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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 2036
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 (EIA) 11

EIA 11 includes the urban area of North San José, the community of Alviso and the San José-Santa Clara Regional Wastewater Facility.

As of January 2021, the United States Fish and Wildlife Service has discontinued their maintenance levee operations. We expect the maintenance levee operations work to resume in fall 2021. 

For more information regarding the United States Fish and Wildlife Service Levee Repair project, please contact Complex Manager Matt Brown at (510) 453-6695. See the United States Fish and Wildlife Service Levee Repair public notice here.

Current Activities:

The United States Army Corps of Engineers (USACE) re-advertised the South San Francisco Bay Shoreline Phase 1 Project Reaches 1, 2 & 3 for construction bidding in January 2021, with construction of Reach 1 (from the Alviso Marina to the Union Pacific railroad) and Reaches 2 & 3 (from Union Pacific railroad to the Artesian Slough) to begin in summer 2021. Valley Water has completed the acquisition of temporary easements required for construction of Reaches 1, 2 & 3. From July 21, 2021 through July 23, 2021, USACE and its contractor will be conducting pre-construction activities on a section of the existing Pond A12/13 and Pond A16 berms.  Please note the construction hours will be from 7 am to 7 pm daily and there will be no public access to trail users across the work area. See the public notification here.

Design of Reaches 4 & 5 are on hold while construction phasing, access points, haul routes, staging, and easements are being addressed with the property owner.   

Reach 1 Design and Permits:

  • 100% Reach 1 levee design Plans and Specifications – Completed

  • San Francisco Bay Regional Water Quality Control Board permit for Reach 1 construction – Received December 2017.

  • San Francisco Bay Conservation and Development Commission permit for Reach 1 construction – Received January 2018.

  • Reach 1 Right-of-Way – Acquired September 2019.

Reach 1 Construction:

  • Valley Water stockpiled approximately 106,000 cubic yards of levee fill material in Pond A12 – Completed December 2019.

  • USACE re-advertised for construction – late January 2021.

  • USACE to begin construction – summer 2021.

Reaches 2 & 3 Design and Permits:

  • 90% Reaches 2 & 3 levee design Plans and Specifications – Completed September 2019.

  • San Francisco Bay Regional Water Quality Control Board permit for Reaches 2 and 3 construction – Received December 2017.

  • San Francisco Bay Conservation and Development Commission permit for Reaches 2 & 3 construction – Received April 2019.

Reaches 2 & 3 Construction:

  • Reaches 2 & 3 right-of-way fully acquired – June 2020.

  • USACE re-advertised for construction – late January 2021.

  • USACE to begin construction – summer 2021.

  Reaches 4 & 5 Design and Permits:

  • 30% Reaches 4 & 5 levee design plans and specifications – Completed April 2020.
  • 60% Reaches 4 & 5 levee design plans and specifications – October 2020 (design on hold).

Completed Milestones:

  • Feasibility Study Phase: September 2005 to July 2016.

  • Environmental Documents: Environmental Impact Report (EIR) was certified by the Valley Water Board on March 22, 2016. Conservancy adopted the EIR as a responsible agency on March 22, 2018.  The USACE and U.S. Fish and Wildlife Services issued their Records of Decision for the Environmental Impact Statement (EIS) in July 8, 2016 and April 6, 2017 respectively.  The San Francisco Bay Restoration Authority adopted the EIR as a responsible agency on April 11, 2018.

  • Preliminary Engineering and Design Phase (including permitting): July 2016 to February 2019.

  • Construction Phase: February 2019 to ongoing.

  • Funding: 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 $512 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. SCC’s and Valley Water’s total local cost share of the project is $371 million. Valley Water’s local cost share is $269 million and SCC’s local cost share is $102 million. Valley Water has secured $17 million from the 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.


Economic Impact Areas (EIA) 1-10

EIAs 1-10 includes the shoreline areas located between San Francisquito Creek and the Lower Guadalupe River 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, initiated the South San Francisco Bay Shoreline Phase II Feasibility Study (Phase II Feasibility Study) in September 2019. The USACE, Valley Water, and State Coastal Conservancy will continue using a phased approach by breaking up EIAs 1-10 into two separate studies. The USACE Phase II Feasibility Study will focus on EIAs 1-4, from San Francisquito Creek in Palo Alto to Permanente Creek in Mountain View. The USACE has requested funds as a part of the regular federal budget cycle for a future Phase III Feasibility Study focusing on the remaining EIAs 5-10, from Permanente Creek in Mountain View to Guadalupe River in San Jose.  

Current activities:

  • USACE Phase II Feasibility Study (EIAs 1-4): The project team is currently developing a focused array of alternatives and collecting and analyzing data to determine the tentatively selected plan. The team held a workshop to develop the ecosystem restoration benefits model in December 2020.  The USACE will be submitting an exemption request to USACE Headquarters to revise the feasibility budget and schedule.  The team plans to hold a public scoping meeting to release a joint Notice of Early Scoping (NEPA) and Notice of Preparation of an EIR (CEQA) in spring 2021.  

  • EIAs 4 and 5: Valley Water is coordinating with the South Bay Salt Ponds Restoration Project (SBSPRP) team to construct the 1% coastal flood risk management levee in EIAs 4 and 5 (Mountain View EIAs).

  • EIAs 6-10: Valley Water has engaged the San Francisco Estuary Institute to develop a visioning document for the Sunnyvale shoreline area and regular collaboration meetings are being held with City of Sunnyvale, USFWS, NASA, Google, and Lockheed Martin.

  • EIA 10: Valley Water is working with the SBSPRP team to plan flood risk management efforts in EIA 10 (San José/Santa Clara and Pond A8 area).

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. The USACE completed a Project Management Plan detailing the Phase II Feasibility Study’s scope, schedule, and budget in May 2020.

Updated April 2021

Reports & Documents

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

For further information, please see

Last updated: August 2019

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.