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E5: San Francisquito Creek Flood Protection*

About This Project

The project is sponsored by the San Francisquito Creek Joint Powers Authority (SFCJPA), of which Valley Water is a member agency, in partnership with the U.S. Army Corps of Engineers (USACE).

Preferred project: A federal-state-local partnership

The project is to construct improvements along San Francisquito Creek from San Francisco Bay to just upstream of the Pop-Chaucer Bridge and additional detention of floodwaters upstream of Highway 280 to provide 1% (100-year event) flood protection, ecosystem restiration and recreational benefits to surrounding communities.

Local-state-funding-only partnership

Highway 101 to Pope-Chaucer Bridge

This stretch of the project will remedy channel constrictions and replace bridges at Newell Road and Pope/Chaucer streets to allow the channel to contain floodwaters of approximately 7,500 cubic feet per second, equivalent to approximately a 1.4% flood event (70-year event). Allowing this level of water to flow through the channel will protect approximately 3,000 parcels in Palo Alto from a flood event close to the February 1998 flood, the largest on record. Currently the channel can only convey approximately a 7% flood event (approximately a 15-year event).

Newell Road Bridge

The Newell Road bridge replacement, unlike the rest of the project elements in this stretch, is sponsored by the City of Palo Alto, which has applied for funding through Caltrans’ Highway Bridge Program (HBP). The project has been programmed by Caltrans to fund approximately 89% of the total cost for replacing the Newell Road bridge, while the local match funds, approximately 11% of the total cost, will be funded by Valley Water through the Safe, Clean Water Program renewal. The City of East Palo Alto and the SFCJPA continue to provide input on the Newell Road bridge replacement.

The SFCJPA continues to pursue partnerships with federal, state and local agencies and grant opportunities for additional construction funding.


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

Palo Alto
Bay to Hwy. 101: Complete; Upstream of Hwy. 101: Design
Start FY 2022 / Finish FY 2025
Safe, Clean Water Fund ($46.5 million); San Francisquito Creek Joint Powers Authority
News and UpdatesNews and Updates
Reports and DocumentsReports and Documents
Environmental and Community BenefitsEnvironmental and Community Benefits
History and BackgroundHistory and Background
News & Updates

Upstream of Highway 101 Reach (Upstream)

SFCJPA prepares for permit applications and Valley Water continues to work on Channel Widening, Top of Bank Improvements, and Pope-Chaucer Street Bridge Replacement Design

The San Francisquito Creek Joint Powers Authority (SFCJPA) continues its effort in preparing applications for regulatory permits to construct the Upstream Reach of the San Francisquito Creek project (Project). Draft regulatory permit applications were submitted in July 2022, the final applications will be submitted by June 2023, and it is anticipated to acquire permits by September 2023.

The City of Palo Alto secured additional Caltrans Highway Bridge Program funding for design and right-of-way acquisitions for the Newell Road Bridge Replacement. Design was completed in March 2023. Construction on the Newell Road Bridge Replacement is expected to begin in the summer of 2024.

The US Army Corps of Engineers (USACE) is leading the implementation of the channel widening sites located upstream of Highway 101. The SFCJPA and USACE are in the process of completing a Feasibility Study through the Continuing Authorities Program Section 205 (CAP 205) process. The draft USACE feasibility study report was completed in July 2022, and the final study report is expected in late 2023. The SFCJPA and Valley Water continue to support the USACE CAP 205 study. Valley Water continues to assist with the engineering and develop the design documents for channel widening sites. The design analysis and various wall type options for the widening sites are being coordinated with the SFCJPA and USACE and the design documents are expected to be completed by the fall of 2023.

Retrofit or replacement of the existing top-of-bank floodwalls along both sides of the creek banks downstream of the Newell Road bridge and upstream of W. Bayshore Road was added to Project. The SFCJPA is preparing a Supplemental EIR and anticipates completing it in late 2023. Valley Water is developing design documents and it is anticipated to complete the design documents by the fall of 2023. Construction is expected in 2025.

Pope-Chaucer Street Bridge Replacement is currently at 80% design. After receiving input from the Palo Alto Architectural Review Board (ARB) at its study session on December 17, 2020, Valley Water and the SFCJPA continue to coordinate with the City of Palo Alto to complete the design. The design documents are expected to be complete by the fall of 2023. 

A winter preparation flood mailer was sent to the properties near San Francisquito Creek that are located in Santa Clara County. 

Previous Updates

The SFCJPA entered into a Feasibility Cost Share Agreement (FCSA) with the USACE in the summer of 2021 and initiated the Continuing Authorities Program Section 205 (CAP 205) process.

At its September 26, 2019 meeting, the SFCJPA Board unanimously certified the San Francisquito Creek Upstream of Highway 101 Project FINAL Environmental Impact Report, approved the project, and authorized the Executive Director to secure the permits, funding and land rights necessary to build it.

This milestone follows an intense period of work to improve the Final EIR since the Draft EIR became available for public comment on April 22, 2019, and we discussed the document at several public hearings, City Council meetings, and SFCJPA Board meetings. 

After receiving input from the community in 2013, the SFCJPA determined the need for a smaller scale project that addresses creek flooding similar to the 1998 flood, and that is achievable within the funding constraints of the partner agencies. Four public scoping meetings were held in January and February 2017 and the SFCJPA was tasked to develop a Draft Environmental Impact Report (Draft EIR) to evaluate the environmental impacts of each alternative.

The Draft EIR was released for public review on April 22, 2019. After considering 17 different alternatives, three alternatives advanced through the screening process: 1) Replace the Pope-Chaucer Bridge and Widen Channel Downstream, 2) Construct One or More Detention Basins, 3) Replace the Pope-Chaucer Bridge and Construct Floodwalls Downstream.

Three public hearings, in Menlo Park, East Palo Alto, and Palo Alto, were held to solicit the public’s comments on the Draft EIR.

The SFCJPA has begun the lengthy process of acquiring permits from multiple agencies to construct the Upstream Reach of the San Francisquito Creek project. Permit applications will be submitted by the spring of 2021.

The City of Palo Alto addressed City staff’s comments on the Newell Road Bridge draft EIR and the desired bridge replacement alternative. The final EIR was certified by the City Council in June 2020 with final design of the replacement bridge and permit applications to follow. For more information, visit the city’s website.

Caltrans replaced the Highway 101 bridge and frontage roads crossing over the creek to improve traffic flow and allow channel widening. The new bridges were completed in 2018.

Bay to Highway 101 Reach (Completed)

The flood protection features of the Bay to Highway 101 Reach of the San Francisquito Creek Flood Protection Project are now complete.  Improvements to this stretch of about one and a half miles of the creek constitute the necessary first step in an overall plan to provide more than 5,700 homes and businesses with creek flood protection. The project also provides improved access to trails. 

The Operations and Maintenance Agreement between Valley Water, East Palo Alto, and the SFCJPA was executed by all parties in Fall 2021 which was then included in final Operations and Maintenance Manual.

March 2023

For more information:

Bay to Highway 101 Reach (Downstream)

Upstream of Highway 101 Reach (Upstream)

Environmental & Community Benefits

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

  1. Preferred project with federal, state and local funding: Protect more than 3,000 parcels by providing 1% (100-year) flood protection.

  2. With state and local funding only: Protect approximately 3,000 parcels by providing 1% (100-year) flood protection downstream of Highway 101, and approximately 1.4% (70-year) protection upstream of Highway 101.


  • Provides 1% flood protection to approximately 3,000 homes and businesses in Palo Alto

  • Local-state-funding-only project provides approximately 1.4% (70-year event) flood protection for approximately 3,000 homes and businesses in Palo Alto

  • Reduces bank erosion and sedimentation-related impacts along San Francisquito Creek

  • Provides new or improved habitats for endangered species

  • Improves water quality

  • Enhances recreational opportunities for the community

  • Leverages dollars via cost-shares and grants from the state Department of Water Resources and the California Department of Transportation

  • Addresses climate change

Geographic Area of Benefit

Palo Alto 

History & Background

Flooding History and Project Background

San Francisquito Creek is one of the last continuous riparian corridors on the San Francisco Peninsula, and is also home to 1 of the few remaining viable steelhead trout runs. The creek can cause severe flood damage with very little warning and has overflowed 7 times since 1910.

During the February 1998 El Niño event, record flooding caused an estimated $28 million in damages in Palo Alto, East Palo Alto and Menlo Park. More than 1,100 homes were flooded in Palo Alto, and Highway 101 was closed, as were numerous other roadways. The largest flood on record prior to 1998 occurred in December of 1955 when the creek overtopped its banks in several locations, inundating about 1,200 acres of commercial and residential property. Damages were estimated at nearly $2 million in 1956 dollars. Total damages from a 1% flood event are estimated at $300 million in Santa Clara and San Mateo Counties, as calculated by the USACE in 2011.

In 2019, Valley Water completed the construction of the San Francisco Bay to Highway 101 reach of the project to provide 1% flood protection  and ecosystem benefits to the neighboring communities. Major improvements included construction of approximately 4,000 feet of floodwall and creating a significantly wider creek marsh plain. Therefore, completion of this stretch protects approximately 3,000 parcels in Palo Alto from a flood event close to the February 1998 flood, the largest on record.

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.