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E4: Upper Penitencia Creek Flood Protection*

About This Project

Preferred project: A federal-state-local partnership

This project continues a partnership with the U.S. Army Corps of Engineers (USACE), to plan, design and construct improvements along 4.2 miles of Upper Penitencia Creek from the confluence with Coyote Creek to Dorel Drive. Part of the project will protect the area around the Bay Area Rapid Transit’s (BART) Berryessa station near King Road, which would otherwise be subject to flooding.

In addition to providing flood protection, this multi-objective project will provide ecological restoration and recreation benefits while preserving the water supply. The natural creek channel will be preserved while adjacent existing open space and parkland will remain as recreational areas, only rarely taking the role as a temporary floodplain so that floodwaters do not enter surrounding neighborhoods and commercial areas. Proposed construction measures may include modified floodplains, limited levees/ floodwalls, a bypass channel, and fish passage improvements.

Local-funding-only project

The original local-funding-only project was to acquire all necessary rights-of-way and construct a 1% (100-year event) flood protection project from Coyote Creek confluence to King Road, which would have protected 450 parcels. In December 2019, the Valley Water Board directed staff to use the available local funding to complete the design and construction of the locally funded project as well as build the reaches of the preferred project that can be constructed with the available funding. This approach extends the local-funding-only project from King Road to Capital Avenue and provides 1% flood protection for an additional 800 parcels. As a result, the new local-funding-only project is to construct flood improvements along Upper Penitencia Creek from the confluence of Coyote Creek to Capital Avenue to increase the 1% flood protection provided with local available dollars to 1,250 parcels, including the new Berryessa BART station.


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

Upper Pen Along Commodore Park
On Target
San José
Start FY 2022 / Finish FY 2036
Safe, Clean Water Fund ($22.0 million)
News and UpdatesNews and Updates
Reports and DocumentsReports and Documents
Environmental and Community BenefitsEnvironmental and Community Benefits
History and BackgroundHistory and Background
News & Updates

The Upper Penitencia Creek Project is a unique and multi-benefit effort currently in the planning stage with goals to:

  • Reduce flood risk.
  • Maintain and enhance water supply.
  • Provide for trails and recreation.
  • Maintain and improve the creek’s habitat.

Preferred project with federal and local funding:

  • No federal funding has been provided from USACE for this project.

Local-funding-only project: 

  • Valley Water continues to work on the local-funding-only option planning study with a streamlined planning process.
  • Valley Water completed the Problem Definition Report in spring 2019.
  • In winter 2017, the Capital Improvement Program (CIP) Committee recommended that the Upper Penitencia Creek Project be reduced to only the planning phase and that the funds be reallocated to complete flood risk reduction along 9 miles of Coyote Creek from Montague Expressway to Tully Road. However, on May 23, 2018, the Valley Water Board of Directors (Board) decided to take “no action” on the proposed modification to the Upper Penitencia Creek Project and instead decided to re-evaluate both projects after the planning study report for each project is completed or substantially advanced. After further analysis, the planning team decided to divide the Upper Penitencia Creek Project into the following three phases:
    • Phase I – Reach 1 (Coyote Creek confluence up to King Rd);
    • Phase II – Reaches 2 & 3 (King Rd up to Capitol Ave); and 
    • Phase III – Reaches 4 through 7 (Capitol Ave up to Dorel Dr).
  • The Recommended Project was to move forward with Phases I & II: complete design and construction. The Recommended Project was presented to the CIP Committee and, with their support, presented to the Board.
  • On December 10, 2019, The Board approved the Recommended Project and the project team prepared to move forward with design and construction of reaches 1, 2, and 3 (Coyote Creek confluence up to Capitol Ave).

The project team is currently nearing the end of the planning phase and expects to transition into design by the end of calendar year 2021. The project team continues to work on the Planning Study Report (PSR), the preliminary Plan & Profile Sheets (Plans), and a geomorphology study to assist in the channel restoration aspects.  The PSR went through QC review in June and is currently being finalized with the QC comments and the results from the geomorphology study. The PSR and preliminary Plans are expected to go through Districtwide review in December 2021.

Updated November 2021 


For more information:

Reports & Documents

Inundation Maps


SFEI Vision Report


Public Meeting Materials

May 15, 2019:

Staff provided an update on the feasible alternatives which reflected the public input received at the October 2018 public meeting.


October 2, 2018:


Environmental & Community Benefits

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

  1. Preferred project with federal and local funding: Construct a flood protection project to provide 1% (100-year) flood protection to 8,000 parcels.

  2. With local funding only: Construct a 1% (100-year) flood protection project from Coyote Creek confluence to Capital Avenue to provide 1% (100-year) flood protection to 1,250 parcels, including the new Berryessa BART station.


  • Preferred project provides up to 1% flood protection to approximately 8,000 homes, schools and businesses

  • Local-funding-only project provides 1% flood protection to 1,250 parcels, including the new Berryessa BART station

  • Restores/enhances ecological and riparian habitat

  • Reduces sedimentation and maintenance requirements

  • Improves water quality in Upper Penitencia and Coyote creeks

  • Provides opportunities for recreation improvements consistent with the City of San José and Santa Clara County
    Park master plans

  • Addresses climate change

Geographic Area of Benefit

San José 


History & Background

Flooding History and Project Background

Upper Penitencia is a major tributary of Coyote Creek, flowing westerly from Alum Rock Park through the residential neighborhoods of Berryessa and Alum Rock in San José. More than 5,000 homes, schools and businesses are located in this floodplain, including many high-tech and commercial industries supporting the greater Silicon Valley.

With the capacity to carry less than a 10-year event, Upper Penitencia Creek has spilled its banks at least 7 times since the District began preparing flood reports in 1967. Damaging flood events occurred in 1978, 1980, 1982, 1983, 1986, 1995, and 1998, impacting many homes, businesses and surface streets.

Potential damages from a 1% (or 100-year) flood event are estimated at $455 million (in 2004 dollars, according to a USACE economic analysis), with average annual damages estimated at $30.5 million for the full reach from the Coyote Creek confluence to Dorel Drive.

The preferred project would build on a 1981 tri-party agreement between the District, the City of San José, and Santa Clara County to preserve open land and provide flood protection along the Upper Penitencia Creek corridor. As a result of the agreement, 78 acres have been permanently preserved as Penitencia Creek County Park and Penitencia Creek Trail. A 4-mile, intermittent trail follows Upper Penitencia Creek from 700-acre Alum Rock Regional Park to its confluence with Coyote Creek. In addition to much-needed flood protection, this project will help provide the opportunity for the City of San José and Santa Clara County to complete the long-planned trail and linear park.

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.