1. What is Water Quality? Images Caption slide show Text TEMPLATE 1
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What is Water Quality?
QUESTIONS ANSWERED
How and where is water quality monitored in the SFE?
What are water quality trends in the SFE?
How do we determine the quality of water in the SFE?
What’s being done to protect water quality in the SFE?
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Caption
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2. Map with locations and icons for what’s monitored where
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How and Where is Water Quality Monitored in the SFE?
QUESTIONS ANSWERED
How and where is water quality monitored in the SFE?
What are water quality trends in the SFE?
How do we determine the quality of water in the SFE?
What’s being done to protect water quality in the SFE?
Map with locations and icons for what’s monitored where
Select water quality constituent, sites of interest and time frame to view animations
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The water quality data used for this animation come from the Department of Water Resources CDEC, Water Boards CEDEN, and Federal NWIS databases. General water quality parameters (e.g., salinity, temperature, dissolved oxygen, pH, and nutrients) are monitored relatively quickly and inexpensively; whereas, chemical analysis for the presence and concentrations of contaminants (e.g., pesticides and metals), and biological testing for the effects of those contaminants take more time. Changes in water quality parameters over time help elucidate the suitability of aquatic habitats for wildlife, human uses like swimming and drinking, and other Beneficial Uses.
Where are the Data?
Another summary of programs that are monitoring for water quality can be found at the Central Valley Monitoring Directory. Programs focused on monitoring water quality include the Citizen Monitoring Program, Interagency Ecological Program, Irrigated Lands Regulatory Program, National Pollutant Discharge Elimination System Program, Non-Point Source Program, Regional Monitoring Programs, Surface Water Ambient Monitoring Program, and Total Maximum Daily Load Program.

3. Which Programs are Monitoring Water Quality?
Citizen Monitoring-linked to section below
Interagency Ecological Program-linked to section below
Irrigated Lands Regulatory Program-linked to section below
National Pollutant Discharge Elimination System-linked to section below
Non-Point Source-linked to section below
Regional Monitoring Programs-linked to section below
Total Maximum Daily Load-linked to section below
Citizen Monitoring
Citizen monitoring is monitoring performed by community members interested in the health and protection of their watersheds. Activities include collecting water quality data, evaluating fish habitat, counting birds, or making visual observations of stream health. Learn more about the SWAMP Clean Water Team’s citizen monitoring here.
Interagency Ecological Program
The Interagency Ecological Program (IEP) is a collaborative effort among multiple state and federal agencies to monitor, research, model, and synthesize critical information for adaptive management, water project operations, planning and regulatory purposes relative to endangered fish and the aquatic ecosystem in the San Francisco estuary (Bay-Delta). The IEP agencies have conducted cooperative long-term monitoring of aquatic resources in the Bay-Delta since 1970.
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Irrigated Lands Regulatory Program
In 2003, the Central Valley Regional Water Quality Control Board adopted the Conditional Waiver of Waste Discharge Requirements for Discharges from Irrigated Lands. These regulations provide for a watershed approach that includes a basin-wide monitoring program to assess impacts of irrigation water discharge. Since that time, several agricultural coalitions throughout the basin have performed characterization monitoring at sites dominated largely by agricultural effluent. You can visit their site here.
National Pollutant Discharge Elimination System
The National Pollutant Discharge Elimination System (NPDES) permit program is authorized by the Clean Water Act and controls water pollution by regulating point sources that discharge into waters of the United States. Point source discharges to waters of the state are discrete conveyances such as pipes or man-made ditches. The NPDES Program is a federal program which has been delegated to the State of California for implementation through the State Water Resources Control Board (State Water Board) and the nine Regional Water Quality Control Boards (Regional Water Boards), collectively Water Boards. In California, NPDES permits are also referred to as waste discharge requirements (WDRs) that regulate discharges to waters of the United States. Since its introduction in 1972, the NPDES permit program is responsible for significant improvements to our Nation's water quality.
More information on California’s NPDES permits and requirements is available through the State Water Board website or US EPA’s website.
Non-Point Source Program
Non-Point Source (NPS) is pollution that does not meet the definition of “point source” in section 502(14) of the Clean Water Act. Point sources are any discernible, confined and discrete conveyance (i.e., pipes). Thus, NPS pollution comes from multiple diffuse sources over relatively large areas, and is caused by irrigation runoff, rainfall or snowmelt moving over and through the ground and depositing pollutants into waters of the state.
NPS pollution originates from sources related to either land or water use, and can include:
Excess fertilizers, herbicides and pesticides from agricultural and residential areas;
Oil, grease and chemicals from urban runoff;
Sediment from improperly managed construction sites, crop and forest lands, and eroding streambanks;
Salt from irrigation practices and acid drainage from abandoned mines;
Bacteria and nutrients from livestock, pet waste and faulty septic systems; and
Atmospheric deposition and hydromodicitaion.
Since there is no one particular source (e.g. pipe) to identify to address NPS pollution, it presents challenges to control. Therefore, regulations and solutions that have worked for point sources do not readily apply to these multiple diffuse sources of NPS pollution. Learn more from US EPA here, or from the Water Board here.
Regional Monitoring Programs
There are many programs that coordinate their monitoring due to shared interests or region. Regional programs include monitoring and data assessment to provide a comprehensive assessment of aquatic health on a region-wide basis. Regional monitoring programs for the Bay and Delta are described below.
San Francisco Bay Regional Monitoring Program (Bay RMP). The Bay RMP has been in place since 1993, and is an innovative collaborative effort between San Francisco Estuary Institute (SFEI), the Regional Water Quality Control Board, and the regulated discharger community. The Bay RMP provides water quality regulators and policy-makers with information they need to manage the Bay effectively. Monitoring performed in the RMP determines spatial patterns and long-term trends in contamination through sampling of water, sediment, bivalves, bird eggs, and fish, and evaluates toxic effects on sensitive organisms and chemical loading to the Bay. The Program combines RMP data with data from other sources to provide for comprehensive assessment of chemical contamination in the Bay.
Delta Regional Monitoring Program (Delta RMP). There is currently no comprehensive contaminants monitoring and assessment program in place for the Sacramento and San Joaquin River Delta. In response to the need for collaborative and credible Delta science, the Central Valley Regional Water Quality Control Board (CVRWQCB) is currently leading the development of a Delta RMP in collaboration with the Aquatic Science Center. The RMP steering committee and technical advisory committee are currently developing the monitoring and assessment framework for the RMP. A wide range of stakeholders including publically owned treatment works (POTWs), municipal stormwater agencies, agricultural coalitions, water supply agencies, CVRWQCB, coordinated monitoring groups, and EPA hold seats on the Steering Committee.
US EPA along with the Coalition for Urban/Rural Environmental Stewadship (CURES) is in the process of developing a regional monitoring program for the San Joaquin River watershed. More information on the project can be found here.
Sacramento Coordinated Monitoring Program
The Sacramento Coordinated Monitoring Program (CMP) is a joint effort of the Sacramento Regional County Sanitation District and the Sacramento Stormwater Management Program to monitor the American and Sacramento Rivers, and has been in place since CMP partnering agencies collect river water samples and test for a variety of water quality constituents and contaminants. The fundamental purpose of the CMP is to develop high-quality data to aid in the development and implementation of water quality policy and regulations in the Sacramento area. You can find more about the program here.
Surface Water Ambient Monitoring Program
The Surface Water Ambient Monitoring Program (SWAMP) was created to fulfill the State Legislature’s mandate for a unifying program that would coordinate all water quality monitoring conducted by the State and Regional Water Boards. SWAMP’s mission is to provide resource managers, decision makers, and the public with timely, high-quality information to elevate the condition of waters throughout California. SWAMP uses externally reviewed monitoring programs and generates comparable data statewide for integrated assessments.
The Sacramento Watershed Coordinated Monitoring Program (SWCMP) is a coordinated monitoring effort between Department of Water Resources (DWR) and the Central Valley Regional Water Quality Control Board’s SWAMP in the northern portion of the Sacramento River Watershed, monitoring ambient water quality at locations in the Sacramento River upstream of Lake Shasta, south to Verona, and at the lower end of all large streams tributary to the Sacramento River. It is funded jointly by DWR Northern District Water Quality Section and the Central Valley Water Board.
Total Maximum Daily Load
A Total Maximum Daily Load (TMDL) is the maximum amount of a pollutant that a waterbody can assimilate in a day while supporting the Beneficial Uses of that waterbody. Monitoring can be required to gain information to determine whether or not a TMDL needs to be developed, or required once a TMDL is in place, to track the success of control measures that were put in place. Under section 303(d) of the Clean Water Act, states are required to develop lists of impaired waters that do not fully support Beneficial Uses. These are waters for which technology-based regulations and other required controls are not stringent enough to meet the water quality standards set by states. The law requires that states establish priority rankings for listed waterbodies and develop TMDLs, for these waters. You can learn more general information about TMDLs here, or visit other areas of this Portal to learn about five specific TMDLs.

4. What are Water Quality Trends in the SFE?
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What are Water Quality Trends in the SFE?
QUESTIONS ANSWERED
How and where is water quality monitored in the SFE?
What are water quality trends in the SFE?
How do we determine the quality of water in the SFE?
What’s being done to protect water quality in the SFE?
Line graph with multi constituents one site at a time
Animations of DO, EC, pH, turb and temp
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General water quality parameters dissolved oxygen (DO), electrical conductivity (EC), pH, turbidity, and temperature are the most commonly collected in the San Francisco Estuary. These parameters are measured manually with meters from grab samples, or by real-time stations at select sites. Scientists can use these as a proxy to determine if the “vital signs” of the San Francisco Estuary appear to be healthy or not. Temperature is a “vital sign” for humans as well as waterbodies, similarly, DO can be viewed like our blood’s oxygen saturation, EC can be viewed like our body’s electrolyte balance. If these coarse measurements are showing unexpected changes, it may indicate that something is not working properly and the need to perform more sophisticated diagnoses or analyses.
Nutrients
Looking at nutrients and the balance of difference nutrients types is one form of more sophisticated analysis. Nutrient analyses are typically performed in a laboratory. Elevated nutrient concentrations may indicate potential for overgrowth of phytoplankton, and likewise, depressed nutrient concentrations may indicate insufficient support for primary production. There are many confounding factors that should be considered when assessing nutrient effects. In addition to nutrient concentrations, seed populations, light intensities, residence times, and the presence of contaminants should be evaluated.
Chemical Analysis
Field samples can also be analyzed for the presence of chemicals (e.g., pesticides, metals, pharmaceuticals). These analyses are performed with high-tech machinery including mass spectrometry, liquid chromatography, and gas chromatography. These types of analyses can determine not only the presence, but also estimates the concentrations of those chemicals.
Affects on Biology
Biological effects can be assessed with toxicity testing or bioassessments. These assessments have been the initial linkages between water quality and what effects water quality may have on organism health. New tools (e.g., genomics, proteomics) are being developed to compliment toxicity testing and better elucidate organism health beyond mortality. The Surface Water Ambient Monitoring Program has recent summaries of toxicity testing and biological assessments here.

5. Photos of very good and very impacted sites
Home   Eco Health   Estuaries   Healthy   San Francisco   Water
How do we Determine the Quality of Water in the SFE?
QUESTIONS ANSWERED
How and where is water quality monitored in the SFE?
What are water quality trends in the SFE?
How do we determine the quality of water in the SFE?
What’s being done to protect water quality in the SFE?
Photos of very good and very impacted sites
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Water Quality Indicators
There are many different things that can be measured as indicators of water quality like dissolved oxygen (DO), electrical conductivity(EC), pH, turbidity, and temperature. Other parameters like chlorophyll a, nutrients, metals, pesticides, and chemicals of emerging concern can also be used to address specific issues. Scientists can use multiple water quality indicators to determine the health of the ecosystem. For example, if you wanted to know if the ecosystem had enough primary productivity to support the system, you might look in the water and sediment to find the amount of nutrients, types of nutrients, and amount of time they were available to phytoplankton. You might also want to look at the intensity and amount of time light was available to them. You would also want to know how many things would eat the phytoplankton and how much they would typically eat. It’s like preparing for a meal, you want to make sure you have the ingredients and time to make the right amount of food for your guests, and hopefully it’s food they will like to eat. Scientists use this type of information to determine whether or not certain waterbodies are impacted or not.
Water Quality Goals and Objectives
Water quality objectives are numeric or narrative limits or levels of water quality constituents or characteristics which are established for the reasonable protection of beneficial uses of water, or the prevention of nuisance within a specific area. In order to evaluate compliance with water quality objectives, the Water Board will consider all relevant and scientifically valid evidence, including numeric criteria and guidelines developed and/or published by other agencies and organizations. These criteria and guidelines are summarized in the Water Quality Goals database.
Clean Water Act 303(d) List
The purpose of the Federal Clean Water Act (CWA) is to restore and maintain chemical, physical, and biological integrity of the nation’s waters and wetlands by preventing point and nonpoint pollution. The CWA and Porter-Cologne Act give the State and Regional Water Boards the authority and responsibility to assess the health of the state’s waters. Under sections 303(d) and 305(b) of the CWA, states are required to regularly assess and report on the health of its waters. Water quality indicator data is evaluated against water quality goals or objectives, and if it is determined that segments of a waterbody are not meeting these goals or objectives for its designated beneficial uses, they are placed on the 303(d) list of impaired water bodies.

6. What’s Being Done to Protect Water Quality in the SFE?
Home   Eco Health   Estuaries   Healthy   San Francisco   Water
What’s Being Done to Protect Water Quality in the SFE?
QUESTIONS ANSWERED
How and where is water quality monitored in the SFE?
What are water quality trends in the SFE?
How do we determine the quality of water in the SFE?
What’s being done to protect water quality in the SFE?
Slide show of the five highlighted TMDLs that they can click on for details (like SFE LR page)
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Pollutant Control Through Cooperation Among Regulatory Agencies and Stakeholders
There are a number of control programs that help protect water quality, but sometimes, cooperation among interested parties can accomplish a lot to protect water quality. Agencies like US EPA, the Water Boards, and the Department of Pesticide Regulation work together and with industry representatives and other stakeholders to cooperatively decrease risks to aquatic ecosystems. Some examples of such cooperation are implementation of best management practices like installation of drip irrigation to minimize the movement of pollutants, or changing labels on pesticides to encourage safer applications.
Pollutant Control Through Total Maximum Daily Loads
Control of pollutants (e.g., the prevention or correction of pollution) can also come from the implementation of Total Maximum Daily Loads (TMDLs). If the Water Boards and US EPA adopt a TMDL, goals and timelines for decreasing the magnitude and frequency of detections are detailed in the implementation plan. There are 14 TMDLs associated with the Delta and it’s tributaries. Detailed summaries for the Delta Organophosphate (OP) TMDL, Lower Sacramento-Feather River OP TMDL, Lower San Joaquin River OP TMDL, Sacramento Urban OP TMDL, and Stockton Dissolved Oxygen TMDL can be viewed by clicking on the links within this sentence. Of these five TMDLs, conditions need improvement for one constituent-waterbody combination, three show that conditions are improving, and one has achieved the TMDL target.

7. What’s Being Done to Protect Water Quality in the SFE?
Home   Eco Health   Estuaries   Healthy   San Francisco   Water
What’s Being Done to Protect Water Quality in the SFE?
QUESTIONS ANSWERED
How and where is water quality monitored in the SFE?
What are water quality trends in the SFE?
How do we determine the quality of water in the SFE?
What’s being done to protect water quality in the SFE?
Slide show of the five highlighted TMDLs that they can click on for details (like SFE LR page)
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(additional language for TMDL section below-the first 5 bullets will be linked to pages that are slides 8-12)
Restoring Water Quality and Aquatic Ecosystems using the Watershed Approach
The Watershed Approach is a cooperative framework for improving water quality and protection for aquatic ecosystems that identifies pollution sources, ecosystem stressors, and solutions for the entire watershed. Actions that address water quality and aquatic ecosystem problems are likely to be more effective and persistent when a diverse group of stakeholders are invested in identifying pollution sources, stressors, and solutions. Science and technical information can be generated with direction from stakeholder groups and used to identify cost effective options for addressing the most pressing watershed vulnerabilities. The community investment generated by this process is important for ensuring that water quality improvements persist over time. Some examples of such cooperation are implementation of best management practices like installation of drip irrigation to minimize the movement of pollutants, or changing labels on pesticides to encourage safer applications.
Adopting and implementing a “Total Maximum Daily Load” (TMDL) is one tool for improving water quality and aquatic ecosystem conditions using the Watershed Approach. TMDLs identify quantitative targets for pollutants and stressors, outline methods for controlling pollutant and stressor sources, allocate responsibility for source control, and establish milestone dates for progress toward achieving targets.
There are 28 adopted TMDLs addressing water pollutants and aquatic ecosystems stressors in watersheds that drain to the San Francisco Estuary. At least 14 of these TMDLS directly address pollutants and stressors that may contribute to declines in several San Francisco Estuary fishes and/or threaten public health.
US EPA worked with its partners to produce TMDL progress reports for several stressors that contribute to aquatic life impairments. Regularly assessing and reporting TMDL progress is important for improving water quality and aquatic ecosystem protection, establishing accountability, and identifying controls that produce the best water quality results for the lowest cost in the shortest time to accelerate water quality improvements. The list below contains the progress reports that have been completed to date:
-Stockton Deep Water Ship Channel Low Dissolved Oxygen
-Sacramento-San Joaquin River Delta Diazinon & Chlorpyrifos
-Lower San Joaquin River Diazinon & Chlorypyrifos
-Lower Sacramento – Feather River Diazinon & Chlorypyrifos
-Sacramento County Urban Streams Diazinon & Chlorpyrifos
-Bay Area Urban Creeks Diazinon & Pesticide Related Toxicity
-Lower Feather River and Lower Sacramento River Diazinon & Chlorpyrifos
-Grasslands Marshes Selenium
-Lower San Joaquin River Selenium
-Salt Slough Selenium   
Pollutant Control Through Cooperation Among Regulatory Agencies and Stakeholders
There are a number of control programs that help protect water quality, but sometimes, cooperation among interested parties can accomplish a lot to protect water quality. Agencies like US EPA, the Water Boards, and the Department of Pesticide Regulation work together and with industry representatives and other stakeholders to cooperatively decrease risks to aquatic ecosystems. Some examples of such cooperation are implementation of best management practices like installation of drip irrigation to minimize the movement of pollutants, or changing labels on pesticides to encourage safer applications.
Pollutant Control Through Total Maximum Daily Loads (TMDLs)
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9. Trend graph from CEDEN and NWIS
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10. Trend graph from CEDEN and NWIS
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11. Trend graph from CEDEN and NWIS
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12. Not likely to be updated live (all stormwater)
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