Fish Down, Invasions Up, Flooding Soon

Fish Down, Invasions Up, Flooding Soon

Ariel Rubissow Okamoto

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Download: Estuary News, October 2013 PDF

Whether you’re a fat salmon or a skinny smelt, life in the watershed of the San Francisco Estuary remains far from “natural.” Dams and levees block Estuary fish from swimming freely in rivers and creeks and through marshlands and floodplains. Alien clams compete for fish food. Invasive weeds clog habitats. And exotic predators threaten life and fin. Hatcheries crank out thousands of coddled, cookie-cutter Chinook salmon every year, and the best fishery in the Delta is no longer salmon and sturgeon but largemouth bass that hail from the Mississippi basin. A few native species, like Sacramento splittail, are “holding their own” according to scientists, but others, like Delta smelt, have declined to such a degree that there are too few to count.

Green Sturgeon. Photo courtesy of Brian Scheier, DWR

Clearly, we have failed to “stem the decline” and “ensure the recovery” of native fish as we set out to do twenty years ago in the CCMP. But over the last two decades, we’ve certainly tried. We’ve built more habitat, released more water from the reservoirs, made more fish food by restoring floodplains and wetlands. We’ve battled in court, in the legislature, and in hearings and meetings on this coast and in the nation’s capital. In fact, for two solid decades we’ve been steadily trying to find a way to bolster the ecosystem without impacts to water available for human uses, and to reroute fish away from the deadly pumps in the South Delta. In all that time, progress has rarely been clear-cut, and the water politics remain heady. But to those in the know, there has been a big change in how we manage the system’s aquatic resources.

“When the fish numbers look bad, we no longer point fingers,” says biologist Bruce Herbold, an insider on interagency fish issues in the California water wars for thirty years. “Everyone knows now that with different years and different conditions, it’s not anybody’s particular fault all the time. There’s much more communication and shared planning. It’s the way we expect to do business now, and the CCMP was where this all started.”

Back in the early 1990s, most fish-friendly interests blamed only one thing for species declines: the state and federal water projects. All the focus was on the pumps, and their dysfunctional screens and fish salvage operations, says Herbold. “At the time, we knew very little about contaminants, poaching, food supplies, Microcystis, and all the other interacting, complicated, multifarious factors affecting fish.”

In those days, people still counted on ever-expanding water exports from the Delta. “The expectation of San Joaquin Valley farmers was that they could go ahead and plant orchards because there would be a reliable and increasing source of water by way of the pumps,” says UC Davis’ Peter Moyle, the watershed’s most well-known fish scientist. Then came the listing of Delta smelt in 1993. “Endangered species created a reliability issue—the farmers never know, these days, when the pumps are going to be turned off to protect smelt.”

Though they can’t promise farmers a consistent water supply, especially not with a number of pelagic fish species seemingly in a downward spiral, much has been done to reduce some of the impacts of the projects on sensitive species, says Herbold. The projects are doing more than just installing better screens and following less harmful salvage procedures; they are now managing flows, when they can afford to, to mimic natural conditions.

“In the 1990s, the agencies tended to think more water was needed all the time, there wasn’t much thought about subtleties of how and where and when you put the water in,” says Moyle. Now, both dam and project operators have been enlisted in providing more or cooler water at certain times of year, with an eye to helping vulnerable young fish or those spawning, growing or migrating. “You can do a lot of things for fish below dams with a fraction of the water we used to think we needed,” says Moyle.

A Paradigm Shift

Just how much water fish should get has always been contentious. Indeed, when the CCMP was still a startup, the feds, who were leading the effort, agreed not to focus directly on flows and water rights but instead on demand-side management in their policy discussions. But not everyone was happy about tackling so many important estuarine management topics in the CCMP while not addressing flows. Environmentalists continued to press for more flows as they sat at the CCMP negotiating table and in other forums. Eventually, the solid science that CCMP partners invested in opened a window.

“Twenty years ago, we were still managing the estuary based on the health of an introduced species—striped bass,” says Barry Nelson, a veteran environmental advocate who sat at those first negotiating tables when he ran Save The Bay, and who now consults on western water issues. “The CCMP came up with a new paradigm for protecting the Delta, which has become the cornerstone of state oversight of the system, and which recognizes the simplest thing in the world: estuaries need water.”

That new paradigm centers on a concept known as “X2.” At that time, research had begun to show that if the saltiness of the water in and around Suisun Bay was two parts per thousand (ppt) in spring, the food web was healthier and fish had more to eat. Where that 2 ppt isohaline occurs in the estuary varies with how much fresh water is flowing out, and how strong the tides.

Applying that science into management, the San Francisco Estuary Partnership organized, hosted and mediated a series of high-level technical workshops at which leading scientists eventually agreed upon an estuarine habitat standard, based on the 2 ppt isohaline. The X2 standard, memorialized in the 1994 Bay-Delta Accord and subsequent state water board actions, requires the water projects to release enough fresh water in spring to keep X2 in the most optimal Delta location.

It was more than a decade before another critical milestone in the flow debate occurred, this too fueled by good science. In 2010, the State Water Board reviewed the best-available research and concluded that, at certain times of year, the estuarine ecosystem and its fish need 75 percent of the Delta’s flow to be unimpaired in order for the habitat to be healthy. That’s a far cry from the 25 percent the fish and the waterway have gotten since the 1970s. While the full 75 percent would be nearly impossible to achieve while supporting all other beneficial uses, such leaps in applied science, embraced at the state level, helped legitimize fish needs for water.

Over time, more and more agencies tasked with protecting fish and wildlife, and the beneficial uses of estuarine waters, have embraced CCMP goals of doing careful ecosystem science, applying it to management, and then monitoring the results. Over the last twenty years, the Interagency Ecological Program, CALFED, the San Francisco Estuary Institute and others have all in some part fulfilled these goals. “We now have incredible amounts of information,” says Moyle. “We know better how to manage endangered fish, and how to bring them back, but it may take such massive changes in how we manage water that no one will want to do it.”

The leaps in understanding are both foundational and cutting edge. It’s only recently, for example, that USGS scientists finally convinced water managers that tides can have just as big of an influence on fish habitat as freshwater flows. Both the fresh and salty sides of the equation are important for fish.

More dazzling, perhaps, is the latest science on fish genetics and behavior. “We’ve got the whole darn genome for Delta smelt mapped out,” says Herbold. “We can tell which parts of the genome react to which stressors, and we can examine their otolith (ear bone) and see what day of their life they entered salt water. We can track individual salmon of a pretty small size as they move through the Delta, and see where each one ends up, and how many make it out to sea. We’ve even learned what happens to fish run through salvage operations. This is all stuff I never imagined we could do.”

Downstream, meanwhile, the Partnership recently started reminding everyone that the Bay, not just the Delta, needs freshwater too. In 2012, the Partnership took Bay Area city and county supervisors on a boat ride to show them why, netting fish from the depths and sharing recent science lessons about the ecosystem at the heart of their municipalities. After that, ABAG took a stronger interest in flows, eventually passing a resolution in 2012 calling for improved flows for the entire Estuary.

“It’s important for the Bay Area to speak with one strong voice, and weigh in on how the Bay should be protected in any proposed statewide water plan,” says ABAG Executive Board member and Contra Costa County Supervisor John Gioia.

Restoring Habitats

Beyond science, there have been many other notable accomplishments on the ground and in the water since the CCMP was published. Most visibly, the upper San Joaquin River is wet for the first time in decades (apart from during big storms). Years of court battles finally gave way to water releases, a restoration plan, and the reintroduction of salmon.

Elsewhere in the system, large-scale restorations along the Tuolumne, Sacramento, Napa and Cosumnes Rivers, among others, have restored flood plains, nursery grounds and fish food supplies. Engineers have also rebuilt gravel beds, and planted shade trees along river banks to cool the water—things fish need to flourish. In the 1990s, water managers removed barriers from Battle, Clear and Butte Creeks so the salmon could move more easily upstream, and in the 2010s more barriers are coming down along the Napa River and Alameda Creek on the edges of San Francisco Bay. Major restorations are also planned for the Cache Slough area of the North Delta, and many agreements have been negotiated to release more flows for fish below dams. On the lands along many rivers, meanwhile, farmers are turning to more “fish-friendly” agricultural practices.

CCMP partners carrying torches for such endeavors are too numerous to name. Upstream in the Delta, much of the restoration work evolved out of early Central Valley anadromous fish restoration and recovery plans and the 1992 Central Valley Water Project Improvement Act, then grew through the CALFED Bay-Delta Program. Most recently, they are reflected in the Bay Delta Conservation Plan’s habitat conservation program, and the EIR for the plan, scheduled for public review in November. These efforts seek to balance ecosystem health with water supply reliability, the dual goals of recent state legislation. Around San Francisco Bay, the restoration of vast tracts of wetlands, championed by other CCMP partners, has also improved the lot of the Estuary’s native fishes. Scientists monitoring levee breaches in both North and South Bay salt ponds are finding fish swim quickly into new habitats.

Preventing Invasions

Despite the groundswell of habitat enhancements, few ecosystems can be said to be healthy if they are invaded by hundreds of exotic species. Whether it’s an Asian overbite clam gobbling up the plankton or a mitten crab burrowing into levees and clogging pump screens, invaders make estuarine management substantially harder. The CCMP called explicitly for new regulations and controls on this front, with good results.

For one, ships can no longer discharge ballast water taken on in foreign harbors in San Francisco Bay or within 200 miles of the coast. The state has steadily tightened regulations promoting better ballast water management over the last two decades, shifting from voluntary to mandatory compliance, and from covering just ocean-crossing ships to embracing coastal traffic as well. Inspectors now board 26 percent of ships visiting California ports, and review ship’s logs and ballast water reports to make sure ballast water has been exchanged in the ocean, rather than in West Coast harbors. More recently, the state has spearheaded research into shipboard treatment systems to kill organisms in ballast before discharge, and is considering new regulations targeting the various organisms that cling to, or foul, vessel hulls.

While the crackdown on new invasions is promising, little can be done about the alien species already turning various parts of the estuarine ecosystem upside down. Using herbicides and mechanical removal methods, however, the state continues to clear Delta waterways of water hyacinth, egeria, and other aquatic weeds, and has also invested in clearing San Francisco Bay wetlands of Atlantic cordgrass. To be effective, such programs often require a level of vigilance and follow-up difficult to sustain amid government budget cuts and impacts on endangered species. But dealing with such challenges and tradeoffs remains the norm for managers of the nation’s most altered and invaded estuary.

The newest menace on the invasion horizon are quagga and zebra mussels, whose appearance in California in 2007 and 2008 sparked more border inspections of trailered boats and a new state plan to counter the spread of these mollusks before they can take hold. These mussels clog water pipes and could be the last straw for native fish already fighting for scarce food.

The Partnership has consistently had staff working on the frontlines against invasions — from the first educational outreach programs on the West Coast to tackling the Chinese mitten crab problem to chairing committees, preparing California action plans, and serving on the nation’s Aquatic Nuisance Species Task Force.

“We’ve pushed hard for prevention and early detection programs. We’ve helped keep the issue on everyone’s radar, year after year, so we can be proactive instead of reactive,” says the Partnership’s Karen McDowell.

The invasions continue, however, a sign that despite all our efforts, the estuarine ecosystem is losing its natural resiliency. Without this resiliency, it’s no surprise that fish managers continue to struggle with challenges such as the precipitous decline of several pelagic fish species. Multiple, interactive stressors seem to be gaining on native fish, and climate change could shove them over the brink. Invading species often move into new niches opened up by floods and rising seas with better success than the locals.

Dealing with such complexities, more flooding and associated changes in California’s water supply is once again placing the spotlight on San Francisco Bay and the Delta. What were once freshwater habitats for fish could soon become salty, and what were once sunken islands could become new bays. Fortunately, the 20 years of science, management and monitoring have given us great insights into what can and cannot be done to make the Estuary as resilient as possible. Several recent publications bring together these insights in a new way — the new historical ecology of the Delta produced by the San Francisco Estuary Institute, and books exploring and comparing scenarios for delta water management and ecosystem preservation in the future (see Log). Both are accomplishments because they synthesize much that has been learned about the past, and establish parameters for future stewardship.

Herbold is both hopeful for the fish, and impatient with slow pace of reaction to new constraints on the Delta’s future. “Fifty years out, we may not be able to take water from the South Delta because either all the levees will have collapsed, or the quagga mussel will have arrived. Instead of having a premise for planning that everything is going to stay the same, the premise needs to be that it won’t,” says Herbold.

Projects Implementing Aquatic Resources Goals 1993-2013: 129

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