B1: Impaired Water Bodies Improvement*

Status

Active

Location

Countywide

Schedule

Start FY 2022 / Finish FY 2036

Funding

Safe, Clean Water Fund ($33.5 million)

This project reduces pollutants in streams, reservoirs and groundwater of Santa Clara County by supporting surface water quality pollution prevention activities. These programs address water quality concerns currently identified by local and state regulatory agencies, as well as contaminants of emerging concern. Initiatives under this project are consistent with the Regional Water Quality Control Board (RWQCB) impaired water bodies designation and Total Maximum Daily Loads (TMDLs), which are the maximum amount of a pollutant that a water body can receive and still safely meet water quality standards. Under this project, Valley Water studies and implements methods to reduce methylmercury formation in reservoirs, and helps create and carry out realistic plans to reduce contaminants, such as nutrients, bacteria, pesticides, polychlorinated biphenyls (PCBs) and others, in local creeks and reservoirs.

This project addresses both greenhouse gas (GHG) reduction and climate change adaptation, as reservoirs are a major source of GHG emissions (i.e. methane, a potent greenhouse gas) during low oxygen conditions. Microbes in the low-oxygen bottom waters of reservoirs and lakes produce methane seasonally. Oxygenation and other interventions may reduce methane production in reservoirs. Oxygenation is the current mechanism to control mercury in fish and may reduce methane emissions. Oxygenation can also reduce the formation of harmful algal blooms, which may become more frequent with warmer temperatures.

*This project was voter approved as part of the Safe, Clean Water and Natural Flood Protection Program.

See Environmental & Community Benefits section for complete description of Key Performance Indicators (KPIs).

KPI #1: (Reduce methylmercury)

The TMDL Monitoring Plan calls for monthly water quality monitoring and spring and summer fish monitoring. Valley Water completed monthly water quality monitoring at Almaden, Calero, Guadalupe, and quarterly monitoring at Stevens Creek Reservoir and Almaden Lake. In spring and summer 2025, fish were sampled at Almaden, Calero, Guadalupe, and Stevens Creek reservoirs. All data were analyzed and included in the biennial progress report submitted to the Water Board in December 2025
In accordance with the adaptive implementation plan for the Guadalupe River Watershed Mercury TMDL Program, Valley Water continued a collaborative research project with the University of California, Merced (UC Merced) to study sorbent treatment methods for mercury control as an alternative to reservoir oxygenation. Sorbents are solid materials that bind to specific compounds. In this case, the study is researching sorbents that preferentially bind to mercury or methylmercury, making it unavailable for entry into the food web. Sorbent treatment methods have the benefit that they do not cause warming or mixing of reservoir water. The project aims to identify effective and appropriate sorbents and application methods that could be used in a field trial in Guadalupe Reservoir. The project began in FY23 and will continue into FY26.
Valley Water coordinated with Santa Clara County, Midpeninsula Regional Open Space District, Guadalupe Rubbish Disposal Company, and the Regional Water Quality Control Board to complete the second 5-year phase of the Coordinated Monitoring Program for the Guadalupe River Watershed Mercury TMDL project. According to the Monitoring Plan, two of the several large storms in January 2023 were sampled for suspended sediment, mercury, and methylmercury in water. The final report was submitted in April 2024 and approved by the Water Board after edits in July 2024. In FY25, the partners continued to collaborate with Regional Water Quality Control Board staff on the next steps for the TMDL. More information on the TMDL project is available here.
In June 2023, Valley Water entered into an agreement with the University of California, Davis (UC Davis) to study methylmercury sources and formation pathways in Guadalupe Reservoir. In FY24, researchers partnered with Valley Water staff to conduct augmented monthly sampling and analysis of various parameters to achieve the goals of the study. Monthly sampling was completed in July 2025. More intensive bi-monthly sampling was carried out from April 2024 to September 2024. These intensive sampling events investigate the seasonal formation pathways of methylmercury production by examining the biological and chemical makeup of bottom water and sediment. The project has been extended through FY27.
In December 2021, Valley Water entered into a collaborative agreement with the University of California, Santa Cruz (UC Santa Cruz) to study local atmospheric mercury deposition near the New Almaden Mining District using lichens as bioindicators. Field data collection was completed in the spring of 2022. Sample analysis and reporting were completed in FY23. Following this study, a second agreement was established to study the sources of atmospheric mercury using lichen. The study began in FY23 and was completed in FY25. Results were published in a peer-reviewed journal. For more information, visit https://doi.org/10.3389/fenvc.2025.1568188.
Valley Water deploys hypolimnetic oxygenation systems (HOSs) to reduce toxic methylmercury production in some reservoirs' bottom waters. HOSs consist of a large oxygen gas generator and distribution lines that bubble oxygen into the bottom waters. This prevents the waters from being hypoxic, an environment low in oxygen that promotes the production of toxic methylmercury. However, HOS operation can increase the temperature of reservoir releases and stimulate surface algae growth, particularly when reservoir storage volume is low. In FY26, HOSs were not operated at Almaden and Calero Reservoirs to better document baseline conditions before piloting a new treatment measures that avoid the negative effects of the line diffuser HOSs

KPI #2: (Prioritization plan)

Valley Water periodically reviews the Prioritization and Implementation of Pollution Prevention and Reduction Activities Plan to Address Impaired Water Bodies in Santa Clara County (Prioritization Plan). The review uses various sources of information, including the San Francisco Bay RWQCB Triennial Review of the Basin Plan and the State’s list of impaired water bodies, to evaluate potential projects in water bodies within our jurisdiction. Since RWQCB priorities change over time as impairments are addressed and new problems are identified, the Prioritization Plan is a living document that is updated according to changing priorities. In FY23, Valley Water surveyed all data available in the California Environmental Data Exchange Network and internal environmental data to develop an objective assessment to identify and prioritize potential projects. A review of the existing data was completed in FY24, and a draft updated Prioritization Plan was completed in FY25. The final plan will be published in FY26. The June 2017 Prioritization Plan can be accessed here.

KPI #3: (Surface water quality improvement activities)

Surface Water Quality Improvement Activity #1: Accumulation Point Mapping and Removal (Coyote Creek and Guadalupe River)
- Valley Water staff developed the Trash Accumulation Assessment and Removal Plan for FY26 in Q2 and began assessments in January 2026.
Surface Water Quality Improvement Activity #2: Reservoir Greenhouse Gas Emission Study
- Valley Water is collaborating with UC Davis to study greenhouse gas emissions from the surfaces of Almaden, Chesbro, Stevens Creek, and Uvas reservoirs. Since January 2021, researchers have completed sampling events to measure gas storage in reservoir sediments (measured quarterly) and greenhouse gas (primarily methane) fluxes from reservoir surfaces in conjunction with atmospheric and water quality data (measured monthly). Data collection continued through 2023, and results were synthesized in a manuscript (https://doi.org/10.1029/2024JG008080) in FY25. A second agreement with UC Davis for additional study in FY25/FY26 to further refine methane flux estimates and collect additional data on carbon dioxide and nitrous oxide began in June 2025. The goal is to improve emissions estimates from all Valley Water reservoirs. Results will inform whether to include reservoir emissions in Valley Water’s greenhouse gas inventory.
Surface Water Quality Improvement Activity #3 Microbial Source Tracking Support
- In FY25, Valley Water supplemented Upper Pajaro Watershed water sampling to add microbial source tracking for various fecal bacteria source markers as part of the Bacteria Special Study Monitoring Report (Water Year 2025) for South Santa Clara County Regional Partners. Fecal bacteria from human sources are much more likely to co-occur with pathogens (usually viruses) that cause human illnesses. However, identifying additional sources can provide a more representative understanding of microbial water quality, including sites previously identified as potential recreational sites (i.e., locations where close human contact with the water may occur, such as swimming or wading). Preliminary results shared in Q1 found that three out of twenty-four samples from receiving waters and outfalls detected human markers, but in extremely low concentrations. This suggests human sources of bacteria were not the main contributors during sampling events. While the following was found for the additional source markers in six receiving water samples. Dog marker was detected in all samples, but the level was low, and it was unclear whether it was caused by pet dogs or wild canine species. Chicken marker was detected at four out of six receiving water samples, but at extremely low levels, suggesting it is not a high priority source of bacteria. Horse marker was not detected in any of the samples collected. Cow marker was detected in all samples, suggesting cattle waste may be present in the larger receiving water watersheds. South County Partners discussed their next steps in Q2 for FY26 monitoring, which focuses on upstream investigations. Valley Water will continue collaboration and potential monitoring support when proposed.

February 2026

For more information:

James Downing, (408) 630-2679

See Environmental & Community Benefits section for complete description of Key Performance Indicators (KPIs).

KPI #1: (Reduce methylmercury)

The TMDL Monitoring Plan calls for monthly water quality monitoring and spring and summer fish monitoring. Valley Water completed monthly water quality monitoring at Almaden, Calero, Guadalupe, and quarterly monitoring at Stevens Creek Reservoir and Almaden Lake. In spring and summer 2025, fish were sampled at Almaden, Calero, Guadalupe, and Stevens Creek reservoirs. All data were analyzed and included in the biennial progress report submitted to the Water Board in December 2025
In accordance with the adaptive implementation plan for the Guadalupe River Watershed Mercury TMDL Program, Valley Water continued a collaborative research project with the University of California, Merced (UC Merced) to study sorbent treatment methods for mercury control as an alternative to reservoir oxygenation. Sorbents are solid materials that bind to specific compounds. In this case, the study is researching sorbents that preferentially bind to mercury or methylmercury, making it unavailable for entry into the food web. Sorbent treatment methods have the benefit that they do not cause warming or mixing of reservoir water. The project aims to identify effective and appropriate sorbents and application methods that could be used in a field trial in Guadalupe Reservoir. The project began in FY23 and will continue into FY26.
Valley Water coordinated with Santa Clara County, Midpeninsula Regional Open Space District, Guadalupe Rubbish Disposal Company, and the Regional Water Quality Control Board to complete the second 5-year phase of the Coordinated Monitoring Program for the Guadalupe River Watershed Mercury TMDL project. According to the Monitoring Plan, two of the several large storms in January 2023 were sampled for suspended sediment, mercury, and methylmercury in water. The final report was submitted in April 2024 and approved by the Water Board after edits in July 2024. In FY25, the partners continued to collaborate with Regional Water Quality Control Board staff on the next steps for the TMDL. More information on the TMDL project is available here.
In June 2023, Valley Water entered into an agreement with the University of California, Davis (UC Davis) to study methylmercury sources and formation pathways in Guadalupe Reservoir. In FY24, researchers partnered with Valley Water staff to conduct augmented monthly sampling and analysis of various parameters to achieve the goals of the study. Monthly sampling was completed in July 2025. More intensive bi-monthly sampling was carried out from April 2024 to September 2024. These intensive sampling events investigate the seasonal formation pathways of methylmercury production by examining the biological and chemical makeup of bottom water and sediment. The project has been extended through FY27.
In December 2021, Valley Water entered into a collaborative agreement with the University of California, Santa Cruz (UC Santa Cruz) to study local atmospheric mercury deposition near the New Almaden Mining District using lichens as bioindicators. Field data collection was completed in the spring of 2022. Sample analysis and reporting were completed in FY23. Following this study, a second agreement was established to study the sources of atmospheric mercury using lichen. The study began in FY23 and was completed in FY25. Results were published in a peer-reviewed journal. For more information, visit https://doi.org/10.3389/fenvc.2025.1568188.
Valley Water deploys hypolimnetic oxygenation systems (HOSs) to reduce toxic methylmercury production in some reservoirs' bottom waters. HOSs consist of a large oxygen gas generator and distribution lines that bubble oxygen into the bottom waters. This prevents the waters from being hypoxic, an environment low in oxygen that promotes the production of toxic methylmercury. However, HOS operation can increase the temperature of reservoir releases and stimulate surface algae growth, particularly when reservoir storage volume is low. In FY26, HOSs were not operated at Almaden and Calero Reservoirs to better document baseline conditions before piloting a new treatment measures that avoid the negative effects of the line diffuser HOSs

KPI #2: (Prioritization plan)

Valley Water periodically reviews the Prioritization and Implementation of Pollution Prevention and Reduction Activities Plan to Address Impaired Water Bodies in Santa Clara County (Prioritization Plan). The review uses various sources of information, including the San Francisco Bay RWQCB Triennial Review of the Basin Plan and the State’s list of impaired water bodies, to evaluate potential projects in water bodies within our jurisdiction. Since RWQCB priorities change over time as impairments are addressed and new problems are identified, the Prioritization Plan is a living document that is updated according to changing priorities. In FY23, Valley Water surveyed all data available in the California Environmental Data Exchange Network and internal environmental data to develop an objective assessment to identify and prioritize potential projects. A review of the existing data was completed in FY24, and a draft updated Prioritization Plan was completed in FY25. The final plan will be published in FY26. The June 2017 Prioritization Plan can be accessed here.

KPI #3: (Surface water quality improvement activities)

Surface Water Quality Improvement Activity #1: Accumulation Point Mapping and Removal (Coyote Creek and Guadalupe River)
- Valley Water staff developed the Trash Accumulation Assessment and Removal Plan for FY26 in Q2 and began assessments in January 2026.
Surface Water Quality Improvement Activity #2: Reservoir Greenhouse Gas Emission Study
- Valley Water is collaborating with UC Davis to study greenhouse gas emissions from the surfaces of Almaden, Chesbro, Stevens Creek, and Uvas reservoirs. Since January 2021, researchers have completed sampling events to measure gas storage in reservoir sediments (measured quarterly) and greenhouse gas (primarily methane) fluxes from reservoir surfaces in conjunction with atmospheric and water quality data (measured monthly). Data collection continued through 2023, and results were synthesized in a manuscript (https://doi.org/10.1029/2024JG008080) in FY25. A second agreement with UC Davis for additional study in FY25/FY26 to further refine methane flux estimates and collect additional data on carbon dioxide and nitrous oxide began in June 2025. The goal is to improve emissions estimates from all Valley Water reservoirs. Results will inform whether to include reservoir emissions in Valley Water’s greenhouse gas inventory.
Surface Water Quality Improvement Activity #3 Microbial Source Tracking Support
- In FY25, Valley Water supplemented Upper Pajaro Watershed water sampling to add microbial source tracking for various fecal bacteria source markers as part of the Bacteria Special Study Monitoring Report (Water Year 2025) for South Santa Clara County Regional Partners. Fecal bacteria from human sources are much more likely to co-occur with pathogens (usually viruses) that cause human illnesses. However, identifying additional sources can provide a more representative understanding of microbial water quality, including sites previously identified as potential recreational sites (i.e., locations where close human contact with the water may occur, such as swimming or wading). Preliminary results shared in Q1 found that three out of twenty-four samples from receiving waters and outfalls detected human markers, but in extremely low concentrations. This suggests human sources of bacteria were not the main contributors during sampling events. While the following was found for the additional source markers in six receiving water samples. Dog marker was detected in all samples, but the level was low, and it was unclear whether it was caused by pet dogs or wild canine species. Chicken marker was detected at four out of six receiving water samples, but at extremely low levels, suggesting it is not a high priority source of bacteria. Horse marker was not detected in any of the samples collected. Cow marker was detected in all samples, suggesting cattle waste may be present in the larger receiving water watersheds. South County Partners discussed their next steps in Q2 for FY26 monitoring, which focuses on upstream investigations. Valley Water will continue collaboration and potential monitoring support when proposed.

February 2026

For more information:

James Downing, (408) 630-2679

Coordinated Monitoring Program

Safe, Clean Water Program Documents

FY22-36 Key Performance Indicators for the Safe, Clean Water Program

Investigate, develop, and implement actions to reduce methylmercury in fish and other organisms in the Guadalupe River Watershed.
Prepare and update a plan for the prioritization of surface water quality improvement activities, such as addressing trash and other pollutants.
Implement at least two (2) priority surface water quality improvement activities identified in the plan per 5-year implementation period.

Benefits

Reduces contaminants in streams and reservoirs
Improves water quality, including water slated for drinking water treatment plants
Increases understanding of mercury cycling in reservoirs to develop strategies that reduce toxic methylmercury in fish consumed by people and wildlife
Increases the scientific understanding of environmental pollutants to assist in developing actions to manage them
Supports regulatory compliance with surface water quality standards for local creeks and reservoirs
Addresses climate change by providing data on the production of methane in reservoirs to estimate the magnitude of those emissions

Geographic Area of Benefit

Countywide

About the Safe, Clean Water and Natural Flood Protection Program

In November 2020, voters in Santa Clara County overwhelmingly approved Measure S, a renewal of Valley Water’s Safe, Clean Water and Natural Flood Protection Program.

The program was first passed by voters in 2000 as the Clean, Safe Creeks and Natural Flood Protection Plan, then again in 2012 as the Safe, Clean Water and Natural Flood Protection Program. The renewal of the Safe, Clean Water Program will continue to provide approximately $47 million annually for local projects that deliver safe, clean water, natural flood protection, and environmental stewardship to all the communities we serve in Santa Clara County.

While evaluating ways to improve the 2012 program, Valley Water gathered feedback from more than 21,000 community members. That helped Valley Water create the six priorities for the renewed Safe, Clean Water Program, which are:

Priority A: Ensure a Safe, Reliable Water Supply
Priority B: Reduce Toxins, Hazards and Contaminants in our Waterways
Priority C: Protect our Water Supply and Dams from Earthquakes and Other Natural Disasters
Priority D: Restore Wildlife Habitat and Provide Open Space
Priority E: Provide Flood Protection to Homes, Businesses, Schools, Streets and Highways
Priority F: Support Public Health and Public Safety for Our Community

Each year, Valley Water prepares a report providing a progress update for each of these program priorities, along with fiscal year accomplishments.

To ensure transparency and accountability to the voters, the ballot measure also created an Independent Monitoring Committee, appointed by the Santa Clara Valley Water District Board of Directors. The Independent Monitoring Committee annually reviews the program’s progress to ensure the outcomes are achieved in a cost-efficient manner and reports its findings to the Board. Additionally, the IMC also reviews each proposed 5-year implementation plan prior to its submittal for Board approval.

In addition, the program requires three independent audits.

View the Safe, Clean Water Program’s annual reports, annual IMC audit reports, and independent audits, including a staff response, on the Valley Water website.