Estuary News

March 2023
Estuary News March 2023

VA Agreement Highlights Habitat Questions

Restoring marsh and wetland habitat can have significant benefits for dozens of species throughout the Bay and Delta—that’s beyond dispute. But when it comes to saving the Estuary’s most imperiled fish, how much habitat improvements can help in the absence of dramatically increased freshwater flows is a question that has dogged and divided scientists and policy makers for years. As the State Water Resources Control Board considers the latest proposal from the State and water agencies for a flows agreement that would restore thousands of riparian and wetland acres—while dedicating less water to the environment than proposed under an alternative regulatory framework—critics argue that science doesn’t support its underlying assumptions. The debate highlights how much there still is to learn about what restoration efforts can and cannot do for the Delta’s ravaged ecosystem.

In January the State Board released the Draft Scientific Basis Report analyzing a voluntary agreement (VA) on freshwater flows into and through the Delta from the Sacramento and Mokelumne Rivers that was proposed by a group of water districts and state and federal resource agencies last spring. The Board is considering adopting the agreement as a pathway to implementing its long-delayed update to the Bay-Delta Plan Water Quality Control Plan. The new report supplements a 2017 Scientific Basis Report supporting Board staff recommendations for minimum unimpaired flows to protect native fish and wildlife. 

The proposed agreement outlines an eight-year program that proponents say would add up to 825,000 acre-feet of freshwater flows for the environment annually and restore more than 27,000 acres of spawning, rearing, and floodplain habitat to reverse the decline of salmon and other native fish populations. Twenty-thousand acres of that habitat would consist of restored and reconnected floodplain in the Sacramento River. (See Setbacks and Swallows.)

The new science basis report finds that the proposed flows would benefit longfin smelt, Sacramento splittail, starry flounder, and California bay shrimp, among other species. “The results show that we would see an improvement in abundance indices for some Delta species related to flow measures,” says Department of Water Resources lead scientist Louise Conrad. The report does not, however, measure the effect of the proposed flows on salmon or steelhead abundance.

Sacramento River flows after January 2023 storms. Photo: Kenneth James, DWR
Floodwaters from recent winter storms spike flows on the Sacramento River. Photo: Ken James, DWR

The proposed flow regimes aren’t nearly large enough to protect endangered species and fisheries, critics say.

For starters, the amount of water the VA would actually provide depends on the baseline used. Critics say the 825,000 acre-feet number is misleading, since it uses a baseline that includes the flows required under discredited 2019 Biological Opinions for endangered fish that dramatically increased permissible water exports. (California sued the federal government to invalidate those BiOps on the grounds that they did not protect fish, and in 2021 the Bureau of Reclamation launched a process that will lead to new BiOps, probably by 2024.) The new science basis report notes that the VA baseline “does not fully reflect the Delta outflow conditions of the environmental baseline” used in the 2017 science basis report, and adjusts its analysis accordingly. Using this “apples to apples” approach, a chart included in the report indicates that the VA would provide much less than 825,000 af in all year types—although the report does not spell that out, leaving the reader to compare flows using different baselines and do the math.

And whatever the baseline, critics also like to point to the State Board’s own 2018 framework for the Sacramento River, which called for 45% to 65% of unimpaired flows from the river and its tributaries into and through the Delta—much more than 825,000 acre-feet. 

Critics are not entirely convinced, either, that more habitat necessarily means more fish, an assumption upon which the voluntary agreement rests.

“They’re trading habitat for flow, but this doesn’t have a basis in science,” says San Francisco Baykeeper science director Jon Rosenfield.

Jennifer Pierre, general manager for the State Water Contractors, who helped negotiate the voluntary agreement, rejects the premise that it trades water for habitat. “We are certainly combining habitat and water, but it’s a huge amount of water,” she says.

Drone footage of salmon struggling in warm water near Shasta Dam in 2021. Photo: Cole
Drone footage of salmon struggling in warm water near Shasta Dam in 2021. Photo courtesy Baykeeper

Finding the balance of  habitat and water needed for a healthy ecosystem is the holy grail of restoration in the Estuary. The Bay-Delta Plan calls for doubling wild salmon populations relative to the 1967 to 1991 average; the VA’s target is to restore 25% of the habitat needed to meet that goal by the end of its eight-year term. The draft science basis report evaluated the effect of the agreement on spawning and rearing habitat in the American, Feather, Mokelumne, Sacramento, and Yuba river watersheds and concluded that although habitat would increase under the VA, the program would not meet its target for rearing habitat in three of the five watersheds. Spawning habitat would meet the target in all the watersheds whether the VA is implemented or not. (The Mokelumne watershed already exceeds 100% for both types of habitat.)

Underlying the VA proposal is the assumption that physical habitat in the Delta is a limiting factor for salmonid populations. However, says BayKeeper’s Rosenfield, “We have research that shows that at current levels of flow, and current levels of returning adults, the habitat we already have in the Delta is not limiting. It’s not occupied in most years, so creating more of this habitat is not expected to do anything.”

Another hypothesis built into the voluntary agreement proposal is that restoring tidal marsh will benefit native fish by exporting zooplankton like copepods, small crustaceans that are a mainstay of fish diets, throughout the Estuary. But, in keeping with previous research addressing this question, a 2022 study led by San Francisco State University biologist Rowan Yelton found that a restored tidal marsh in the Delta did not provide a net delivery of copepods to a nearby channel. “The idea that tidal wetlands export copepods to adjacent areas is not supported,” wrote Yelton and his co-authors. “No study yet has found a persistent export of zooplankton from wetlands to open water in the San Francisco Estuary or, as far as we know, anywhere else.” 

DWR’s Conrad notes that even if they don’t export zooplankton, shallow-water habitats like wetlands and floodplains are “more likely to be productive of other types of fish food, such as drift invertebrates.” This also benefits native fishes, she says.

Efforts to allow more Yolo Bypass flooding, via Fremont Weir pictured here in 2023 and other projects, have long been aimed at creating more floodplain habitat and food for young fish. Photo: Andrew Innerarity, DWR
Floodplain habitat created at the Fremont Weir by recent storms and restoration interventions around the Yolo Bypass. Photo: Andrew Innerarity, DWR

A different multi-year study published in 2017 by Department of Water Resources environmental scientist Lynn Takata found that Chinook salmon raised on floodplains had an increased growth rate. However, there was no evidence that restoring floodplains would boost salmon populations. “Despite the known growth advantages of floodplain rearing, we did not detect significant differences in survival to the ocean fishery between releases in the Yolo Bypass and the Sacramento River,” wrote Takata and her co-authors. 

“Failure to find evidence is not the same as disproving a hypothesis,” Rosenfield allows. “But if we’re banking an entire program on less flow, we’d better know that more habitat works and we don’t have that.” In contrast, he continues, “we know flow works.” 

But survival isn’t the whole story, says Conrad. “Life history diversity is a key factor for population viability of salmon, and it is related to habitat diversity. When you have increased diversity of habitats, you build resilience into the population,” she says. “I think that we are on very firm ground to say that by restoring access to floodplains we are supporting outmigration to occur in a way that [gives fish] more options, so that it’s not a simple firehose,” pushing fish out through the Estuary to the sea.

Everyone seems to agree that flows and habitat improvements need to go hand in hand for ecosystem restoration to succeed. “It’s not enough to have flow without habitat. It’s also not enough to have habitat without flow,” says Conrad. “The voluntary agreement proposal as a package is trying to meet both of those needs.” 

The sticking point is whether the VA will provide enough water to make habitat restoration successful.  

“You need to put flow down the river to make restoration work,” says Julie Zimmerman, who directs The Nature Conservancy’s Science for Water Program in California. Habitat and flows work hand in hand, she says, adding that one issue is how the VA defines habitat. “They’re defining habitat as simply depths and velocity of water, and it’s more than that. When you create habitat with flow, there’s a lot more going on,” she says, citing the effects of flows on temperature, gravel flushing, and sediment deposit. “We need to start with these functional flows and then shape the habitat to support them. With the voluntary agreements, there’s not enough water to do this.” 

The scale of the habitat improvements in the VA are also a concern, says Zimmerman. “The basic river ecology concept is that flow is the master variable of a river,” she says. “If you put flow down a river, you’re affecting all these different ecosystem processes, and you’re doing it everywhere. [But] when you go out with a bulldozer and you create habitat, you’re [mainly affecting] this one little parcel in one place in the system. Even if habitat was limiting, the scale of it relative to the whole river isn’t enough to change the trajectory of a population.”

The Dutch Slough tidal marsh restoration project site, pictured here in 2021, is restoring 1,187 acres into a tidal marsh to provide habitat for salmon and other native fish and wildlife. Photo: Jonathan Wong, DWR
The Dutch Slough tidal marsh restoration site, which is restoring 1,187 acres to provide habitat for salmon and other native fish and wildlife. Photo: Jonathan Wong, DWR

The water contractors’ Pierre believes that implementation of the voluntary agreement may provide for new scientific insights. “I’m hoping that this is enough of a resource for us to really start to test some of our hypotheses, to understand what are the effects of restoration on its own, as well as the effect of restoration combined with targeted flows,” she says.

Jeffrey Mount, a Public Policy Institute of California geomorphologist specializing in rivers and wetlands, also says the science supporting the voluntary agreement proposal is lacking. But, in the face of tremendous pushback on environmental flows from water users, he supports the concept of a collaborative approach that integrates flows and habitat. “We think voluntary agreements are the way to go,” he says. “Just more water for fish is not enough. The only way to manage risk is to take risks—you can’t set rigid flow standards that won’t make anyone happy; you need to manage them as a package with physical habitat.”

The science basis report concluded that the combination of flows and habitat restoration proposed in the VA “is expected to improve conditions for salmonids and other estuarine species,” while noting that the “actual outcomes…are not certain at this time,” due to “uncertainty arising from assumptions and simplifications.” The Board held a public workshop on the draft on January 19. Staff are now reviewing comments and revising the draft, which will undergo independent peer review before becoming final.

Reporting support by Robin Meadows. 

Top Photo: Hatcheries produce most of the remaining salmon and steelhead in the estuary system. Photo: Jonathan Wong, DWR

Prior Estuary News Stories

About the author

Cariad Hayes Thronson covers legal and political issues for Estuary News. She has served on the staffs of several national publications, including The American Lawyer. She is a long-time contributor to Estuary News, and some years ago served as its assistant editor. She lives in San Mateo with her husband and two children.

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