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E7: San Francisco Bay Shoreline Protection*

About This Project

This project is a partnership with the California State Coastal Conservancy, the U.S. Army Corps of Engineers (USACE) and regional stakeholders to provide tidal flood protection, restore and enhance tidal marsh and related habitats, and provide recreational and public access opportunities along Santa Clara County’s shoreline.

This project relies on federal participation from the USACE to develop the project and prepare the plans. Without federal participation, Valley Water cannot implement planning, design and construction on our own due to limited available funding. The Safe, Clean Water funding provides a portion of the local share of funding for planning, design and construction phases for Economic Impact Areas (EIAs) 1-4, and a portion of the local share of funding for the planning study and design phases for EIAs 5-9.

The 2012 Safe, Clean Water Program has already provided $15 million as a portion of Valley Water’s  local share of funding for flood protection improvements in Economic Impact Area (EIA) 11, which is the urban area of North San José and the community of Alviso. Once completed, EIA 11 will provide flood protection to more than 1,000 residential structures and 100 non-residential structures, and allow for the restoration of 2,900 acres of tidal marsh and related habitats.

The project will provide coastal flood protection from a rising sea level, and will restore and enhance tidal marsh by using a combination of flood protection levees, wetlands and transitional zone habitats also known as ecotones. Ecotones will provide an additional protective buffer for the levee and allow marsh habitat to migrate upslope as the sea level rises. This approach of using natural infrastructure will help develop a resilient and adaptable flood protection system that can evolve in the future.

(Photograph by Cris Benton)

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

Shoreline - Chicago Marsh Cris Benton
On Target
Milpitas, Mountain View, Palo Alto, San José, Santa Clara and Sunnyvale
Start FY 2022 / Finish FY 2028
Safe, Clean Water Fund ($30.4 million); Watershed Stream Stewardship Fund
News and UpdatesNews and Updates
Reports and DocumentsReports and Documents
Environmental and Community BenefitsEnvironmental and Community Benefits
History and BackgroundHistory and Background
News & Updates

Economic Impact Area 11

Economic Impact Area (EIA) 11 includes the urban area of North San José, the community of Alviso and the San José-Santa Clara Regional Wastewater Facility. The 2012 Safe, Clean Water Program provided $15 million as a portion of Valley Water’s local share of funding for flood protection improvements in EIA 11. There are five reaches under EIA 11 (Phase I).  See map here.

Construction work on Reaches 1 through 3 began in December 2021 and is estimated to continue until Summer 2025. Reach 1 extends from Alviso Marina to Union Pacific Railroad and Reaches 2 and 3 stretch from the Union Pacific Railroad to Artesian Slough. Daily construction hours are 7 a.m. to 5:30 p.m., Monday through Friday, excluding weekends and holidays. Work to date has consisted primarily of removing water from the work area, demolishing the existing berm, and replacing it with a more suitable material foundation for the levee. As well, crews are moving more than 500,000 cubic yards of material to build the levee. Works crews have set up coffer dams and sheet pile wall systems to isolate the construction area from the surrounding pond areas and have relocated about 25,000 fish from the work area to the Bay. There will be no public access to trail users across the Pond A12, A13, A16 and A17 berms that are within the construction work area. See the fact sheet here

Design of Reaches 4 and 5, which extend from the Artesian Slough East to Coyote Creek, are on hold while construction phasing, access points, haul routes, staging, and easements are being addressed with the property owner.  USACE and the non-federal partners are looking for alternative measures that meet project objectives and reduce construction costs.  Before being put on hold, 60% levee design plans and specifications were completed in October 2020.

Weekend hours added for levee work

Beginning Saturday, Feb. 5, 2022, the USACE and its contractor began working on weekends to monitor and maintain the dewatering equipment, to demo and construct levee (excluding truck hauling of fill materials), and to maintain best management practices. Work activities will be within the controlled construction site which is fenced off from the public. Typical weekend hours are from 7 a.m. to 5:30 p.m. but may also occasionally occur outside these hours as well. 

A multi-agency partnership

The Shoreline Project is a strongly supported project as evidenced by the signing of the USACE Chief's Report in December 2015, with a total Feasibility Study cost of $22 million, followed by its authorization for design and construction in the Water Infrastructure Improvements for the Nation Act in December 2016. 

The total project cost is $545 million to implement coastal flood risk management, ecosystem restoration, and recreational project elements. The project has received $124 million under the USACE 2018 Disaster Supplemental Appropriations Bill. California State Coastal Conservancy’s (Conservancy) and Valley Water’s total local cost share of the project is $400 million. Valley Water’s local cost share is $298 million and the Conservancy’s local cost share is $102 million. Valley Water has secured $15 million from the 2012 Safe, Clean Water program and $61 million from the San Francisco Bay Restoration Authority’s Measure AA program. Remaining share of Valley Water funds will be from the Watershed Stream Stewardship Fund and Senate Bill 881 will allow Valley Water to be eligible for reimbursement from the Department of Water Resources (DWR) State Subventions Program pending DWR funding availability. Future federal appropriations of $17 million will be required for restoration monitoring.

For significant EIA 11 project milestones reached, click here.


Economic Impact Areas 1-10

Economic Impact Area (EIAs) 1-10 include the shoreline areas located between San Francisquito Creek in Palo Alto and the Lower Guadalupe River in San José and includes the communities of Palo Alto, Mountain View, NASA, Sunnyvale, San José, and Santa Clara. The USACE in partnership with Valley Water, and the California State Coastal Conservancy (Conservancy) are using a phased approach by breaking up EIAs 1-10 into two separate studies. The South San Francisco Bay Shoreline Phase II Feasibility Study (Phase II Feasibility Study) focuses on EIAs 1-4, from San Francisquito Creek in Palo Alto to Permanente Creek in Mountain View. The Shoreline (Sunnyvale) Feasibility Study focuses on the remaining EIAs 5-10, from Permanente Creek in Mountain View to Guadalupe River in San José.  The Phase II Feasibility Study was initiated in September 2019, and the Shoreline (Sunnyvale) Feasibility Study was initiated in August 2023.

Current activities:

  • USACE Phase II Feasibility Study (EIAs 1-4):  The USACE Economic Feasibility Analysis determined that the future economic damage from coastal flooding is not great enough to justify investing federal dollars in a project until approximately 2060. USACE is finalizing study documentation, which will include information on when the study should be resumed in the future based on increasing sea level rise levels.  In addition, Valley Water is considering alternate means of working with USACE on smaller projects in the study area to address near-term coastal flooding.

  • EIAs 5-10: The Shoreline Phase III Feasibility Study has received federal funding and the Feasibility Cost Share Agreement between Valley Water and USACE was signed and a kickoff meeting was held in August 2023.  The Conservancy will sign on as a local sponsor via an amendment in October 2023. 

  • EIA 10: Valley Water is working with the SBSPRP team to plan flood risk management efforts in EIA 10 (Calabazas/San Tomas Aquino Creek-Marsh Connection Project)

EIAs 1-10 Completed milestones:

  • Valley Water’s Preliminary Feasibility Study: Began in June 2015 and was completed and finalized in March 2017. The preliminary study’s goal was to identify a preliminary 1% coastal flood risk management alignment with related benefits and costs for the EIAs 1-10 coastal area to aid in determining the Valley Water’s next study phase or phases and to identify potential study partnership opportunities. The preliminary alignment was identified and used to move forward with conducting the preliminary feasibility study analysis. The City of Palo Alto, City of Mountain View, City of Sunnyvale, City of San José, NASA Moffett Field, US Fish and Wildlife Service, State Coastal Conservancy and Mid-Peninsula Open Space Authority were all consulted in the identification of the preliminary alignment.

  • USACE Phase II Feasibility Study (EIAs 1-4): On September 26, 2019, USACE, Valley Water, and State Coastal Conservancy signed the Feasibility Cost Share Agreement for the next study phase. A kickoff for the planning charette was held on October 9, 2019. The USACE held the Alternatives Milestone Meeting in January 2020. USACE leadership approved an exemption request to increase the feasibility study budget and extend the schedule on Sept. 29, 2021. The study was scheduled to be completed in 2025. The ecosystem restoration benefits model was approved and certified for regional use by the USACE Ecosystem Restoration National Planning Center of Expertise on November 5, 2021. A geotechnical investigation of the existing levee system around Palo Alto flood basin was completed in early November 2021. In October 2022, the USACE completed an Economic Feasibility Analysis that determined that the future economic damage from coastal flooding is not great enough to justify investing federal dollars in a project until approximately 2060.

  • Sunnyvale Shoreline Resilience Vision: In 2019, Valley Water engaged the San Francisco Estuary Institute to develop a visioning document for the Sunnyvale shoreline area, called the Sunnyvale Shoreline Resilience Vision. The Vision group stakeholders include Valley Water, the City of Sunnyvale, Lockheed Martin, the Midpeninsula Regional Open Space District, NASA, the US Fish and Wildlife Service, the South Bay Salt Pond Restoration Project, and Google. During the first phase of collaboration between 2019 and 2021, the Vision group successfully advanced preparatory actions for the future Shoreline Phase III Feasibility Study for the Moffett Airfield and Sunnyvale shoreline, including lobbying Congress for dedication of funds, increasing alignment between stakeholders, exploring synergies between individual planning efforts, and gathering data USACE will need for their analysis. An executive summary documenting the Vision group’s efforts was finalized in December 2021 and can be accessed here

August 2023

For more information:

South San Francisco Bay Shoreline Project, Phase I (EIA 11, San Jose / Alviso)

South San Francisco Bay Shoreline Project, Phase II Feasibility Study (EIAs 1-4, Palo Alto / Mountain View)

South San Francisco Bay Shoreline Project, Phase III Feasibility Study (EIAs 5-10, Mountain View / Moffett Federal Airfield / Sunnyvale)


Reports & Documents

Public Notification 

Project Fact Sheets

Economic Impact Area 11

Appendix A: NEPA/CEQA Supporting Documents 

Appendix B: Supporting Planning and Environmental 

Documentation and Information (Appendix B1-B6 and Appendix B7-B12

Appendix C: Economics 

Appendix D: Hydrology and Hydraulics 

Appendix E1: Civil Design and Cost Engineering 

Appendix E2: Basis of Cost Estimate Memorandum 

Appendix F: Monitoring and Adaptive Management Plan for Ecosystem Restoration 

Appendix G: Geotechnical Engineering 

Appendix H: Real Estate 

Appendix I: Public Comments 

Appendix J: Support Letters 

Errata to Final EIR + CEQA Summary 020916

Addenda to FEIR/FEIS:


Economic Impact Areas 1-10

  • The Preliminary Feasibility Study for EIAs 1-10 can be downloaded from the following links:

Executive Summary

Final Evaluation Report

Appendix 1: Long Wave Modeling Report

Appendix 2:  Statistic Analysis of Water Surface Elevation

Appendix 3: Coastal Storm Damage Risk Analysis 

Appendix 4: Hydraulic Analysis



Environmental & Community Benefits

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

  1. Provide a portion of the local share of funding for planning, design and construction phases for the Santa Clara County shoreline area, EIAs 1-4.

  2. Provide a portion of the local share of funding for planning and design phases for the Santa Clara County shoreline area, EIAs 5-9.


  • Provides planning and design to protect nearly 4,700 acres and more than 5,000 structures, including roads, highways, parks, airports and sewage treatment plants in Santa Clara County

  • Allows for restoration of tidal marsh habitat for endangered wildlife such as the salt marsh harvest mouse and Ridgway’s rail; rich feeding grounds for shorebirds; and nursery areas for young fish such as leopard sharks and steelhead

  • Provides educational, recreational and public access opportunities

  • Protects more than 4,300 structures (EIAs 1-4)

  • Allows for the restoration of 400 acres of tidal marsh and related habitats (EIAs 1-4)

  • Addresses climate change

Geographic Area of Benefit

Milpitas, Mountain View, Palo Alto, San José, Santa Clara and Sunnyvale 

History & Background

Flooding History and Project Background

This project stems from the 2003 acquisition of thousands of acres of former South Bay salt production ponds, purchased for restoration with combined public and private funding. The South Bay Shoreline Protection Project is an important component of the South Bay Salt Ponds Restoration Project, a large, multi-agency effort to restore 16,500 acres of tidal wetlands which involves all South Bay cities that meet the San Francisco Bay. Without incorporating flood protection measures, proposed recreational use and environmental restoration is likely to reduce the effectiveness of existing shoreline levees formerly maintained for salt production. Project E7 would upgrade levees to protect Silicon Valley’s “Golden Triangle,” bounded by Highways 101, 237 and 880, and extending north into the Baylands of Milpitas. Multiple flood events since the mid-1990s have damaged business operations in this area, now home to major high-tech corporations including Intel, Google, Yahoo, Cisco, and others. The project would also protect Alviso neighborhoods, as well as important infrastructure such as airports and sewage treatment plants.

The existing multi-agency partnerships for the South Bay Salt Ponds Restoration project and the San Francisco Bay Shoreline Study ensure that all goals for this largest wetland restoration on the West Coast will be incorporated. The Safe, Clean Water measure provides a share of the total funding needed for planning and design phases for the full shoreline project area. It also provides the funding needed to purchase lands, easements and rights-of-way as necessary to construct improvements in EIA 11, and a share of the construction costs for that portion of the project.

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.