Back to top

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 2029
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

Local-funding-only project: 

The Planning Study Report (PSR) for the Upper Penitencia Creek Flood Protection Project is completed. The PSR describes the planning process used to develop a recommended multi-objective solution for the project. The PSR further discusses the current creek conditions, defines objectives, analyzes alternatives based on the project's alternative ranking methodology, describes public input, and identifies the staff-recommended alternative, including its operation and maintenance and potential mitigation requirements. The PSR's appendices A and B through I are also available.

With the completion of the PSR, the project will transition to the design phase to further analyze and develop a preferred alternative for the project. Public input meetings will be held during this phase.

On-going activities:

  • Valley Water continues to work on the local funding-only option and actively looking for state and federal funding opportunities.
  • Valley Water continues coordinating with property stakeholders along the creek, including the San Jose Flea Market and the City of San Jose.
  • Public meetings will be held during the design phase.


  • Valley Water presented the project and the preferred alternatives at a meeting with state and federal resource agencies in 2021. The Environmental Protection Agency, the U.S. Army Corps of Engineers, the California Department of Fish and Wildlife, the U.S. Fish and Wildlife Services, the National Marine Fisheries Service, and the San Francisco Bay Regional Water Quality Board participated in the meeting, providing feedback. The feedback received from the resource agencies will help the design team develop the California Environmental Quality Act (CEQA) and resource agency permitting strategy.
  • A geomorphology study was conducted to determine the creek's geomorphic conditions and develop the project's channel restoration/enhancement details. The geomorphology study was finalized in March 2022 and incorporated into the PSR.

Preferred project with federal and local funding:

  • No federal funding was provided by the United States Army Corps of Engineers (USACE) for this project.

Updated January 2023

For more information:

Reports & Documents

Planning Study Report (PSR) and Supporting Appendices

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.