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In recent years, invasive aquatic plants have increased exponentially in the shallow waters of California’s Sacramento-San Joaquin River Delta, clogging about 17,400 acres (nearly 30 square miles) of the waterways. Among the plants’ many effects are changes in the way mud and sand move through the region.

A marshy edge of a river choked with weeds.
Tips of Brazilian waterweed (Egeria densa) break the surface at low tide in Lindsey Slough in the northern Sacramento-San Joaquin River Delta. More commonly, this invasive plant is completely submerged.

This article is part of the August 2018 issue of the Sound Waves newsletter

Lately, U.S. Geological Survey (USGS) research oceanographer Jessie Lacy has been spending a lot of time thinking about really small things—particles of mud and fine sand that float in the shallow waters of California’s Sacramento-San Joaquin River Delta. “The Delta” comprises a broad expanse of winding channels and low islands in the tidal, fresh waters at the confluence of the Sacramento and San Joaquin rivers east of San Francisco Bay. In recent years, invasive aquatic plants have increased exponentially here, clogging about 17,400 acres (nearly 30 square miles) of the waterways. Among the plants’ many effects are changes in the way mud and sand move through the region.

Two women stand together smiling on a boat wearing life jackets and sun hats with other safety gear.
Shruti Khanna (left, California Department of Fish and Wildlife) and Judy Drexler (USGS California Water Science Center) on the USGS Pacific Coastal and Marine Science Center’s research vessel Parke Snavely during fieldwork in the Sacramento-San Joaquin River Delta.

Why does it matter? These tiny particles are vital to the health of the Delta, the bay, and the beaches beyond. When suspended in the water, they make it “turbid” or cloudy. Adequate turbidity levels are required to protect many native fish, including the endangered Delta smelt, from predation. Sediment is also essential for marshes, which protect shoreline communities from extreme storms, help filter water pollution, and nurture fish, birds, and other wildlife. The steady accumulation of mud and sand settling out of turbid water at high tide is what makes marshes grow. Current efforts to restore tidal marshes in the Delta and around the edges of San Francisco Bay will succeed only if there’s enough natural sediment to build up the marshes, especially as sea level rises. Looking beyond the bay, the movement of sediment from the Delta through the bay and out through the Golden Gate Bridge is crucial for beaches “downstream,” like San Francisco’s Ocean Beach. Erosion at this strand’s southern end is outpacing sand input, threatening a major roadway and a sewage-treatment plant.

Map of a large bay and delta area with shades of color to show water depth and land elevation.
The Sacramento-San Joaquin River Delta runs along the right of the image, a bathymetric/topographic digital elevation model. See the USGS data release for more information.

“Sediment movement through the Delta to the bay has been decreasing over the same time period as the invasion of aquatic vegetation,” says Lacy. She and her collaborators know that dam construction and urban development have reduced sediment input to the bay, and they want to know whether and to what extent invasive vegetation is also a factor. Lacy says: “There’s a lot of evidence that the invasive vegetation traps sediment.”

Lacy is studying that trapping as part of a three-year project led by USGS wetland ecologist Judith Drexler of the California Water Science Center. Drexler says: “We want to provide information about the effect of invasive aquatic plants on fish habitat and marsh health to agencies that control invasive vegetation in the Delta.” These agencies include the California Department of Fish and WildlifeDivision of Boating and Waterways, and Department of Water Resources. Project scientists come from the USGS California Water Science Center and Pacific Coastal and Marine Science Center, and the California Department of Fish and Wildlife. The USGS San Francisco Bay-Delta Priority Ecosystems Science Program and the USGS Coastal and Marine Hazards and Resources Program are funding the study.

“To accomplish our goal,” says Drexler, “we’re measuring impacts on sediment transport, turbidity, and marsh-accretion rates. This study is the first of its kind to address these research questions in a quantitative way.”

examples of fieldwork done in the Sacramento-San Joaquin River Delta
Top row, left to right: Cordell Johnson (left) and Evan Dailey use the USGS R/V Fast Eddy to collect water samples. Cordell Johnson (left) and Jessie Lacy prepare to deploy a tripod holding instruments to measure water level, currents, and suspended sediment. USGS divers Jenny McKee (left) and Tim Elfers assemble the gear they will need to measure vegetation density in Middle River. Bottom row, left to right: Tim Elfers (left) and Jenny McKee mark locations for vegetation-density measurements in Middle River. Brazilian waterweed clings to an instrument package that Cordell Johnson is pulling onto the R/V Parke Snavely after the instruments recorded data for about two weeks in Lindsey Slough.

Several species of invasive aquatic plants grow in the Delta, but the scientists eventually focused on Brazilian waterweed (Egeria densa), a submerged aquatic plant that dominates the three Delta sites they have chosen to investigate. Lacy and her team from the USGS Pacific Coastal and Marine Science Center put instruments inside and outside patches of Brazilian waterweed at each of the three sites. The instruments, mounted on steel platforms, included gauges to record water level, current meters to measure water movement at various depths, and optical devices to quantify sediment suspended in the water. Lacy’s team left the instruments in place to collect data for about two weeks. Additionally, they mapped the depth and shape of the channels at each site, determined the density of plants in the vegetation patches, and sampled bed sediment inside and outside the patches.

“Our Delta fieldwork drew on the wide skills and the flexibility of our field operations team,” says Lacy, referring to participants from the center’s Marine Facility, aka Marfac. This group operates vessels, designs and fabricates equipment, and supports field sampling and mapping. “The equipment and excellent technicians we have at Marfac put us in a great position to carry out this work.”

Map shows an area of detail from an index map, with towns and waterways labeled.
Sites where USGS scientists made measurements in the Sacramento-San Joaquin River Delta.

The first site they studied was Lindsey Slough, a quiet tidal channel in the north Delta where they deployed instruments in April 2017. In March 2018, they placed instruments in two more sites: Middle River in the south Delta, and lower Mokelumne River in the east-central Delta.

“Lindsey is very much a backwater,” says Lacy, with weak currents and very fine sediment. “Mokelumne is the most active,” she says, with energetic currents and the coarsest sediment, including lots of sand. Middle River, in keeping with its name, is somewhere between, with currents a little stronger and sediment a little coarser than those at Lindsey Slough.

The scientists hypothesized that bed sediment below the vegetation patches would be finer than outside the patches, and that is what they found at the Mokelumne and Middle River sites. Water flowing relatively quickly in channels outside vegetation patches carries fine particles in suspension, leaving larger particles below on the bed. But water slowed by the dense Brazilian waterweed drops even the finer sediment particles to the bed.

“So, it looks like some fine sediment is getting trapped beneath the vegetation patches” at two of the three study sites. “In the Lindsey site,” however, “we did not get the result I was picturing,” says Lacy. Sediment on the bed below the Brazilian waterweed, although as fine as in the other vegetated sites, was not significantly different from sediment in the channel outside the patch. Lacy says, “I think the overall lesson about grain size is that the degree of sorting by vegetation depends on the range of particles in the system. In a system [like Lindsey], where all the particles are incredibly fine, you're not going to see big sorting due to vegetation, because there are no larger particles to provide contrast.”

Learning new lessons and tackling new challenges are part of the excitement of working on this project. “Most of the approaches in this study are new,” says Drexler, “because no direct measurements of sediment trapping by invasive aquatic vegetation have been made.” Lacy’s efforts to measure vegetation density provide an example. Initially she tried to use a standard approach: mark out squares of known area (quadrats) and count all the stems in each quadrat.

An object of two circular pieces of mixed materials are partially covered with mud and plant debris.
Patches of dark sand cling to an instrument package that collected data for approximately two weeks at the Mokelumne River site—evidence that currents at the site were strong enough to carry sand, which is heavier than mud, probably during elevated river flows following two storms in the watershed. Photo credit: Jessie Lacy, USGS

“The problem,” says Lacy, “is that the Brazilian waterweed plants have so many branches, it’s really hard to know what’s a stem and what’s a branch.” What’s more, the Marfac divers trying to count stems “couldn’t see anything because it’s so turbid in there. Melissa Foley [one of the divers] just came up and said, ‘Stem count is not going to happen.’” The team decided to harvest everything within each quadrat, measure its mass, and develop techniques for relating mass to cross-sectional area, the number they need to determine how much the plant material is slowing water flow. “I feel pretty happy about it,” says Lacy. “We had to make this up on the fly.”

Lacy’s findings will complement data collected by other project scientists at and near the same locations. One group measured the transport, or “flux,” of suspended sediment flowing into vegetation patches from upstream and flowing out of them downstream, to quantify the patches’ “trapping efficiency.” Drexler’s team took core samples in the channel bed beneath vegetation patches and in adjacent marshes to measure and compare accretion of inorganic and organic material in each of these locations. The project scientists will synthesize all their results in an estimate of total sediment trapping by submerged vegetation in the Delta. They have already begun sharing their findings at formal and informal meetings and will work on publications in the coming year.


Map shows river channels in farmland with labels to show distance, latitude and longitude, and spots where data was collected.
Edge of vegetation (red lines) and bathymetry (depths indicated by rainbow colors, with cooler colors deeper) of the channel at Lindsey Slough, mapped from the USGS research vessel Parke Snavely.
Photo shows a very large, dense clump of weeds that grow in water picked up with a hook, plus a close-up photo of the plant.
Brazilian waterweed, with dozens of branches on every plant, forced the scientists to devise new techniques for measuring its impact on water flow.
Image of a plant with many long, sinuous stalks and tiny leaves and scale bars to show how large it measures.
One technique for calculating plant impact on water flow was to harvest individual plants and determine their cross-sectional area with photogrammetry. The area of this plant, from Lindsey Slough, is 0.35 square meters (about 3.8 square feet). The plant is nearly 2 meters (6 feet) in its longest dimension.
A small boat sits on calm waters with trees in the distance, and a cloudy sky.
USGS research vessel Fast Eddy at the Mokelumne River site in the Sacramento-San Joaquin River Delta, March 14, 2018.

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