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California Estuary Monitoring Workgroup’s Estuary Portal Instructions for 34 North
This pages are for general layout guidance and for guidance on the Questions/Answered Box development. Text in the main part of each page doesn’t not reflect recent edits and should not be used. The text that should be used in those areas is the text that has been loaded into the estuary workgroup website.
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Instructions for left navigation bar:
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us …………………………………..………………………………………………………………………………………………………………………………..……… 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 Instructions for left navigation bar: Estuaries: links to the “California Estuaries” introduction page (slide 3) Laws, Regulations, and Standards: links to the “What’s being done to protect California’s estuaries (slide 6) Research: links to “What research is being performed in the SF Estuary?” (slide 8) Monitoring…: links to the “what monitoring programs…” (slide 9) Restoration and Management: can we get rid of this link for now? Combined this information with research
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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 California’s estuaries? How can I be part of the solution? Main image/map would be of SF Bay, followed by Sacramento-San Joaquin Delta, followed by Sacramento River, followed by Morro Bay. People will be able to click directly to the SF Estuary pages (slide 10 and following) from the SF Bay and Delta images. Other images will be other California estuaries that won’t be clickable until those pages are developed later. Each of the questions in the “Questions Answered” box will link to introduction pages on each of those questions, except “what are estuaries, and why are they important?” which is bolded to indicate that this is the page you are on, and the one that is grayed out which will need to say “Content in Development” or something when you click/hover on it. Clicking on the blue text will open a wiki 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.
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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 Elkhorn Slough 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. - You get to this page by clicking on the “Where are California’s Estuaries?” question in the Questions Answered box on the intro page (slide 3) - Clicking on “San Francisco Estuary” will take you to the “What is the San Francisco Estuary, and why is it important page? (slide 10)” Clicking on the other estuaries takes to you a wiki that will pop up with basic information on each of them. These pages will be developed further in the future. In the Questions Answered Box, “Where are CA’s estuaries?” is bolded to indicate that that is the page you are on at the moment. Clicking on it wouldn’t do anything. It’s for general organization.
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Water Habitat Living Resources Ecological Processes Stewardship
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home Eco Health Estuaries Health How Healthy are California’s Estuaries? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Water Habitat Living Resources Ecological Processes Stewardship QUESTIONS ANSWERED How healthy are California’s estuaries? SF Estuary Health How 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. 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 3). Eventually, each estuary will have their own health page, but for the moment, only the SF Estuary health information is presented (see slide 11 for SF Estuary health page). The photos in this sliding viewer thing do NOT link to other pages. Will just be a representative photo for each one and a caption. (this is different from what happens on slide 11). In the Questions Answered Box, “how healthy are Ca’s estuaries?” is bolded to indicate that that is the page you are on at the moment. Clicking on it wouldn’t do anything. It’s for general organization.
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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? Laws, Regulations, and Polices Stewardship 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. 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 Federal Laws, Regulations, and Policies Protect CA Estuaries? (links to the federal part of the laws and regs page [next slide]) - This is the introductory page to what is being done to protect CA’s estuaries. You would get here by clicking on that same question on the introductory page (slide 3). - In the Questions Answered Box, “what’s being done to protect Ca’s estuaries?” is bolded to indicate that that is the page you are on at the moment. Clicking on it wouldn’t do anything. It’s for general organization - “Laws, Regulations, and Policies” in the Questions Answered box links to slide 7. - Stewardship is grayed out and would need to indicate “Content in Development” - “What Federal Laws, Regulations, and Policies Protect CA Estuaries?” (links to the federal part of the laws and regs page [next slide]) - “What State Laws, Regulations, and Policies Protect CA Estuaries?” [links to the state part of the laws/regs page (next slide)} - “What Policies and Plans Protect the SF Estuary?” [links to the policies and plans specific to the SF Estuary part of the laws/regs page (next slide)] What State Laws, Regulations, and Policies Protect CA Estuaries? [links to the state part of the laws/regs page (next slide)} What Policies and Plans Protect the SF Estuary? [links to the policies and plans specific to the SF Estuary part of the laws/regs page (next slide)]
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What Policies and Plans Protect the SF Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home Eco Health Estuaries Protection Laws What Laws, Regulations, and Policies Protect California’s Estuaries? …………………………………..………………………………………………………………………………………………………………………………..……… QUESTIONS ANSWERED What’s being done to protect California’s estuaries? What laws, regulations, and polices protect California’s estuaries? Federal State SF Estuary Policies and Plans 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 Federal Laws, Regulations, and Policies Protect California’s Estuaries? Clean Water Act (CWA) Purpose: To govern water pollution and regulate water quality standards for surface waters Agencies: 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 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. 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. Additional Resources: USACE Jurisdiction Mitigation Guidance (Section 404(b)(1)) What You Need to Know About Section 404 Permits (PowerPoint presentation) Endangered Species Act (ESA) Purpose: To protect and recover imperiled species and the habitat upon which they depend 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 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. 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 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 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 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.” 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 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. Regulatory Instruments 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 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) 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 EPA logo USFWS logo USACE logo In the Q/A box, “Federal” jumps to the federal laws section on this page, “State” jumps to the state laws section on this page, and “SF Estuary…” jumps to the SF Estuary policies and plans section on this page. Arrange logos and images as you think best. Just keep certain logos near/next to certain sections of text, and there are notes on the estuary website page to guide you. Image of clapper rail NOAA logo Image of eelgrass What State Laws, Regulations, and Policies Protect California’s Estuaries? [more logos will be used below, but didn’t use a blue box again. You get the idea.] What Policies and Plans Protect the SF Estuary?
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What Research is Being Performed in the SF Estuary?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home Eco Health Estuaries Research What Research is Being Performed in the SF Estuary? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Many groups are conducting and funding original research in the San Francisco Estuary, including those listed below. 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 - You get to this page from clicking on “research” on the left blue navigation bar.
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What Monitoring Programs, Data Sources, and Reports Are Available?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home Eco Health Estuaries Monitoring What Monitoring Programs, Data Sources, and Reports Are Available? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Many groups are 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 San Francisco Invasive Spartina Project (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 get to this page from clicking on “monitoring programs, data sources, and reports” on the left blue navigation bar.
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< > 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 San Francisco 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?” or from the image/map on the introductory estuaries slide (slide 3) In the Q/A box, “how healthy is the SF Estuary?” links to the introductory page for that (slide 11), “what’s being done?” links back to “what’s being done to protect CA’s estuaries?” (slide 6), and “how can i…” needs to indicate “Content in Development” Need to have a caption beneath the video with a short description of what it shows to entice the public the view it
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Ecological Processes Picture
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 What is the San Francisco 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? Water Picture Habitat Picture Living Resources Picture Ecological Processes Picture Stewardship Picture 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. In the blue sliding viewer thing, clicking on “living resources” links to “why are living resources a key attribute?” (slide 12), clicking on “water” links to “why is water a key attribute” (slide 54), clicking on habitat links to “why is habitat a key attribute?” (slide 57), clicking on ecological processes links to “why are ecological processes a key attribute?” (slide 58), and stewardship (which will still have a picture) will be grayed out and will not link to anything, will say “Content in Development” when you hover on it, if possible. “What’s being done to protect the SF estuary?” question links to slide 8
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Why are Living Resources 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 Living Resources Why are Living Resources 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 How healthy is the SF Estuary? Why are living resources a key attribute? How do we determine the health of living resources? Zooplankton Benthic Organisms Phytoplankton Fish Birds Plants Mammals Why are living resources a key attribute? 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 healthy are SF Estuary 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) - You would get to this slide by clicking on living resources from previous slide. Pictures in sliding thing would be phytoplankton, zooplankton, etc. and clicking on them links to their “what is it and why is it important” pages. In Q/A box, “how do we determine the health of living resources?” links to next slide (slide 13). “Why are living resources… is bolded to indicate that is the page you are on and will not link anywhere.” It is there for general organization. Clicking on “how healthy is the SF Estuary?” will take you back to slide 11
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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 Where San Francisco Health Living Resources Health Diagram How do We Determine the Health of Living Resources? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management Identify Key Attributes Water Habitat Ecological Processes Stewardship Describe Health Indicators Species Composition (e.g. native v. exotic) Species Distribution Species Abundance STEP 1 STEP 2 Phytoplankton 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 Drivers Fish Birds Mammals Living Resources Zooplankton Benthic Organisms Plants We are here! Make diagram web friendly but static. How do we determine the health of 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.
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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 to protect them? 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. In the Q/A box: The first question link is bolded to indicate that is the page you are on (“What are phytoplankton?”). Clicking on it wouldn’t do anything. Keeping it because we think it helps to have a standardized Q/A box on each phytoplankton page and will give people an easy, clear way to get back to a particular phytoplankton section. The “How and where” question links to the next slide (slide 15). The “trends” question links to slide 16. The healthy question links back slide 11 (“how healthy is the SF Estuary” until more content on drivers/stressors is developed. “What’s being done to protect them” links to the “what’s being done to protect CA’s estuaries” (slide 6). These last two questions link to these same places for all of the living resources. -pH, dissolved oxygen, algal blooms, and water transparancy all link to wikis with basic information on these topics - “Learn more “ links to phytoplankton monitoring page (next slide (15))
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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 to protect them? 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. In the Q/A box: The first question links to that page (slide 14) The “How and where” question link is bolded to indicate that is the page you are on. Clicking on it wouldn’t do anything. Keeping it because we think it helps to have a standardized Q/A box on each phytoplankton page and will give people an easy, clear way to get back to a particular phytoplankton section. The “trends” question links to slide 16. The healthy question links back slide 11 (“how healthy is the SF Estuary” until more content on drivers/stressors is developed. “What’s being done to protect them” links to the “what’s being done to protect CA’s estuaries” (slide 6). These last two questions link to these same places for all of the living resources.
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< > 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 to protect them? 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. In the Q/A box: The first question links to that page (slide 14). The “How and where” question links to that page (slide 15). The “trends” question link is bolded to indicate that is the page you are on. Clicking on it wouldn’t do anything. Keeping it because we think it helps to have a standardized Q/A box on each phytoplankton page and will give people an easy, clear way to get back to a particular phytoplankton section. The healthy question links back slide 11 (“how healthy is the SF Estuary” until more content on drivers/stressors is developed. “What’s being done to protect them” links to the “what’s being done to protect CA’s estuaries” (slide 6). These last two questions link to these same places for all of the living resources. The blue box on the page would present a carousel of graphs (and their captions) about phytoplankton trends.
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Note: The graphs on slides will be presented as a slide carousel on slide 16. 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 17 will be viewed individually, but all graphs on slide 18 will be viewed together for comparison.
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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 ( ) – Central Delta Chlorophyll a Trends ( ) – Rivers Chlorophyll a Trends ( ) - Downstream 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. Instructions for graphs in the estuary workgroup website and in second PowerPoint. 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.)
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Phytoplankton Species Composition Trends
Text for this chart. Text for this chart Text for this chart, Phytoplankton Species Composition Trends Instructions for graphs in the estuary workgroup website and in second PowerPoint. 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.)
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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 to protect them? 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)). In the Q/A box: The first question link is bolded to indicate that is the page you are on (“What are zooplankton?”). Clicking on it wouldn’t do anything. Keeping it because we think it helps to have a standardized Q/A box on each zooplankton page and will give people an easy, clear way to get back to a particular zooplankton section. The “How and where” question links to the next slide (slide 21). The “trends” question links to slide 22. The healthy question links back slide 11 (“how healthy is the SF Estuary” until more content on drivers/stressors is developed. “What’s being done to protect them” links to the “what’s being done to protect CA’s estuaries” (slide 6). These last two questions link to these same places for all of the living resources. If there are wikis created for “copepods,” “cladocerans,” etc., then the blue links in the text would open those wikis. If those wikis are not created, then remove the links and make the text static. “Learn more…” links to next slide (slide 21).
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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 to protect them? Zooplankton Monitoring Stations In the Q/A box: The first question links to that page (slide 20) The “How and where” question link is bolded to indicate that is the page you are on. Clicking on it wouldn’t do anything. Keeping it because we think it helps to have a standardized Q/A box on each zooplankton page and will give people an easy, clear way to get back to a particular zooplankton section. The “trends” question links to slide 22. The healthy question links back slide 11 (“how healthy is the SF Estuary” until more content on drivers/stressors is developed. “What’s being done to protect them” links to the “what’s being done to protect CA’s estuaries” (slide 6). These last two questions link to these same places for all of the living resources. 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.
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< > What are SF Estuary Zooplankton Trends? - In the Q/A box:
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 to protect them? < > Slide carousel of graphs Zooplankton Trends in the SF Estuary to 2011 - In the Q/A box: The first question links to that page (slide 20). The “How and where” question links to that page (slide 21). The “trends” question link is bolded to indicate that is the page you are on. Clicking on it wouldn’t do anything. Keeping it because we think it helps to have a standardized Q/A box on each zooplankton page and will give people an easy, clear way to get back to a particular zooplankton section. The healthy question links back slide 11 (“how healthy is the SF Estuary” until more content on drivers/stressors is developed. “What’s being done to protect them” links to the “what’s being done to protect CA’s estuaries” (slide 6). These last two questions link to these same places for all of the living resources. The blue box on the page would present a carousel of graphs (and their captions) about zooplankton trends. 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.
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Note: The graphs on slides will be presented as a slide carousel on slide 22 . 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 24 will be viewed together for comparison, and all on slide 25 will be viewed together for comparison. Instructions for graphs in the estuary workgroup website and in second PowerPoint.
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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. Instructions for graphs in the estuary workgroup website and in second PowerPoint.
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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). These graphs will be shown together for comparison. Instructions for graphs in the estuary workgroup website and in second PowerPoint.
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< > 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 to protect them? < > Pictures of benthic organisms that you can click on to get to details In the Q/A box: The first question link is bolded to indicate that is the page you are on (“What are benthic organisms?”). Clicking on it wouldn’t do anything. Keeping it because we think it helps to have a standardized Q/A box on each benthic page and will give people an easy, clear way to get back to a particular benthic section. The “How and where” question links to the next slide (slide 27). The “trends” question links to slide 28. The healthy question links back slide 11 (“how healthy is the SF Estuary” until more content on drivers/stressors is developed. “What’s being done to protect them” links to the “what’s being done to protect CA’s estuaries” (slide 6). These last two questions link to these same places for all of the living resources. In text blue links: - Phytoplankton – link to “what are phytoplankton page” - zooplankton – link to “What are zooplankton page” - “Learn more “ – link to benthic measuring page (next slide (27)) 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.
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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 to protect them? 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. In the Q/A box: The first question links to that page (slide 26) The “How and where” question link is bolded to indicate that is the page you are on. Clicking on it wouldn’t do anything. Keeping it because we think it helps to have a standardized Q/A box on each benthic page and will give people an easy, clear way to get back to a particular benthic section. The “trends” question links to slide 28. The healthy question links back slide 11 (“how healthy is the SF Estuary” until more content on drivers/stressors is developed. “What’s being done to protect them” links to the “what’s being done to protect CA’s estuaries” (slide 6). These last two questions link to these same places for all of the living resources.
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< > 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 to protect them? < > 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. - In the Q/A box: The first question links to that page (slide 26). The “How and where” question links to that page (slide 27). The “trends” question link is bolded to indicate that is the page you are on. Clicking on it wouldn’t do anything. Keeping it because we think it helps to have a standardized Q/A box on each benthic page and will give people an easy, clear way to get back to a particular benthic section. The healthy question links back slide 11 (“how healthy is the SF Estuary” until more content on drivers/stressors is developed. “What’s being done to protect them” links to the “what’s being done to protect CA’s estuaries” (slide 6). These last two questions link to these same places for all of the living resources. - Graphs in blue box are a carousel. Each have their own caption.
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Note: The graphs on slide 30 will be presented as a slide carousel on slide 28. The viewer would see each graph and its caption by clicking on it in the carousel. Instructions for graphs in the estuary workgroup website and in second PowerPoint.
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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.
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< > Why is Water a Key Attribute?
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home Eco Health Estuaries Where San Francisco Health Water Why is Water a Key Attribute? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management QUESTIONS ANSWERED Why is water a key attribute? What do we mean by water quantity? What do we mean by 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 in the sliding viewer on slide 11. - In Q/A box, - “What is water quantity…” links to next slide (slide 54). - “What is water quality …” links to slide 55. 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)
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< > What Do We Mean By Water Quantity? - In Q/A box:
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home Eco Health Estuaries Where San Francisco Health Water Quantity What Do We Mean By 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 QUESTIONS ANSWERED Why is water a key attribute? What do we mean by water quantity? What do we mean by water quality? < > Water related pictures that you can click on to get to details What Is Water Quantity? 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. Why is Water Quantity Important? 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. - In Q/A box: - “why is water a key attribute?” links to slide 53. - “what is water quantity” is bolded to indicate that this is the page you are on. Clicking it wouldn’t do anything. For organization. - “what is water quality?” links to slide 55.
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< > What Do We Mean By Water Quality? - In Q/A box:
Home Safe to Drink Safe to Swim Safe to Eat Fish Ecosystem Health Stressors & Processes Contact Us Home Eco Health Estuaries Where San Francisco Health Water Quality What Do We Mean By Water Quality? …………………………………..………………………………………………………………………………………………………………………………..……… Cal/EPA Natural Resources Agency About the California Water Quality Monitoring Council ESTUARIES Stressors Laws, Regulations & Standards Research Monitoring Programs, Data Sources & Reports Restoration & Management < > QUESTIONS ANSWERED Why is water a key attribute? What do we mean by water quantity? What do we mean by water quality? Water related pictures that you can click on to get to details - In Q/A box: - “why is water a key attribute?” links to slide 53. - “what is water quantity” links to slide 54. - “what is water quality?” is bolded to indicate that this is the page you are on. Clicking it wouldn’t do anything. For organization. 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.
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< > Why is Habitat 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 Habitat Why is Habitat 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 < > Habitat related pictures that you can click on to get to details - You get to this slide by clicking on the habitat tab in the sliding viewer on slide 11. Why is habitat a key attribute? [text on website]
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Why are Ecological Processes 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 Ecological Processes Why are Ecological Processes 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 Why are ecological processes a key attribute? 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. - You get to this slide by clicking on the ecological processes tab in the sliding viewer on slide 11.
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