ESTUARY PEARLS: Water management and riparian forests; Primary production in the Delta; The “SmeltCam”; Predicting ecosystem change; Delta salinity; Dr. Ted Sommer retires

This issue dives into current uncertainties and innovations in Estuary science and features research from the latest issue of San Francisco Estuary and Watershed Science. Topics include threats to riparian forests and an analysis of the Delta’s lost productivity.

Modern water management practices that damp down natural river patterns produce streamside forests that “live fast and die young,” hastening the destruction of an important and dwindling habitat.

Melissa Rohde of the State University of New York College of Environmental Science and Forestry (SUNY-ESF) and colleagues analyzed five years of high-resolution satellite and water resource data showing vegetation greenness along California rivers.

Trees growing alongside the 30% of state rivers with natural flows decreased in greenness from the wet spring through the dry summer months, the scientists report in the Proceedings of the National Academy of Sciences, demonstrating they rely on groundwater to make it through the dry season. By contrast, woodlands along the 70% of streams receiving water from dams, wastewater treatment plants, and other human sources kept up the same vigorous levels of photosynthesis and water use throughout the summer.

One would initially think, well, that’s great, the extra water is really helping the environment,” says Dr. John Stella, a professor of ecohydrology at SUNY-ESF. But while extra water enables established riparian trees to grow bigger faster, that benefit comes at a high cost: earlier mortality and poor regeneration. In nature, spring snow-melt floods normally cause riverbanks to erode and channels to migrate across the floodplain, exposing bare, moist sandbars ideal for nurturing the seedlings of riparian trees. Managed river channels, however, seldom migrate much, eliminating spaces for new forests to take root. Meanwhile, on regulated water supply streams such as the Sacramento River, the stable elevated flow during summer followed by severe draw-downs in early fall often leave new seedlings high and dry.

These riparian forests are what we call disturbance-dependent communities. When you eliminate the disturbance, in this case, the spring floods, you eliminate the conditions to which they’re adapted,” Stella says.

Considering riparian forests in water management practices can go a long way toward protecting them. For example, when pumping groundwater, “we need to be cognizant of where, how far, and how fast we draw” to ensure riparian trees can still access a supply of moisture, Stella says. Unfortunately, at present, “if we change water deliveries on managed streams, there’s no backup plan for these trees; their dependence on the altered flow is a vulnerability.”

Author: Kathleen Wong | Photo courtesy of John Stella


Loss of wetland habitat in the Delta has reduced net primary productivity by 94%, but achieving current restoration goals could restore 12% of this loss.

In a new study published in the September 2021 issue of Science of The Total Environment, researchers modeled net primary production of the Delta under historical and contemporary conditions in order to project the potential benefits of restoration.

The loss of net primary productivity—the amount of energy available to pass up the food chain—associated with human modification of the Delta since the early 19th century has reduced the energy available to support biodiversity and ecosystem services. Using the San Francisco Estuary Institute’s Historical Ecology Project, which modeled the early Delta based on archival photos, maps, and texts from the early 1800s, researchers estimated the total area for five specific habitat types: open water, tidal marsh, non-tidal marsh, riparian forest/scrub, and seasonal floodplains. The 94% loss of net primary productivity is even greater than the estimated 77% loss of total wetland extent (defined as hydrologically connected habitat), as the Delta lost high-productivity marsh habitat and gained lower-productivity open water habitat.

Not only have we reduced the magnitude of net primary production, but we’ve also transformed the marsh fuel ecosystem into one fueled more by aquatic plants, many of which are non-native, and phytoplankton,” says James Cloern, one of the study’s lead authors, when presenting results at the 2021 Bay-Delta Science Conference.

Although habitat restoration could potentially restore an estimated 12% of lost primary production, factors such as invasive species, water management, and climate change mean that these efforts are unlikely to return Delta ecosystem function to its historical state. However, Cloern says the study’s methods could be used to help inform more rigorous wetland restoration programs around the world.

Author: Elyse De Franco | Image: PANPP refers to potential aquatic net primary production, an estimate of what primary production would be in today’s environment but in the historical Delta landscape.


Monitoring Delta smelt and other sensitive species with an underwater camera could be both safer and more effective than with a traditional trawl.

Standard smelt surveys rely on the use of boat-driven nets, which trap fish by funneling them from the wide mouth of the net to the closed end (known as the cod end). To check their catch, researchers must pull the net and its contents from the water. But this additional handling can harm and even kill the same fish that wildlife agencies are trying to save with the support of robust, long-running monitoring efforts.

There may be a better way: According to a new study in the June 2021 issue of San Francisco Estuary and Watershed Science, the use of an underwater camera—the “SmeltCam,” developed about a decade ago by U.S. Geological Survey (USGS) research fish biologist Frederick Feyrer—could provide comparable data with less stress by simply filming the fish as they pass through the net. In this case, the cod end would be left open, so that the fish return to open water on their own.

But to estimate the retention efficiency of the SmeltCam (how well it “captures” fish that enter the net), Feyrer and fellow USGS fish biologists Brock Huntsman and Matthew Young instead paired the device with a closed-end net and pulled the whole thing to the surface as in a traditional trawl. Because virtually no Delta smelt have been caught in recent trawls, the researchers instead targeted similarly sized Northern anchovy, specifically in San Pablo Bay and the Napa River.

If [the SmeltCam] is going to be used as a valid alternative, then we need to know how it compares to conventional approaches,” says Huntsman. What they found was that the camera was often as efficient as the closed-net approach, if not more so—due, they hypothesize, to smaller fish escaping the net after being recorded on camera but before being hauled on board. Still, Huntsman says retention efficiency is just one aspect of gear performance, and no guarantee that the SmeltCam will be adopted for smelt or any other species. (Read prior stories on similar efforts – a pontoon designed for flow-through fish monitoring, and a network listening for passing salmon).

Author: Nate Seltenrich | Photo: SmeltCam on deck, ready to be deployed | Credit: Fred Feyrer


Scientists are finding it increasingly difficult to predict how ecosystems will respond to sudden and rapid changes such as extreme droughts, wildfires, and flooding.

Writing in the June 2021 issue of San Francisco Estuary & Watershed Science, a group led by environmental economist Richard Norgaard note that due to the increasing pace of ecological change associated with a warming world, models derived using past data are less able to provide reliable predictions, particularly as extreme events create conditions outside historic reference points.

This has global implications for environmental management, but the authors—many of whom have served on the Delta Independent Science Board—center their focus on the Sacramento-San Joaquin Delta. Environmental managers often speak of ecosystem resilience but the authors argue it’s just as important to apply the concept of resilience and adaptability to our human systems of policy-making and management.

Without a concerted effort, scientists, policy-makers, and managers may be overtaken by the rapidity of change and find themselves reacting to, rather than anticipating, changes,” the authors point out.

They also propose a Delta Science Visioning process that brings together experts from across the biological and social sciences, as well as policymakers and environmental managers, to collectively envision a more adaptive and integrated strategy. Norgaard says that building support for more integrative approaches hasn’t been easy, as scientific institutions aren’t organized that way.

There’s a lot of awareness of climate change and the need to adapt, but the structure of the system makes it difficult… what was really helping bring scientists along with this argument was the extreme drought, the extreme flooding, the extreme wildfires. All of this was building up as this paper was coming about.”

Author: Elyse De Franco | Above: In 1800 the Delta was mostly marshes and native fish habitat (green). By 2016, farmland had reclaimed wetlands (orange), and invasive species had moved in (purple); by 2050, sea level rise will flood more of the Delta, except some well-placed patches of restored habitat | Source: The Delta on Fast Forward (2016)


When it comes to managing Delta salinity, a new research paper suggests we treat public policy like a science experiment.

As anthropogenic factors like salt accumulation through irrigation and freshwater storage combine with drought and sea-level rise, the Delta is headed for a saltier future.

The June 2021 paper, published in San Francisco Estuary and Watershed Science, integrates biological and physical sciences to draw a comprehensive picture of Delta salinity and changing freshwater inflow. Changing salinity patterns could have a profound impact on the region’s ecology, affecting how and when fish like the Delta smelt or Coho salmon spawn, and which aquatic plants survive.

The paper insists that the patterns observed suggest that the future will be difficult to predict, as extreme weather events will lead to bigger fluctuations in salt levels, and recommends that management agencies encourage interdisciplinary coordination when approaching future challenges. The paper concludes that researchers and policy-makers should work more closely together, and consider water-management projects as science experiments.

Co-author Ted Sommers believes that this type of management will require substantial investments in science support and flexibility from regulators and water managers, but “the good news is that there is an increasing interest in using science to guide annual decision-making.” As with any experiment, “clearly-stated assumptions, alternative hypotheses, and predictions should be part of the planning process.” Funding can then be structured in a way that permits monitoring before and after implementation, and enable managers to more effectively respond to a rapidly changing system.

Author: Michael Hunter Adamson | Above: Building a temporary drought barrier at False River to deter the tidal push of saltwater from San Francisco Bay into the central Delta in June 2021 | Photo: Andrew Innerarity / California Department of Water Resources.


The SF Estuary will lose a leading fish researcher and big picture thinker in October with the retirement of Ted Sommer, Lead Scientist for California Department of Water Resources.

Sommer began his long career at DWR in 1991, and early on founded the Feather River fish monitoring program. His work moved progressively downstream to the Bay-Delta, where he has helped manage the Interagency Ecological Program since the late 1990s.

Ted helped develop a commonality between DWR and other resource agencies and universities, creating a solid, collaborative approach to Delta science and showing its relevance to decision-making,” says former EPA fish biologist Bruce Herbold. “That was not always an easy task, because some of the science was unpopular with management and water users.” Earlier this summer Ariel Rubissow Okamoto asked Sommer to reflect on his accomplishments and hopes for the future. Check out their conversation here.

Print Friendly, PDF & Email
%d bloggers like this: