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Placing instruments into San Francisco Bay, California, for 6 weeks of gathering data on how bay waters move sediment.

by Stephen Wessells, Jessica Lacy, Lissa MacVean, and Helen Gibbons

On a bright day in early February, 2011, U.S. Geological Survey (USGS) research oceanographer Jessica Lacy and USGS Mendenhall Fellow Lissa MacVean supervised the placement of aluminum platforms bristling with instruments into San Francisco Bay, California, for 6 weeks of gathering data on how bay waters move sediment. The scientists' goal is to determine how sediment is transported among the shallow environments of the bay—one factor that controls whether the sediment will reach marshes at the bay's edge. Their findings may improve the ability to predict the outcome of marsh-restoration projects around the bay. A recently released USGS video highlights some of their goals and activities.

San Francisco Bay is a dynamic and complicated estuary where seawater entering through the Golden Gate mixes with freshwater from the San Joaquin and Sacramento Rivers and numerous local streams. The water is commonly clouded by muddy sediment lifted from the bottom or delivered by streams and kept afloat by the near-constant motion of the water in response to winds, waves, and tides. At times, the turbid water in the shallows looks like chocolate milk.

Maps show California, location of San Francisco Bay, location of San Pablo Bay, and depth of the water of San Pablo Bay.
At left, San Francisco Bay and surroundings in a photograph acquired April 21, 2002, by astronauts aboard the International Space Station. Note brown plumes of suspended sediment in bay waters. Yellow box outlines study area in the San Pablo Bay portion; triangles are sites where instruments were deployed. Image courtesy of NASA's Earth Observatory. At right, The study area, with triangles marking sites where instruments were deployed. Labels indicate each site's water depth relative to MLLW (mean lower low water), the average of the lowest water levels for each day. Regions below MLLW are virtually always submerged (subtidal); regions above MLLW are regularly exposed to the air (intertidal). Background image courtesy of Esri's ArcGIS Online map service and Aerials Express.

Fringing the bay are wetlands and tidal marshes that play an important role in bay ecosystems. More than 80 percent of the wetland habitats that existed before the 1850s and the Gold Rush have been lost because of human activities, including diking, draining, and filling. The USGS provides science support to many of the local, state, and federal efforts to improve the health of the bay by restoring tens of thousands of acres of commercial salt ponds, diked agricultural lands, and other lands to functioning tidal marsh and shallow ponds.

"Some wetlands-restoration projects actually deposit sediment to bring the marsh plain elevation up to the appropriate level for plants," said Lacy, "but it's considered a much better option to rely on natural processes because that is a sustainable restoration. And [relying on natural processes] means assuming that the turbid waters of the bay will deposit enough sediment in the marsh to restore it."

How long this process may take varies for different parts of the bay and is typically not well known at the beginning of a restoration project. Where the newly delivered sediment will come from is also not well known, raising concerns that large-scale marsh restoration might impact other bay habitats. For example, adjacent mudflats, which are critical foraging grounds for shorebirds, could be altered if natural processes carry significant amounts of sediment from the mudflats to the restored marshes.

The USGS study now underway will begin to address the question of how sediment is supplied to marshes by looking in detail at how bay sediment moves from areas that are always inundated, or are subtidal, into intertidal mudflats that are alternately wet and dry. The forces that drive sediment from subtidal to intertidal regions also influence how—and whether—it gets transported into marshes. Tides, winds, and storms all function in different ways and over different timescales. USGS observations of how the bay's shallow regions respond to such forces will provide answers to such essential questions as:

  • On average, do tides transport sediment into or out of the shallows?
  • When storms occur, is sediment from the watersheds washed into the shallow habitats, or does it bypass them, heading instead for the Golden Gate?
  • On windy days, do waves pick up more sediment from the intertidal regions or the subtidal regions, or equal amounts from each?

The answers to these questions will help scientists understand where the sediment deposited in marshes comes from and what that means for nearby habitats like mudflats, as well as the rate at which sediment deposition will build up the marsh plain.

The study was designed by MacVean as part her work in the USGS Mendenhall Research Fellowship Program, which provides postdoctoral scientists an opportunity to conduct original research with USGS scientists. MacVean recently completed her Ph.D. in civil and environmental engineering at the University of California, Berkeley, with a focus on environmental fluid mechanics. Her Mendenhall project is titled "Sediment Cycling Between Estuarine Habitats," and Lacy is one of her USGS advisors.

"We're making field measurements of water velocities, salinities, and suspended sediment in order to determine exactly what's controlling how sediment moves in really shallow environments in an estuary," said MacVean.

The scientists placed instrumented platforms at four sites in San Pablo Bay, a northern embayment of San Francisco Bay. The four sites lie along a gradient from the 12-m deep channel in the southern part of San Pablo Bay to intertidal mudflats that are exposed to air at each low tide. The platforms hold instruments to measure such variables as currents, waves, salinity, and suspended sediment.

One photo shows instruments on a metal frame going into the water off a boat, the other shows the frame submerged.
At left, USGS Marine Technician Jenny White steadies an instrumented platform as it is winched into the water at the Middle station (see map of study area), where the depth of the bay floor is 0.5 m below MLLW. Photograph taken February 2, 2011, by Lissa MacVean. At right, the platform, deployed at high tide, is now resting on the bay floor, and all that's visible is a warning flag to alert boaters. During low tide, all but 0.5 m of the platform (which is a little more than 2-m tall) will be exposed to the air.

"We have more than one [of each type of instrument] on each platform," said Lacy, "because we're looking at different elevations above the seafloor, and that's because current speed and suspended-sediment concentration change a lot with height above the bed. If you can resolve those changes with depth, you can learn something about the mechanisms that are bringing sediment up into the water column and then moving it around."

During the 6-week deployment, the instruments gathered a massive amount of data, making measurements as fast as 10 times per second. Among other things, the data will show how sediment concentrations and water velocities change over a range of time scales—as the seasons change, when storms come and go, when it's windy or not windy, through each tidal cycle, and during the passage of a single wave.

Photos show people preparing data and sample collection devices to go into the water.
At left, USGS Pacific Coastal and Marine Science Center scientists Pete Dal Ferro, Jenny White, and Joanne Thede Ferreira deploy a platform at the Lower station, where the depth of the bay floor is 1 m below MLLW. Photograph taken February 2, 2011, by Jessie Lacy. At right, to supplement data collected by the instruments, MacVean made periodic trips to each site to collect sediment samples. Here she extracts a small core of sediment collected from the bay floor on March 9, 2011. Cores from all sites will be analyzed to identify differences in sediment characteristics—such as grain size and porosity—that affect susceptibility to erosion. This knowledge will help the scientists understand whether sediment at the different sites will respond differently to the forces of tides and wind. Photograph by Pete Dal Ferro.

"An even shorter time scale is the turbulence time scale," said Lacy. "Although waves pick the sediment up off the bed, it's the turbulence—the tiny, random motions caused by the interaction of currents with the bed and wind with the water surface—that actually mixes sediment up through the water column. In previous experiments, mostly in deeper water, we've been able to resolve that combination of processes. In this experiment, we'll be examining those processes right at this intertidal zone, where there are very few measurements."

This type of data is essential for verifying the accuracy of sediment-transport models, which can then be used to predict the impacts of long-term processes such as marsh restoration and sea-level rise.

Two photos show a metal frame that holds instruments to collect data in murky water.
February 25, 2011, San Pablo Bay data collection. At left, the platform at the Lower station is partly exposed to the air shortly after low tide. At right, the platform on mudflat at the Upper station is completely exposed to the air shortly after low tide on February 25, 2011.

MacVean is excited about exploring unknown territory at their study sites: "The water is really turbid and murky, so you can't see to the bottom, even in a very shallow depth," she said. "It's sort of inhospitable for science, which is really why it's interesting. There's still a lot that isn't known about how these systems work."

The instruments were recovered in mid-March. After downloading the data, MacVean began using a combination of data analysis and numerical modeling to provide a picture of how sediment is carried from shallow bay water to intertidal areas. When her work is complete, it will not only shed light on the mechanisms that transport sediment from the bay into recently restored marshes but will also provide information that can be used to address another important question: Will the bay-fringing marshes—both those that exist now and those that will be produced by restoration—survive in the face of accelerating sea-level rise? A 2007 report by the Intergovernmental Panel on Climate Change estimates that the global average sea level will rise between 0.18 and 0.59 m (0.6 and 2 ft) in the next century. The results of MacVean's project will help resolve one piece of the puzzle of whether sediment deposition in marshes can keep up.

Additional information is available in "South Bay Science Symposium," Sound Waves, March 2011. Learn more about the USGS Mendenhall Research Fellowship Program. To watch MacVean, Lacy, and their field team in action, view the new USGS video below, "Turbid Bay: Sediment in Motion."

Turbid Bay: Sediment in Motion

USGS scientists from the Pacific Coastal and Marine Science Center explore how sediment moves across San Francisco Bay tidal flats.  The research team deploys a suite of large instrumented tripods to record sediment movements over a six-week period in early 2011.  Answers from this work will help determine whether deposition of sediment at high tide is occurring quickly enough to preserve marshes in the face of sea-level rise.  

The program also highlights the value and function of the USGS Mendenhall Fellowship Program. The Mendenhall Program at the USGS provides recent PhD graduates an opportunity to conduct cutting-edge research on pressing scientific questions with the guidance and mentoring of established scientists.

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