San Francisco Bay’s salt ponds derive their rich colors from a complex mix of algae, minerals, micro-organisms and brine shrimp, which change hues as the pond’s salinity increases during the five years it takes to yield a bed of salt.

Photo credit: Courtesy South Bay Salt Pond Restoration Project

By David Pescovitz

As you fly into San Francisco International Airport, the aerial view is a mosaic of color. The waters of south San Francisco Bay are a patchwork of shapes ranging in hue from deep navy to teal green to intense orange, the result of salt ponds. Areas of the bay cordoned off years ago for salt production, these ponds supply the stuff we use in everything from manufacturing glass and soap to flavoring our scrambled eggs. But the view from on high may soon change. UC Berkeley research is informing major efforts to restore San Francisco Bay—including more than 16,000 acres of salt ponds—to an ecosystem better suited to the flora and fauna that enjoyed coastal living long before we did.

“More than a century ago, we decided that the San Francisco Delta was useful agricultural land and that the edge of the bay was good for development and salt ponds,” says UC Berkeley professor of environmental engineering Mark Stacey. “Now there’s momentum to reverse that trajectory and restore a lot of these habitats.”

For the last four years, one of Stacey’s laboratories has been the South Bay salt ponds. There, the South Bay Salt Pond Restoration Project (SBSPRP)—the umbrella organization that funds some of Stacey’s research—is working on the second largest ecosystem restoration project in the country following the Florida Everglades.

“Many of the lands simply can’t be restored to marsh habitats,” Stacey says. For example, “Foster City was built on landfill in what was once baylands. It’s not going anywhere. But there are many areas that are good candidates.”

Restoration, he says, will take time, dedication and cross-disciplinary science and engineering. Stacey and his students embody all of that. Their efforts to understand the physical and mechanical processes that govern water flow could impact restoration projects throughout the bay for decades to come.

Why go to all this trouble to turn back the clock?

Restoration will not only recover lost tidal wetlands and native species; it will also replace a makeshift flood control infrastructure dating from the first half of the 20th century.

“The salt ponds were constructed by throwing up cheap earthen berms that weren’t even engineered,” says Steve Ritchie, SBSPRP project manager. “They have accomplished flood protection for the Silicon Valley, even though they weren’t built for that purpose.” Sixty percent of the restoration project’s estimated cost—about  $1 billion over the next 50 years, Ritchie says—will be spent on building new flood-control levees.

“We should be thankful to the salt makers,” Ritchie adds. “If they hadn’t built these salt ponds, we would have developed right up to the edge of the bay. Not only would those areas be under water, but we would have zero opportunity to achieve any restoration.”

The San Francisco Bay, a 1,600-square-mile waterway between the Pacific Ocean and the Sacramento–San Joaquin Delta, is the largest estuarine habitat in the Western Hemisphere. Before the Gold Rush, it is estimated that the bay was 133 percent larger than it is today, with wetlands, salt marshes and tidal marsh surrounding much of its perimeter. But over the past two centuries, the bay has been filled in, drained, diked, bridged, dredged and dammed into agricultural fields, salt ponds, cities and other developments. Now, only 2 percent of the original marsh habitat is left.

Mark Stacey grew up on the lakes of Minnesota and studied physics and political science at Stanford. His work on San Francisco Bay, he says, provides “the right mix of childhood associations with exciting physics and policy issues in the midst of a thriving metropolitan area.”

Photo credit: Courtesy Mark Stacey

The bay supports 750 native species of fish, birds, and other animals and plants. But the surrounding Bay Area is also home to 7.2 million people who depend on the estuary to meet their needs for salt as well as commerce, agriculture, fresh water, transport, building, recreational access and more. The delta of the Sacramento and San Joaquin rivers has been fashioned into a 1,100-mile system of water channels and subsided islands for agricultural production. It’s also an important source of fresh drinking water and irrigation for more than two-thirds of the state. With its rich population of herring, bait shrimp and Dungeness crab, the bay supports the country’s only urban commercial fisheries. It’s also the largest harbor on the coast, a gateway to the Pacific for 67 million tons of cargo per year. That traffic in itself exposes the estuary to risks like last November’s Cosco Busan oil spill. (see Bay watch: Outsmarting future oil spills).

The pristine estuary that existed before the mid-1800s is long gone, Mark Stacey observes, but it can be restored to some degree. The trick, he says, will be balancing the human needs with those of the many wetlands ecosystems, some predating development and others that have emerged as a side effect of development.

The South Bay Salt Pond Restoration effort involves opening designated salt ponds to tidal flow and observing how the altered flow affects both sediment and salt movement throughout the entire bay. That’s where Stacey brings his long history of research on tidal dynamics into play. Along with sediment, changes in tidal dynamics affect salt concentration in the restoration areas. Salinity, in turn, affects which plants will develop in the new marshlands and which animal species can thrive there.

“We’re effecting change in an estuary in ways that have never been done before,” Stacey says. “Fortunately, we have laws of physics that govern these processes and, with some predictive modeling, I think we can get a handle on how this restoration will affect tidal dynamics throughout the bay.”

Since salt production began in San Francisco Bay in 1854, the ponds, owned mostly by Cargill Incorporated, have overtaken almost the entire area surrounding the bay south of the San Mateo Bridge, approximately 26,000 acres.

In October 2000, Cargill struck a deal, negotiated by Senator Dianne Feinstein, to consolidate its operations and sell more than 60 percent of its South Bay salt ponds to the state, in addition to 1,400 acres along the Napa River. The U.S. Fish and Wildlife Service and the Department of Fish and Game are now responsible for stewardship of the ponds. It’s a complicated dynamic with numerous stakeholders.

In the South Bay, for example, of major concern are the migratory birds that use the area as a stopping-off point; one species may rely on marsh habitat, while others depend on the intertidal zones for feeding at low water. In the delta, endangered fish such as smelt take top priority. And throughout the bay, maintaining flood-control systems is a primary concern.

“The issue isn’t whether restoration will occur but what the flavor of that restoration will be in each area,” Stacey explains. “What are the trade-offs in each area? And what does the endpoint look like?”

Right now, the perimeter of the South Bay is largely a hardened rock-walled shoreline of levees. Historically, however, the transition from the bay was gradual, from channels to shallows to mudflats to marsh, high marsh, and then uplands. These habitats were all connected to each other and to the bay.

According to Stacey, restoration efforts are likely to soften the transition and once again link those habitats. The levees cannot be removed, since their flood-control function remains vital, especially in anticipation of rises in sea level from weather systems and climate change. Instead, channels will be built through the rock walls to connect the habitats in specific places.

Environmental engineering graduate student Lissa MacVean

Photo credit: Bart Nagel

However, opening up the levees also leads to a cascade of new challenges. In the time since the shoreline was leveed, the land has subsided. In the South Bay, what was once marsh is now a couple meters below water, and, in the delta, that land is as much as 10 meters below sea level. Opening up the levees will create a tidal salt lake, where sedimentation can proceed until enough sediment builds up on the bottom for plants to grow and marsh to reemerge.

To conduct their research, Stacey, graduate student Lissa MacVean and colleagues frequently embark on bay cruises aboard a small boat outfitted with a variety of sensing instruments. They use an acoustic Doppler current profiler, which converts the echoes of audio waves into three-dimensional representations of the current. Sensors are immersed in the water to keep track of temperature and salinity and measure chlorophyll concentration, an indicator of what’s living in the water.

Stacey’s team recently received a National Science Foundation grant of $667,000 to study the physics of sediment movement around the bay and the role of wind and tides in that transport. The key to gathering useful data, he says, is measuring flows and currents on wide time scales, from “turbulent scales” lasting only a few seconds, to 12-hour tidal scales, to lunar and annual cycles.

The researchers have begun to analyze how the first holes in the levees, opened as part of the Salt Pond Restoration effort, have affected sediment transport. MacVean has spent months in the field monitoring the exchange between one of those ponds and Coyote Creek to track the movement of sediment. Her project is now being parlayed into a large-scale collaboration with Stanford to develop a hydrodynamic and sediment transport model for the entire San Francisco Bay with three years of funding from the Coastal Conservancy.

“I’m interested in the details of hydrodynamics because it’s so firmly rooted in real physics,” MacVean says. “But what motivates me is that this basic science has the potential to influence how restoration is performed.”

Only by exposing those subtle dynamics hidden under the water’s surface can we hope to re-engineer San Francisco Bay and turn back time 200 years.

“Some day, when you fly into the airport, you won’t see the mosaic of reds, oranges and yellows anymore,” Stacey sums up. “But the mix of habitats you’ll be looking at will much more closely resemble a healthy San Francisco Bay as it once was.”

David Pescovitz (david@pesco.net) is a research director at Institute for the Future, co-editor of BoingBoing.net and editor-at-large for MAKE: magazine.