From salt pond to salt marsh: Transforming the Bay

Updated to reflect passage of 9-county parcel tax.

Walk along levees where the community of Alviso meets the San Francisco Bay, and you can see for miles. The view along the flat expanse of marsh takes in homes, railroad tracks, faraway hillsides, NASA hangers, old landfills and a 7-story-high pile of salt.

Closer in, birds of every variety swoop and call; the wind whips through the marsh grasses, and the shallow water glints in the afternoon sun.

What you can’t see are the property lines in the New Chicago Marsh, where a real estate developer subdivided the land for single-family homes along the San Francisco Bay more than 100 years ago. That land is now 8 feet below sea level.

In fact, much of Alviso has subsided. Situated between the Guadalupe River and Coyote Creek, the community, now a part of the city of San José, exists under the threat of tidal and street flooding as well as sea-level rise. In 1983, the area was evacuated for 30 days due to severe flooding, in some places as much as 10-feet deep.

1-Alviso Post Office - 1983-color


But now, a project to protect and restore the area has reached a major milestone. This project, a collaboration between the State Coastal Conservancy, federal government and the Santa Clara Valley Water District, stands poised to protect thousands of people and businesses from tidal flooding and sea level rise. Last December, the U.S. Army Corps of Engineers’ Chief of Engineers recommended that Congress authorize the Army Corps to begin the design and ultimately construction of the first phase of the South San Francisco Bay Shoreline Project.

The project will not only protect against tidal flooding and rising seas, it will also enhance habitat for endangered species and provide important recreation opportunities to the South Bay. It includes construction of 4 miles of a flood risk management levee, restoration of 2,900 acres of tidal marsh habitat, reduction of tidal flood risk for about 5,500 people, protection of the San José-Santa Clara Regional Wastewater Facility that serves 1.4 million people and businesses, and protection of State Route 237, a major Silicon Valley commute artery, and the water district’s Silicon Valley Advanced Water Purification Center.

The Shoreline Project and the concurrent South Bay Salt Pond Restoration Project will return former salt production ponds that once ringed the southern part of San Francisco Bay back to the tidal wetland that previously teemed with insects, animals and birds.

The Shoreline Project’s flood risk management levee must be completed before the later phases of the South Bay Salt Pond Restoration project can proceed in the Alviso area. The Salt Pond restoration project includes breaching old salt pond berms which will allow sediment-laden bay water to flow back into the former salt ponds, building up the pond elevation and allowing marsh vegetation to grow.

Minneapolis-based Cargill sold and donated 16,500 acres around the Bay and the Napa River to the state and federal government for $100 million. The old berms that formed the salt ponds today serve as de facto flood protection levees, though that was never their intent.

John Bourgeois, executive project manager for the South Bay Salt Pond Restoration Project for the State Coastal Conservancy, walked along a berm that extended from the Don Edwards National Wildlife Refuge’s Environmental Education Center, where the former salt ponds were located. The low, dirt levee is visibly crumbling along the sides.

“Most are in worse shape,” he said. “No engineering or design went into these.”

Yet these berms and a few ponds restored to marshes are all that stand in the way of the community of Alviso, SR 237 and the wastewater treatment facility just up the road.

“I think the big piece of infrastructure is the wastewater treatment plant,” Bourgeois said. “If you’ve got 1.4 million people who can’t flush the toilet, that’s going to shut down Silicon Valley.

“All of our sewage treatment plants are at the edge of the bay at the lowest spots,” he added. “They’re all at risk.”

Bourgeois also points out that with Hurricane Katrina, people were relocated, and many never made their way back.

“A flooding event of the type we’re talking about could result in billions of dollars of damage and a permanent mark on our economy,” he said. “Silicon Valley is one of the leading economies in the world. The economic impact affects everybody.”

In fact, a 2015 report by the Bay Area Council, a business-sponsored public policy advocacy organization for the 9-county San Francisco Bay Area, notes that an extreme storm in the Bay Area could have an economic impact of more than $10 billion.

Cue the 4-mile-long flood risk management levee. When complete, the levee, which will tie into existing FEMA-accredited levees and improve salt pond berms, some by as much as 6 feet, will provide combined flood protection from both a 100-year river and tidal flood event, or a flood that has a 1 percent chance of occurring in any given year. It will also protect against a scenario of 3 feet of sea-level rise over the next 50 years, said Caleb Conn, Army Corps project manager for the Shoreline Project. The project will also provide habitat restoration.

“It’s an opportunity to restore right around 2,900 acres of former salt production ponds to tidal marsh. There are benefits to endangered species in the area, and what we’re proposing will allow habitat to adapt to sea-level rise over the years, Conn said. “One of our missions is flood risk management and another mission is ecosystem restoration. It allows us to move forward and accomplish two missions we’re tasked to do.”

In the past 100 years, 90 percent of the tidal marsh ringing the San Francisco Bay has been lost, and with it, the habitat for multiple species who depend on tidal marsh insects, animals and vegetation for food and shelter. The project will bring about 2,900 acres of that important habitat back.

In fact, remnant pathways for the water are still visible under the former salt ponds. As the salt pond berms are breached to create the tidal marsh, those channels will serve as a guide once again.

“The water will find its old path,” said Rechelle Blank the water district’s project manager for the Shoreline Project.

Against much of the levee, there will be an “ecotone,” or buffer area, a sloping transition between the bay and the levee that will provide a unique suite of wetland plant habitat.  The buffer area will benefit the recovery of listed species such as Ridgway’s rails, black rails and the salt marsh harvest mouse.

The ecotone will also help provide protection to the levee from erosion caused by wind and waves. The ecotone may extend out from the levee by up to 400 feet, and that buffer between the levee and the bay will help lower the maintenance cost of the levee over its lifetime, Blank said. That’s because the wetland and ecotone bear the brunt of wave action instead of the levee itself.

The buffer area will also tend to keep pace with sea-level rise, as it can accumulate sediment and organic matter and grow vertically. But there has to be enough sediment in the water to get deposited every tidal cycle.

“We have a very high suspended sediment concentration in the Bay,” Bourgeois said. “That’s why this is such a unique project. An engineered levee and wetland together make a great adaptation to sea-level rise.”

Currently the berms are used as recreation trails, providing a place to observe nature, hike and ride bikes. When complete, the project will provide a connecting trail that will tie into and become a portion of the San Francisco Bay Trail, a 500-mile, as-yet-incomplete trail circling the Bay.


The Shoreline and Salt Pond Restoration projects go hand-in-hand and involve coordination among a number of agencies, from local to federal. The Shoreline Project is a collaboration between the U.S. Army Corps of Engineers, the State Coastal Conservancy, and the Santa Clara Valley Water District, Santa Clara County’s wholesale water provider and flood protection agency. The Army Corps and the U.S. Fish and Wildlife Service are co-leads for the federal environmental impact statement, and both will issue a record of decision on that document. The water district is the lead agency under the California Environmental Quality Act (CEQA) and is responsible for certifying the project’s environmental impact report and complying with CEQA.

Collaboration will continue into the next phases of both the Shoreline and Salt Pond Restoration projects. In the next phases, the water district’s role includes providing monetary and resource support, staffing and coordination with other cities, private companies and the federal airfield Moffett Field, home to the NASA/Ames Research Center.

“It takes a lot of coordination,” said Blank. The water district is working closely with state, federal and local partners, Moffett Field and local cities to come up with a preliminary alignment. “It needs to be tailored to the shoreline, salt pond restoration efforts and take into account how creeks flow to the bay and existing and on-going flood protection infrastructure projects, etc.”

The Phase I Shoreline partners are also working with the Union Pacific Railroad, whose tracks carry freight and commuter trains just a few feet above the water level. The new levee will include a swing gate across the tracks that will close under the pressure of the water when it reaches a certain elevation.


Now that the Shoreline Project has gotten the green light from the Army Corps, it’s Congress’s turn – the project needs congressional approval to begin construction.

The Shoreline Project is estimated to cost $174 million, with the federal share expected to be $70.3 million. The coastal conservancy and water district will fund the remaining $103.8 million.

In June, voters passed a $12-a-year parcel tax for the 9-county Bay Area. That tax is expected to generate as much as $500 million for Bay restoration over its 20-year life, and Santa Clara County could get as much as $60 million which could go toward funding the local share.

The water district will look at possible grants and cost savings from other projects to help meet the funding needs.

One thing is certain: flood protection that starts here won’t stop here.

“For people along the southern part of the bay, this is one phase of a much larger project,” Conn said. “We’re going to be able to use information from this project for future flood protection projects along the bay.”


Project Timeline

2016-2018: Detailed design and permitting process

2018-2021: Construction of levee, tidal gate and flood gate

2019-2022: Construction of ecotone and pre-breach restoration features

2021-2022: Breaching of certain salt ponds

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

%d bloggers like this: