The massive infrastructure project to extend BART through Downtown San José and into Santa Clara is inching closer to getting underway.

Valley Transportation Authority officials expect the $76 million tunnel boring machine ordered from Germany to be ready to start digging around 2026, making way for two side-by-side tracks along with three underground stations in San José’s Little Portugal neighborhood, Downtown and at Diridon Station.

Between the tunneling of nearly 5 miles and other excavation work, officials said the project overall will remove roughly 3.5 million cubic yards of dirt from the ground.

But it’s not just potential riders, politicians and transit advocates who are anxiously waiting for the major work to begin; environmentalists working for years to restore historic marshlands in the San Francisco Bay are set to receive a major portion of that dug up earth to support their efforts.

The goal is to take the dirt from VTA’s BART to Silicon Valley Phase II project and dump it into the bottoms of former salt production ponds in the South Bay near North San José and Sunnyvale and not far from San José’s Alviso neighborhood.

Experts said the material will help accelerate the conversion of those ponds back into tidal marshes — nearly all of which were destroyed by human development in the Bay Area stretching back more than a century.

“It’s just a terrific benefit if we can make it work with all the parties in to help us,” said Donna Ball, a senior scientist at San Francisco Estuary Institute.

Ball is the lead scientist on the South Bay Salt Pond Restoration Project, a multi-decade effort run by the California Coastal Conservancy and one of several active Bay restoration projects in the region.

A walkway leading to pond A12 at Alviso Marina County Park in Alviso on May 1, 2024. (Martin do Nascimento/KQED)

The restoration project plans to convert 15,000 acres of former Cargill salt ponds — sold to federal and state wildlife agencies in 2003 — back into marshes, which provide a slew of benefits to the region.

“Tidal marshes do a lot of things. They do a lot of things for nature, for wildlife, they also do a lot of things for people,” said Dave Halsing, the executive manager for the restoration project.

“Marshes clean the waters of the Bay. They absorb greenhouse gasses,” Halsing said. “And then from the human end, they absorb the wave energy, and the tidal flows, and high tides and storm surges, and so they, on their own, provide a certain amount of flood protection benefits to human communities.”

And while Bay restoration projects have often made good use of dirt from other construction and infrastructure projects previously, this is the first time the region has seen the use of what’s known as “tunnel muck” specifically to raise the bottoms of a former salt pond.

Dave Halsing, Executive Project Manager at South Bay Salt Pond Restoration Project, beside A12 pond at Alviso Marina County Park in Alviso on May 1, 2024. (Martin do Nascimento/KQED)

To make the boring machine’s job easier and ensure all the dirt can be funneled out the back end, the soils will be injected with liquifying and softening agents just ahead of each section of the tunnel being cut.

“So what they’re digging through, it starts off as pure, deep bay mud, but when it comes out, it’s a little wetter and a little softer because of all these things they add to it, these conditioners,” Halsing said. That’s the muck.

A raft of water regulatory and oversight agencies will take part in evaluating the environmental impact of the whole project, including examining the conditioners and testing the muck to ensure it’s safe to go into the Bay.

With the curve of sea level rise estimates expected to get steeper, experts estimate the Bay Area will need 548 million metric tons of sediment to keep up and to complete critical restoration projects, allowing marshes to form before those areas are inundated with water.

Pinkish water at pond A12 Alviso Marina County Park in Alviso on May 1, 2024. (Martin do Nascimento/KQED)

The naturally available supply of Bay mud and dirt is expected to fall short of what’s needed, making muck, dirt and sediment a hot commodity.

Once the material is removed from the tunnel, it’ll need to be brought to the ponds. That might happen by rail, truck, or a pipeline that could be built for this effort, but officials said it’s a bit too soon to say what method will be chosen.

However it gets there, though, Halsing is hopeful it’ll be a big boon to the Bay.

The restoration project team has been systematically trying to build marshes back up, in part by letting Bay water back into these ponds, like a levee breaching in Menlo Park in December. The aim is to bring pond bottoms up to a level where marsh plants, like prolific pickleweed, can grow and spread, creating buffers between the tides and settled areas of the region.

The marshes, once established, behave like a sponge, soaking up energy, absorbing water, and protecting infrastructure behind them, Halsing said.

But without the aid of fill soil, the process of restoring marshes depends largely on the natural high and low tides that occur twice daily, which deposit only minuscule amounts of sediment with each pass, Halsing said.

Pinkish water at pond A12 at Alviso Marina County Park in Alviso on May 1, 2024. (Martin do Nascimento/KQED)

The millions of yards of muck from the BART extension could shave decades off restoration work.

One of the ponds near the Alviso neighborhood where officials are contemplating putting the material, known as pond A12, is today still a deep reddish pink color from bacteria that thrive in deeply salty water. The shores are crusted with white crystallized chunks of salt.

“As we move further along and sea level rise is more of a risk, this goal of raising the bottom elevation of these ponds with this imported tunnel material will be a huge kick-start, a jump-start to the natural processes that we would otherwise have to wait for,” Halsing said.

Ann Calnan, VTA’s lead for the soil reuse project, said while the agency hopes to bring all 3.5 million cubic yards of soil to the ponds, the final amount will likely be lower. Some of the soil, especially near the surface, might not make the cleanliness cut.

Ann Calnan, Environmental Lead at Santa Clara Valley Transportation Authority, at Alviso Marina County Park in Alviso on May 1, 2024. (Martin do Nascimento/KQED)

Other factors, like weather conditions and breaks in the work periods for nesting seasons and duck hunting, could result in some soil being hauled off to quarries or landfills.

Bernice Alaniz, a spokesperson for VTA’s BART project, said while the environmental benefit of the reuse project is one of the main selling points, using the soil for a climate-friendly project could have financial benefits, too.

[aside label="Related Stories" postID="science_1974464,science_1979603,quest_54442"]Every truckload of soil taken to a landfill or quarry would cost the agency a “tipping fee” to dump the load. For every truckload, railcar, or pipeline full of soil, the agency can divert it to the ponds, and it can cut those fees, she said.

Alaniz said the agency couldn’t provide a total cost for the soil reuse project until further decisions are made during the environmental review and design phases.

The transit agency has already received a $1.5 million grant from the California State Coastal Conservancy to help cover the environmental review costs for the project, and the California Wildlife Conservation Board awarded VTA with a $2.98 million grant to help cover the cost of designing the project.

Alaniz said the agency plans to seek more grants to cover other costs of the project, as well.

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From Tunnel Muck to Tidal Marsh, BART Extension Could Benefit the Bay