is the introduction page to “how healthy are CA’s estuaries?” You would get to this page by clicking on the question “How healthy are CA’s estuaries” on the main introduction page (slide 2). Eventually, each estuary will have their own health page, but for the moment, only the SF Estuary health information is presented (see slide 8 for SF Estuary health page). How healthy are California’s estuaries? The health of the human body as a whole depends upon the health of its parts – the brain, the bones, the heart. The health of California’s estuaries is no different and depends on the well-being of its parts, also known as attributes, as defined by the authors of The State of the San Francisco Bay Report. These attributes include living resources, water, habitat, ecological processes, and stewardship. 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.

What is Being Done to 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 is Being Done to 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’s being done to protect California’s estuaries? What’s being done to protect them? California’s estuaries are being protected in a number of ways with Laws, Regulations, and Policies, Federal State SF Estuary Policies and Plans Research and Restoration, Monitoring Programs, Data Sources, and Reports, and Stewardship. [content in development] The initial focus of the Portal is on an evaluation of the policies and programs protecting the SF Estuary. More information on other California estuaries is under development. What laws, regulations, and policies protect California’s estuaries? California’s estuaries, and the organisms that live in them, are protected by many federal laws, regulations, and policies designed to prevent the degradation and destruction of Water Quality, Habitat, Living Resources, and Ecological Processes. Some of these protections, which government agencies enforce and uphold, and how they relate to California’s estuaries are described below. Please note: Simply having laws, regulations, and policies in place is not enough to protect California’s estuaries and other natural resources. Constant vigilance and effort are necessary to ensure healthy ecosystems and the continued existence of rare and listed species. Federal Laws, Regulations, and Policies 1. Endangered Species Act (ESA) Purpose: To protect and recover imperiled species and the habitat upon which they depend Agencies: The US Fish and Wildlife Service (USFWS) Responsible for protecting terrestrial and freshwater species National Oceanic and Atmospheric Administration (NOAA) Fisheries Responsible for protecting marine and anadromous [link to definition] species How This Relates to CA Estuaries: California’s estuaries provide essential habitat for a number of plant and animal species listed as endangered, threatened, or other special status categories by the federal government. The ESA protects these species by prohibiting “take” and preserving their habitat. Some of these federal listed species include Delta smelt, Giant garter snake, Western snowy plover, Chinook salmon, and Southern sea otter. Additional Resources: NOAA ESA Fact Sheet USFWS ESA Fact Sheet USFWS Permits for Native Species under ESA Regulations under ESA Section 7 Consultation (ESA Section 7(a)(2)) Purpose: To ensure that federal agency actions do not jeopardize the existence of any listed species Agencies: USFWS and NOAA Fisheries All federal actions, including those that agencis fund or authorize, are reviewed to protect listed species. Because California estuaries are habitat for listed species, any federal actions that may negatively affect the species or their habitat would require a Section 7 Consultation. A Brief Explanation of Section 7 Consultations 2. Habitat Conservation Plans (HCPs) (ESA Section 10(a)(1)(B)) Purpose: To minimize or mitigate impacts to listed and non-listed species from proposed, non-federal projects and to authorize incidental take of listed species HCPs are required when applying for federal incidental take permits. The permit applicants design, implement, and secure funding for a conservation plan that minimizes and mitigates harm to the impacted species during the proposed project. Some HCPs that include CA Estuaries in their plan areas are East Contra Costa County HCP/NCCP and Solano Multispecies HCP/NCCP. USFWS HCP Fact Sheet NOAA Endangered Species Permits FAQ 3. Estuary Restoration Act Purpose: To promote the restoration of estuary habitat, develop a national Estuary Habitat Restoration Strategy, provide financial and technical assistance to restoration projects, and to develop and enhance monitoring, data sharing, and research capabilities Agency: Estuary Habitat Restoration Council (NOAA, US Environmental Protection Agency, US Army Corps of Engineers, USFWS, US Department of Agriculture) Estuary habitat restoration would benefit the health of CA estuaries. The Estuary Restoration Act and NOAA USACE Estuary Restoration Act Summary 4. Clean Water Act (CWA) Purpose: To govern water pollution and regulate water quality standards for surface waters US Army Corps of Engineers (USACE) Responsible for managing the nation’s waterways and wetlands. US Environmental Protection Agency (USEPA) Responsible for regulating water quality standards and overseeing USACE regulatory activities The health of California estuaries and estuarine species depend on water quality. Habitat, living resources, and ecosystem processes thrive with clean water. Regulations under CWA Section 404 Permits Purpose: To regulate the discharge of dredged or fill material (such as soil or sediments) into water waters of the U.S. Agencies: USACE and USFWS Dredged or fill materials can be almost any substance or pollutant that can adversely affect water quality or navigation. Section 404 permits are issued 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. These permits would protect water quality for CA Estuaries from local or upstream project activities. USACE Jurisdiction Mitigation Guidance (Section 404(b)(1)) What You Need to Know About Section 404 Permits (PowerPoint presentation) 5. Coastal Zone Management Act (CZMA) Purpose: To manage US coastal resources and balance economic development with environmental conservation Agency: NOAA Office of Ocean and Coastal Resource Management The Coastal Zone Management Act (CZMA) outlines two national programs, the National Coastal Zone Management Program and the National Estuarine Research Reserve System. These 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.” 6. Eelgrass Mitigation Policy Purpose: To protect eelgrass for its ecological and economic benefits through mitigation Agency: NOAA Fisheries Eelgrass and other seagrasses provide valuable habitat for federally protected marine species. The protection of eelgrass would benefit the conservation and protection of these species. What is Eelgrass? Article on NOAA Eelgrass Restoration State Laws, Regulations, and Policies 1. California Endangered Species Act (CESA) Purpose: To protect California native species and their habitats from extinction and significant decline that would lead to extinction Agency: California Department of Fish and Wildlife (CDFW) California’s estuaries provide essential habitat for a number of plant and animal species listed as endangered, threatened, or other special status categories by the state. The CESA protects these species by prohibiting “take” and preserving their habitat. Some of these state listed species include Longfin smelt, Salt marsh harvest mouse, Chinook salmon, Greater sandhill crane, and Bald eagle. Regulations under CESA Consistency Determinations (FGC Section ) Purpose: To ensure that federal actions are consistent with CESA, this is similar to the ESA Section 7 Consultations [link to Section 7 description] Agency: CDFW Federally authorized incidental take of state listed species must be approved by CDFW to uphold CESA protections. This is one of many ways the state can protect CA estuarine species, by reviewing federal projects and planning ahead to minimize and avoid species and habitat loss. Incidental Take Permits (FGC Section ) Purpose: To work with development projects to avoid potential impacts to rare, endangered, and threatened species and to offset project caused species and habitat loss Incidental take permits allow us to balance human use and the environment of CA Estuaries. It supports responsible planning and development to protect listed species but without preventing growth. 2. Natural Community Conservation Planning Act (NCCPA) Purpose: To provide an early planning framework for proposed development projects within a planning area to avoid, minimize, and compensate for project impacts to wildlife and their habitat Similar to federal Habitat Conservation Plans (HCPs) [link to HCP description] and CESA incidental take permits (see above), Natural Community Conservation Plans (NCCPs) protect species and their habitat while allowing for responsible economic development. There are several NCCPs that include CA Estuaries in their plan areas (e.g., East Contra Costa County HCP/NCCP, Solano Multispecies HCP/NCCP). 3. Porter-Cologne Water Quality Control Act (Porter-Cologne) Purpose: To establish and enforce water quality standards in California for beneficial uses, such as drinking water, endangered species habitat protection, and recreation Agency: State Water Resource Control Boards (State Water Boards) Additional Resources: Summary of Porter-Cologne 4. Regulations under the Clean Water Act (CWA) [link to CWA discussion] Total Daily Maximum Load (TMDL) Program (CWA Section 303(d), California Code Section ) Purpose: To protect and maintain water quality, waters that do not meet water quality standards are listed as “impaired.” TMDLs are developed to restore impaired water bodies. Agency: State Water Boards How this Relates to CA Estuaries: The health of California estuaries and estuarine species depend on water quality. Habitat, living resources, and ecosystem processes thrive with clean water. TMDLs improve water quality by controlling the amount of pollutants that enter impaired water bodies. Additional Resources: California's Impaired Waters List Section 401 Certification Purpose: Requires federal agencies to certify that their actions under CWA Section 404 [link to 404 Permit description] do not violate state water quality standards Agency: State and Regional Water Boards Section 401 of the CWA ensures that federal 404 permits within California do not harm estuarine ecosystems by impacting water quality with the discharge of dredged or fill material. Wetlands, riparian areas, and headwaters are vulnerable to filling, which can affect the health of these areas. 5. The California Coastal Act Purpose: To protect coastal resources, including recreation, agriculture, water quality, development, and habitat protection Agency: California Coastal Commission The Coastal Commission's primary role in regards to estuary protection is the regulation of coastal development. Under California’s federally-approved Coastal Management Program, the California Coastal Commission manages development along the California coast except for San Francisco Bay, where the San Francisco Bay Conservation and Development Commission oversees development. 6. California Senate Bill 1070, Coordination of Monitoring, Assessment and Reporting Purpose: Established the Water Quality Monitoring Council to standardize, enhance, and improve coordination for water quality and related ecosystem monitoring, assessment, and reporting and to increase public accessibility to data and information Agencies: Water Quality Monitoring Council The California Estuary Monitoring Workgroup (CEMW), a workgroup under the Water Quality Monitoring Council, is developing methods to assess the health of the San Francisco Estuary and shares its findings, data, and information on the California Estuaries Portal. 7. Governor’s Executive Order #S-13-08: Climate Adaptation Strategy Purpose: Directed state agencies to plan for sea level rise and climate change impacts through coordination of the state Climate Adaptation Strategy Agencies: Natural Resources Agency; Department of Water Resources; California costal management agencies, such as California Coastal Commission; and the California Energy Commission Sea level rise and climate change would cause habitat loss and put additional stressors on fragile species and ecosystems. Additional Resources: California Climate Adaptation Strategy 8. Governor’s Executive Order #S-03-05: Greenhouse Gas Emission Reduction/Climate Action Team Purpose: Established greenhouse gas (GHG) emission reduction targets, created the Climate Action Team, and directed the Secretary of Cal/EPA to coordinate efforts with other state agencies. Agencies: Cal/EPA and Climate Action Team The efforts to reduce GHG include assessing GHG impacts and developing mitigation and adaptation plans. CA Estuaries may be sensitive to GHG and climate change impacts. What policies and plans specifically protect the SF Estuary? 1. Delta Plan Purpose: To improve California’s water supply reliability, protect and enhance the Delta ecosystem and as a unique and evolving place, improve water quality, reduce flood risk, and set an example by using “best available science” Lead Agency: Delta Stewardship Council 2. Bay-Delta Water Quality Control Plan Purpose: To identify beneficial uses of the Bay-Delta, develop water quality objectives to protect the beneficial uses, and develop an implementation program to meet water quality objectives Lead Agency: State Water Resources Control Board (State Water Board) 3. Strategic Workplan for Activities in the San Francisco Bay Sacramento-San Joaquin Delta Estuary Purpose: To protect the beneficial uses of water in the Bay-Delta estuary, including water rights, quality, and adequate flows. Lead Agencies: Central Valley Regional, San Francisco Bay, and State Water Quality Control Boards 4. Local Habitat Conservation Plans (HCPs) and Natural Community Conservation Plans (NCCPs) Purpose: To allow for economic activities to continue will while minimizing and mitigating the impact of authorized incidental take of covered species and to conserve these species and their habitats Completed Plans in the Delta: San Joaquin Multispecies HCP and East Contra Costa County HCP/NCCP Plans under Development: The Bay Delta Conservation Plan, Yolo Natural Heritage Program Plan, South Sacramento HCP, and Solano Multispecies HCP. 5. Bay Delta Conservation Plan (BDCP) Purpose: To protect and restore the Bay-Delta estuary and create a reliable water supply. Lead Agencies: Department of Water Resources (DWR) Please note: The BDCP is still under development. 6. Suisun Marsh Habitat Management, Preservation, and Restoration Plan Purpose: To restore 5,000-7,000 acres of tidal wetlands and manage wetlands in Suisun Marsh through cooperative, multi-stakeholder efforts Lead Agencies: USBR 7. Endangered Fish Species Biological Opinions USFWS Biological Opinion for the Long-Term Operations of the State Water Project (SWP) and Central Valley Project (CVP) Purpose: To assess the impacts of the state and federal water projects on Delta smelt and provide requirements to avoid jeopardizing the species Lead Agency: US Fish and Wildlife Service (USFWS) • USFWS State and Federal Water Projects Biological Opinion: An Overview (PowerPoint Presentation) 8. NMFS Biological Opinion (BiOp) for the Long-Term Operations of the SWP and CVP Purpose: To assess the impacts of the state and federal water projects on Chinook salmon and provide requirements to avoid jeopardizing the species Lead Agency: National Oceanic and Atmospheric Administration's (NOAA’s) National Marine Fisheries Service (NMFS) • NMFS 2011 BiOp Amendment • NMFS 2009 BiOp on California’s Central Valley Water Project (PowerPoint Presentation) 9. Fish Restoration Program Agreement Purpose: To address specific habitat restoration requirements of the USFWS and NOAA Fisheries biological opinions for the SWP and CVP operations and the Department of Fish and Wildlife (DFW) longfin smelt incidental take permit for SWP operations Lead Agencies: DWR and DFW 10. Delta Levees Special Flood Control Projects Program Purpose: To fund local agencies in the Delta for habitat projects linked to flood management improvements Lead Agency: DWR, Delta Levees Program 11. Central Valley Flood Protection Plan (CVFPP) Purpose: To reduce the risk of flooding and provide more ecosystem and habitat protection Lead Agency: Central Valley Flood Protection Board Additional Resources: CVFPP Website SF Estuary Habitat Restoration Guidance 1. Baylands Ecosystem Habitat Goals: A Report of Habitat Recommendations Purpose: To guide the public in restoring and improving the baylands and adjacent habitats of the SF Estuary Lead Agencies: US Environmental Protection Agency and SF Bay Regional Water Quality Control Board Preparer: San Francisco Bay Area Wetlands Ecosystem Goals Project 2. San Francisco Bay Subtidal Habitat Goals Project Purpose: To achieve, over the next 50 years, a net improvement of the San Francisco Bay’s subtidal ecosystem through science-based protection and restoration of habitats Lead Agency: San Francisco Bay Conservation and Development Commission (BCDC), California Ocean Protection Council (OPC)/California State Coastal Conservancy (SCC), NOAA Habitat Conservation, NOAA Restoration Center, and the San Francisco Estuary Partnership (SFEP) • San Francisco Bay Subtidal Habitat Goals Project website 3. The Conservation Lands Network: San Francisco Bay Area Upland Habitat Goals Project Report Purpose: To identify the most essential lands needed to sustain the biodiversity of the San Francisco Bay Area and to guide informed investments in biodiversity conservation Lead Agency: Bay Area Open Space Council • The Conservation Lands Network website • A summary of the Conservation Lands Network • Article on biologist and landowner perspectives on the Conservation Lands Network What research is being performed in the SF Estuary? Many groups are conducting and funding original research in the San Francisco Estuary, including those listed below. This is not an exhaustive list. Ca Department of Fish and Wildlife Ecosystem Restoration Program (link to Delta Sceince Program (link to Grants (link to Fellows (link to Interagency Ecological Program (link to National Science Foundation (link to National Center for Ecological Analysis and Synthesis (link to San Francisco Estuary Institute (link to San Francisco Invasive Spartina Project (link to San Francisco National Estuarine Research Reserve System (link to and State and Federal Contractors Water Agency (link to University of California, Davis (link to University of California, Davis Information Center for the Environment (link to University of California, Berkeley (link to US Geological Survey (link to What monitoring programs, data sources, & reports are there for the SF Estuary? Many groups are monitoring and reporting various water-related components in the San Francisco Estuary, including those listed below. The Central Valley Monitoring Directory (link to is a good source of metadata for much of the monitoring being performed in the Central Valley. Monitoring Programs (link below) Additional Data Sources (link below) Reports (link below) Monitoring Programs Ca Department of Fish and Wildlife (link to Ca Department of Pesticide Regulation (link to Ca Department of Water Resources Water Data Library (link to Interagency Ecological Program (link to Irrigated Lands Regulatory Program (link to Point Reyes Bird Observatory Conservation Science – San Francisco Bay Program (link to San Francisco Bay Joint Venture (link to San Francisco Bay Regional Monitoring Program (link to Surface Water Ambient Monitoring Program (link to US Fish and Wildlife Service (link to Additional Data Sources Ca Environmental Data Exchange (link to Ca Data Exchange Center (link to US Geological Survey National Water Information System (link to Reports Delta Bay-Delta Strategic Workplan (link to Ca Department of Fish and Wildlife Ecosystem Restoration Program Conservation Strategy (link to Delta Atlas (link to Delta Historical Ecology Study (link to Delta Science Plan (link to Delta Vision Foundation Report Card (link to Pelagic Organism Decline Reports (link to Public Policy Institute of California Reports (link to Pulse of the Delta (link to The State of the Bay-Delta, 2008 (link to San Francisco Bay National Coastal Conditions Reports (link to Pulse of the Estuary (link to San Francisco Estuary Partnership Comprehensive Conservation Management Program (link to San Francisco Habitat Goals Project (link to State of The Bay Report (link to State of the Birds Report (link to You would get here by clicking on the “what is being done to protect CA’s estuaries” question on the main page (slide 2). This page is long, and thus clicking on the blue links at the top of the page will drop you to that section of the page that deals with that topic. For example, clicking on “Monitoring Programs, Data Sources, and Reports” will drop you down to the Monitoring Programs section about halfway down the page. The blue links under research and monitoring will not be presented this way. Instead, the name of the group will be the actual link.

< > What is the San Francisco Estuary, 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 What is the San Francisco 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 Estuary? The San Francisco Estuary (SF Estuary) is a partly enclosed body of water where salt water from the Pacific Ocean mixes with freshwater from rivers draining the surrounding watershed. The SF Estuary is the largest estuary on the west coasts of North and South America and includes the Golden Gate Strait, San Francisco, San Pablo, and Richardson Bays (western Bays), Carquinez Strait, Suisun, Grizzly, and Honker Bays (eastern Bays), and the Sacramento-San Joaquin River Delta (Delta). The mixing of sea water and freshwater creates characteristic estuarine aquatic habitat that transitions from salty sea water to brackish (less salty) to freshwater. Tides bring water from the Pacific Ocean through the Golden Gate Strait into the estuary while California’s two largest rivers, the Sacramento and San Joaquin, contribute the greatest amount of freshwater to the estuary. The Sacramento and San Joaquin Rivers carry water from the Sierra Nevada and Cascade mountain ranges to the Delta where the transition from freshwater to sea water is observed. The river channels combine and fresh and salty water mix and move back and forth with the tides throughout the SF Estuary. Why is the San Francisco Estuary Important? The SF Estuary is a valuable ecological and economic resource. The natural resources in the SF Estuary are the building blocks of the economy, our communities, and ecosystems. Ecology The continual mixture of salt and fresh water is the foundation of the ecological richness observed in the estuary. The estuary provides food and shelter for more than 750 species of plants, fish, and other wildlife including several endangered or threatened species. 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 year-round. Economy and Community The San Francisco Estuary region attracts and supports a vibrant economy and many communities. The visually striking shorelines and beautiful bays and beaches make it one of the country’s most desirable places to live, work, and visit. The SF Estuary provides water to approximately 30 million Californians and their communities where it is used for drinking water supply, residential yards, community parks, schools, and businesses. The region is home to Silicon Valley, the international hub of the high-tech industry, and is a global tourist destination for water and land recreation including boating, fishing, surfing, swimming, hiking, and biking. SF Estuary resources support important parts of the regional and national 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. How Healthy is the Estuary? The SF Estuary aquatic ecosystem is in a state of crisis, however some parts of the aquatic ecosystem are improving. Changes over the last 150 years have diminished the resiliency of natural resources in the SF Estuary. Conversion of natural landscape and aquatic environments to urban uses, industrial sites, agriculture and managed recreational areas has resulted in removal of more than 90% of aquatic habitat including tidal and freshwater wetlands, sloughs, and riparian areas in SF Estuary and its upper watershed. More than 90 species of plants and animals have regulatory protection to prevent losing them from the SF Estuary ecosystem. The San Francisco Estuary Project State of the Bay Report (2011) shows water quality has improved over the last fifty years due to better sewage treatment systems, solid waste disposal, and chemical regulation. These changes have improved water quality, substantially decreasing observed aquatic toxicity and protecting water for safe swimming. However, persistent water quality problems such as mercury, selenium, and toxicity remain in some portions of the estuary and new water quality concerns are emerging such as negative aquatic life impacts from personal care and pharmaceutical products. The SF Estuary is in crisis due to rapidly declining resident and migratory fish populations, the collapse of California’s salmon fishing industry, changes and declines in the aquatic food web, and water supply limits for aquatic life, agriculture, urban, and industrial uses. The impact of these changes is magnified and concentrated in the eastern part of the SF Estuary, the Sacramento-San Joaquin River Delta, where the high demand for fresh water combined with substantial landscape and hydrological modification amplifies California’s vulnerability to natural drought cycles that can drastically reduce water supply needed to support aquatic habitat, commercial fisheries, agriculture, industry, and communities. - Video at top will be a flyover with specific sites marked – 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?”

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  Where  San Francisco  Health How Healthy is 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 healthy is the SF Estuary? Living Resources Water Habitat Ecological Processes Stewardship Water Habitat Living Resources Ecological Processes Stewardship Links: clicking on “living resources” where it is blue in the text or in the “Questions Answered” box will take you to the next slide (slide 8). Clicking on “water” in either place will take you to slide 44 . “The State of the Bay report” link would take you to How healthy is the SF Estuary? The health of the human body as a whole depends upon the health of its parts – the brain, the bones, the heart. The health of California’s estuaries is no different and depends on the well-being of its parts, also known as attributes, as defined by the authors of The State of the San Francisco Bay Report. These attributes include living resources, water, habitat, ecological processes, and stewardship. 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.

< > 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? …………………………………..………………………………………………………………………………………………………………………………..……… 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 Mammals Plants 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 carousel would be phytoplankton, zooplankton, etc. To get to each living resource page, you can click its name in the “questions answered” box or in the blue link in the text. 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 phytoplankton, zooplankton, benthic organisms, fish, birds, plants, and mammals. 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)

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? Living Resources Water Habitat 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 Phytoplankton Fish Define Focal Categories 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 Zooplankton Benthic Organisms The location of where this page falls is still being determined. How do we determine the health of each living resources? 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.

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? …………………………………..………………………………………………………………………………………………………………………………..……… 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? How healthy are they 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, 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 monitored in the SF Estuary. -pH, dissolved oxygen, and algal blooms all link to viewer windows with basic information on these topics - “Learn more “ links to phytoplankton monitoring page (next slide) - The first question in the “Questions Answered” box links to this page. The “How and where” question links to the next slide (slide 11). The “trends” question links to slide 12. The healthy question links back slide 6 (to the health section there) until more content on this question is developed. “What’s being done about it” links to the laws, regulations, and polices slide (slide 5). These last two questions link to these same places for all of the living resources.

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? …………………………………..………………………………………………………………………………………………………………………………..……… 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 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? How healthy are they in the SF Estuary? What’s being done about it? 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. Twenty-two 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 monitor phytoplankton. Where are the data? More information on phytoplankton monitoring can be found in the Phytoplankton Study Meta Data. Links: - IEP links to - Environmental Monitoring Program links to “Learn more . . “ links to the D1641 report – phytoplankton methods content Meta Data links to

< > 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? How healthy are they 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 < > Pictures off trends graphs that you can click on to get to details 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, species that are not as nutritious for zooplankton. Cyanobacteria, some of which can produce toxins that make humans and pets sick, have been increasing in portions of the SF Estuary. The blue box on the page would present a carousel of graphs (and their captions) about phytoplankton trends. These graphs are on the following slides. These graphs will draw from the live phytoplankton data. 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.)

Note to Reviewer The graphs on slides will be presented as a slide carousel on slide 12. The viewer would see each graph and its caption by clicking on it in the carousel. There are 7 total graphs. Each graph on slide 14 will be viewed individually, but all graphs on slide 15 will be viewed together for comparison.

Instructions for graphs.
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. 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
Text for this chart. Text for this chart Text for this chart, Phytoplankton Species Composition Trends Additional comment about these graphs (to be developed): “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.” 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 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 What are zooplankton, and why are they important? How and where are they monitored in the SF Estuary? What are their trends in the SF Estuary? How healthy are they in the SF Estuary? What’s being done about it? Slide show – Photos SF Estuary zooplankton species (pictures on next slide are part of what will go here) 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)).

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

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 What are zooplankton, and why are they important? How and where are they monitored in the SF Estuary? What are their trends in the SF Estuary? How healthy are they in the SF Estuary? What’s being done about it? 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: 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. Nineteen 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? …………………………………..………………………………………………………………………………………………………………………………..……… 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 zooplankton, and why are they important? How and where are they monitored in the SF Estuary? What are their trends in the SF Estuary? How healthy are they in the SF Estuary? What’s being done about it? < > Slide carousel of graphs Zooplankton Trends in the SF Estuary to 2011 - For the moment, these graphs will be static images and will not link to the live zooplankton data. 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.

Note to Reviewer The graphs on slides will be presented as a slide carousel on slide 19 . The viewer would see each graph and its caption by clicking on it in the carousel. There are 2 total graphs. All graphs on slide 21 and on slide 22 will be viewed together for comparison.

- These graphs will be shown together for comparison.
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). - These graphs will be shown together for comparison.

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? …………………………………..………………………………………………………………………………………………………………………………..……… 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 in the SF Estuary? What are their trends in the SF Estuary? How healthy are they 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) What are benthic organisms? Benthic organisms live at 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 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. Certain fish species, including juvenile salmon, striped bass, and sturgeon, also consume many types of benthic organisms. A large percentage of the benthic organisms found in the SF Estuary are invasive and thus can have negative effects on the health of the estuary. 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? …………………………………..………………………………………………………………………………………………………………………………..……… 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, and why are they important? How and where are they monitored in the SF Estuary? What are their trends in the SF Estuary? How healthy are they 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. EMP monitoring sites are not good for accurately sampling shrimp and crabs, but the CDFW Bay study surveys collect crabs and shrimp monthly using an otter trawl, which is towed near the boom and selectively captures shrimp, crabs, and bottom-feeding fish. Thirty-five fixed stations that are distributed evenly throughout four sub-regions of the estuary, including South, Central, San Pablo, and Suisun Bays. 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 CDFW Bay Study – links to the CDFW bay study page. Benthic Dictionary links to Heather Fuller links to Meta Data links to Benthic BioGuide links to

< > What are Benthic Organism 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  Living Resources  Benthics  Trends What are Benthic Organism 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 QUESTIONS ANSWERED What are benthic organisms, and why are they important? How and where are they monitored in the SF Estuary? What are their trends in the SF Estuary? How healthy are they in the SF Estuary? What’s being done about it? < > Slide carousel of graphs 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 (Potamocorbula amurensis) 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 there has been an obvious collapse of the phytoplankton community in Suisan Bay since the late 1980s. Such declines have had negative impacts on the zooplankton that eat these phytoplankton and the fish that feed on the zooplankton. Notes: - Graphs above are a carousel. Each have their own caption.

Note to Reviewer The graphs on slide 27 will be presented as a slide carousel on slide 25. The viewer would see each graph and its caption by clicking on it in the carousel. There are 3 total graphs.

Live Graph from monitoring data.
Benthic Organism Trends ( ) Live Graph from monitoring data. Abundance of Shrimp in the SF Bay ( ) Abundance of Crabs in the SF Bay ( ) Overall crab abundance has generally increased over time in the SF Bay. Overall shrimp abundance has increased over time in the SF Bay. ”Live graph” comments: - Going to show Potamocorbula abundance from 1987 to present (yearly averages and maybe just show two sites in Suisan Bay that usually have the highest Potamocorbula abundances (D6 and D7). Also going to show seasonal abundances of Potamocorbula. Pie chart with 4 seasons. Also make species composition pie charts (like done with phytoplankton) to show other species besides Potamocorbula. Show two time periods. One from pre-Potamocorbula years (early-mid 80s) and post-Potamocorbula (anything recent). Will sum either sum data from all sites or split up the data regionally.

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 the Types of Fishes 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 fishes in the SF Estuary, and why are they important? How and where are they surveyed in the SF Estuary? What are their trends in the SF Estuary? How healthy are they in the SF Estuary? What’s being done about it? Insert slide show with clickable images of the different types of fish. 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 (that, for the most part, complete (or can complete) their entire life cycle in or very close to the estuary), migratory fish (that must transition between freshwater and marine habitats beyond the Estuary to complete their life cycle), and marine fish (that lay their eggs (spawn) and/or rear in bay habitats). 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 Estuary. 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. Links: Resident fish (in blue type) links to “what are resident fish” page Migratory fish (in blue type) links to “what are migratory fish” page Marine fish (in blue type) links to “what are marine fish” page

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 Resident Fish in the SF Estuary, and Why are They Important? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What are types of fishes in the SF Estuary, and why are they important? What are resident fish? What are migratory fish? What are marine 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 representative species of resident fish health: Delta Smelt Longfin Smelt Sacramento Splittail Delta Smelt (native) Represents: estuarine dependent, short-lived, open shallow water resident Delta smelt (Hypomesustranspacificus) 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] Longfin Smelt (native) Represents: short lived, deep water resident Longfinsmelt (Spirinchusthaleichthys) 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 wiki]. 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. Sacramento Splittail (native) Represents: floodplain spawners, shallow water resident Sacramento splittail (Pogonichthysmacrolepidotus) 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]. Learn more about how resident fish are surveyed. (link to resident fish surveying page) Images of species Alternate Language Delta Smelt Delta smelt are native to the SF Estuary, particularly to the areas upstream of San Pablo Bay including Suisan Bay and the Delta. They are important because the SF Estuary is the only place in the world where these small fish are found, and thus they are part of what makes the Bay area unique from other areas of the country. Delta smelt are nearly translucent in water, with a steel blue sheen to their sides, and are found in open water, mostly away from shorelines and vegetated inshore areas. They move into tidal freshwater habitats, mostly in the Delta, to lay their eggs (spawn) in late winter and spring. Once the eggs hatch, the small fish move downstream throughout low salinity habitats, generally moving into Suisun Bay, Montezuma Slough, and the lower Sacramento River below Rio Vista to rear. Feeding on plankton helps the small fish grow. By the fall, the fish have reached adulthood and begin their gradual migration back upstream into freshwater areas to spawn. Most Delta smelt live for one year – they perish after they spawn --, but some can live up to two years. Because these fish are estuarine-dependent--they spend their entire lives in the estuary--they are also good indicators for the health of the estuary as a whole. Delta smelt are currently protected as a threatened species under state and federal law. Longfin Smelt Longfin smelt are native to California’s bay, estuary, and nearshore coastal environments from the SF Estuary north to the Oregon border. The SF Estuary supports the largest population in California. These small, silvery fish lay their eggs in the freshwater of the upper estuary (Suisan Bay and Marsh and the Delta) and move downstream into the saltier Bay and, occasionally, coastal waters to grow. Most live for two years, but can live up to three years. Longfin smelt are not listed as endangered or threatened under federal law, but the State of California identifies them as a Species of Special Concern. Sacramento Splittail Sacramento splittail are native to the Central Valley of California, and most of their population today can be found in the SF Estuary. They live 7-9 years and can tolerate a variety of environmental conditions. In late winter and early spring, they move upstream to spawn in large, open, shallow, freshwater floodplains in and around the Delta and its tributaries. In May, the hatched fish migrate back downstream into the tidal upper estuary, including Suisun Bay, where they grow in shallow, saltier feeding grounds for a year or two before starting the cycle again. Early flows in winter that open the way for the fish to migrate upstream and the extended duration of floodplain inundation, particularly at Yolo Bypass, for spawning and rearing are two of the most important environmental conditions for the splittail. Splittail feed on zooplankton and benthic organisms including clams and shrimp. The species was delisted in 2003 as a threatened species by the USFWS, but it is still considered at Species of Special Concern by the state. - 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. Images 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 What are the Types of Marine Fish in the SF Estuary, and Why are They Important? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What are types of fishes in the SF Estuary, and why are they important? What are resident fish? What are migratory fish? What are marine 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 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. For more information on other species, see the Report on the fish, shrimp, and crab Sampling in the San Francisco Estuary. These types of marine fish include: Pacific herring [link to heading below] Starry flounder [link to heading below] English sole [link to heading below] California halibut [link to heading below] Shiner perch [link to heading below] Pacific Herring Represent: Commercially important fishery, and brackish spawning and rearing habitat. • Pacific herring (Clupeapallasii) 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. Starry Flounder Represents: Recreationally important fishery, brackish benthic spawning and rearing habitat • 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. English Sole Represents: Commercially important fishery and intertidal and subtidal rearing habitat. California Halibut Represents: Commercially important fishery, recreationally important fishery, benthic and brackish juvenile rearing habitat. Shiner Perch Represents: Eelgrass beds and vertical structure habitat Learn more about how marine fish are surveyed. (link to fish surveying slide) Images of species Alternate Language Pacific Herring Pacific herring are native marine fish that are found along the Pacific coasts of North America and northeast Asia. The SF Estuary is one of the most important spawning areas in the eastern Pacific for these dark blue and olive colored fish with silvery bellies. Once a year, the herring enter the estuary and lay their eggs in Central and Richardson Bays from late fall through early spring, beginning their lives in the shallow areas of the estuary before gradually migrating into deeper water and finally back into the ocean. They can live up to 19 years. The fish support a commercial fishery--mainly for roe (herring eggs)—that is the last commercial finfish fishery left in the Bay. They are also important prey for marine fish and bird predators. In 1993, the total North American Pacific herring fishery collapsed due to overfishing and is slowly recovering. They are not listed under the Endangered Species Act. Starry Flounder Starry flounder are a native marine fish that are found along the Pacific coasts of North America and Asia. They are bottom-dwelling, predatory flatfish that depend on estuaries like the SF Estuary for spawning and rearing before migrating back into the ocean. During December and January, the fish enter the estuary to spawn. Once the eggs hatch, the young fish spend their days eating plankton and benthic organisms and growing big enough to return to the ocean. The fish are preyed upon by herons, harbor seals, and other marine life. Starry flounder are also a sport fishery in California. English Sole English sole are native marine flatfish, brown on one side and white or pale yellow on the other, found in coastal waters from Baja California to Alaska. They tend to spawn in nearshore and estuarine environments, including the San Francisco Bay. Because English sole are a type of flatfish (like flounder), juveniles undergo metamorphosis: their left eye migrates to their right side, and the fish starts living demersally, or along the sea floor. Females grow twice as large as males and can live up to twenty years. English sole are an important species for commercial trawl fishing, though the majority of the catch is taken in Washington and Oregon. This species has become more abundant in recent years, benefiting from fishing restrictions aimed at protecting other bottom-dwellers. California Halibut California halibut are native marine flatfish, brown or blackish with light and dark splotches on one side and white on the other, found in coastal waters from Baja California to British Columbia. Most adult halibut live in these coastal waters, but they enter estuarine environments, such as the SF Estuary, to spawn. Once the eggs hatch, the juvenile halibut spend time growing and maturing in the estuary before returning to the ocean. They prefer shallow, sandy environments and feed almost exclusively on anchovies and other small fish. They are relatively abundant and are a popular sport fish in California. Shiner Perch Shiner perch are native fish that are found in marine, bay, and estuarine environments along the Pacific coast of North America. These silver to gray fish, that can live up to 7 years, move into the SF Estuary when they are ready to spawn. Once the eggs hatch, the young fish spend time in the estuary, feeding mostly on zooplankton and growing in the protective waters, before returning to the ocean. They are plentiful in the SF Estuary and are a popular sportfish. Images of species Images 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 Migratory What are the Types of Migratory 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 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 migrate to the ocean where most of their growth occurs. Anadromous fish species traverse the San Francisco Estuary twice during their lives, on their way to and from their spawning grounds on the rivers of the Central Valley. There are many anadromous fish species in the San Francisco Estuary’s fish fauna, too many to describe all of them here. Below, we describe a few of the anadromous fish species that are commonly used to track the health of the San Francisco Estuary. For more information …. [websites] These types of migratory fish include Chinook salmon [link to heading below] Steelhead [link to heading below] Green and white sturgeon [link to heading below] Pacific lamprey [link to heading below] Striped Bass [link to heading below] Chinook Salmon Chinook salmon (Oncorhynchus tshawytscha), also known as King salmon, are the largest members of the Pacific salmon. These fish once spawned in most of the perennial rivers between central California and Alaska. However, their behavior of returning to spawn in the same waterway where they incubated as eggs leads to divergence among populations of different rivers; even within rivers, different distinct populations (known as runs) can co-exist without interbreeding. The Sacramento River and its tributaries support four distinct runs of Chinook salmon, more different types than any river system in North America. These runs – winter, spring, fall, and late-fall – are distinguished by the season during which adults return to freshwater to spawn and other behavioral, life history, ecological, and genetic differences. As a result, each run may represent the health of different estuarine and riverine habitats. Sacramento winter run Represents: Native Endemic, Sacramento river mainstem habitat during summer and fall; shallow water estuarine conditions during winter The Sacramento River winter-run Chinook salmon once spawned in high elevation habitats on the Sacramento River and its tributaries in the far northern and northeastern parts of this state. After the construction of Shasta and Keswick Dams in the middle of the last century, this run’s spawning habitat was limited to short stretches of river below these dams. This run, which is unique throughout the world, enters freshwater in the winter, but delays spawning until spring; its eggs incubate in late-spring and summer and are thus exposed to very warm water (temperatures >56oF are lethal to Chinook salmon eggs). Winter-run Chinook salmon were listed under the federal and state Endangered Species Acts in Commercial and sportfishing for this run is minimized by fishing regulations. Central Valley spring run Represents: Native, Sacramento river mainstem and small tributary habitat during summer and fall; shallow water estuarine conditions during spring The Central Valley spring-run Chinook salmon once spawned in smaller rivers and creeks at high elevation throughout the Sacramento River and San Joaquin River watersheds. The construction of major dams in the middle of the last century, limited this run’s spawning habitat. The San Joaquin River Valley’s spring run were extirpated following construction of Friant Dam. Today, spring-run Chinook salmon spawn in significant numbers on the mainstem of the Sacramento River below Keswick Dam, the Feather River, and several small creeks on the slopes of Mt. Lassen. This run enters freshwater in the spring, but delays spawning until fall; they spend several months holding in small creeks (without eating!), waiting for water temperatures to fall to levels that will support successful egg incubation. Spring-run Chinook salmon were listed under the federal and state Endangered Species Acts in the mid-1990’s. Commercial and sportfishing for this run is minimized by fishing regulations. Sacramento late-fall run Represents: Native, Sacramento river mainstem habitat during late- fall; shallow water estuarine conditions during winter The Sacramento River’s late-fall run Chinook salmon spawn are larger and migrate and spawn later in the fall than fall run Chinook salmon. This run predominantly spawns below Keswick Dam immediately after arriving. Their offspring quickly migrate downstream, towards the Estuary and Ocean. This run is not protected under the Endangered Species Act and are caught in the marine commercial and sport fishery. Central Valley fall run Represents: Native, Important Commercial Fishery, Important Sport Fishery, Sacramento and San Joaquin and tributary river mainstem habitats during fall and winter; shallow water estuarine conditions during spring Now, the most abundant run of Chinook salmon using the San Francisco Estuary, the Central Valley’s fall run of Chinook salmon supports a commercial and sport fishery from Central California through Southern Oregon. This run enters freshwater during the fall and reproduces soon after reaching spawning grounds on the mainstem of most of the Central Valley’s larger rivers. These fish hatch in winter and migrate to the Estuary and ocean in the spring. Paradoxically, their juvenile migrations occur at approximately the same time as spring run Chinook salmon. This run is not protected under the Endangered Species Act and commercial and sport-fishing are regulated by state and federal agencies. Steelhead Steelhead (Oncorhynchus mykiss) are a migratory form of rainbow trout and are distant cousins of Chinook salmon. Unlike the Central Valley’s Chinook salmon, Central Valley steelhead may live in freshwater for several years before migrating to the ocean. Also, they are capable of surviving spawning, migrating to the ocean again, and returning to spawn again. Steelhead historically spawned in the highest accessible elevations of most Central Valley River systems. Construction of multiple dams on most of the Central Valley’s rivers has reduced their range substantially. Steelhead are listed as threatened under the federal Endangered Species Act. Green and White Sturgeon Two species of sturgeon (genus: Acipenser) spawn in the Central Valley. These fish can live for many decades and spawn multiple times. They may grow to sizes greater than 6 feet in length. Sturgeon spawn in the mainstem of large rivers. They feed mostly on benthic macroinvertebrates but will eat fish when available. Because of their large, dermal scales (bony plates), sturgeon are impervious to most predators. Green sturgeon in the San Francisco Estuary are listed as threatened under the federal Endangered Species Act. The more abundant white sturgeon support a sportfishery in the San Francisco Estuary’s main bays. Pacific Lamprey •Pacific lamprey – rest of text Striped Bass Striped bass (Morone saxatilis) were intentionally introduced to the San Francisco Estuary from the Atlantic Coast in These predators eat other native and non-native fish (piscivorous) as well as large macro-invertebrates. They support a vibrant sportfishery in the Sacramento-San Joaquin Delta and the bays of the San Francisco Estuary. Striped bass enter the lower mainstems of the Central Valley’s major rivers to spawn during the summer. Their eggs float downstream and (if they are not eaten by other fish) hatch in or near the Sacramento-San Joaquin River Delta. These fish rear in the Estuary’s Low Salinity Zone (LSZ: Link to Portal’s Water Quality Page) and the size of their juvenile (young-of-year) population is considered to be a good indicator of estuarine health. Learn more about how migratory fish are surveyed. (link to fish monitoring page) Images of species QUESTIONS ANSWERED What are types of fishes in the SF Estuary, and why are they important? What are resident fish? What are migratory fish? What are marine fish? Alternative Language Chinook Salmon Chinook (king) salmon are native to California. These white, pink, or red fish are anadromous, meaning that they are born in freshwater streams, migrate to the ocean to feed and grow, and return to the streams where they were born to spawn and die. Four genetically distinct runs—the upstream migrations—of Chinook spawn in the Sacramento-San Joaquin River system and pass through the SF Estuary. These runs are named for the season when the majority of the run enters freshwater as adults and include the Central Valley fall and late fall-run, the Central Valley spring-run, and the Sacramento River winter-run. The fall run—the migration occurs from July to December and spawning takes places from October through December—and the late fall run—the migration occurs from mid-October through December and spawning takes place from January through mid-April—are the most abundant of the Central Valley races and are part of large commercial and recreational fisheries in the Pacific ocean and popular sport fisheries in the rivers and streams. They are currently a species of concern under the federal Endangered Species Act. The spring run migration occurs from late March through September and spawning occurs from mid-August through early October. Historically, spring-run Chinook were the most abundant race in the Central Valley, but more recently, their numbers have been greatly reduced. They are listed as threatened under state and federal endangered species acts. The winter-run Chinook migrate from the ocean under the Golden Gate Bridge from November through May and pass into the Sacramento River from December through early August. Spawning occurs in the upper main-stem of the Sacramento River from mid-April through August, after which the juvenile fish move downstream and enter the Delta from September through June. Most of their historic spawning grounds are now blocked by dams, but cool summer water releases from the dams have helped the population recover in the past. They are listed as endangered under the state and federal endangered species acts. Steelhead Steelhead trout, a type of rainbow trout, are native to California. These silvery, black-spotted, and red-striped fish are anadromous, meaning that they are born in freshwater streams, migrate to the ocean to feed and grow, and return to the streams where they were born to spawn. Typically, the juvenile steelhead will live in freshwater for one to three years before they migrate to the ocean, where they may spend one to two years growing and maturing before returning to their native streams to spawn. Unlike salmon, steelhead may make this spawning journey between two and four times in their life-times. Most live for around six years but can live up to nine. They tend to eat estuarine insects, benthic organisms, and eventually other fish. In the SF Estuary, steelhead are listed as threatened by the federal Endangered Species Act. It is estimated that the number of steelhead in California has declined 50% in the last 30 years—from an estimated 500,000 to only 250,000 adults (McEwan and Jackson 1996). Steelhead runs in the SF Bay tributaries are estimated to be below 10,000 fish (Leidy 2000). The CDFW operates a regulated recreational steelhead fishery on hatchery-produced steelhead, and regulations vary by stream. Green and White Sturgeon Green and white sturgeon are native fish that are known to feed in estuaries and bays up and down the west coast of North America. Both are anadromous, meaning that they are born in freshwater streams, migrate to the ocean to feed and grow, and return to the streams where they were born to spawn. Green and white sturgeon are believed to spend the majority of their lives in near-shore oceanic waters, bays, and estuaries where they feed on benthic organisms by sucking them up their snout. These fish are long-lived—ages up to 42 years have been documented, but their maximum life span may be between 60 and 70 years. Historically, green sturgeon have had limited distribution in California, with most of their spawning taking place in the Klamath and Sacramento Rivers. Today, most of their spawning takes place in the Klamath and its tributaries, and they are listed as threatened under the federal endangered species act. White sturgeon, however, are abundant in the SF Estuary and are managed as a popular sport fish. Pacific Lamprey Pacific lamprey are native fish whose range extends along the west coast of North America and along the eastern coast of Asia. These eel-like fish are anadromous, meaning that they are born in freshwater streams, migrate to the ocean to feed and grow, and return to the streams where they were born to spawn. When they are born, lamprey burrow into the bottom of the stream and can live there between five and seven years. Afterwards, they migrate downstream to the Pacific Ocean where they become predatory and prey on other fish, including salmon and various types of flatfish, for several years before returning to their natal streams to spawn and die. Although lamprey populations seem to be declining, they have not yet been identified as threatened or endangered by state or federal law. Striped Bass Striped bass are not native to the SF Estuary. They were introduced into the San Francisco Bay in 1879 and grew to large enough numbers to support a commercial fishery. The fishery closed in 1935, but a sport fishery continued and remains popular today. These long-lived fish can tolerate a range of salinities. They spend most of their lives in the protective bays of the estuary but will occasionally move out into the ocean. They also move upstream when they are ready to spawn. As young fish, the bass prey on zooplankton and benthic organisms. Once they are large enough, however, they become predatory, eating other fish, including juvenile salmon. Images of species Images of species

< > 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? How are resident fish surveyed? How are migratory fish surveyed? How are marine 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 < > Slide carousel of graphs How and where are fish surveyed? The San Francisco Estuary fish fauna is surveyed regularly by numerous fish sampling programs operated by state and federal fish and wildlife agencies. The methods used to survey fishes vary depending on their behavior and size as well as by the habitats (depth, clarity, currents) where they live. A short sample and description of the fish sampling programs whose data are used in this portal is provided below. New data sets are continuously uploaded to this portal as the need arises; for descriptions of additional fish sampling programs in the Estuary, visit these websites: for resident and marine fishes (link to: and for migratory fishes (link to: [INSERT SLIDE SHOW -- Slides include: Bay study sampling program map (AMYE -- Ali sent you some files for this that were too big/numerous for her to manage), Fall midwater trawl sampling map (link to: beach seine image (link to: fall midwater trawl sampling image (link to: 20mm Survey (link to Since 1995, CDFW has sampled 41 fixed locations throughout the Delta and downstream to the eastern portion of San Pablo Bay and Napa River. Bi-weekly surveys are taken from mid-March through early July using a weighted sled to access the bottom. This survey catches mm fishes best. In 2008, six stations were added. Adult Striped Bass Program (link to CDFW staff calculate adult striped bass abundance, relative abundance, harvest rate, and survival rate by using data from Commercial Passenger Fishing Vessels (Party Boats; CPFV), various creel surveys, and a mark-recapture program. They monitor the relative abundance of adult striped bass by calculating catch per unit effort (CPUE) from data submitted by Commercial Passenger Fishing Vessels. The Department’s Marine Region compiles the data. Fall Midwater Trawl Survey (FMWT) (link to: Since 1967, California Department of Fish and Wildlife (CDFW) has sampled 100 fixed locations in San Pablo Bay, Suisun Bay, Suisun Marsh, and the Sacramento-San Joaquin Delta once a month between September and December using a net that is towed behind a boat. This survey counts, identifies, and measures mainly resident (link to: Portal's Resident Fish page) fish that occupy open-water habitats. The original intent of this survey was to measure striped bass abundance, but more recently, 22 additional stations were added to monitor delta smelt distribution. Fish Salvage Monitoring (link to Since 1957, the US Bureau of Reclamation (BoR) has salvaged fish at the Tracy Fish Collection Facility (TFCF). The Department of Fish and Game's Fish Facilities Unit, in cooperation with DWR, began salvaging fish at the Skinner Delta Fish Protective Facility (SDFPF) in The salvaged fish are trucked daily and released at several sites in the western Delta. Salvage of fish at both facilities is conducted 24 hours a day, seven days a week at regular intervals. Sampling of entrained fish at the SDFPF and TFCF is the source for DFG's daily salvage and loss estimates for the monitoring of incidental take of listed fish species. Salmon Surveys (link to: Salmon are among our most iconic, ecologically and economically important migratory (link to: Portal's Migratory Fish page) fish species. CDFW's Fisheries Branch Anadromous Resource Assessment Unit compiles annual population estimates of adult (spawning) Chinook salmon in the Central Valley into its "GrandTab" report (link to: from a variety of sources estimating population size for late-fall, winter, spring, and fall-runs of Chinook salmon. These estimates are based on counts of fish entering hatcheries and migrating past dams, carcass surveys, live fish counts, and ground and aerial redd (salmon nest) counts conducted by CDFW, the US Fish and Wildlife Service, the California Department of Water Resources, the East Bay Municipal Utilities District, the US Bureau of Reclamation, the Lower Yuba River Management Team, and the Fisheries Foundation of California. Estimates of the number of fish returning to Central Valley waterways (termed "escapement") are converted by the US Fish and Wildlife Service into salmon production estimates, that include the number of Chinook salmon taken in the commercial and sport salmon fishery; Central Valley salmon production [link to: estimates are used in the portal. San Francisco Bay Study (Bay Study) (link to: Since 1980, CDFW has sampled fixed stations throughout the Estuary once a month throughout the year at numerous fixed sampling locations. This survey counts, identifies, and measures resident (link to: Portal's Resident Fish page) and marine (link to: Portal's Marine Fish page) fish that occupy open-water and bay floor habitats. Smelt Larva Survey (link to Since 2009, CDFW has sampled 35 locations throughout the Delta and upstream into the Sacramento and San Joaquin Rivers. Bi-weekly surveys are taken from early January through early April by towing a net behind a boat. This is the newest CDFW fish survey and is meant to specifically monitor delta smelt larvae. Spring Kodiak Trawl (link to In the mid-90’s, this gear was shown to effectively capture delta smelt, and in 2002, the survey started being used to monitor distribution of delta smelt. CDFW samples 39 locations over the course of 4-5 days annually from San Pablo Bay upstream to Stockton on the San Joaquin River, Walnut Grove on the Sacramento River, and the Sacramento Deep Water Ship Channel. Monthly surveys are taken from January through May by towing a net behind two boats. Suisun Marsh Survey (link to: UC Davis has sampled the fishes and invertebrates of Suisun Marsh every month since 1980 using an otter (bottom) trawl towed behind a small boat at numerous fixed sampling stations throughout the Marsh's many channels. The Suisun Marsh survey captures mainly resident fish species in shallow openwater and shallow marsh habitats featuring brackish and fresh water. The abundance of juvenile Chinook salmon emigrating from the Central Valley's tributaries on their way to the ocean are estimated by a variety of Fish and Wildlife service juvenile fish sampling programs [link to: that operate in and around the Delta). Townet Survey (link to Since 1959, CDFW has sampled 32 locations throughout the Delta to monitor small, juvenile striped bass. Bi-weekly surveys are taken from early June through late August by towing a sled with mesh behind a boat. In 2011, eight locations were added to the survey.

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? …………………………………..………………………………………………………………………………………………………………………………..……… 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 fish trends? What are resident fish trends? What are migratory fish trends? What are marine fish trends? Slide carousel of resident, marine, and migratory fish trend graphs What are SF Estuary Fish Trends? Many native fish abundance trends are declining in the San Francisco Estuary. Learn more about resident, migratory, and marine fish trends in the SF Estuary. - 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 migratory, and for marine). - It seems like this page is a little unnecessary, but somehow we need a launch to three trend groups. Consider combining all pages? Might be too much information.

< > What are SF Estuary Resident 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 Resident 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 QUESTIONS ANSWERED What are SF Estuary fish trends? What are resident fish trends? What are migratory fish trends? What are marine fish trends? < > Slide carousel of graphs What are SF Estuary Resident Fish Trends? There are numerous resident fish species in the SF Estuary. This portal depicts the estuary's resident fishes by presenting data on three native resident species that use the estuary in very different ways. Specifically, the FMWT abundance indices for Delta smelt, longfin smelt, age-0 striped bass, and Sacramento splittail are presented below.The abundance indices for these three species rapidly declined to record low levels around In 2005, the IEP formed a team to evaluate the potential causes of these and other declines. (link to: - There will be a carousel of graphs in the blue box area showing resident fish trends. 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.

CAPTION: 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. CAPTION: 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. All longfin smelt populations in the state were listed under the California Endangered Species Act in The US Fish and Wildlife Service declared that the SF Estuary population of longifn smelt warranted listing, but listing was precluded by budgetary constraints. CAPTION: 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.

< > Trend Graph What are SF Estuary Marine 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  Marine What are SF Estuary Marine Fish Trends? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What are SF Estuary fish trends? What are resident fish trends? What are migratory fish trends? What are marine 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 < > Slide carousel of graphs What are Marine 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. Five species were selected to demonstrate abundance trends for a diverse assemblage of life history traits within the marine habitat of the San Francisco Estuary, including Pacific Herring, Starry Flounder, English Sole, California Halibut, and Shiner Perch. All data presented here is from the San Francisco Bay Study. Trend Graph

Trend Graph Trend Graph Trend Graph Trend Graph Trend Graph
CAPTION: 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. CAPTION: Abundance indices for Starry Flounder indicate a declining trend through time, particularly in the most recent five years. CAPTION: Abundance indices for this species show increases in English Sole since the late 1990s. CAPTION: Increases in abundance index for California Halibut began in the 1980s and 1990s with recent increases in water temperature. However, species have been declining with increases in cold water temperatures. CAPTION: Shiner Perch abundances have varied widely over the studies period, but have been decreasing for the last five years, fluctuating partially with salinity changes in the Estuary. Trend Graph Trend Graph Trend Graph Trend Graph

< > What are SF Estuary Migratory 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 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 QUESTIONS ANSWERED What are SF Estuary fish trends? What are resident fish trends? What are migratory fish trends? What are marine fish trends? < > Slide carousel of graphs What are Migratory 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. There are many anadromous fish species that pass through the SF Estuary on their way to and from the ocean. Learn more about these fish and efforts to recover them. [link to: This portal depicts migratory fish population trends with four distinct populations of Chinook salmon and non-native striped bass. Chinook salmon: 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 (in-river returns plus fish caught in the commercial or sport fishery) is presented above for Sacramento fall-run, San Joaquin fall run, Central Valley spring-run, and Sacramento winter-run Chinook salmon. The blue box above represent where a carousel of graphs will be that the viewer can click on to see the graph and its captions. These graphs are depicted on slide 42.

CAPTION: The fall run of Sacramento River Chinook salmon is a major (and in some years, the only major) contributor to the commercial ocean fishery for this species throughout most of northern California and southern Oregon. Production of this population between 1967 and 1991 averaged over 115,000 fish per year and was targeted to increase to 230,000 fish per year (indicated by the AFRP Production Target line on this graph) by the federal Central Valley Project Improvement Act of However, natural production of this fish continues to decline and averaged 72,595 between 1992 and Recent major declines led to the unprecedented closing of California’s commercial salmon fishery in 2008, 2009 and most of 2010. CAPTION: 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. Since then, winter run Chinook have depended on habitat created by cold-water releases from Shasta Reservoir. The population has experienced a catastrophic decline since the late 1960's and was listed under the federal and California Endangered Species Acts in the early 1990's. The AFRP (Anadromous Fish Restoration Program) Production Target of 110,000 fish indicated on this graph is a target set under the federal Central Valley Project Improvement Act of Winter run Chinook salmon production averaged 6,320 fish per year from ] CAPTION: Believed to be the most abundant Chinook salmon population historically, spring run populations have declined substantially over the past half century or more. 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. The population was listed under the federal and California Endangered Species Acts in the early 1990's. The AFRP (Anadromous Fish Restoration Program) Production Target of 68,000 fish indicated on this graph is a target set under the federal Central Valley Project Improvement Act of Production in the period averaged 13,654 fish per year, slightly more than half the production in the period. CAPTION: Historically, fall run Chinook salmon spawned in the mainstem San Joaquin River and its major tributaries. The San Joaquin spawning population was eliminated in the middle of the last century following the construction of Friant Dam. Production on the San Joaquin's major tributaries (the Stanislaus, Tuolumne, and Merced Rivers) has continued to decline in recent decades, from more than 38,000 fish per year between 1967 and 1991 to less than half of that (18,700 fish per year) over the last two decades. CAPTION: Despite its success since being introduced to the Estuary in 1879, production of juvenile striped bass has declined substantially over the past two decades.

Slideshow of birds 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  Birds What Birds are 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 Slideshow of birds in the SF Estuary What birds are in the SF Estuary, and why are they important? How and where are birds surveyed in the SF Estuary? What are SF Estuary bird trends? How healthy are they in the SF Estuary? What is being done about it? QUESTIONS ANSWERED Tri-colored blackbird – links to Ducks – link to Tidal marsh birds (song sparrow, common yellowthroat, clapper rail) - Snowy plover - Least tern - Shorebirds - Double-crested cormorant Other resources: State of the Birds San Francisco Bay The San Francisco Estuary provides critical habitat for a wide variety of bird species. Birds are an ecologically diverse group, and this diversity is reflected in the wide range of bird species dependent on different portions of the Estuary’s ecosystems. Birds breed, feed, rest, and find refuge from predators in tidal marshes, tidal flats, seasonal marsh, permanent freshwater marsh, salt ponds, diked wetlands, open water, rocky areas, sandy beaches, riparian areas, river banks, agricultural areas, pastures, grasslands, woodlands, and urban areas. Some bird species are present year-round, while others are migratory. Some species are present only during the breeding season, some only during the winter, and some only during migration. Some bird species rely more on aquatic food web resources, others more on the terrestrial food web resources. Many bird species feed on fish, birds and invertebrates, using specialized hunting techniques to exploit particular prey species. Others primarily eat seeds or other plant parts, at least during certain times of year when insects are less available.

How and Where are Bird Populations Tracked 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  Birds  Surveyed How and Where are Bird Populations Tracked 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 birds are in the SF Estuary, and why are they important? How and where are birds surveyed in the SF Estuary? What are SF Estuary bird trends? How healthy are they in the SF Estuary? What is being done about it? QUESTIONS ANSWERED Notes. Bird survey map: see if we can access data from the Avian Knowledge Network. Not sure if they have web syndication. For this page, we could request the map of survey locations and data summaries as shown above. Birds are have been surveyed in many places in the SF Estuary. The map above shows a subset of the bird survey locations. For more bird survey locations, data, and other information, please see the following: California Avian Data Center: California Partners in Flight data: Point Blue Conservation Science / PRBO: California Department of Fish and Game: data, including Bird Species of Special Concern: Breeding waterfowl surveys: Breeding Bird Surveys (BBS)-

What are SF Estuary Bird Population 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  Birds Trends What are SF Estuary Bird Population 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 birds are in the SF Estuary, and why are they important? How and where are birds surveyed in the SF Estuary? What are SF Estuary bird trends? Tidal Marsh Birds Herons and Egrets Wintering Waterfowl Breeding Waterfowl How healthy are they in the SF Estuary? What is being done about it? QUESTIONS ANSWERED Nesting tidal marsh birds- San Francisco Bay Nesting herons & egrets San Francisco Bay Breeding waterfowl – Napa-Sonoma Marsh, Suisun Marsh, Sacramento – San Joaquin Delta Wintering waterfowl San Francisco Bay - Content here is still under development. Bird population trends in the San Francisco Estuary are variable. Many species are decreasing, while a few are decreasing.

What are SF Estuary Tidal Marsh Bird Population 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  Birds Trends  Tidal marsh birds What are SF Estuary Tidal Marsh Bird Population 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 Tidal marsh birds – San Francisco Bay, San Pablo Bay, and Suisun Bay These species are rare to common year-round residents of tidal salt, brackish, and freshwater marshes, where dense vegetation and water meet. Some also live in non-tidal marshes and riparian wetlands. All are considered special status species or subspecies by the State of California. What are SF Estuary bird trends? Tidal Marsh Birds Herons and Egrets Wintering Waterfowl Breeding Waterfowl QUESTIONS ANSWERED Suisun, San Pablo and Alameda Song sparrow (Melospiza melodia maxillaris, M. m. samuelis, and M. m. pusillula) Conservation status: There are four subspecies of song sparrow in the San Francisco Estuary, including one in the Delta (Modesto song sparrow, not reported here), all considered Species of Special Concern by the California Department of Fish and Game. Residence status: This species is quite common in tidal marsh, non- tidal marsh and riparian areas with dense understory vegetation. The species is resident year-round in tidal marshes, and defends breeding territories from late February to late July. Habitat use: This species prefers densely vegetated tidal marshes with song perches and cover for nesting and predator avoidance. Dominant plant species vary with salinity. Trends: Trends for this species are based on density (birds per hectare) calculated from point count surveys in San Francisco, San Pablo, and Suisun Bay tidal marshes. Density has been decreasing in San Pablo and Suisun Bays since In San Francisco Bay, density increased substantially but in more recent years has been decreasing again. More information: Bird Species of Special Concern Species Account PRBO Riparian Bird Conservation Plan - Species Account PRBO newsletter PRBO tidal marsh songbird monitoring Cornell species account Wikipedia species account Click graphs to enlarge California black rail (Laterallus jamaicensis coturniculus) Conservation status: The California black rail is a Threatened and Fully- protected Species in the state of California. Residence status: This species is found year-round in dense tidal marsh in San Pablo Bay, Suisun Bay, and the Sacramento-San Joaquin Delta; in the Delta it is also found in non-tidal marshes. Habitat use: in SF Bay, this species prefers high tidal marsh pickleweed and bulrush habitat with open understory and dense canopy. In the Delta, black rails use densely vegetated in-channel islands with willow and dogwood, as well as managed marshes dominated by tules. Trends: Trends for this species are based on density (birds per hectare) calculated from point count surveys in tidal marshes in San Pablo Bay and Suisun Bay. Density of Black Rails has increased overall since In San Pablo Bay, the positive trend has occurred since 1996; in Suisun Bay, the positive trend is only evident in recent years ( ). This positive trend is likely attributed to increased availability and quality of habitat due to restoration. More information: PRBO Secretive Tidal marsh bird monitoring UC Berkeley Black Rail Project Cornell Lab species account Wikipedia species account Click graphs to enlarge Common yellowthroat (Geothlypis trichas) Conservation status: There are two subspecies in the SF Estuary. The salt marsh common yellowthroat of San Francisco and San Pablo Bay is considered a Species of Special Concern by the California Department of Fish and Game. Other subspecies are found in the Delta and riparian areas around the SF Estuary. Residence status: The species is resident year-round in the SF Estuary but is migratory elsewhere in California, wintering in Latin America. The species breeds in tidal marshes, and in non-tidal freshwater marshes, including riparian areas. Habitat use: This species prefers wetlands with a tall, dense understory including cattails and tules. Trends: Trends for this species are based on density (birds per hectare) calculated from point count surveys in San Francisco, San Pablo, and Suisun Bay tidal marshes. Density of Common Yellowthroats in the SF Bay has not changed significantly since In San Pablo and Suisun Bays, density has increased significantly since 1996, but the trend has abated in recent years in San Pablo Bay. More information: Bird Species of Special Concern Species Account PRBO Riparian Bird Conservation Plan - Species Account PRBO Tidal marsh songbird monitoring Cornell Lab species account Wikipedia species account Click graphs to enlarge HS’s and DM-T’s work Source: State of San Francisco Bay Report Technical appendices More information: PRBO San Francisco Bay monitoring PRBO Tidal marsh songbird monitoring

What are SF Estuary Heron and Egret Bird Population 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  Birds Trends  Herons & Egrets What are SF Estuary Heron and Egret Bird Population Trends? …………………………………..………………………………………………………………………………………………………………………………..……… What are SF Estuary bird trends? Tidal Marsh Birds Herons and Egrets Wintering Waterfowl Breeding Waterfowl QUESTIONS ANSWERED Heron and egret nesting 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 Great blue heron and Great egret (Ardea herodias and Ardea alba) Conservation status: The great blue heron and great egret are not listed species, but, as both are important predators, these species are considered as useful indicators of ecosystem health. The locations of their nesting colonies are tracked by the California Department of Fish and Wildlifes’ California Natural Diversity Database (CNDDB) (link to website) Residence status: This species is found year-round throughout the SF Estuary in a variety of habitats. Habitat use: In the SF Estuary, these species nest colonially in tall stands of trees in marshes, along river banks and sloughs, near agricultural areas, and sometimes in suburban neighborhoods. Egrets and herons forage within several kilometers of their nest trees, in wetland habitats. They eat fish, frogs, amphibians, large aquatic and terrestrial invertebrates, and small birds. Trends: Trends for this species are based on nest density (nests per 100 square km) and nest success (nests with 1 chick surviving to fledge) calculated from colony surveys conducted in San Francisco, San Pablo, and Suisun Bays. Heron and egret nest density has decreased in central SF Bay since In San Pablo Bay, nest density has increased more than nine-fold in that time, although density values were lower than the other regions; in Suisun Bay, nest density has remained stable. This positive trend in San Pablo Bay is likely attributed to increased availability and quality of habitat due to restoration. (If decide to include nesting success: Heron and egret nest success has declined since 1991.) More information: Audubon Canyon Ranch Cornell Lab species account Wikipedia species account Danika Melcer – Tsao’s work Acknowledgements: State of the Bay 2011

What are SF Estuary Wintering Waterfowl Bird Population 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  Birds Trends  Wintering waterfowl What are SF Estuary Wintering Waterfowl Bird Population Trends? …………………………………..………………………………………………………………………………………………………………………………..……… What are SF Estuary bird trends? Tidal Marsh Birds Herons and Egrets Wintering Waterfowl Breeding Waterfowl QUESTIONS ANSWERED 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 Dabbling ducks Diving ducks Click graph to enlarge Click graph to enlarge What are Wintering Waterfowl? “Over-wintering” is when an animal migrates to another habitat for the winter. “Wintering waterfowl” are what waterfowl are called when they are over-wintering. What is the Difference Between Dabbling and Diving Ducks? Diagram of Diving and Dabbling Duck Foraging (Source: Dabbling and diving, as seen in the diagram, are simply two feeding behaviors. Ducks are differentiated by their feeding behavior. Winter waterfowl population trends show a difference in abundance depending on feeding behavior (see graphs above). Dabbling Ducks Feeding Behavior: Dabbling, feed at or just below the surface in shallow water. Diet: Seeds, aquatic vegetation, invertebrates (e.g., insects, worms, snails) Habitat: Wetlands, ponds with shallow water and submerged vegetation Trends: Trends for diving ducks are based on density (birds per unit hectare) using aerial and on-the-ground counts in South SF Bay, Central SF Bay, North SF Bay, and Suisun Bay. Examples of Dabbling Ducks: Diving Ducks Feeding Behavior: Diving, feed in deeper waters by diving below the surface. Diet: Fish, crustaceans Habitat: Subtidal, submerged coastal areas Trends: Trends for diving ducks are based on density (birds per unit hectare) using aerial and on-the-ground counts in South SF Bay, Central SF Bay, North SF Bay, and Suisun Bay. Examples of Diving Ducks: Acknowledgements: State of the Bay 2011

What are SF Estuary Breeding Waterfowl Bird Population 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  Birds Trends  Breeding Waterfowl What are SF Estuary Breeding Waterfowl Bird Population Trends? …………………………………..………………………………………………………………………………………………………………………………..……… What are SF Estuary bird trends? Tidal Marsh Birds Herons and Egrets Wintering Waterfowl Breeding Waterfowl QUESTIONS ANSWERED 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 Breeding waterfowl abundance Delta trendsl Suisun trendsl Napa-Sonoma trendsl State-wide trendsl Click graphs to enlarge Click here: Methods for Breeding waterfowl surveys Mallard (Anas platyrynchos) Conservation status: Residence status: Habitat use:. Trends:. Population estimates….. More information: Calif Dept of Fish and Wildlife Waterfowl Program Central Valley Joint Venture USGS Western Ecological Research Center – Breeding Waterfowl Breeding Ecology USGS Waterfowl Identification Guide Mallard identification Department of Water Resources Suisun Marsh Program Cornell Lab species account Wikipedia species account Acknowledgements: California Department of Fish and Wildlife Waterfowl Program:

< > 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? Water Quantity Water Quality How do we determine the health of water quantity? How do we determine the health of water quality? < > 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. Why is Water a Key Attribute? Water is a key attribute of estuaries because it is a necessary ingredient of any aquatic ecosystem. Estuaries are aquatic environments defined by the interaction and mixing of fresh water from rivers and streams with saltwater from the ocean. The position and size of this mixing zone are controlled by the tides and freshwater inputs. Water quantity and (link to WATER QUANTITY) water quality (LINK TO WATER QUALITY) are two measurable properties that have direct effects on the health of an estuary. Learn more about the most recent evaluation of the state of the SF Bay. (link to SOTB Report 2011)

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 Water Quantity …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What is water quantity, and why is it important? How and where is water quantity monitored in the SF Estuary? What are trends in water quantity in the SF Estuary? How do we determine the health of water quantity? What Is Water Quantity And Why Is It Important? Water Quantity: The quantity and timing of freshwater inputs to the estuary from rivers, tidal exchange of sea water, and the volume, frequency, and duration of water diversions are measurable properties that directly affect estuarine aquatic habitat, water quality, water supply, and the abundance and distribution of aquatic life in the SF Estuary. Tides vary predictably throughout the year but are largely unaffected by human activities. On the other hand, freshwater flows vary seasonally (e.g. storms and the timing of snowmelt) and across years (e.g. wet years and dry years); freshwater flow is affected by human use (diversions) and storage practices (behind dams). Variation in the flow of freshwater is a major determinant of water quality, ecosystem processes, and habitat distribution that varies greatly from year-to-year and can be influenced by human water management activities. Measurable water quantity properties in an estuary are focused on freshwater because of the importance of freshwater to the system, the influence humans have over freshwater flows, and the demand for freshwater diversions to supply irrigation, drinking, and industrial uses. Two important measurable properties of fresh water quantity in the SF Estuary are unimpaired runoff[create a definition box for this DEFINITION: an estimate of the amount of water that would flow out of the Sacramento-San Joaquin Delta if there were no dams or water diversions) and net outflow from the Sacramento-San Joaquin Delta (Net Delta Outflow, NDO) [DEFINITION: The amount of water that actually flowed out of the Delta to the west of Chipps Island; this is the flow that affects organisms and processes in the estuary west of the Delta and excludes water that has been diverted or stored for human uses upstream of and within the Delta]). The difference between Unimpaired runoff and Net Delta Outflow is one reflection of human impact on the water quantity attribute of ecosystem health. The panel depicts the year-to-year variation in freshwater that falls into the Central Valley (i.e., unimpaired runoff [DEFINITION-- an estimate of the amount of water that would flow out of the Sacramento-San Joaquin Delta if there were no dams or water diversions]. Bar colors reflect six different Water Year classifications [DEFINITION: A categorization of “water years” (which run from October through the following September) into groups with different amounts of precipitation/runoff] --wet, above normal, below normal, dry, critically dry, and super-critically dry; super-critically dry years are the driest 5% of years on record. The lower panel depicts year-to-year variation in actual Net Delta Outflow (NDO). NDO is a fraction of what it would be if water were not diverted for irrigation, drinking, and industrial uses. Note that the actual frequency of supercritically dry years (black bars) and critically dry years (red bars) is much greater than would occur without human water diversions and storage. Conversely, the frequency of “wet” years experienced by the SF Estuary is much lower than would occur under unimpaired conditions. How and Where is Water Quantity Monitored in the SF Estuary? [PROVIDE DESCRIPTION OF CDEC and OTHER WATER FLOW MONITORING PROGRAMS (if data the portal uses or may use would come from elsewhere] What are Trends in Water Quantity in the SF Estuary? Unimpaired Runoff and the quantity of fresh water that actually enters the San Francisco Estuary vary daily, seasonally, and annually. Although human uses for fresh water are somewhat constrained by the amount of precipitation in any given year (unimpaired runoff), our diversion and storage of water have generally increased over the past 80 years. Water that is diverted from rivers or stored behind dams is generally not available to the estuarine environment. As a result of increasing water diversion and storage, the trend in the quantity of water flowing into and through the San Francisco Estuary has declined over time. The fraction of water that falls as precipitation in the Central Valley that made it to the estuary has declined over time; in the most recent decades, humans diverted slightly more than half the unimpaired runoff. In the worst years, 70% or more of the Central Valley’s unimpaired water resources were diverted before they could become NDO. 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 questions in the “Questions Answered” box link to sections on this page.

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? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What is water quantity, and why is it important? How and where is water quantity monitored in the SF Estuary? What are trends in water quantity in the SF Estuary? 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 What Is Water Quality? Water quality refers to the physical, chemical, and biological characteristics of water. There are many measurable properties of water that determine the overall condition of water for aquatic life and other beneficial uses such as drinking water, irrigation, fishing, and swimming. Some of the most common water quality properties measured include: Water quality parameters can include such as: salinity temperature conductance dissolved oxygen pH nutrients pathogens contaminants, such as pesticides (e.g., DDT, dieldrin, chlordane, and pyrethroids) and heavy metals (e.g., mercury and selenium). Some water quality properties are indicators of physical aquatic habitat condition such as salinity, temperature, and dissolved oxygen. Sometimes, these properties are called ""vital sign" indicators. Other water quality properties refer to maximum contaminant levels that aquatic or human life can tolerate. Why Is It Important? Water quality is important for supporting aquatic life and other users of aquatic resources in the estuary. Poor water quality can negatively impact the health of the estuary by contributing to the reduction of aquatic life populations, increase water treatment costs for uses drinking, and reducing the supply of water for irrigation, industrial, and aquatic life uses. How and Where is Water Quality Monitored in the SF Estuary? [content in development] What are Trends in Water Quantity in the SF Estuary? Monitoring and assessment information shows that water quality is considered “impaired” in all San Francisco Estuary waterways despite water quality improvements from sewage treatment and chemicals control upgrades. These water quality impairments are published in California’s 2010 CWA Section 303(d) List of Impaired Waters. Water quality standards are exceeded for pesticides, manufacturing compounds, metals (mercury, selenium), pathogens, nutrients, invasive species, sediment, and toxicity from unknown sources. Similarly water quality standards are not being met for dissolved oxygen and temperature. These persistent water quality problems negatively affect aquatic life, drinking water, recreation, agriculture, the economy and public health. California issues health advisories to warn the public about eating fish with unsafe levels of contaminants from certain waterways. The salinity gradient and ammonia concentrations are important water quality properties for aquatic life that are not addressed on the 2010 CWA 303(d) List of Impaired Water Bodies. Salinity Gradient: The meeting of ocean and rivers waters creates a dynamic balance between freshwater and saltwater in the estuary. The mixing of marine and freshwater creates zones of intermediate salinity called brackish water (CREATE DEFINITION). Marine water salinity is approximately 35 parts per thousand (ppt) while freshwater salinity is less than 0.5 ppt. Extensive persistent brackish water zones that occur in estuaries represent important and unique and productive habitats for fish and wildlife species. In the San Francisco Estuary, the position and extent of low salinity brackish habitats is estimated by the location in the estuary where salinity is approximately 2 ppt. This Low Salinity Zone (LSZ), see figure below, is characterized by salinity that ranges between 0.5 and 6.0 ppt. The location of the LSZ center is referred to as “X2” which is the distance (X) in kilometers from the Golden Gate Bridge to the location in the estuary where water is 2 ppt (near the bottom of the estuary). Water becomes fresher (less than 2ppt salt) upstream of X2 while water becomes progressively more salty (more than 2 ppt salt) downstream of X2 until it reaches the ocean (35 ppt salt). The salinity gradient is an important indicator of water quality because shows the position of the LSZ which is important for access to food sources and exposure to water diversions, many species of benthic organisms, phytoplankton, zooplankton, and fish are found only in habitats with specific salinities, and the population size for many organisms is strongly correlated with the average seasonal position of X2 in any given year. INSERT GRAPHIC FROM Delta Modeling Associates Low Salinity Flip Book. June 15, Version 0.9. It is a file in this project page (X265DMA.pdf). Ammonia Concentrations -- content to be developed. The questions in the “Questions Answered” box link to sections on this page.

Food web conceptual model. [Click to navigate to other portal pages].
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 SF Estuary 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 < > Slide show carousel of species representing main components of the food web. Food web conceptual model. [Click to navigate to other portal pages]. What is the SF Estuary Food Web, and Why is It Important? The SF Estuary food web includes fish [link to fish pages], birds [link to bird pages], other wildlife, and the microscopic organisms, plants, and invertebrates that are food for them. The food web diagram above 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) [link to phytoplankton page] and larger terrestrial and aquatic vegetation. Phytoplankton is consumed by microscopic aquatic animals (zooplankton) [link to zooplankton page] 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. - The placement of this slide is still being decided.

California Estuary Monitoring Workgroup’s Estuary Portal Instructions for Comments Please send all comments to Stephanie Fong (State and Federal Contractors.

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California Estuary Monitoring Workgroup’s Estuary Portal Instructions for Comments Please send all comments to Stephanie Fong (State and Federal Contractors.

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Presentation on theme: "California Estuary Monitoring Workgroup’s Estuary Portal Instructions for Comments Please send all comments to Stephanie Fong (State and Federal Contractors."— Presentation transcript:

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