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OPENING pursue diverse activities, including sor of the conference. CALFED is a REMARKS shipping, fishing, recreation, and cooperative state-federal effort, of commerce. Finally, the Estuary hosts which U.S. EPA is a part, to balance This Report describes the current a rich diversity of flora and fauna. efforts to provide water supplies and state of the San Francisco Bay- Two-thirds of the state's salmon and restore the ecosystem in the Bay- Sacramento-San Joaquin Delta nearly half the birds migrating along Delta watershed. Estuary's environment — waters, the Pacific Flyway pass through the wetlands, wildlife, watersheds, and Bay and Delta. Many government, the aquatic ecosystem. It also high- business, environmental, and com- TABLE lights new restoration research, munity interests now agree that bene- OF CONTENTS explores outstanding science ques- ficial use of the Estuary's resources tions, and offers take home notes for cannot be sustained without large- Executive Summary...... 2 those working to protect California's scale environmental restoration. Keynote Address...... 7 water supplies and endangered This 2004 State of the Estuary Vital Statistics ...... 9 species. Report summarizes restoration and San Francisco Bay and the Delta rehabilitation recommendations Pollutants ...... 27 combine to form the West Coast's drawn from the 43 presentations and Emerging largest estuary, where fresh water 129 posters of the October 2003 Pollutants ...... 35 from the Sacramento and San State of the Estuary Conference and Joaquin rivers and watersheds flows on related research. The report also Restoring the Estuary provides some vital statistics about out through the Bay and into the Watershed...... 39 Pacific Ocean. In early the 1800s, the changes in the Estuary's fish and Wetlands ...... 45 Bay covered almost 700 square miles wildlife populations, pollution levels, Salt Ponds ...... 57 and the Delta's rivers swirled through and flows over the past two years, The Delta ...... 61 a vast Byzantine network of 80 atoll- since the last State of the Estuary Focus on Fish...... 65 like islands and hundreds of miles of report was published. braided channels and marshes. Back The report and conference are all Politics then, almost a million fish passed part of the San Francisco Estuary and Plumbing ...... 71 through the Estuary each year and 69 Project's ongoing efforts to imple- million acre-feet of water crashed ment its Comprehensive Conservation Bibliography ...... 81 down from mountain headwaters and Management Plan (CCMP) for toward the sea. But in 1848 the Gold the Bay and Delta and to educate and Rush began and hydraulic mining involve the public in protecting and plugged the rivers and bays with restoring the Estuary. The S.F. more than one billion cubic yards of Estuary Project's CCMP is a consen- sediments. Over time, farmers and sus plan developed cooperatively by city builders filled up more than 750 over 100 government, private and square miles of tidal marsh, and engi- community interests over a five-year neers built dams to block and store period and completed in 1993. The the rush of water from the mountains project is one of 28 such projects into the Estuary and massive pumps working to protect the water quality, and canals to convey this water to natural resources and economic vitali- thirsty cities and farms throughout ty of estuaries across the nation under the state. the U.S. Environmental Protection Today's Estuary encompasses Agency's National Estuary Program, roughly 1,600 square miles, drains which was established in 1987 more than 40% of the state (60,000 through Section 320 of the amended square miles and 47% of the state's Clean Water Act. Since its creation in total runoff), provides drinking water 1987, the Project has held six State of to 20 million Californians (two-thirds the Estuary Conferences and provided of the state's population), and irri- numerous publications and forums on gates 4.5 million acres of farmland. topics concerning the Bay-Delta envi- The Estuary also enables the nation's ronment. In 2001, CALFED joined fifth largest metropolitan region to the Estuary Project as a major spon-

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hum of mountain bikes or the drum EXECUTIVE SUMMMARY of hiking boots can also disrupt shoreline birds and mammals, but Reprint of a December 2003 decide how and where to maximize regulators and scientists are still try- ESTUARY Newsletter article. habitat potential for the many differing to figure out just how much is too much. The S.F. Bay Commission’s Though the words "changes and ent species of birds that currently use Caitlin Sweeney told the crowd that challenges" dominated the banners the ponds, continued the Point Reyes two field studies along the Bay Trail and brochures of October’s State of Bird Observatory’s Nils Warnock. show differing results—one that the Estuary conference, another "C" There will be tradeoffs in transform- humans have an adverse effect; the word kept springing to the lips of its ing the ponds to tidal marsh, with other that there is no correlation speakers: choices. The 800-plus dabbling ducks benefiting the most, between bird use and human use of crowd gathered at the Henry J. he said. trails. "We still have a lot to learn Kaiser Convention Center in Oakland about the relationship between fre- heard experts talk about difficult "We are entering quency and intensity of human use choices ahead, as we try to reach and effects on wildlife," admitted ambitious restoration goals for huge an era of choices, Sweeney. areas of our watershed without bringing on more pollution, mosqui- and they won’t be Because the South Bay ponds are toes, invasions, or clashes over which located in such a heavily populated city or island or bird or fish gets what easy ones." urban area, said the Coastal water. "We are entering an era of Conservancy’s Amy Hutzel, resource choices, and they won’t be easy SAM LUOMA managers will need to decide how to ones," announced one of the first CALIFORNIA balance many competing interests, BAY-DELTA AUTHORITY speakers, CALFED’s Sam Luoma. among them endangered species, birds, flood management, and Tackling tough choices will require wildlife-oriented public access and science, education, and especially Tidal marsh restoration could dis- recreation. Planners are applying leadership, according to keynote place the threatened snowy plovers what has been learned about restor- speaker Leon Panetta. Too often it is that nest in and around the salt ponds ing salt ponds in the North Bay, but not these things, but a crisis that and levees in the South Bay and that the South Bay is a different animal, drives environmental policy said the need to be handled with kid gloves. said Hutzel, who explained that the 16-year congressman from Monterey, According to U.S. Fish & Wildlife’s Conservancy and its partners are who served as White House Chief of Joy Albertson, the Bay supports 100- working on a phase-out and steward- Staff from 1995 to 1997. Panetta 150 breeding plovers, about 10% of ship plan that will deal with such pointed to the collapse of Monterey the entire U.S. population of the issues as formulating a long-term Bay’s valuable sardine fishery as an Pacific Coast Western Snowy Plover. water circulation plan for the ponds, example of shortsighted stewardship The birds nest in shallow scrapes on and minimizing mercury methylation, and called for a national commitment salt pond levees or flat open areas introduced species, and mosquitoes. to protecting our oceans and estuar- within 100 meters of water, lining Said Hutzel, "We hope to compress ies on the order of Roosevelt’s early their nests with pebbles and salt crys- the 10 years of work done in the commitment to our national parks. tals. But California gulls—which also North Bay to five years in the South "We need to decide what kind of roost on dry salt ponds and levees— Bay." quality of life we want to pass on to prey on plover nests and chicks. Like the next generation," he said. gulls, ravens and crows are thriving as But how will we pay for long-term the Bay Area continues to urbanize. maintenance and operations of the Many of the decisions that loom They "hang out" in the landfills built restored South Bay ponds? That was ahead involve birds. The last few gen- next to the wetlands years ago, and the question posed by the Bay erations of Bay shorebirds have also eat plover eggs and chicks. Institute’s Marc Holmes in his talk the greatly benefited from the large con- Choosing where to locate and second day. The Bay lacks a distinc- stellation of salt ponds in the South restore salt pans and ponds will be tive identity 3,000 miles away in Bay, but they may need to make way critical to the plover’s future, said Washington, D.C., said Holmes, for other avians unless careful choices Albertson, along with deciding how which makes it challenging to get are made about what the U.S. to manage water levels, salinities, and federal funding. It doesn’t have the Environmental Protection Agency’s predators. poetic "River of Grass" image of the Mike Monroe called the largest single Everglades, or the strong, multi-state habitat restoration project ever envi- Ravens and crows are not the only constituency of Chesapeake Bay, said sioned for the Estuary. We must interlopers on sensitive bird turf. The

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Holmes, and "historic diked baylands" ‘pretty up’ an ugly engineering proj- "...Sediment loads don’t necessarily inspire East Coast ect—is over. Plants are our new engi- politicians. "When people think of San neering materials." Soil bioengineering from small tributaries Francisco Bay, they think about the techniques similar to those used in Golden Gate Bridge and the urban stream restoration—creating may be having a Transamerica Pyramid building," he willow fascines and bundles to trap said. The Bay needs not only a strong sediment—are also being used in the greater impact on the identity that will resonate in Delta, said Lauren Hastings in her Bay than those from Washington (Holmes suggested John overview of Delta restoration proj- Hart and David Sanger’s "Hollow ects, the idea being to work with the larger rivers that Lands"), but also a planned funding nature instead of trying to control it strategy to finance restoration, opera- with hard structures. Working with flow to the Estuary. " tions, and maintenance—not merely nature—the tides—was also the U.S. acquisition. Geological Survey’s Jon Burau’s focus, LESTER MCKEE SFEI Once we have the money we need who described recent experiments at for restoration (and ongoing mainte- Frank’s Tract. By synchronizing water lutants, our only choice may be to do nance), we will need to decide where project operations with tidal ebbs and nothing—or try to reduce their loads, we will get the best return on invest- flows, said Burau, we can control which is not always possible. The ment, to use the banking-based ter- salinity and improve water quality. Estuary Institute’s Mike Conner men- minology common in several talks. Riparian restoration may not tioned mercury, PCBs, DDT, dieldrin, We tend to put restoration money receive the attention marsh restora- and chlordane as problem pollutants into highly visible projects, like tidal tion does, but new science indicates in the Bay, which he christened "the wetlands and urban streams, said Jeff that it should. Lester McKee pointed Big Muddy" because sediments—and Haltiner of Phil Williams & Associates, out that recent research by the S.F. contaminants from the bottom— but we also need to develop stew- Estuary Institute on sediment loads become resuspended with every tide. ardship around mudflats, upper from small tributaries shows that they Conner’s colleague, Jay Davis, watersheds, and grazing lands—to may be having a greater impact on described the efforts the Institute has take a broader look at the Bay. And in the Bay than the larger rivers that undertaken over the past few years doing restoration, we need to better flow to the Estuary. Why? Because as part of the Regional Monitoring train the next generation. We are there is proportionately more sedi- Program (RMP) to model the long- practicing by "learning on the patient," ment in less volume of water, term fate of persistent organic pollu- said Haltiner, who also pointed out explained McKee, and particles are tants in the Bay. The degree of con- that while we have regional goals for more likely to be deposited along tamination is most severe for PCBs, wetland restoration, we have nothing channel banks and bottoms. These said Davis, which continue to "load" comparable for fluvial systems. same small waterways are also large the Bay as bottom sediments are contributors of mercury and PCBs— In fact, riparian restoration is the resuspended and recirculated, and at least equal to inputs from Central "poor cousin" of marsh restoration, contaminated sediments are eroded Valley rivers, according to McKee. according to the S.F. Regional Board’s from the watershed. According to Part of the problem is that many of Ann Riley, despite enormous citizen the Institute’s model, if all these loads these small tributaries historically interest and the fact that riparian could be eliminated, we could reduce entered the Bay in sloughs or season- restoration has evolved from city- PCBs in the Bay by 90%, but it al wetlands, but now discharge their block-long-sized projects to mile-long would take about 70 years. PAHs are water—and contaminants—directly projects, an evolution due in part to another problem, and are at the into the Bay in flood-control channels opportunities to rehab old flood-con- threshold for concern, said Davis. or pipes without first being filtered by trol projects. One of the myths about When it comes to a relatively new wetlands. restoring urban streams, said Riley, is pollutant, the flame retardant PBDEs, that you cannot have a healthy eco- Restoring the mouths of creeks is we don’t know enough about the logical system in a city. If project one choice we could make to see threshold for concern, said Davis. We designers get the length and width of multiple benefits from our restoration do know that concentrations of the active channel right, she said, a dollars, as such projects would help PBDEs are increasing exponentially fully functional channel is possible. filter sediment and pollutants while and that we are "loading up our sedi- Working with nature is a part of the creating habitat. Meanwhile, other ments." The partial ban on PBDEs new restoration paradigm, she added. pollutants lurking at the bottom of signed by former Governor Davis will "The era of planting streams with the Bay will be harder to get rid of, help address the problem, but over- container stock from nurseries—to said several speakers. For some pol- all, the Bay is slow to respond to a

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decrease in loadings of persistent the highest in the world. One con- land foraging patterns in and along chemicals, said Davis. "Even small cern about PBDEs is that they may be the edges of primary sloughs, and loads of persistent chemicals can have endocrine disruptors, the focus of their endangered status. Schwarzbach significant consequences, and con- NOAA Fisheries’ Tracy Collier’s talk. found that slough channel order influ- tamination of the watershed will pro- Endocrine disruptors mimic or block ences methyl mercury concentra- long recovery." hormones or alter hormonal balance tions, with greater methylation taking in humans and other creatures, such place in primary—or smaller, more as fish, explained Collier, who has dendritic—channels. One of the most "Riparian studied the effects of PAHs (another timely questions that needs to be problem Bay pollutant and endocrine addressed, said Schwarzbach, is restoration is the disruptor) on zebra fish and found whether wetland restoration will ‘poor cousin’ of that they suffer from arrhythmia and increase or decrease mercury lev- loss of cardiovascular function. els—and whether the benefits of marsh restoration… So what can be done? Some solu- restoration outweigh any associated tions are simple, said the S.F. Regional problems. despite enormous Board’s Keith Lichten, who described Another potential risk associated citizen interest and how post-construction stormwater with wetland restoration is West Nile management measures, such as Virus, which is headed for the Bay the fact that it has swales, ponds, wetlands, media fil- Area in 2004, according to the ters, green roofs, and even something Contra Costa Mosquito and Vector evolved from city- as simple as narrower streets, can fil- Control District’s Karl Malamud- ter and improve what runs off to the Roam. Some wetlands will present block-long-sized Bay. Those measures can have other more trouble than others, said benefits too, like controlling floods Malamud-Roam. High-risk wetlands projects to mile- and giving people a sense of place. include seasonal wetlands, wetlands long projects." "As people see runoff flow across the with dense vegetation (in which mos- landscape, they better understand quitoes can hide from fish), wetlands ANN RILEY their connection to the Bay and how with no plumbing or operations and S.F. BAY REGIONAL WATER their actions affect it," said Lichten. maintenance budget, and small, dis- QUALITY CONTROL BOARD "The Bay becomes more than some- persed wetlands (for which it is hard- thing they just drive over." Another er to track down landowners about regulatory approach to cleaning up maintenance concerns). Good tidal Emerging pollutants—PBDEs and the Bay is through TMDLs, or stan- flushing helps prevent mosquitoes, endocrine disruptors—were the dards that limit the maximum amount explained Malamud-Roam, because focus of a trio of speakers during the allowable from all dischargers on a most juvenile mosquitoes need three- first day’s afternoon session. Tom daily basis. Lichten’s colleague Dyan plus days of standing water in order McDonald with the Office of Whyte explained that regulators are to breed. "Wetland restoration is pos- Environmental Health Hazard continuing to define and refine water sible and compatible with mosquito Assessment described health con- quality standards for the Bay. Whyte control, but it has to be done right," cerns related to PBDEs, which are told the audience to "stay tuned" for a Malamud-Roam concluded. now ubiquitous in our environment: TMDL for PCBs in the Bay, an urban Regardless of fears about West Nile Even house dust may be a pathway creek pesticide toxicity TMDL, a Virus, wetlands restoration efforts into the human body. Kim Hooper report on Napa River sediment and continue to burgeon around the Bay. characterized humans as the prover- pathogens, sediment reports for San Wetlands and Water Resources’ bial canaries in a coalmine, making Francisquito and Sonoma creeks, and Stuart Siegel gave a bird’s eye tour of the case for measuring body burdens an amendment to the S.F. Basin Plan planned and in-progress projects, of contaminants like PBDEs. We for mercury, which remains one of while Keith Merkel of Merkel & measure chemicals in air, soil, water, the Bay’s most problematic contami- Associates showed us where the few and animals, said Hooper, but not in nants and was one of the confer- remaining eelgrass beds are located people. Yet body burden data—par- ence’s most popular topics. and described the efforts being ticularly from human breast milk—is Mercury—in the form of undertaken to map them, in order to very useful for analyzing risks associ- methylmercury, which bioaccumu- better understand where to try to ated with neurodevelopment, said lates in birds and their eggs—was restore them. Currently, only 0.1% Hooper. The bottom line is that per- chronicled by Steve Schwarzbach of of the Bay’s bottom supports eel- sistent organic pollutants are "not a the U.S. Geological Survey, who grass, compared to 11% in San Diego good idea." PBDE levels in humans found that clapper rails are particular- Bay and 55% in Mission Bay, for and biota in the Bay are now among ly vulnerable due to their tidal wet- example, although there is more eel-

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grass in the Bay now than in the late Such considerations were the focus California’s perspective, Kern County 1980s. What is thriving in and around of the conference’s third day. The Water Agency’s Brent Walthall the Bay are weeds, such as invasive Resources Agency’s Tim Ramirez described ag’s point of view, and spartina, pepperweed, and other kicked things off by reminding us that Steve McAuley covered that of the troublemakers, according to coastal Southern California is tied to the California Urban Water Agencies. plant ecologist Peter Baye. Klamath, and the Bay to the Environmental Defense’s Spreck Restoration will affect the spread of Colorado River by virtue of our Rosekrans offered his critique of the all plants, including invasive species, plumbing and political systems. Environmental Water Account (EWA). warned Baye, who suggested that CALFED’s Patrick Wright agreed, The Department of Water Heron’s Head Marsh in San Francisco emphasizing that our old approach to Resources’s Jerry Johns said that the could be used as a model for other meeting water needs—by expanding EWA is working, calling it the "glue tidal marsh restoration projects. existing projects—is "out the door," that put CALFED together," guaran- There, Atlantic cordgrass was and suggesting that new approaches teeing water supply reliability and fish removed prior to restoration and need to be regionally and partner- recovery. "There have been two dry nearby colonies controlled to mini- ship-based. "It’s not an accident that years and one above-normal water mize reinfestation. in an area like the Klamath, conflict is year," said Johns. "And no big fights. Phil Williams took the long-range more prevalent than in areas where The fish have benefited, and the view in discussing wetlands restora- we have a process," said Wright. The water supply is stable." But DWR’s tion, attempting to predict the future S.F. Regional Board’s Loretta Kamyar Guivetchi predicted that by of Bay habitats. "We need to recognize Barsamian stressed the importance 2030, California will have "half as that the Estuary as a geomorphic sys- her agency has placed on building many new people as today," and tem is dynamic and evolving whether partnerships with businesses, envi- pointed out that "because California or not humans are on its periphery," ronmental groups, and dischargers in agriculture is producing 50% more said Williams. He cautioned that the resolving Bay-related conflicts. today than 20 years ago, we cannot time to do restoration is sooner rather Analyzing conflicts on the Klamath afford to keep taking water away than later. "The Estuary is still a River was also the focus of U.C. from ag to meet our urban water drowning river valley that has not Davis’ Jeff Mount, who shared his needs." He suggested that perhaps achieved equilibrium between sedi- perspective as a member of the cotton and rice should be phased out. ment deposition and erosion yet," said National Research Council team con- "We need to subsidize crops that can Williams. Because we are faced with a vened to investigate last year’s fish be used to promote things that will diminishing sediment supply in the kill. The Council concluded that while have statewide benefits." Estuary and accelerated sea level rise, the primary cause of the die-off was we will get a vegetated marsh more disease, resource managers in the "We need to recognize quickly in restoring subsided sites now Klamath Basin are not taking full than if we wait until later, he advantage of the tools available to that the Estuary is explained. Phyllis Faber, of Phyllis M. them under the Endangered Species Faber & Associates, has monitored Act. "The Klamath Basin lacks an dynamic and evolving several wetland restoration projects ecosystem-based approach," said over the years, comparing Warm Mount, who felt that an important whether or not humans Springs in the South Bay, and Muzzi lesson to apply to the Bay-Delta is Marsh and Sonoma Baylands in the that single-species management is are on its periphery." "destined to fail." North Bay, to China Camp, a "control" PHIL WILLIAMS site. Plants will establish themselves Managing for multiple species is PHILIP WILLIAMS AND ASSOCIATES naturally where elevations and soil part of what we need to do in figuring conditions are appropriate, said Faber. out whether we can pump more But a mature pickleweed marsh can water south and still protect the In the afternoon, Senator Mike take 30 to 40 years to develop, and Estuary, the hot topic of the third Machado said that while we have the she stressed that restorationists need day’s late morning session. If you are tools to manage our water, we need to cultivate patience. Visiting scientist a small fish near the pumps, said Cal to better choose how to use them. Denise Reed from the University of Fish & Game’s Diana Jacobs, you will Assemblymember Joe Canciamilla New Orleans echoed Faber, suggest- be drawn into the central and south agreed, but went one step further, ing that we shouldn’t "mess with stuff" Delta. "Will flow changes add to saying that the state "is at a pivotal too much, but rely on nature and time cumulative impacts or be barely per- point in resolving water issues, all of instead. We also need to consider how ceptible?" asked Jacobs. "The stakes which have a direct and indirect the Bay’s wetlands are influenced by are high for people and ecosystems." effect on the Bay-Delta." The chal- water management decisions, said The Metropolitan Water District’s lenge to public agencies, said Reed. Tim Quinn presented Southern Canciamilla, is "whether the CALFED

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ROD will be followed. What’s being which pesticides might be causing the the S.F. Bay-Delta is unique among proposed now is ‘trust me.’" We can problem. In the future, said U.S. estuaries in the accuracy and consider increased pumping, said Anderson, genotoxins, such as cap- amount of temporal data collected, Canciamilla, but we need to take care tan, ziram, carbaryl, malathion, said Russ Flegal of U.C. Santa Cruz, of the Delta in the process." methyl bromide, and trifluralin, making it possible to quantify current One way to make sure we have should be studied. metal contaminants in the Bay. Other enough water to meet multiple needs reasons for hope include increased is to increase our use of recycled "We need to public awareness about the Bay. Save water. DWR’s Fawzi Karajeh said his the Bay’s David Lewis pointed out agency sees possibilities for using examine the that, under supervision of his organi- more recycled water in agriculture zation alone, over 12,000 people and landscape irrigation. At the top of gravity of the have removed 20,000 pounds of inva- the list of the state’s recycled water sive species and planted more than task force are public safety and the changes we’ve 20,000 native plants on several sites environment, said Karajeh. If we can around the Bay. John Wise (retired, assure the public that recycled water wrought as we’ve EPA), said he is optimistic about pub- is safe, 1.5 MAF of it could contribute made ourselves lic engagement in Bay issues, citing a 1.2 MAF of "new" water supply. Gary "continuous agenda of public involve- Wolff, of the Pacific Institute for comfortable and ment" as the driving force behind Studies in Development, public policy over the past 40 years. Environment, and Security, told the prosperous living We will need to continue making an audience that California’s economy effort to involve the public, said Wise, can continue to grow without taking along the Bay." and the public is eager for a way to more water from the environment. measure the success of restoration Cost-effective conservation tech- SAM LUOMA and adaptive management. "What CALIFORNIA niques for homes and businesses are gets measured gets done," said Wise. BAY-DELTA AUTHORITY available now, said Wolff, who sum- The Bay Institute’s Report Card is marized some findings from the one important step in that direction. Institute’s new publication, Waste The S.F. Estuary Institute’s Bruce Not, Want Not. With all these chemicals in our Thompson and the Bay Institute’s Anitra Pawley presented the results Water saved by urban users could waters, can we ever hope to restore our fisheries? Gordon Becker from of the S.F. Bay Index published in benefit both human quality of life and October 2003. Several speakers men- fish, said Wolff. But flows may not be the Center for Ecosystem Management and Restoration added tioned that the only way the public all fish need, according to the will fully support restoration is University of Washington’s Jim water supply issues, flood control, and fish migration barriers to the list through good science. "Science has Anderson, who has found that tem- never been more important," said perature is more important, at least of challenges facing steelhead in Bay tributaries. While historical abun- CALFED’s Sam Luoma. "The Bay is a to fish in the Columbia River. U.C. constantly changing place, and we are Davis’ Bill Bennett wondered if we dance will never be attained, said Becker, we should focus on improv- still learning better ways of operating can truly separate human impacts our existing systems and how to from natural influences on fish popu- ing passage and flows and on habitat improvements based on natural chan- work with Mother Nature." But most lations, concluding that the issue importantly, said Luoma, the public needs to be researched further. nel processes. "Restoration should focus on priority watersheds," said needs to understand that we are liv- Human and natural influences may be ing in an era of choice. "We need to co-occurring and interacting in com- Becker, who believes that too few resources are being expended to examine the gravity of the changes plex ways, causing population we’ve wrought as we’ve made our- declines, said Bennett. "It’s not just restore Bay Area streams. "We should integrate steelhead restoration selves comfortable and prosperous pumps and pollution, but effects at living along the Bay." local and regional scales. We can into watershed management efforts measure these things." Another underway." Becker concluded on an human impact that remains a puzzle optimistic note, citing great public is the genotoxic effects of agricultural support for restoring fish in Walnut, runoff in the San Joaquin River, said Alameda, and Coyote creeks, among Susan Anderson, also from U.C. other Bay Area streams. Davis. While Anderson saw elevated Other speakers, too, were opti- DNA strand breaks in fish exposed to mistic, despite the challenges and the San Joaquin River, it wasn’t clear choices ahead. As a result of the RMP,

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question is, how many more future. The report is titled America’s PROTECTING Montereys will there be? How many Living Oceans: Charting a Course OUR RESOURCES — more communities will suffer for Sea Change, and is a comprehen- because of poor stewardship? sive look at the depths of our oceans THE CHALLENGE OF and the impact of human behavior. STEWARDSHIP Too often we take our natural resources for granted. In And that’s why I term the situation a the hearings we had on the crisis. Because many of the same stresses that you have identified here FROM THE KEYNOTE ADDRESS BY Pew Commission it became as impacting the Estuary are impact- THE HONORABLE obvious that the public gen- ing our oceans. LEON PANETTA erally takes our oceans for THE PANETTA INSTITUTE AND granted. They take our We’re looking at the equivalent of PEW OCEANS COMMISSION estuaries for granted, too: the last buffalo hunt when it comes to they see the estuary, but our fisheries. We have depleted our The San Francisco Bay Estuary is they don’t see what goes on oceans of 90 percent of the large one of the greatest ecosystems of the beneath the surface. So we take it marine fish—the tuna, the marlin, world. It is a meeting place for for granted, and we pay a price for and the swordfish. Populations of waters, weather, tides, salmon, stur- that. The question is whether we are cod, haddock, yellow-tailed flounder, geon, for migratory birds, for visi- going to protect the great natural and rockfish have reached historic tors from throughout the world, a splendors and resources that are so lows and in many cases are nearing meeting place for the eight million important not only to life itself, but the point where they will become people who live along its coastlines. also as the legacy we pass on to extinct. Only 22 percent of fish But a tremendous challenge faces us future generations. stocks are fished sustainably. As you in trying to protect that fine, fragile cycle of life, that balance between life on land and life beneath the sea. "Every eight months we have the The challenge we have is also the equivalent of an Exxon Valdez oil spill — challenge of what we pass on to our children. I think what drives us and 10.8 billion gallons of oil — as runoff should drive us is passing on to our children the opportunity to enjoy a from streets and highways into our better quality of life. For quality of life is related to protecting the most coastal waters.” important resources we have. To those of us in California, that means We govern our democracy either places like the Big Sur coast, the through leadership or crisis. If leader- have found in the San Francisco Bay Mendocino coast, the Farallones, the ship is there and is willing to take the Estuary, pollution is an increasing life, the wonderful life and habitats risks of leadership, then we can take problem, not only within our estuar- we have in our oceans, our coastlines. steps to avoid the consuming crisis ies, but along our coastlines as well. In Monterey it’s not only the bay; it’s that ultimately develops in every pol- Discharges of nitrogen have Elkhorn Slough. And here obviously, icy area. But if leadership is not increased five-fold. And we expect it’s not only the wonder of the coast there, crisis will drive policy. Too that they could increase another 30 but also this wonderful Estuary. often today, we govern more by crisis percent within the next few years. As a result, we have huge dead zones As a boy I grew up in Monterey, than by leadership, whether in ener- appearing off of our coastlines. A in a fishing village that was driven gy, health care, the budget, social dead zone is exactly that: no life by the sardine industry. Families security, Medicare, foreign policy, or within that area. We have degraded were there for that purpose; Cannery indeed, too often, the natural environ- about two-thirds of our estuaries and Row developed, and John Steinbeck ment. We wait for a crisis to happen our bays as a result of pollution. wrote about it. But ultimately you in order to respond. And sometimes Thirteen thousand beaches are closed know what happened. As a result of that can be too late. Our oceans and or on pollution advisories. According overfishing and poor stewardship, many of our estuaries are in crisis. to a study by the National Science the sardines disappeared. The fami- The Pew Oceans Commission that I Foundation, we have the equivalent lies and community that depended chaired engaged in three years of of an Exxon Valdez oil spill—10.8 on the sardine industry were impact- work and a journey of discovery to billion gallons of oil—as runoff from ed, seriously. Because of poor stew- determine the state of our oceans and streets and highways into our coastal ardship, we lost a very important our estuaries and the steps needed to waters every eight months. In addi- part of the legacy of that area. The ensure that we protect them for the tion, invasive species are crowding

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out our native species and altering at different levels, whether federal or to be amended to do that. But first, habitats. In San Francisco Bay, you local. And so what oftentimes hap- Congress and the President must have identified about 175 invasive, pens is that issues have to be taken make a commitment to protecting introduced species. to court to have a federal judge our oceans and our estuaries. We decide them. have recommended that Congress Coastal development is another pass a national ocean policy act that stress we found to be significant. clearly expresses the commitment of Here in California, 54 percent of our the nation to protecting these areas population lives on 17 percent of our "Too often today, as a public trust. Very little will be land. And we estimate that 25-27 we govern more accomplished unless there is a funda- billion more people will move to our mental commitment recognizing that coastlines in the next 15 years. by crisis than by these areas must be protected the We’ve lost 20,000—and continue to same way we protected Yellowstone lose 20,000—acres of wetlands each leadership…we or Yosemite. year in this country. California alone has lost 95 percent of its historic wait for a crisis to One hundred years ago, Teddy wetlands. So all of this tells us that Roosevelt made a national commit- we have a problem that has to be happen in order to ment to protect our land; today, 100 confronted. But the good news, to a respond." years later, this President and this large extent confirmed by the work Congress—all of us—need to make that you have done here, is that it is the same kind of commitment when not too late to reverse what has hap- So we govern much more by crisis it comes to protecting our oceans and pened, to repair the damage, to than by leadership. Some of the pri- our estuaries. It will not just happen restore these great resources. mary recommendations of the Pew on its own. It requires a call to action. Commission were that we need to As John Wise pointed out, it The problem is, we can’t deal with reform ocean management, that we demands that people come together this kind of challenge on a hit-and- need greater coordination of ocean with clear goals. We live in a time miss basis. We can’t just address it policy at the federal level, that we when we’re confronting crisis on a with court orders. We can’t just deal need to have an ocean agency number of fronts—whether Iraq, with it by simply waiting for crisis to responsible for dealing with these North Korea, or the Middle East. drive policy. This kind of challenge agencies, that we need to develop Problems of the economy, deficits— requires leadership—not just by ecosystem councils that manage all of these things consume us. The elected leaders but by all of us. The ecosystems on land and in water. The challenge is to point out to citizens biggest challenge we face is how to Chesapeake Bay Plan was one of best that when it comes to problems change the laws and attitudes of the models we saw—it involved several involving estuaries and oceans, these past so that they can meet the reali- states plus the federal government, are issues that relate to life itself—to ties of the present. Our ocean laws— plus the local government, which our health, nutrition, the quality of air the laws that deal with our coastline came together to set goals to try to we breathe, to our climate, to the waters—date back to an era when restore life in Chesapeake Bay. And it fisheries that are important to our our primary concern was preventing worked because everybody was com- communities, to our economies, to other nations from stealing our ocean mitted; everybody was sitting at the our recreational enjoyment, and to resources before we got to them. It same table. Those kinds of ecosystem our very souls. That’s the case we was not about sustainability; it was councils need to be established for have to make. It is vital to the future not about good management. It was other major ecosystem areas such as and to that American dream my about protecting the resource from the one you’re dealing with here. It is father talked about, that we pass on a others who might try to seize it. And also important to develop and reform better quality of life to our children so what developed is a conglomera- fisheries policies in a way that advo- when it comes to our oceans and our tion of laws that oftentimes do not cates sustainability and gets away estuaries. And that will require a work together. Governance may be from single species management. tremendous commitment by all of us. one of the biggest problems we face It will require fighting for what we when it comes to dealing with our We need to protect coastlines, believe in. If we’re willing to fight I oceans crisis. There are 60 commit- marshes, and wetlands from develop- think we can establish such an impor- tees in Congress that deal with our ment and identify areas that need to tant national commitment, that this is oceans and estuaries; there are 140 be protected. We need to clean our a national trust that all the people laws; there are 30-40 agencies. There waters, particularly of non-point care about, that this great resource— is a lack of science to look at these source pollution. We’ve done a pret- the oceans and estuaries—belong not problems. As a result, there is very ty good job on direct pollution but just to us but to our children as well. little coordination, and there is con- haven’t done enough on non-point flicting guidance by various agencies sources. The Clean Water Act needs

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vital statistics 2002-2004

"Organisms constantly adapt to their environment. So must policies. And so must policymakers. Learning from small failures is often more important than celebrating huge successes. Adaptive management is implicit in how we currently seek to manage the Estuary. We need to bring adaptive management — based on the goals and indicators being formulated, such as those the Bay Institute has presented — explicitly into the realm of public engagement." JOHN WISE U.S. ENVIRONMENTAL PROTECTION AGENCY (RETIRED)

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FRESHWATER FLOWS TO THE SAN FRANCISCO ESTUARY, 1980-2003 Flows IN MILLIONS OF ACRE FEET

Recent Inflows 70 Total Delta Inflow Normal or above normal rainfall 60 Net Delta Outflow has meant improved Delta inflows in 50 recent years. Inflows to the Delta 40 and Estuary were 15.4 million acre- feet (MAF) in water-year 2002 30 (October 1, 2001 - September 30, 20 2002) and 21 million acre-feet 10 (MAF) in water-year 2003 (October 0 1, 2002 - September 30, 2003). '80'82 '84 '86 '88 '90 '92 '94 '96 '98 '00 '02 Delta outflows were 9 MAF in 2002 and 14 MAF in 2003 (Interagency Source: DWR, , Dayflow QTOT Ecological Program, 2004). Water Use San Ramon Valley Recycled Water Efficiency Program (SRVRWP), which will Diversions for serve areas of Blackhawk, Danville, Beneficial Use Water use efficiency, conservation, and recycling projects within the Dublin, and San Ramon. When com- Water is diverted both within the Bay-Delta region aim to provide a plete, this multi-phased 6.7-mgd proj- Delta and upstream in the Estuary’s "drought-proof" source of water to ect is expected to deliver 3.3 mgd to watersheds to irrigate farmland and help meet the needs of cities, indus- DSRSD’s service area and 2.4 mgd supply cities. In-Delta exports have tries, and agriculture. From 2001- to EBMUD’s service area with 1 mgd largely remained within the range of 2003, CALFED’s water use efficien- available to either. The project’s ini- 4 to 6 MAF per year since 1974, but cy program provided $39 million in tial phase is now under construction, the percent of Delta inflow diverted grants to more than 100 different and first recycled water deliveries are can vary widely from year to year. local water conservation and recy- expected in summer 2005. In water-year 2002, 5.5 MAF were cling projects statewide. Prop. 50 Meanwhile, EBMUD currently diverted, and in 2003, 6.3 MAF. The provides an additional $180 million produces almost 6 mgd of recycled average percentages of total Delta over the next three years to fund por- water. In addition to its joint project inflows diverted were 39.9 in 2002 tions of the program. Prop. 13 also with DSRSD, EBMUD’s multi- and 38.3 in 2003 (Interagency provided funding for water recycling phased East Bayshore Recycled Ecological Program, 2004). projects. CALFED expects that these Water Project (EBRWP) is currently projects will make a significant con- under construction, with first deliver- tribution toward meeting its water ies expected after mid-2005. The PERCENT OF INFLOW DIVERTED use efficiency goals. EBRWP will ultimately include near- 50 At the local level, the Bay Area ly 30 miles of pipeline through parts Water Recycling Program’s (BAR- of Alameda, Albany, Berkeley, WRP) Master Plan, now complete, Emeryville, and Oakland and will save 2.5 mgd (2,800 acre-feet/year) 40 calls for recycling 125,000 af/year in the Bay Area by 2010, and about once all recycled water customers are 240,000 af/year by 2025. Many Bay hooked up to the system. 30 Area agencies are forging ahead with MORE the design, construction and opera- INFO ?http://calwater.ca.gov/ tion of water recycling projects. For or www.ebmud.com example, the Dublin San Ramon 20 Services District (DSRSD) recycling facility’s current treatment capacity is 3 mgd, with 10 miles of distribution 10 ‘97 ‘98 ‘99 ‘00 ‘01 ‘02 ‘03 installed. Planned capacity for this facility is 9.6 mgd. DSRSD and the Source: DWR, Exports TOT East Bay Municipal Utility District (EBMUD) are jointly developing the

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SALMON RUNS OF CONCERN IN THOUSANDS OF ADULT FISH RETURNING TO SPAWN Fish & Aquatic Organisms

70 Winter-Run to Upper Sacramento River Central Valley Salmon 60 Fall-Run to San Joaquin River Most populations of Central Valley Spring-Run to Upper Sacramento River chinook salmon seem to be holding 50 relatively steady. Central Valley chi- 40 nook salmon occur in four discrete 30 runs—winter-run, spring-run, fall- 20 run, and late fall-run (run refers to the season in which adults return to 10 their native streams to spawn). The 0 winter-run chinook salmon, with the '80'82 '84 '86 '88 '90 '92 '94 '96 '98 '00 '02 lowest population, has been listed as New counting methods for winter run implemented after 2000 shown in chart below. Source: CDFG both a state and federal endangered species since 1994. As a result of fish had to use the ladders. An alter- S.F. Estuary, was listed as a federal more regular interagency scrutiny of native method, counts of spawned and state threatened species in 1993. operations, a new counting method female carcasses upstream, backed Delta smelt are considered environ- for chinook winter-run salmon criti- up by earlier surveys, revealed a vari- mentally sensitive because of their cal to assessing "incidental take lim- ation up to a factor of five in the total primarily annual lifecycle, limited its" was put into place recently. estimates of spawning adults. The diet, low fecundity, and restricted Federal incidental take limits for new higher estimates of adult escape- distribution within the Estuary. winter-run allow up to two percent of ment translated into a higher estimate Possible reasons for the Delta smelt’s "juvenile production" to be lost at the of juvenile production and meant that decline include reductions in Delta pumps. The formula for setting take the take limit was never reached in outflow, extreme high outflows limits combines the number of off- 2001, for example, changing the need (which displaces them away from spring produced ("juvenile produc- to reduce pumping and use EWA suitable rearing habitat), entrainment tion") with the number of adult fish resources to protect fish. losses at major water diversions, prey item changes, competition, toxicants, returning to spawn each year ("adult MORE disease, and predation. escapement"). The latter number— INFO ? [email protected] based on how many fish passed After a dramatic decline in the through the Red Bluff Dam fish lad- Delta Smelt 1980s, Delta smelt abundance gener- ders—became questionable in recent ally increased throughout the 1990s. The Delta smelt, a 55-70 mm long years as the dam gates remained Scientists attribute this population translucent fish once common in the open for longer periods and fewer increase to the above-normal outflow conditions, which aided in the transport of larval/juvenile ENVIRONMENTAL WATER ACCOUNT EXPENDITURES fish from the Delta to their rear- JAN 2001 THRU SEPT 2004 ing grounds around the Suisun 2001 2002 2003 2004 Bay area. More recently, abundance indices indicate another 200 Delta Smelt 200% Winter Run Salmon downward trend, starting in

Reconsultation Level 2001. Most likely, lower outflow 150 150 through the Delta in recent years has been a major factor in the decline. Cal Fish & Game moni- 100 100 tors the relative abundance of Delta smelt through two long-

Amount of Water Amount of Water term monitoring programs: the 50 50 (Thousands of Acre-feet) Summer Townet Survey (TNS) (since 1959) and the Fall 0 0 Midwater Trawl Survey (MWT) JFMA AMSON JJ DJFMASON AM JJ DJFMASON AM JJ DJFMASON AM JJ D (since 1967). The 2003 TNS index for Delta smelt is 1.6, a EWA expenditures are used to take proactive measures (release water from reservoirs and/or ramp decrease from 2002 (4.7) and down Delta pumping plant rates) to AVOID the reconsultation levels (100%, or “red light) for delta smelt and winter run chinook salmon. In previous years - without the EWA - protective actions could not be taken UNTIL the reconsultation levels were reached. Note that a single EWA action often provides benefits to more than one listed species (including spring run chinook salmon and steelhead). 11 SOE layout 1 8/12/04 8:27 PM Page 12

STATE OF THE ESTUARY

2001 (3.5). Meanwhile, the 2003 Splittail occurred only briefly prior to the MWT index was 210, up slightly Young splittail production has splittail spawning period in 2002 from 2002 (139), but well below the been low in the past two years as a and 2003, but a late season pulse in MWT 36-year average (556). To result of low river flow during the late April-early May 2003 resulted reduce the impact of Delta pumping splittail spawning period in late in some successful spawning. Upper operations on Delta smelt, CALFED February-May. Nonetheless, in Estuary trawl surveys collected few developed the Environmental Water September 2003, U.S. Fish & or no young of the year in 2002, and Account (2000), which has been Wildlife removed splittail from the those captured by the Fish & used primarily to reduce Delta smelt list of threatened species. The sil- Wildlife Seine Survey were mostly take by reducing pumping. It is too very-gold minnow, found only in upstream of the Delta. In 2003, most soon to determine whether this effort tributaries to the S.F. Estuary and surveys captured low numbers of will provide population-level bene- the Delta, is the only fish species to young of the year. Although splittail fits. (Mayfield, Pers. Comm., 2004) be de-listed for reasons other than was de-listed, it remains a species of concern because of its limited access MORE extinction. Splittail are known to to spawning habitat during low flow INFO [email protected] spawn on inundated terrestrial vege- ? tation, and recruitment appears most years and the potential for future strongly associated with the magni- water management decisions to Longfin Smelt tude and duration of floodplain inun- exacerbate its situation. (Baxter, Longfin smelt in the Estuary repre- dation during spawning period Pers. Comm., 2004) sent the southernmost spawning pop- (Sommer et al. 1997, Moyle et al. MORE ulation in North America, and their (in press)). Floodplain inundation INFO [email protected] abundance continues to be positively ? correlated with Delta outflow during their December-May larval period STRIPED BASS INDEX (Baxter 1999). Since the extremely 1961-2003 wet winter of 1998, Delta outflow for FMWT Index the December-May period has generally declined through 2003, and so 20000 has the abundance of longfin smelt, as measured by Cal Fish & Game’s Fall Midwater Trawl Survey. In 2002, the 15000 abundance index increased slightly from 247 in 2001 to 707, before declining to 191 in 2003. These repre- 10000 sent some of the lowest abundance levels observed for longfin smelt, and probably reflect poor early survival 5000 conditions resulting from recent low outflow years and changes in food web dynamics brought about by the 0 introduced Asian clam, Potamocorbula 61 63 65 67 69 71 73 75 77 79 81 83 85 87 89 91 93 95 97 99 01 03 amurensis (Kimmerer 2002). On a positive note, Cal Fish & Game has TNS Index continued to collect 115 -140 mm 120 spawners (about three years old) in trawl sampling, which suggests that 100 survival has increased from juvenile to adult (age two) and beyond. These 80 age-three females can produce over twice as many eggs as age-two 60 females, and such spawners can help

buffer against poor year-classes. 40 (Baxter, Pers. Comm., 2004)

MORE 20 INFO ? [email protected] 0 61 63 65 67 69 71 7375 77 79 81 83 85 87 89 91 93 95 97 99 01 03

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Striped Bass Commercial Fisheries in the Estuary (Kelly & Klimley Adult striped bass numbers are Since the 1997 El Niño, the 2004, Cal Fish & Game 2001). While increasing, while the abundance esti- spawning biomass of Pacific herring, green sturgeon are long-lived (up to mates of striped bass in their first which supports the Bay’s largest 70 years), delayed reproduction com- year of life (young-of-the-year or commercial fishery, has remained bined with habitat destruction and YOY) remain at very low levels. below the long-term (since 1978) pressure from fishing make it diffi- Using data from an ongoing mark average of 52,234 short tons. In cult for them to replenish their popu- and recapture study, Cal Fish & response to this decline, the Fish and lations quickly. In 2001, a coalition Game reported a population increase Game Commission, which manages of environmental groups petitioned of 70% from 1998 to 2000 (State of the fishery, has lowered catch quotas. NMFS to list the green sturgeon as the Estuary 2002). However, abun- Although ocean productivity has either endangered or threatened. As dance indices of YOY fish as indicat- been favorable for herring over the part of its review, NMFS identified ed by Fish & Game’s Midsummer last several years, a large recruitment two distinct population segments: the Townet Survey (TNS) and Fall of young fish to the spawning popu- northern population (found north of Midwater Trawl Survey (FMWT) are lation has yet to occur, and older age the Eel River along the coast) and the at or near their lowest levels. classes have been declining. southern population (includes any Following record high biomass levels coastal or Central Valley populations In 2003, Fish & Game biologists of 99,050 short tons in 1995-1996 south of the Eel River, with the only investigated potential mechanisms and 89,570 short tons in 1996-1997, known population in the Sacramento that would explain how low numbers spawning biomass plunged to 20,000 River). NMFS declined to list the of YOY fish could result in large short tons following the 1997 El green sturgeon in 2003, but placed numbers of adult fish: 1) Was Niño. Since then, spawning biomass both population segments on its can- increasing water clarity leading to estimates have been 39,500 short didate species list. Green sturgeon decreasing YOY striped bass catch? tons for 1998-1999, 27,400 short tons status will be reassessed within five 2) Were YOY striped bass shifting for 1999-2000, 37,300 short tons for years if warranted (NMFS 2003). toward the lower half of the water 2000-2001, 35,400 short tons for Meanwhile, scientists are studying column where the oblique tow used 2001-2002, and 34,400 short tons for parameters influencing sturgeon by the TNS and FMWT would sam- 2003-2004 (a biomass number has movement within the Estuary, pre- ple them for a shorter period of time? not been finalized for 2002-2003). ferred spawning locations and envi- 3) Were higher proportions of YOY (Watters, Pers. Comm., 2004) ronments, and residence time within striped bass using shallow water (less the river and Estuary system (Kelly then 4 feet) habitat? 4) Were abun- MORE & Klimley, 2004). The results of dance trends depicted by the TNS INFO [email protected] such studies could inform improved and FMWT representative of abun- natural resource management and dance in the upper Estuary? Results Green Sturgeon protection efforts for the species. suggest that some other mechanism, Limited evidence suggests that such as increased survival after the MORE overall, the population of the anadro- first year of life, is responsible for INFO [email protected] mous green sturgeon (Acipenser ? the increasing numbers of adult medirostris) may be declining in striped bass. California. It is known to spawn in Future lines of investigation the Klamath, Trinity and Sacramento include how spatial and temporal dis- rivers, as well as the Rogue River in tributions of larval striped bass relate Oregon. Little is known about its his- to survival, and a reassessment of the toric or current distribution and potential for density-dependent mor- movement throughout the Estuary, tality to affect fall YOY abundance but abundance estimates do not sug- as suggested by Kimmerer, et. al. gest that the population has declined (2000). MORE INFO [email protected]

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Invasive Species this point, the National Green Crab A "boom-and-bust" cycle has been Management Plan includes several reported for some introduced Green Crabs recommendations for local popula- species, although this may not be tion control strategies. These include universally true for all introductions. The European green crab early warning methods for new MORE (Carcinus maenas) is now estab- range expansions, prevention meas- INFO [email protected] lished in every significant bay and ures against new introductions, and ? estuary between Monterey, coordinated monitoring of popula- California, and Gray's Harbor, tion trends, new outbreaks, and loss- Pike Washington. It appeared in South es to commercial fisheries. The voracious Northern pike, S.F. Bay in the early 1990s and has native to Canada and the Midwest, MORE spread north at least as far as the was illegally planted in the 85,000- INFO [email protected] Carquinez Strait. Salinity limits the ? acre-foot Lake Davis reservoir in the crab’s distribution: crabs have been early 1990s. In 1997, Cal Fish & collected from water ranging from Chinese Mitten Crab Game treated the lake with Rotenone 5-31 parts per thousand (ppt) salt to The Chinese mitten crab (Eriocheir to prevent pike from eating lake trout water, but few have been collected sinensis) population has increased and escaping into and corrupting the from water with less than 10 ppt. A rapidly since it was first reported in Delta ecosystem. The treatment tem- 10-year study in Bodega Bay found the S.F. Estuary in the early 1990s. porarily shut the lake to all recre- that in contrast to their slow growth Numbers of downstream migrating ational uses and compromised local rates in Europe, green crabs here adults peaked at the BurRec fish water supplies. In May 1999, about a grew rapidly and reached sexual facility in 1998, while adult numbers year after more than a million trout maturity in their first year. Over the in northern S.F. Bay peaked in 1998 were planted and the lake had course of the study, the green crab and 2001. All data sources support a reopened, the pike reappeared. severely reduced the abundance of population decline in 2002 and 2003. Biologists have pulled approximately three common invertebrate species, When numbers are low, the mitten 38,000 pike from the lake since 1999, but did not impact the shorebird crab’s major impact is stealing bait mainly from shallow areas such as food web (Grosholz et al. 2000). from sport anglers at some locations Mosquito Slough, a weedy channel Another consequence of green crab in the Delta and Suisun and San into the lake. In February 2000, a predation is the accelerated invasion Pablo bays. Lake Davis steering committee, of another invasive species, the east- comprised of Plumas County and What controls mitten crab popula- ern gem clam, which was introduced Cal Fish & Game officials and local tion in the Estuary is not understood, into Bodega Harbor nearly 50 years citizens, released a management plan although winter temperatures and ago and is now much more abundant recommending 13 "control-and- outflow are hypothesized to control than it has been in past decades. contain" measures, including several larval survival and settlement time. While eradication is not possible at types of barrier nets, increased elec- tro-fishing, underwater explosions, MITTEN CRAB STATUS and fishing derbies. By the spring of 2003, those recommended activities 800000 4 were complete, and a three-year sum- USBR mary of those efforts was released CDFG (see http://www.dfg.ca. gov/ north- 600000 3 ernpike/ index.html). Despite the increased numbers of pike in the 400000 2 lake, they have not been found outside of Lake Davis, and the steering CDFG CPUE (thousands) USBR Catch committee is assessing next steps. 200000 1

0 0 96 97 98 99 00 01 02 03

Year

Total catch of adult mitten crabs at BurRec’s fish facility (bars) and catch per tow (CPUE) of adult mitten crabs from Cal Fish & Game’s S.F. Bay Study otter trawl survey (line), 1996-2003.

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SITES SELECTED BY THE INVASIVE SPARTINA PROJECT VITAL STATS FOR TREATMENT OF NON-NATIVE CORDGRASS IN 2004. NUMBERS CORRESPOND TO THE SPARTINA PROJECT’S "TREATMENT SITE NUMBER" FOR THAT LOCATION. future tidal marsh restoration throughout the Estuary. The impacts associated with the spread of Atlantic cordgrass (Spartina alterniflora) include hybridization with and likely local extinction of native Spartina foliosa, regional loss of unvegetated tidal flat habitat, elimination of small tidal channels, and loss of pickleweed habitat essential to the endangered salt marsh harvest mouse. Preliminary results from mapping at a limited number of infested sites in 2003 indicate that coverage increased three- to five-fold in approximately two years. If this holds true for the entire population of non-native cordgrass mapped in 2001 (469 acres), there are now between 1,400 and 2,300 acres of the invader. More detailed analysis of the 2003 monitoring data is currently underway, and full Bay-wide monitoring is planned for 2004. Meanwhile, the Coastal Conservancy and U.S. Fish & Wildlife completed the program- matic EIS/EIR for the S.F. Estuary Invasive Spartina Project. The Coastal Conservancy adopted the EIR, and Fish & Wildlife is preparing Asian Clams od, clam biomass is very low and the ROD. The Spartina Project iden- The Asian clam (Potamocorbula thus the clam’s grazing pressure is tified and prepared site-specific con- amurensis) continues to be the domi- too low to restrict phytoplankton trol plans for 13 priority sites encom- nant benthic organism in the North bloom formation. (Thompson, Pers. passing more than 250 acres of non- Bay. The seasonal decline of the Comm., 2004) native Spartina; more than $250,000 in CALFED-funded grants will allow bivalve continues to occur through- MORE seven local agencies to carry out out the North Bay in winter of most INFO [email protected] years, and is followed by peaks in ? these plans in 2004. With adequate density after reproduction in spring funding, the Spartina Project expects and fall. There have been some short Cordgrass to control the invasive Spartina by duration phytoplankton blooms in the Species of Spartina (cordgrasses), 2010, but a dedicated funding source northern bay for the last several years introduced into the Estuary in the for the effort has not yet been estab- during early spring, when 1970s, have spread rapidly and pose lished. a serious threat to the success of Potamocorbula biomass is at an MORE annual minimum. These blooms have INFO ? www.spartina.org been earlier and shorter in duration RESTORATION PROJECTS (INCLUDING MITIGATION SITES) KNOWN than historic blooms. Potamocorbula TO BE INVADED BY NON-NATIVE was first seen in the South Bay in CORDGRASS. 1988 and had become a dominant bivalve by 1990. Unlike in the North Bay, however, the South Bay phytoplankton bloom has not been depleted by Potamocorbula filter-feeding. This is due to the seasonal cycle of Potamocorbula in that part of the Bay—during the spring bloom peri-

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Wetlands & Wildlife Bay Area Wetlands Restoration Program (WRP), a partnership of 18 Wetlands federal, state, and local public agencies, is working to implement the S.F. Bay Joint Venture partners CCMP’s wetlands action items and completed several major acquisitions the broad recommendations of the around the Bay, including the Cargill Baylands Ecosystem Habitat Goals property (16,000 acres) and the Report. Gobies Bahia wetlands (600 acres). Current Four species of non-native gobies efforts include restoration planning MORE (all of which were probably intro- for the South Bay salt ponds and INFO ? duced via ballast water release) con- restoration projects on Petaluma and For a comprehensive list of wetland tinue to inhabit Estuary waters. Cal restoration projects that have been Triangle marshes, Simmons Slough, implemented around the Bay, see the Fish & Game S.F. Bay Study catch Pacheco Marsh, Hamilton Air Force database and maps compiled by of the shimofuri goby (Tridentiger Base-Bel Marin Keys, Napa- Wetlands and Water Resources bifasciatus) has remained relatively Sonoma Marshes, Cullinan Ranch, (www.swampthing.org). For wetlands stable over the past five years, Napa River Flood Control Project, creation, restoration, mitigation, and whereas catch of the chameleon enhancement projects, see the S.F. American Canyon, Dutch Slough, Estuary Institute’s Wetland Project goby (T. trigonocephalus) has Eden Landing Ecological Reserve, Tracker (www.wrmp.org/projectsin- declined slightly. The yellowfin and West Stege Marsh. In the North tro.html), S.F. Bay Joint Venture goby (Acanthogobius flavimanus) Bay, efforts are underway to acquire (www.sfbayjv.org/), and Central has historically been the most abun- and permanently protect privately Valley Joint Venture (www.cvjv.org). dant and widespread of the intro- For detailed information about owned tidal wetlands and diked bay- CALFED’s extensive activities and duced gobies. Yet in 2002 and 2003, lands. Nearly 300 other projects to accomplishments, see the CALFED Bay Study catch of shokihaze gobies protect and restore wetlands and Bay-Delta Program Annual Report (T. barbatus) exceeded the catch of riparian habitats are also in progress. 2003 (http://calwater.ca.gov/). yellowfin gobies. The impact of the Both the Central Valley and S.F. Bay For information about restoration of shokihaze goby in the Estuary has the Cargill property, see Joint Ventures are updating their www.southbayrestoration.org not yet been determined. Within the implementation plans, and the Estuary, shokihaze gobies are found Central Valley Joint Venture has primarily in Suisun Bay and the identified the Delta as a high priority California lower Sacramento River, where they area for habitat work. While water- Clapper Rail have the potential to harm native fowl habitat will remain a key focus Current Bay- fishes (e.g., sculpin, Delta smelt, and for both joint ventures, updated wide population longfin smelt) and shrimp and other plans will also include specific goals estimates for the invertebrates by competing for for breeding and wintering water- endangered resources and through predation. fowl, shorebirds, grassland and California clapper rail (Rallus lon- Adult shokihaze gobies have been riparian birds, and other wetlands- girostris obsoletus) are not available, found in salinities ranging from 0.44 associated birds, and will address but surveys in the mid-1990s placed to 28.81 parts per thousand. In agricultural practices and protection. their numbers at about 1,200 (up February 2002, the Bay Study Central Valley partnerships have from a low of 300-500 birds in caught two shokihaze gobies south resulted in three recent North 1991). While Central and South Bay of the Dumbarton Bridge. The American Wetland Conservation Act populations continue to hold steady, potential exists for the shokihaze (NAWCA) grants totaling nearly $3 there is some indication that North goby range to expand within the million for wetland conservation Bay populations are in precipitous Estuary and also into other bodies of activities in Suisun Marsh and in the decline, at least at some locales. water within California. Yolo and Delta basins. Meanwhile, Recent field studies suggest that MORE regional interests continued with rails in the more pristine North Bay INFO ? [email protected] wetlands-related planning, partner- marshes are faring less well than ships, and fundraising. CALFED those in areas closer to residential completed a draft regional imple- and urban areas. The estimated 13 mentation plan that includes eight pairs present in Sonoma Creek in restoration priorities and continued 1993 dropped to one to three pairs in to provide significant funding for 1998, and in 2001, no rails were restoration projects and ecosystem found. Along the Napa River, an planning and processes. The S.F. estimated 16 to 23 pairs surveyed in

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the 1990s dropped to four to seven mated approximately 14,500 black rails between one-fourth (minimum) to pairs in 2001 and perhaps to as few in the entire S.F. Bay system, with one-half (maximum) of the state’s as three pairs by 2004. Heavy rains approximately 7,200 black rails in the total fledgling population. in the winter of 1997-1998 may have San Pablo Bay system and a similar Farther north, the number of terns caused some declines in the North number in Suisun Bay and Carquinez at the Southern Power (formerly Bay, as residual high water, particu- Strait, but the true number may be PG&E) cooling ponds in Pittsburgh larly along the North San Pablo higher or lower (Evens & Nur 2002); decreased from 13 pairs in 2001 to 8 Bayshore, impacted nesting success new population studies are currently in 2003. Southern Power is continu- (Albertson & Evens 1998), and there underway. Key predictive factors in ing PG&E’s voluntary monitoring is concern that predation by non- black rail distribution are vegetation program at the site. A colony site was native mammalian predators (prima- height, absence of amphipods (indica- started in 2000 on Caltrans property rily red fox) may be further impact- tors of lower elevation marsh), and, in in Albany. It hosted somewhere ing North Bay populations. The caus- San Pablo Bay, presence of Frankenia between 8-12 pairs in 2000 and 9 es of the dynamism of clapper rail (an indicator of high-elevation marsh pairs in 2001; in 2002 and 2003, populations in S.F. Bay are poorly habitat) (Evens et al. 1986). According there were no nests. The East Bay understood—a regionwide survey to the 2002 study, other variables may Regional Park District recently estab- effort beginning in 2004 will attempt include marsh size (rail abundance lished a least tern breeding site on to clarify many questions. Early tended to increase as the size of the the Hayward Regional Shoreline. results of surveys underway indicate marsh increased), marsh distribution Terns visited this site in 2003, but no that some areas are still depressed (the distributional relationship of each nesting was observed. Least terns (e.g., Sonoma Creek and White marsh to other marshes likely influ- have abandoned the Oakland Airport Slough), while other areas are sup- ences rail presence and abundance), as a breeding site probably due to porting relatively high densities (San marsh configuration (broader marshes predation by feral cats and the non- Pablo Bay shoreline from Gallinas tended to support rails in higher abun- native red fox (last reported breeding Creek north to the lower Petaluma dance than linear marshes), predator attempt in 1995). River). (Evens, Pers. Comm., 2004) populations (sites bound by levees or riprap provide access and habitat to MORE MORE mammalian predators), hydrological INFO (510)521-9624 INFO [email protected] ? ? cycles (tidal marshes with full tidal influence provide the best habitat for Salt Marsh Black Rails rails), and fluctuations in water level Tidal marsh- (inundation above a certain depth may Yellowthroat lands of the S.F. exclude habitat to black rails) (Evens et Surveys of tidal Bay region sup- al. 1989, Flores & Eddleman 1993, marshes in 2000 detected few yel- port most of the Evens et al. 1991). lowthroats (Geothlypis trichas sinu- California black osa), a state Species of Special MORE Concern, in S.F. Bay itself; likely rail (Laterallus INFO [email protected] jamaicensis coturniculus) population in ? only a few hundred are present. In the western United States (Manolis San Pablo Bay, the estimated density 1978, Evens et al. 1991). For the most Least Terns was also low, with an estimated total part, the breeding distribution of black California least terns (Sterna antil- population of 3,000 or fewer breed- rails, state listed as threatened, is con- larum browni), state and federally ing individuals. In many marshes in fined to remnants of historic tidal listed as endangered, continue to nest San Pablo Bay, yellowthroats were marshlands in the Estuary’s northern at Alameda Point, formerly the completely absent. In Suisun Bay, reaches, primarily those associated with Alameda Naval Air Station. While however, densities observed were San Pablo and Suisun bays (Manolis disturbances from low-flying heli- quite high (10-fold higher than in 1979, Evens et al. 1989, Evens et al. copters, mammalian predators, and San Pablo Bay); Point Reyes Bird 1991). Black rails occur in the South raptors have increased, human distur- Observatory scientists estimate Bay as well, but mostly during winter, bance from trespassers has decreased 10,000 to 15,000 breeding individu- and with breeding limited to very few to almost none. Although the number als in Suisun Bay. An additional locations (e.g., Dumbarton Marsh). of tern pairs using the base increases unknown number are present in Small numbers have also been discov- each year, the number of successful brackish and freshwater marshes. ered recently in small wetlands in the fledglings continues to fluctuate. In More recent surveys by PRBO scien- Sierra foothills and at a few isolated 2001, fledgling estimates reached an tists are consistent with 2000 sur- marshes in the Delta. A 1996 study esti- all-time high of 320. In 2002, veys. Salt marsh yellowthroats Alameda’s fledglings represented appear to respond to specific vegeta-

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tion composition and are more abun- song sparrows (Melospiza melodia early 2002, with three male and three dant where there is a greater amount samuelis), found in San Pablo Bay, female rabbits released into an of Scirpus maritimus (alkali and bul- from 65,000-85,000. The presence of enclosed pen during the winter. The rush) and peppergrass (a non-native salt marsh song sparrows is not rabbits successfully bred, and 49 herb). In addition, they are more strongly linked to any one, or even young rabbits were later released into abundant where the vegetation struc- several, species of plants, though the natural riparian habitat at the refuge. ture is more complex; for example, three subspecies of song sparrows do The program was expanded in 2003, where there is more diversity in the appear to respond positively to gum- with two additional enclosures, 194 height of herbs. Finally, salt marsh plant and coyote brush and negative- young rabbits released into the refuge, yellowthroats are more numerous in ly to rush. Nevertheless, the popula- and as many as 70 rabbits still in the marshes that are more compact in tion density of song sparrows is well pens. The rabbits in the pen are not shape, rather than elongated or irreg- correlated with landscape features. released into the wild until they are ular in shape. Density is greatest where land adja- large enough to successfully survive the translocation. All rabbits are MORE cent to the marsh contains less urban- screened by a veterinarian before INFO [email protected] ized areas and less agriculture and a ? being released. or [email protected]; greater extent of natural uplands. www.prbo.org/tm Conversely, density is lowest in MORE small, isolated marshes. All three INFO ? (916)414-6600 Salt Marsh song sparrow subspecies are state or (559)487-5139 Species of Special Concern. Song Sparrows Reproductive suc- MORE Harbor Seals cess of salt marsh INFO ? [email protected] S.F. Bay harbor song sparrows has or [email protected]; seal (Phoca been increasing slowly since 1998, www.prbo.org/tm vitulina) numbers which was the poorest year recorded have remained fairly stable over the to date; in particular, reproductive Riparian Brush Rabbit past decade. Although approximately success levels in 2003 were, overall, Populations of the federally listed 12 haul-out sites are known in the higher than in any year since 1996. (endangered) riparian brush rabbit Bay, harbor seals are found in the Despite the relative increase in repro- (Sylvilagus bachmani riparius) are greatest numbers throughout the year ductive success, the overall success largely restricted to riparian habitat at three sites: Mowry Slough, Yerba observed at most marshes (usually along the Stanislaus River in Caswell Buena Island, and Castro Rocks. between 15% and 20% of nesting Memorial State Park, the San Joaquin Mowry Slough, the largest pupping attempts result in any fledged young River National Wildlife Refuge, and site in the Bay, is used heavily during at all) is below the level necessary to two small parcels of private land the pupping (mid-March-May) and ensure a stable population. along the San Joaquin River. The rab- molting (June-mid-August) seasons. Reproductive success varies among bits were thought to be restricted to Since 2000, approximately 300 harbor seals and 100 pups have been counted marshes, with landscape characteris- the habitat in Caswell until surveys at Mowry Slough each pupping sea- tics (such as proximity to the water’s discovered the two additional popula- son. In the winter (mid-November- edge) being good predictors of nest tions (one of which was recently mid-March) months, when Pacific survival. The greatest cause of nest found to be more extensive than first herring (Clupea pallasi) spawn in the failure is predation. Current efforts thought), and a cooperative state/fed- Bay, seals are typically most plentiful are being directed toward identifying eral effort began a breed-and-release at Yerba Buena Island, with 200-300 predators (potentially mammals, program into the refuge. The numbers harbor seals using this site (1998- snakes, and crows and jays). In addi- in Caswell were extremely low in 2002). Castro Rocks, a chain of rock tion, about 10% of nests fail each 2001, but rebounded slightly in 2002 clusters just south of the Richmond year due to flooding during the high- and 2003. The population remains too Bridge and the second-largest pup- est tides. Estimated numbers of small to allow population size estima- ping site in the Bay, is used by breeding Alameda song sparrows tion tools to function properly, so the approximately 150-250 seals year- (Melospiza melodia pusillula), exact size of the Caswell population is round (2000-2003). Seismic retrofit restricted to Central and South S.F. not known. Efforts are underway in work began on the Richmond Bridge bays, range from 12,000-18,000 indi- the park to improve the habitat for viduals; of Suisun song sparrows in early 2001, and researchers from rabbits, as well as for federally listed S.F. State University are monitoring (Melospiza melodia maxillaris), (endangered) riparian wood rats found in Suisun Bay, from 36,000- what effect, if any, the construction is (Neotoma fuscipes riparia). The cap- 53,000; and of San Pablo or Samuel’s having on seal numbers and behavior. tive breeding program was begun in

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To date, researchers have documented cides, and predation all threaten the approximately 113 plovers utilized a shift in site use to rocks located far- frog, the largest native to the western Bay salt ponds during the breeding ther from the bridge when construction United States. In spring 2004, the U.S. season, an increase from 2003. As of is underway in the immediate area; Fish & Wildlife Service renewed a late June 2004, approximately 50 overall seal numbers have not proposal to declare 4.1 million acres nests had been found and followed declined. (Green, Pers. Comm., 2004). across California, including parts of through to completion to determine the Bay Area, as critical habitat for the hatching success. In addition, avian MORE frog. More than two-thirds of the pro- predator surveys were conducted to INFO [email protected] ? posed habitat is privately owned. A determine what predators may be pos- draft economic analysis is expected in ing the highest risk to plover success. Salt Marsh early 2005. The highest concentration of plovers was found in Eden Landing Nature Harvest Mouse MORE Reserve. (Albertson, Pers. Comm., It is not known INFO ? (510)663-0616 whether the popula- 2004; Strong Pers. Comm., 2004) tion of the Bay’s endangered salt marsh harvest mouse Western MORE INFO (510)792-0222 (Reithrodontomys raviventris) has Snowy Plover ? changed significantly over the past In the Bay Area, or (408)946-6548 three years. Population studies are the federally conducted only when development threatened Pacific Coast western Western projects or changes in land use snowy plover (Charadrius alexandri- Burrowing Owl threaten the mice, and few such stud- nus nivosus) is primarily associated Western burrowing ies have been required during this with commercial salt evaporation owls (Athene cunicu- time. When such studies are conduct- ponds and levees, which means that laria hypugaea) were ed, their piecemeal nature makes it land managers have not to date been once common throughout the West, difficult for scientists to get a take on able to actively manage habitat or but they have declined precipitously in overall population trends. Several resources for this species. However, California in the last several marsh restoration projects that could the recent purchase of more than decades—breeding owls have been impact mice populations are under- 15,000 acres of salt ponds in south eliminated from at least 8%-10% of way in the North Bay, and the South S.F. Bay by Fish & Wildlife and Cal their former range in the state and are S.F. Bay Marsh Restoration Project Fish & Game could aid in plover trending toward extinction in another has begun in the South Bay, but it recovery. Future pond management 25%. Currently, estimates are that will take years to decades for new will include managing several of these more than 70% of California's breed- marshes to be produced and hence ponds as plover nesting and foraging ing owls live in the margins of agricul- increase mouse populations. habitat, as well as conducting predator tural land in the Imperial Valley. (Shellhammer, Pers. Comm., 2004) control and minimizing human distur- Locally, burrowing owls declined 50% bance. These actions are outlined in MORE from the 1980s to the 1990s. The owl Fish & Wildlife’s draft recovery plan INFO [email protected] has been extirpated from San ? for the plover, which calls for increas- Francisco and Marin counties and ing the S.F. Bay breeding population from most of San Mateo and Sonoma Red-Legged Frogs from its current level of 150-200 indi- counties. It can still be found in scat- The once-abundant California red- viduals to 500. While the Bay did not tered spots in the East Bay, including legged frog (Rana aurora draytonii) historically support 500 snowy the Berkeley Marina, and in Santa federally listed as threatened, has dis- plovers, managing salt evaporation Clara County, where a census five appeared from approximately 70% of ponds for plovers is an opportunity for years ago estimated 120-141 pairs. its historical range. It is now found it to play a significant role in the Burrowing owls nest in the burrows of only in coastal wetland areas and recovery of this species, especially ground squirrels and other mammals. freshwater streams from Marin County because many of the plover’s historic They require open fields with adequate south to Ventura and in scattered coastal breeding and wintering sites food supply for foraging, low vegeta- streams in the Sierra Nevada. Across have been degraded by human distur- tive cover (to watch for predators), and the frog’s range there are only four bance and urban development. adequate roosting sites. Burrowing populations with Breeding season surveys conducted in owls are threatened primarily by habi- more than 350 adults. 2004 by the S.F. Bay Bird tat loss due to urban development and Habitat loss, stream Observatory and the Don Edwards by the corresponding eradication of sedimentation, pesti- National Wildlife Refuge indicate that ground squirrels and other burrowing

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rodents. Other factors contributing to abatement activities, trampling by generally be below levels of concern. the decline of owls statewide include over-grazing or human activity in sen- Concentrations of chemicals currently burrow destruction through disking and sitive marshes, and naturally occurring in use, such as pyrethroid insecticides grading, pesticide impacts, increased events also threaten the plant. and polybrominated diphenyl ethers predation by non-native or feral (PBDEs) may be increasing. Also of Researchers planted soft bird’s-beak species, habitat fragmentation, and concern are copper, dioxins and poly- seeds in test plots at Rush Ranch in other human-caused mortality from cyclic aromatic hydrocarbons (PAHs). 2000. They found that the plant does vehicle strikes, electrified fences, colli- Work outside the RMP suggests that best in patchy habitat, with gaps to pro- sions with wind turbines, shooting, and selenium is also a concern. The S.F. vide sunlight for seedlings, and that vandalism of nests. The state-approved Regional Board established a water clipping back the vegetative canopy practice of relocating owls from devel- quality attainment strategy (site-spe- gives the parasites a crucial boost, opment sites is accelerating local extir- cific objectives and prevention-based although exotic plants take advantage pations from rapidly urbanizing areas. of the gaps. High seedling mortality at action plans) for copper and nickel in Owls typically nest in the same burrow the reintroduced and natural population South S.F. Bay (south of the year after year and often try to return to sites was linked to host association Dumbarton Bridge) in May 2002; the their former homes. One study found with non-native plants. The Rush strategy is currently being implement- that only one relocation in eight result- Ranch population is expanding by nated. The Board will establish a mercu- ed in successful nesting at the new site. ural dispersal, and many seedlings have ry TMDL (total maximum daily load) The owl was listed as a state Species of established outside the experimental for S.F. Bay in 2004 and expects to Special Concern in 1994. In December plots. New studies are underway at establish TMDLs for PCBs and for 2003, Cal Fish & Game denied a peti- Rush Ranch and other sites to further pesticides in urban creeks that drain tion that would have granted the owl understand management factors influ- to S.F. Bay in 2005. The Board is cur- endangered status. encing critical life stages of this endan- rently working with the Clean Estuary MORE gered plant, and to test the plant’s Partnership (the Bay Area municipal INFO ? (408)252-3748 response to invasive species control wastewater and urban runoff agen- options. cies) to establish TMDLs, water quality attainment strategies, or other Soft Bird’s-Beak MORE appropriate response plans for legacy Soft bird’s-beak (Cordylanthus mol- INFO ? [email protected] pesticides and selenium in S.F. Bay, lis ssp. mollis), state and federally list- and copper and nickel in S.F. Bay ed as endangered, sur- Water & Sediments north of the Dumbarton Bridge. vives in only 19 wide- MORE ly scattered sites in the Bay Contaminants INFO www.sfei.org; coastal salt and brack- ? www.swrcb.ca.gov/rwqcb2/ ish tidal marshes In the Bay, most contaminant around San Pablo and guidelines are being met, but the level Suisun bays and in of contamination today is probably Delta & Upstream Contra Costa, Napa, high enough to impair the health of Contaminants the ecosystem (indications of impair- and Solano counties, with individual The freshwater side of the Estuary ment include the toxicity of water and populations fluctuating from year to does not have a systematic monitoring sediment samples to lab organisms year. program to evaluate contaminant lev- and the frequent presence of contami- els in water, sediment, or biota. The hemiparasitic bird’s-beak is nant concentrations exceeding water, However, contaminants documented photosynthetic and can fix its own car- sediment, and fish guidelines). A rela- to exceed either water quality objec- bon for growth requirements. It also tively small number of problem con- tives or concentrations toxic to aquat- attaches to a variety of hosts, including taminants makes it rare to find clean ic organisms in the Delta have been pickleweed, saltgrass, and exotic forbs water or sediment in the Bay. Of all given the highest priority by the and grasses. In turn, it supports native the contaminants measured by the Central Valley Regional Water bee pollinators and moth species Estuary's Regional Monitoring Quality Control Board for develop- whose larvae eat its seeds. Ninety per- Program (RMP), results suggest that ment of regional load reduction and cent of its historic habitat has been lost those of greatest concern are mercury control programs (TMDLs) under the with conversion of tidal marsh to farm- and polychlorinated biphenyls Clean Water Act. land. Water pollution, muted tidal (PCBs). While mercury concentra- hydrology, host association with exotic tions remain unchanged, PCB concen- In 2004-2005, the Board is expected winter annual plants, competition with trations appear to be gradually declin- to consider amendments to its Basin invasive plants, habitat fragmentation, ing. Concentrations of DDT, chlor- Plan to address water quality problems excessive seed predation associated dane, and other legacy pesticides have in the Delta associated with elevated with reduced tidal hydrology, mosquito declined more rapidly and may soon levels of diazinon, chlorpyrifos, and

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mercury, along with an amendment to begin control of low dissolved oxygen in the Stockton Deepwater Ship Channel. THE EXPLOSION OF tamination; we’ve knocked the top The Basin Plan amendments for each will NEW SCIENCE ABOUT off, and it will be expensive to do include an implementation plan with a THE BAY: IMPLICATIONS more. We need to understand that just schedule and monitoring to assess compli- FOR MANAGEMENT as the Bay is constantly changing, ance. Each plan will likely contain a our policies are constantly SAMUEL N. LUOMA reopener clause, probably after 5-10 changing as well: the CALFED BAY-DELTA PROGRAM AND EPA’s standard for copper years, to ensure that monitoring results U.S. GEOLOGICAL SURVEY and new scientific findings are incorporat- in the South Bay, for example. The point is that ed into the revised implementation plans. In managing the Bay-Delta in the the experiment continues. future, we will have to choose In the Sacramento basin, the Board We’re now trying to incor- between difficult economic, social, passed a Basin Plan amendment to con- porate a little more flexi- and environmental issues. We are liv- trol diazinon and chlorpyrifos in the bility into regulation, but it ing in an era of choices. Many of these lower Feather and Sacramento rivers. In is very important that we choices have a technical basis, and sci- 2004, the Board will consider whether follow the experiment ence has never been more important. requirements for diazinon and chlorpyri- through and don’t go back to the con- Scientists need to better link to and fos control in Sacramento urban creeks ditions of the 1970s. adopted into the city’s MS4 permit sev- communicate with the public. We need eral years ago can be accepted in lieu of a much closer link between the scien- Probably the ultimate in choices is an actual Basin Plan amendment. The tific community and the community of the CALFED Bay-Delta Program. It’s Board is expected to consider amend- people making policy. a very complicated, ambitious program, but the multi-stakeholder ments for mercury control in Sulfur As we began to understand the approach is the only way to move Creek, Harley Gulch, and Cache Creek gravity of the changes we have forward, and the scientific communi- in 2005. brought to the Bay environment as ty has a major role to play. We’re we made our lives comfortable and In the San Joaquin basin, the Board talking about improving the situation prosperous, some powerful laws were will consider amendments for chlorpyri- for threatened species, improving passed that gave us tools to begin to fos, diazinon, boron, and salt in 2004- water supply reliability, improving change the direction of a downward 2005. Ongoing monitoring shows that water quality, and maintaining a levee environmental trend. Since the 1970s, concentrations of diazinon and chlorpyri- system so that we can maintain water the growth of our understanding of fos continue to fall throughout both the supply for 22 million Californians, all the Bay has exploded. Sacramento and San Joaquin watersheds, while improving the environment. most likely because of decreased agricultural use. Lower ambient pesticide concentrations make passage of the "We need a much closer link between organophosphorus insecticides basin plan amendments less controversial. In con- the scientific community and the trast, controlling salt in the San Joaquin community of people making policy. basin remains highly contentious. Ensuring that all the recently adopted It is our job as scientists now to engage in control actions are implemented is a concern, due to resource constraints. the process. We need to be at the policy The recently approved agricultural table more than we have in the past." waiver may help, but lawsuits by both agricultural and environmental interests are still pending. Nonetheless, agricultural coalition groups have submitted We learned about the stressors; we There are lots of goals, and lots of monitoring plans and watershed evalua- learned that the whole Bay-Delta sys- contradictions. There is also a lot of tion reports. Monitoring is scheduled to tem is linked. Even the South Bay is money involved: The people of begin in summer 2004, and results will linked to the rivers in the North Bay, California have shown—by passing help track the concentration of contami- which are linked to the coastal sys- four different bond measures—that nants of concern. tem. We’ve realized that if we’re they are very interested in finding going to understand this system, we solutions to these problems. MORE have to understand it all. INFO www.swrcb.ca.gov/rwqcb5/ We’re talking about implementing ? There is a lot left to do. We’ve ecosystem restoration projects, about taken the easy steps in terms of con- improving urban water quality by

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ence should be commensurate with “It is so important that the public the stakes. Proposition 50 requires every large project to have a compo- understands that we are living in an era nent that learns about its performance. We are not ready to move sci- of choices, not in an era of black or white, ence to policy until we understand how a process works, and we cannot an all or nothing situation.” predict the rate of discovery. But there is always time for science. reducing agricultural drainage, about drinking water. How do we resolve Those of us in the scientific commu- making some major changes (these this conundrum? Most of our salmon nity can be naïve about policy. It is are proposals from the 2000 Record management policies assume that we our job as scientists now to engage of Decision). We’re talking about want to keep salmon out of the in the process. We need to be at the improving conveyance through the Delta, but others have taught us that policy table more than we have in Delta more effectively, moving more the Delta is a nursery for salmon. the past. Sacramento River water through the We built hatcheries for fish to make MORE giant pumps to the Central Valley up for habitat loss above Shasta INFO [email protected] and Southern California, about eval- Dam so we could continue to have a uating the potential for storing water fall run, but we now know that in the Delta, and improving flood hatchery fish can threaten wild protection. These are proposals, not salmon. Even from an ecosystem decisions. As we start to learn about restoration point of view: Do we the Delta—and we’ve learned a lot restore whole ecosystem processes since 1997—sometimes alternatives or do we focus on individual species to the obvious engineering solutions like winter run salmon or Delta appear. That is our role in the scien- smelt? Do we focus on protecting tific community; that is what grow- endangered species? CALFED has ing knowledge is all about. It is not chosen to walk down the middle, to just about pointing out problems try to do both. (which we have to do), but it is also We are entering an era of choices, about recognizing that with prob- of re-engineering and re-naturaliza- lems come opportunities to learn and tion in an effort to improve the func- to propose creative solutions. We’re tioning of disturbed ecosystems learning that we need to work with while at same time providing stable Mother Nature instead of building and sustainable resource extraction. engineering projects that are less We cannot pretend that the stability flexible. of our lives and the economic pros- In the CALFED Bay-Delta pro- perity of our society aren’t linked to gram, we’re interested in rehabilitat- resources like water. How do we do ing, re-engineering, re-naturalizing, both? One of the important compo- or restoring our ecosystems—this is nents is understanding and respect- a challenge, but this is also the thing ing Mother Nature and working with we hope will balance some of the her as best we can. We have to other choices we have to make. We understand which tradeoffs are most will also need to choose where we effective, which we want to make, do restoration: some places respond and which we don’t want to make. quickly; some don’t respond at all. This is why it is so important that Are we investing in the right places? the public understands that we are Or does it just take some places a living in an era of choices, not in an long time? There are conundrums: era of black or white, an all or noth- Peter Moyle has taught us that ing situation. native fish benefit from variable This has begun to manifest itself salinity in the Delta. But variability in CALFED where the policy is that is just what we don’t want in our investments in environmental sci-

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INDICATORS OF framework and eight indexes com- fresh water that have been diverted ESTUARINE HEALTH posed of 39 indicators to provide a from the Bay since the 1940s: In regional view of the Bay’s condi- 2002, fully half of all the water that tion. The indicators lists from the would have flowed into the Bay nat- ANITRA PAWLEY two projects are converging, testa- urally was used for irrigated agricul- THE BAY INSTITUTE ment to the progress made in devel- ture in the Central Valley or export- oping indicators after numerous such ed to southern and coastal California BRUCE THOMPSON efforts were attempted. We are cur- cities. In 11 of the past 20 years, the SAN FRANCISCO ESTUARY rently aligning these projects to Bay received the same amount of INSTITUTE strengthen the way we evaluate the water it would typically see in a crit- Bay, to provide a stronger funding ically dry year, meaning that the Bay Like the Chesapeake Bay, the base, and to unify the ways in which is experiencing a chronic drought. Great Lakes, and the Everglades, the we describe the Estuary’s health. Many Bay fish depend on healthy San Francisco Bay-Delta watershed Discrete examples from the inflows of freshwater during the comprises one of the nation’s great Scorecard show how these indicators spring—the near collapse of several natural treasures. But unlike these can be developed from existing data species (e.g, longfin smelt), docu- systems, the San Francisco Bay has sources and aggregated into multi- mented by the Bay Fish Index, coin- no agreed-upon, defined suite of metric indexes. The Scorecard used cided with record diversions of indicators to guide and measure the a tiered approach for presenting freshwater from the Bay during the effectiveness of the policy reforms complex information to the public, 1987-1992 drought. Despite several and habitat restoration projects being managers, decision-makers, and sci- wet years since then, and new proposed to improve its health. entists. Each index is supported by inflow protections and restoration Two projects seek to remedy this an overview of the index and score, efforts tracked by the Stewardship situation: the San Francisco Estuary a discussion of each of the compo- Index, fish populations have not Project’s effort to identify Indicators nent indicators, and supporting tech- substantially recovered, a testament of Estuary Condition, and The Bay nical documentation. The unique but to both the challenges of the task Institute’s Ecological Scorecard, a simple scoring system captured the ahead as well as the as yet limited prototype suite of indicators for the attention of the media, policy-mak- implementation of habitat and flow Bay region. These efforts illustrate ers, and the public. Upon its release restoration programs. There is bound the iterative nature of and the chal- in October 2003, a wide array of to be a delay in ecosystem response lenges and complexity involved in newspaper and radio stations carried to these improvements; however, developing compelling and easily the story, many in front page and newly established protections are understood indicators for the prime time spots. already being eroded as new pres- Estuary. Both efforts build on previ- So how is the Bay doing? In gen- sures are placed on the Bay's water ous indicator identification efforts eral, the Scorecard indexes provide a resources. (i.e., Levy et al. 1996; Young et. al. picture of regional ecosystem health Many of the indicators in the Bay 1998; Pawley et. al. 2000; Gunther that has declined dramatically over Index consistently told us that the and Jacobson 2002), and existing the long-term data record; however, upstream portion of the Bay was in Bay region monitoring programs recent trends are stable for most the most trouble. This is a critically (i.e., Interagency Monitoring indexes and in limited cases, some- important part of the Bay's estuary Program, USGS, Regional what improving. For habitat and ecosystem, home to many species Monitoring Program). shellfish populations, there have that are found nowhere else but San The San Francisco Estuary been small but noticeable improve- Francisco Bay. It is also the part of Institute identified a draft set of ments. Although progress is slow, the Bay most affected by reduced assessment questions and indicators we have been acquiring a significant freshwater inflows and, along with in collaboration with the Center for amount of habitat for wetland the South Bay, the most impacted by Ecosystem Management and The preservation and restoration; recent pollution from agricultural, industri- Bay Institute after holding work- numbers are up for the Dungeness al, and urban runoff. Of all areas of shops with a wide range of local sci- crab (the well-known symbol of San the Bay, Suisun Bay is the most entists. The Bay Institute’s Francisco’s Fishermen’s Wharf); and heavily infested with alien species, Scorecard evolved over a three-year several new protections designed to both plant and animal. The invasion improve water quality have been period with input from a panel of by the alien clam Potamocorbula is adopted. nationally recognized experts and centered in Suisun Bay and it is many local scientists. The Bay The Freshwater Inflow Index directly related to the collapse of the Institute developed a conceptual chronicles the increasing amounts of pelagic food web there.

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Also chronicled by the Scorecard SCORECARD: THE STATE OF THE ESTUARY are the improvements in water quali- ACCORDING TO THE BAY INSTITUTE ty that were initiated 30 years ago as a result of the federal Clean Water Act. The open waters of the Bay are substantially cleaner that they were in the 1960s and 1970s. However, water quality standards designed to protect the health of aquatic organisms as well as people are regularly exceeded for several potent toxics, including mercury and PCBs, both of which still enter the Bay in non- point source runoff. Largely because of these two contaminants, most fish caught in the Bay are not safe to eat. More disturbing, improvements in water quality appear to have stalled—neither the Water Quality Index nor the Fishable indicator show any improvement during the past nine years, underscoring the need to make better progress with pollution reduction programs tracked in the Stewardship Index. The Scorecard Index is now being used in outreach around the Bay. A desired outcome is that the public gain a greater depth of understanding about the complexity of the Estuary and its condition, a height- ened awareness of the impacts of individual actions on the Estuary, and a broader understanding of the opportunities and threats that face the ecosystem. The public is clamor- ing for a concise and easy way to understand the Bay’s health. Without this tool and others like it, we are not reaching the people who can help change the way we collectively impact the ecosystem and garner the support that is so urgently needed for programs that improve San Francisco Bay’s health. MORE INFO [email protected] or www.bay.org

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VITAL STATS

REFLECTIONS OF A WRITER AND PHOTOGRAPHER

JOHN HART AND DAVID SANGER

The water is expanding. After years of controversy about encroach- ments on the Bay and Delta, we have to ponder the effects of an estuary that is growing in volume and potentially in area. The nineteenth century "Sierra mudwave" is gone. Diked-off lands are subsiding and threatened with flooding. Sea level is rising. Maintaining the land area of the Delta Photo: David Sanger is a challenge. In many places, the going to be a major source of nutri- deliberate restoration of marginal ents to open water, or not? Can the Public understanding of the wetlands only makes a virtue of estuary be healthy on its reduced Estuary is growing—but slowly. necessity. freshwater budget? What are the People and even governments have a Restoration is a big, big deal. effects of the explosive rise of way to go in seeing the system as a We are struck by the boldness, the Potamocorbula? As one scientist told single, regionally central. Increased promise, and the difficulty of the us, "The system changes faster than contact, as through shoreline parks rehabilitation ("restoration") efforts you can publish." and ferry service, can help forge con- now proposed. The most dramatic Transportation is the source of nections. Explicit educational efforts measure, tidal wetland restoration, is many pressures. If container vessels remain vital: courses, exhibits, youth well defined but challenging. It will are approaching maximum practical programs, publications like our book, require lots of money, lots of knowl- size, channel dredging and port treatments in other media, and of edge, lots of mud to rebuild subsided expansion may recedeg as issues. But course gatherings like the State of the lands, and lots of follow-through ships remain polluters and vectors for Estuary conference. attention once begun. Other than exotic species. Plans for a bigger, wetland enhancement, further steps faster ferry system raise hopes but John Hart and David Sanger spent three in restoration seem rather inchoate. also questions about impact. Most years researching, writing, and photograph- regional airports, not just San ing the book San Francisco Bay: Portrait of There’s a huge amount yet to be an Estuary, University of California Press; learned. Despite years of excellent Francisco International, are sited on www.sanfranciscobaybook.org. research, fundamental questions the estuary’s margins and face pres- remain open. Are expanded wetlands sure to expand.

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STATE OF THE ESTUARY

MEETING OUR GOALS have embraced the report’s recom- CELEBRATING FOR THE BAY mendations and begun to use them THE CCMP as guidance as they seek to improve habitats. Although the Goals Report includes recommendations ranging MICHAEL W. MONROE from conceptual to quite specific, it WILL TRAVIS U.S. ENVIRONMENTAL SAN FRANCISCO BAY provides only the general template PROTECTION AGENCY CONSERVATION AND DEVELOPMENT upon which additional, much more COMMISSION The San Francisco Bay Area detailed planning is required for even the smallest of habitat projects. Wetlands Ecosystem Goals Project At this sixth biennial State of the report, Baylands Ecosystem Habitat Last year, as a follow-up to the Estuary Conference, we celebrate the Goals, the culmination of three Goals Project, the resource and regu- tenth anniversary of the CCMP—the years’ effort by nearly 100 scientists latory agencies established the San Comprehensive Conservation and and resource managers, is one of the Francisco Bay Area Wetlands Management Plan—created by the most widely-used government docu- Restoration Program. The purpose of San Francisco Estuary Project in ments ever read. It recommends the that program is to encourage effec- 1992. kinds, amounts, and distribution of tive implementation of the Goals The folks who put the CCMP wetlands and related habitats needed report recommendations and to together renewed the idea of devel- to sustain diverse and healthy com- improve interagency coordination oping public policy by talking with munities of fish and wildlife involving habitat restoration. The the people who would be impacted resources in the San Francisco Bay Wetlands Restoration Program by the policies and basing the poli- Area. These habitat goals were includes top-level agency managers, cies on the best science available at developed in response to the San senior staff, and technical experts the time. This approach found trac- Francisco Estuary Project’s who work to address both policy and tion in the 1990s and led to lots of Comprehensive Conservation and technical issues. One of the most other efforts: the San Francisco Management Plan and represent sev- exciting sub-groups within the pro- Estuary Institute’s Regional eral years of work by scientists and gram is the design review group, Monitoring Program, the Bay-Delta resource managers. consisting of scientists and engineers, Accord, the San Francisco Bay Joint many of whom were involved in the The Goals Project’s geographic Venture, CALFED, and the Baylands Goals Project, whose role is to pro- scope included the portion of the Ecosystems Habitat Goals publica- vide technical review and assistance San Francisco Bay Estuary down- tions—all based on the principles and to folks considering habitat projects stream of the Sacramento-San approach embodied in the CCMP. Joaquin Delta. Project participants or who are well into habitat projects. focused their attention on the bay- That group sets up review panels, Many of the recommendations and lands—the lands within the histori- and project sponsors come in and policies in the CCMP are being cal and modern boundaries of the make presentations. The final prod- achieved, not because the promised tides—and immediately adjacent uct is a letter that sets forth concerns federal funding has finally come areas. and suggestions for improving the through, but because the people projects, and most people have found involved in formulating and carrying The Goals report calls for restor- it very helpful. out the CCMP keep finding ways to ing more than 60,000 acres of diked advance the Estuary Project goals Bay Area habitat restoration start- baylands to tidal salt marsh. It also using whatever resources are avail- ed several decades ago with a few stresses the need for other large- able. Perhaps ironically, this has small projects. Today, projects rang- scale habitat improvements: manag- given the CCMP more durability than ing from a few acres to thousands of ing large areas of shallow saline lots of federal funding would have. ponds for shorebirds and waterfowl acres are being planned or imple- and restoring and enhancing transi- mented. Their success will depend As we look ahead to the next ten tional habitats, riparian forests, and largely on how well we apply the years, we can expect the San seasonal wetlands. In total, the information in the Goals Report as Francisco Estuary Project to continue report calls for improving habitats well as the science presented at this to provide us with a forum in which on more than 100,000 acres in and conference. we can address important Bay-Delta issues, ranging from non-point source around the Bay. MORE pollution and watershed management INFO [email protected] Several thousand copies of the ? to invasive species and massive wet- Goals report have been distributed, land restoration projects. and many public and private entities

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POLLUTANTS

pollutants

"The 1972 federal Clean Water Act called for ‘best available treatment’ for removing pollutants, and that approach has been largely successful. However, some pollutants are not removed by conventional treatment. There are three ways of dealing with this problem. One is to provide better-than-secondary treatment, typically nitrification and sand filtration. Data indicate that this approach reduces mercury in sewage treatment plant effluents by about 70 percent. A second approach is to seek legal or regulatory action to discontinue use of the offending pollutant. This has been effective for DDT, PCBs, mercury (for most of its former uses), and lead as a fuel additive. A third approach is water reclamation, in which water and the pollutants it contains are applied to plants and soils, where further pollution breakdown can occur without damage to natural waters." LARRY KOLB S.F. Bay Regional Water Quality Control Board

In 2002, SFEI identified five different phthalate compounds—polymers used to make plastics more flexible—in the Bay. "We still don’t have a clear consensus on how much of a risk they pose." MIKE CONNER SFEI

Photo: Norah Rudin

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STATE OF THE ESTUARY

THE LONG-TERM FATE OF Other chemicals PERSISTENT CHEMICALS can be compared and CHOICES AND CONSEQUENCES IN SAN FRANCISCO BAY contrasted with PCBs. Dioxin con- PCBs • No action: Recovery in >100 years tamination is the next • Load reductions of 10 kg could have JAY DAVIS, ET AL. most severe, with significantbenefit over the long-term SAN FRANCISCO concentrations in ESTUARY INSTITUTE white croaker that are DDT • No action or localized action may be five times higher a viable alternative Some simple models developed by than the threshold for concern. Dioxins are • Load reductions would yield relatively the San Francisco Estuary Institute quick reduction in concentrations (SFEI) over the past few years as part quite similar to of the Regional Monitoring Program PCBs, with residual PAHs • No action: Maintain present concentrations for Trace Substances in the San loading from the Francisco Estuary (RMP) can tell us watershed probably • Load reductions would yield relatively a lot about the long term fate of per- comprising a large quick reduction in concentrations sistent organic chemicals such as fraction of inputs, PCBs, PAHs, and legacy pesticides limited degradation, PBDEs • No action: Potentially create a long-term (DDT, chlordane, and dieldrin) in the and limited pathways problem Estuary. The models are useful in for loss from the Bay. • Early detection and load reductions will PAH and legacy pes- illustrating how choices made today minimize a potential long term problem will determine how clean the Bay ticide concentrations will be in decades to come. They are right at thresholds describe simple mass budgets for for concern, so a lesser degree of improvement is need- Davis in August 2003 will help pre- each chemical in the Estuary, based vent the potential long term problem on estimates of masses entering the ed to address these contaminants. PAH concentrations are remaining of PBDE accumulation in the Bay Bay, cycling and degradation within food web. the Bay, and outputs from the Bay. constant in the Bay in spite of large The framework has also been used to continued loadings, primarily due to MORE provide preliminary assessments of their relatively high degradation rates. INFO ? [email protected] dioxins and the flame retardant poly- A reduction in PAH loads would brominated diphenyl ethers (PBDEs). quickly translate into reduced concentrations Of these chemicals, the degree of in the Bay. Legacy • Why are persistent organic contamination is most severe for pesticide concentra- SCIENCE pollutants (POPs) still contami- PCBs, with median concentrations in tions have been falling QUESTIONS nating Estuary fish decades after the key indicator (white croaker more rapidly than bans were implemented? muscle tissue) 10 times higher than PCB concentrations in the threshold for concern. In spite of the past few decades, Mass budget models suggest several key factors are restrictions on PCB use in place probably due to higher responsible: since 1979, concentrations have degradation rates. • Ongoing inputs of POPs: PCBs and legacy pesti- declined slowly in the past 20 years. Legacy pesticide con- cides enter the Estuary, as contaminated sedi- Important features of the PCB budg- centrations may gener- ments throughout the Estuary watershed contin- et that are thought to be responsible ally fall below thresh- ue to erode. The primary sources of PAHs are for the slow decline are the resist- olds for concern, even continuing emissions from cars and trucks. ance of PCBs to degradation, limited if no action is taken. • The long residence time of sediments in the pathways for loss from the Bay, and PBDE concentrations Estuary ecosystem: POPs generally become residual loading from erosion and have risen rapidly in tightly bound to sediment particles in the remobilization of contaminated soils recent years. The Estuary. While the waters of the Estuary pass and sediments in the watershed. The thresholds for concern through to the ocean in a matter of months, model predicts that even if all loads and degradation rates sediments become trapped in the ecosystem for could be eliminated, a 90% reduction for these chemicals decades. would take about 70 years to have not been estab- • Degradation rates of some POPs are slow (e.g., achieve, and that continued loading lished. The partial ban DDTs) or very slow (e.g., PCBs): These charac- of 10 to 20 kg per year would signif- of PBDEs passed by teristics of the Estuary and POPs highlight the icantly delay recovery. former Governor need to prevent the entry of persistent pollutants into the ecosystem.

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POLLUTANTS

TRACKING PESTICIDE Experiments were timed to coincide MONITORING WORKS EFFECTS ON NATIVE FISH with the first rainstorm event after dor- USING BIOMARKERS mant-season application of organophosphate (OP) pesticides to A. RUSSELL FLEGAL orchards. DNA strand breaks (Comet UNIVERSITY OF CALIFORNIA SANTA CRUZ SUSAN ANDERSON, ET AL. Assay), acetylcholinesterase (AChE) DAVIS BODEGA MARINE LABORATORY activities and pesticide concentrations In contrast to many estuaries in were measured. Data from these exper- the United States, the San Francisco Agricultural pesticides contaminate iments indicated that concentrations of Bay-Delta Estuary has been moni- waters of the Sacramento and San dormant season pesticides during 2000 tored for trace metal contaminants Joaquin watersheds at concentrations and 2001 were much lower than in pre- since 1989. Now performed under toxic to test invertebrates, yet effects vious years and did not induce AchE the Regional Monitoring program, on resident native fish species have not enzyme inhibition in exposed fish in those systematic measurements have been examined in much detail. We per- the field or lab. However, DNA strand yielded insights on the temporal, as formed experiments in the field and lab breaks were significantly elevated in well as spatial, variations of trace to test whether pesticide exposures are fish exposed to San Joaquin River metal concentrations throughout the correlated with genetic biomarker water (38.8%, 28.4%, and 53.6% DNA Bay. Initial results showed pro- responses in the Sacramento sucker strand breakage in 2000 field, 2000 nounced seasonal variability in some (Catostomus occidentalis). lab, and 2001 field exposures, respec- metal concentrations in the South tively) compared Bay, associated with temporal gradi- to a nearby ref- ents in the system’s hydraulic DNA STRAND BREAKS IN erence site SAN JOAQUIN RIVER SUCKERS regime: metal concentrations (15.4%, 8.7%, increased as flushing rates and 12.6% in decreased. Subsequent surveys cor- 80 300 2000 field, 2000 roborated that seasonal variability SJ Strand Breaks lab, and 2001 70 OU Strand Breaks but also highlighted the importance 250 field exposures, ChE Inhibitors Conc. of episodic events on the biogeo- 60 respectively). chemical cycles of metals in the 200 DNA strand Estuary. For example, floods that 50 break induction release water from the Yolo Bypass 40 150 was not correlat- markedly alter chromium’s concen- ed with OP pes- tration and speciation in the Bay. 30 ticide concentra- 100 While that seasonal and episodic % DNA in Comet Tail tions. In 2001, 20 variability has complicated assess- Cages In Cages In the Ames muta- 50 ments of longer term variations in 10 Total OP Pesticide Concentration (ng/L) Total genicity assay metal concentrations in the Estuary, was applied to 0 0 recent studies using stable lead iso- 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 1 2 3 4 5 6 field-collected January February topic composition analyses and time water and indi- series models have provided the first cated that San measure of decadal changes in metal Joaquin River contamination in the Estuary. This water was significantly more muta- level of resolution, which is unique genic than the reference site. Further to San Francisco Bay, is only possi- TAKE HOME studies should investigate the cause of ble because of the continuance of the genotoxicity observed. (Anderson, Regional Monitoring Program over NOTES SOE, 2002) the past decade. MORE • Since DNA strand breaks did not MORE INFO ? [email protected] appear to be correlated with OP INFO [email protected] pesticide concentrations, we recommend that other genotoxic pesticides be analyzed for, including captan, ziram, carbaryl, malathion, methyl bromide, and trifluralin.

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TAKE HOME SMALL TRIBUTARY shown that changes in land use and STORMWATER management have increased non-point CONTAMINATION OF sediment supply to streams. Large- NOTES scale hydromodification has caused SAN FRANCISCO BAY many streams to incise, increasing • Our research suggests that the sediment transport and reducing access sediment budget for the Estuary to natural floodplains. We know that is changing. Our best estimates LESTER MCKEE SAN FRANCISCO ESTUARY INSTITUTE annually averaged exports of suspend- suggest that about 60% of the ed sediments from Bay Area streams suspended sediment entering the Small tributaries that flow into San vary spatially by two orders of magni- Estuary annually comes from the Francisco Bay may be having more of tude, and suspended sediment loads Sacramento/San Joaquin River sys- an impact on water quality than previ- from a single watershed can vary tem and the other 40% from the ously thought. Recent studies by SFEI inter-annually by up to four orders of small tributaries draining the nine and its partners suggest that sediment magnitude. Available data also suggest Bay Area Counties (Marin, loads entering the Estuary from the that during about one year in every Sonoma, Napa, Solano, Contra Central Valley are decreasing over seven, sediment loads from local tribu- Costa, Alameda, Santa Clara, San time and currently reflect magnitudes taries are greater than those from the Mateo, San Francisco). This has estimated for the pre-mining period Central Valley. It appears that the aver- the following management impli- (circa 1850). Studies also suggest that age load of suspended sediment from cations: approximately 40% of total sediment local tributaries may form an increas- • Since sediment is the main vector loads to the Estuary (~2 Mt) comes ingly important contribution to the for transport of Hg, PCBs and from local urbanized and agricultural sediment budget of the Estuary. OC pesticides, a downward trend watersheds that comprise less than 5% SFEI, in conjunction with the in sediment load from the of the total watershed area and provide Regional Monitoring Program and the Sacramento/ San Joaquin River only 4% of the annual average runoff Clean Estuary Partnership, is conduct- system suggests that the contri- that enters the Estuary. bution of Hg, PCBs and OC pesticide loads derived from the Stormwater runoff has been identi- Central Valley may also be fied as a significant source of pollution • Is there a trend in the sediment decreasing over time. to San Francisco Bay, and new loads entering the Estuary from TMDLs are likely to call for substan- the small tributaries • A downward trend in sediment tial, quantifiable reductions in these SCIENCE within the nine Bay load from the Sacramento/ San loads. Contaminants of current TMDL QUESTIONS Area counties? Joaquin River system suggests that focus, such as mercury (Hg), polychlo- there may be less sediment avail- rinated biphenyls (PCBs), and • Are the PCB data collected in the able for future wetlands restora- organochlorine (OC) pesticides, are Guadalupe River watershed tion projects. transported into the Estuary primarily indicative of other urban water- • This shift in our understanding of via suspended particles. An improved sheds in the Bay Area? the proportion of Hg, PCBs and understanding of sediment processes OC pesticide loads derived from in the Estuary and its tributaries pro- • Are concentrations of Hg in each pathway suggests that con- vides an important framework for stormwater in the urbanized tinued improvements in stormwa- understanding contaminant processes. drainages of the Bay Area typical ter quality in urban areas sur- of other urban areas in the U.S. or Research carried out by SFEI on rounding the Estuary can help does mercury in rocks and soils of historical and contemporary sediment improve water quality in the the Coast Ranges naturally elevate transport processes supports the Estuary. mercury concentrations and load- hypothesis that sediment loads from ings? small tributaries may have increased over time. For example, many of the • Is the trend of decreasing sedi- small tributaries that once discharged ment loads from the Central to slough systems or ended as distribu- Valley responsible for the taries in seasonal wetlands now have observed erosion in some areas of flood conveyance channels near the San Francisco Bay? Estuary margin that efficiently trans- mit suspended sediments to the • What influence does the Yolo Estuary. Geomorphic studies have Bypass have on annual mercury loadings from the Central Valley into the Estuary? 30 SOE layout 1 8/12/04 8:30 PM Page 31

POLLUTANTS

ing studies on sediment and contami- Six obvious questions to ask are nant loading at the confluence of the THE BIG • What are the contaminants of con- Sacramento and San Joaquin Rivers MUDDY cern? (Hg, PCBs, OC pesticides and polyaro- matic hydrocarbons (PAHs)) and on the MIKE CONNER • What problems are they causing? lower Guadalupe River (Hg, other trace EXECUTIVE DIRECTOR • How can we control them? SAN FRANCISCO ESTUARY INSTITUTE metals, PCBs, and OC pesticides). • Are our control methods working? Preliminary results suggest that previ- San Francisco Bay is "the Big Muddy;" ous Hg load estimates from the Central • Are we focusing on the right it’s a very muddy estuary; the muds Valley were over-estimated by a factor issues, and what else could we be are resuspended with every tide. of 2 to 3 and loads of Hg from the doing? They absorb most of the contami- Guadalupe River were underestimated • If you make the Bay safe for peo- nants we’re worried about; they take by a factor of 2. It now appears that the ple, are you going to make it safe them down into the sediments and loads of Hg from local tributaries are at for everything else? prevent them from being washed out least equal, if not greater, in magnitude of the Bay. That’s the long-term than those coming from the Central problem we’re dealing with. The Bigger policy questions that need to Valley. Preliminary results on PCBs question is, instead of dealing with be debated and discussed include suggest that local tributaries may sup- these things contaminant by contami- ply a significant portion of the external • How much energy do we want to nant, should we start thinking about inputs to the Estuary, perhaps about spend on legacy pollutants versus a sediment strategy for the Bay? That equal to the Central Valley loads. emerging contaminants like the also figures into restoration issues— brominated flame retardants— MORE do we have enough sediment for where will we get the most bang INFO ? [email protected] restoration? for our buck?

STORMWATER LOADS: LARGE RIVERS VS. SMALL TRIBS Area Water Sediment Mercury PCBs

2000

Rivers Rivers (11 kg) Small Tribs no estimate Tributaries

160 tkm 2 26 Mm 3 3.54 Mt 840 kg

2003

160 tkm 2 26 Mm 3 1.7 Mt 630 kg 30-40 kg

This chart compares source and magnitude of water, suspended sediment, mercury, and PCBs entering the Bay from the Central Valley (Sacramento and San Joaquin Rivers) and small local tributaries (entering the Bay from the nine Bay Area counties). Over the past three years, San Francisco Estuary Institute and its partners have carried out a number of desktop evaluations, literature reviews, and empirical field studies. The results of these efforts have changed our understanding of the sediment budget of the Bay, the average loads of contaminants entering the Bay annually, the variation of sediment and contaminant loads entering the Bay between years, and the relative proportion of sediment and contaminants entering the Bay from a variety of pathways. Management measures designed to improve water quality of the Bay will need to be adaptive as new empirical data continues to improve our understanding of Bay processes.

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TAKE HOME STORMWATER cant remaining single sources of pol- CONTAMINATION: lutant loading to waters. As a result, NOTES SIMPLE THINGS in 1987, Congress expanded the NPDES permit program to include THAT WORK • New development and significant urban stormwater runoff. In the Bay redevelopment projects must now Area, each large municipality is cov- clearly incorporate a combination of : ered by an NPDES stormwater per- KEITH H. LICHTEN - Source controls to prevent the dis- mit that requires the municipality to SAN FRANCISCO BAY REGIONAL charge of pollutants; WATER QUALITY CONTROL BOARD act to reduce pollutants to the maximum extent practicable. - Design measures to reduce the amount of directly connected imper- Revised stormwater permits Examples of actions include sten- vious surface; and, requiring municipalities and devel- ciling storm drain inlets with "No - Treatment controls to remove pollu- opers to clean up pollutants in urban Dumping – Drains to Bay" mes- tants from runoff prior to discharge runoff from new development and sages, sweeping streets on a regular to receiving waters. significant redevelopment projects basis, and inspecting industrial and have caused concern and confusion. commercial facilities. Federal law What exactly is required, and how also recognizes that new develop- can those requirements be incorpo- ment and significant re-development found from the Bay Area to the rated into project designs? Is it pos- projects are significant sources of Pacific Northwest, Washington D.C., sible to build controls that really pollutants. Over the last two years, and Europe. Frederick Law work into projects, and can they be existing municipal NPDES storm Olmsted’s 1879 Back Bay Fens in maintained? In fact, a wide variety water permit performance standards Boston provide an excellent example of practices and controls can be for new and re-development projects of how elegant engineering and incorporated into projects at a rea- in the Bay Area and the state have landscape architecture can be used sonable cost. Such measures can been significantly revised. to achieve multiple goals, including improving water quality. reduce urban runoff pollution while Examples of simple measures that increasing property values, reducing can help meet NPDES requirements MORE downstream erosion and costs to include trash enclosures, water qual- INFO [email protected] taxpayers for flood control mainte- ity ponds, vegetated swales, biore- www.scvurppp.org nance, and creating attractive public tention areas, skinny streets, and www.cabmphandbooks.org spaces. more. Geographical examples can be Congress created the National Pollutant URBAN RUNOFF SOLUTIONS Discharge Elimination System (NPDES) Program in 1970 as part of the federal Clean Water Act, to reach the goal of making the nation’s waters fishable, swimmable, and drink- able. In the 1970s, NPDES did substantially reduce pollution from "big pipe" dischargers, such as wastewater treatment plants, refineries, and large manufacturing plants. However, the nation’s waters remained significantly impaired by non-point source pollutants, including those in urban stormwater runoff, one of the most signifi-

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POLLUTANTS

TAKE HOME TMDLS: WATER challenge is to develop implementa- QUALITY SOLUTIONS tion plans that result in tangible NOTES FOR THE BAY water quality benefits. Adaptive implementation plans can address • Urban runoff pollutant loads are a signifi- concerns regarding limitations in our cant concern. Additional work is needed DYAN C. WHYTE knowledge of pollutant fate, trans- to determine how to effectively and efficiently remove (or prevent pollutants S.F. BAY REGIONAL WATER port, and effects, while promoting from entering) urban stormwater runoff. QUALITY CONTROL BOARD immediate actions to remedy the problem. Adaptive management is • While we need to reduce mercury loads The S.F. Bay Regional Water founded on the premise that imple- to the Bay, studies are urgently needed Quality Control Board (Board) is menting actions and observing the to determine how we can minimize methyl mercury production in both committed to using a collaborative Bay’s response will provide the dual newly constructed and existing wetlands. approach to develop scientifically optimum benefit of defining source sound and effective Total Maximum control effectiveness and improving • If control measures are put in place now, Daily Loads (TMDLs) to restore and our understanding of the Bay. it will still take the Bay over 100 years to protect the beneficial uses of San recover from past discharges of PCBs Francisco Bay. San Francisco Bay is In order to be truly adaptive, and mercury. listed as impaired by mercury, PCBs, TMDL implementation plans should • Prevention is still the best approach and pesticide toxicity, legacy pesticides include pollutant load reduction we need to take this lesson to heart (i.e., DDT), selenium, actions commensurate with our when it comes to managing pollutants dioxins/furans, and exotic species. understanding of the problem; a such as PBDEs. TMDLs for these pollutants will monitoring program to assess the identify sources, define how much of effectiveness of control actions and a pollutant the Bay can assimilate, progress towards achieving TMDL The Board will soon consider adopt- allocate responsibility for reducing targets; a list of outstanding manage- ing a mercury TMDL for San pollutant loads, and include reason- ment questions and a framework for Francisco Bay, which we hope will able and feasible implementation addressing such questions; and a exemplify how one of San Francisco plans. clearly defined process for reviewing Bay’s most challenging water quality and modifying the TMDL. problems was jointly solved using Through cooperative efforts such adaptive management. as the Clean Estuary Partnership, the Successful TMDL implementation San Francisco Bay Regional will require continuous dialogue and MORE Monitoring Program, and local trust, both in the process and INFO ? [email protected] stakeholder groups, our collective amongst stakeholders and regulators.

DEFINING THE DESIRED CONDITION OF A WATERBODY BY REFINING WATER QUALITY STANDARDS

Numeric TMDL targets more directly reflect the condition of the beneficial use.

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STATE OF THE ESTUARY

species and locations within both the TAKE HOME METHYLMERCURY IN Delta and the Bay. Slough channel ESTUARINE BIRDS order appears to influence methyl mercury concentrations, with greater NOTES methylation taking place in pri- • Mercury does occur at potentially STEVEN SCHWARZBACH, ET AL. mary—or smaller, more dendritic— embryotoxic concentrations in some WESTERN ECOLOGICAL RESEARCH channels. Mercury concentrations CENTER, USGS BRD among all eggs assessed varied by species of aquatic birds within the SACRAMENTO FISH AND WILDLIFE two orders of magnitude, from less Bay/Delta ecosystem, but concentra- OFFICE, USFWS than 0.02 to 3.33 ppm on a fresh wet tions were highly variable (0.02 to 3.33 weight basis. The lowest concentra- ppm on a fresh wet weight basis) and Because mercury is efficiently tions were found in the eggs of dependent upon species foraging pat- transformed to methylmercury in wet- California and western gulls in the terns and geographic location of nests. land sediments, and methylmercury Bay. Three species had location • In the Delta, great blue herons nest- strongly bioaccumulates in aquatic means above the currently accepted ing along the Sacramento River had foodwebs, we speculated that wide- Lowest Observed Adverse Effect higher mercury concentrations than spread mercury contamination of the Concentration (LOAEC) of 0.8 ppm great blue herons nesting along the Bay/Delta from historic mining in the in avian eggs. These were Caspian San Joaquin River, and mercury con- Coast Range, and the use of a signifi- terns, which had location means centrations in eggs of herons were cant fraction of this mined mercury in ranging from 0.7 to 1.2 ppm, correlated with mercury concentra- extracting gold from stream sedi- Forster’s terns, which had location tions in silversides, a common prey ments and placer deposits in the means between 0.5 and 1.63 ppm, fish found throughout the Delta. Sierra Nevada, could be posing a and California clapper rails, which health threat to piscivorous wildlife. • The highest mercury concentrations had a mean of 0.82. The highest tern in bird eggs were found in birds nest- To assess our hypothesis, we con- egg mercury came from South Bay ing in the Bay rather than the Delta. ducted a systematic survey of mer- locations. Two other species, the Birds foraging in the margins of the cury exposure in aquatic birds in snowy plover and black-necked stilt, Bay generally had greater mercury both San Francisco Bay and the had a location mean concentration bioaccumulation risk than did birds Sacramento/San Joaquin Delta, as just below 0.5, but some had eggs foraging at similar trophic levels in the part of the CalFed mercury project between 0.5 and 0.8. Central Bay. Terns, for example, have in 2000 and 2001. Avian mercury A companion study by Dr. Gary greater egg mercury concentrations exposure was documented by sam- Heinz of USGS’s Patuxent Wildlife than double-crested cormorants. pling 321 eggs from 15 species and Research Center using egg injection analyzing total and methylmercury techniques seemed to indicate the cor- concentrations in their contents. We both the South and North Bay. The morant is less sensitive than the mal- found that nearly all the mercury in sensitivity of clapper rail embryos to lard, the species upon which the wild bird eggs was methylmercury. methylmercury, their elevated expo- LOAEC is based, so the threshold sures to methylmercury resulting from Significant differences in mercury exceedance in this species at Suisun their tidal wetland foraging patterns bioaccumulation were found in Bay in 2000 was probably not indica- along the edges of primary sloughs, tive of a mercury problem for and their endangered population status • Is bioaccumulation of mercury having cormorant hatchability. The may make them the avian species reproductive effects Heinz work also indicated most vulnerable to methylmercury SCIENCE on other species, that clapper rails were likely contamination in the Bay Delta system. QUESTIONS such as terns? much more sensitive than the mallard, and that therefore, MORE even concentrations below INFO ? • Does methylmercury affect migratory stevenschwarzbach@ usgs.gov birds? the 0.8 mallard number could • What is the effect of elevated mercury still be toxicologically signif- INTERTIDAL MARSH STRUCTURE levels in the livers of diving ducks? icant. We concluded that PRIMARY SLOUGHS ARE SMALLEST • Do other non-fish-eating species mercury concentrations have mercury-induced problems? found in clapper rail eggs • What dietary pathways lead to the great- that failed to hatch from est risk of bioaccumulating Wildcat Marsh were likely mercury? embyrotoxic. Hatchability of • Will wetland restoration increase or clapper rail eggs has been decrease mercury levels? Do the demonstrated to be below benefits of restoration outweigh normal in previous studies in the problems? Tidal Source 34 SOE layout 1 8/12/04 8:31 PM Page 35

EMERGING POLLUTANTS

emerging pollutants

“Concentrations of polybrominated diphenol ethers (PBDEs) in fish, marine mammals, and people from the San Francisco Bay region are among the highest in the world. Five years ago, I had never heard of this class of compounds nor had most of the folks at my agency. In five years, they have gone from being completely off the radar screen of most U.S. environmental scientists until the point that in 2003 the State of California signed legislation to ban them."

TOM MCDONALD OFFICE OF ENVIRONMENTAL HEALTH HAZARD ASSESSMENT CALIFORNIA ENVIRONMENTAL PROTECTION AGENCY

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STATE OF THE ESTUARY

TAKE HOME THE RISK POSED BY tissues. Although not well under- FLAME RETARDANTS stood, the primary sources of expo- NOTES sure appear to stem from ingestion of foods, especially fish and breastmilk, • PBDEs are persistent and bioaccumu- THOMAS A. MCDONALD and possibly from inhalation of dust lative toxicants, whose levels are CALIFORNIA ENVIRONMENTAL containing PBDEs in homes and increasing in humans and biota in PROTECTION AGENCY offices. North America. California and the European • Children's health is our greatest con- Concentrations of polybrominated Union have banned two of the three cern, since early exposure to PBDEs diphenol ethers (PBDEs) in fish, commercial mixtures of the PBDEs, results in altered development of the marine mammals, and people from and firms in Japan have voluntarily brain and reproductive organs in the San Francisco Bay region are stopped using PBDEs. animals. among the highest in the world, and these levels appear to be increasing Based on multiple studies in ani- • The current margin of safety is low: each year. Approximately 75 million mals, the greatest health problems tissue concentrations in some U.S. pounds of PBDEs are used each year associated with human environmen- residents are approaching tissue levels in the U.S., added as flame retardants tal exposure to PBDEs are disrup- in animals associated with develop- to plastics in computers, televisions, tion of thyroid hormones and harm mental effects. appliances, building materials, and to the developing brain. PBDE lev- • PBDEs and PCBs, of which we are all vehicle parts, and to foams used in els in people are approaching the co-exposed, may work together to furniture. PBDEs migrate out of levels in animals that have been alter development of the brain and these products and into the environ- shown to cause adverse effects on reproductive organs. ment, where they bioaccumulate. learning, memory, and behavior. PBDEs are now ubiqui- New research suggests that PBDEs tous in the environment and PCBs (which are also present in • Now that the bioaccumulative forms of PBDEs and have been meas- people) may work together to alter have been banned, how long will it take for ured in indoor and out- learning and behavior following tissue levels in the U.S. to start to decline? door air, house dust, exposure early in life. That is, how long of a lag time is there food, streams and lakes, MORE between the use of a persistent, bioaccumula- terrestrial and aquatic INFO [email protected] tive chemical and when it biota, and human body ? SCIENCE QUESTIONS reaches the top of the food chain? PBDE LEVELS ARE RISING IN U.S. PEOPLE • Risk estimates from PCB exposures are usually 100 based on the cancer endpoint, since it is thought to be the most sensitive toxic end- 80 Each point represents ~10 people point. Some regulatory programs currently 60 regulate PCB exposure based only on the PCB

congeners that behave like dioxin, using their ng/g 40 Each point represents "dioxin-like equivalents" to predict risk. ~200 people However, many ortho-substituted (non-diox- 20 in-like) PCBs, which are present by far in the greatest concentrations in fish and people, are 0 neurotoxic to the developing organism. PBDEs 1982 1987 1992 1997 2002 also harm the growing brain, and recent data Collection indicate that some PCBs and PBDEs work PBDE levels have been rising in the North American environment as evident by many additively to alter brain development in mice. time-trend studies in fish, birds, and other wildlife. Recently, researchers have also confirmed that PBDE levels in people in the U.S. have increased over time. Sjodin and col- Some recent estimates of the risk of neurode- leagues from the U.S. Centers for Disease Control (Sjodin et al., 2003, Organohalogen velopmental effects from PCBs are very close Compounds 61:1-4) took archived serum samples from various regions in the U.S. cov- to the risk estimates derived for cancer ering the years 1985 to 2002. For time points before 1992, pooled blood from 9 sep- effects. With the high (and increasing) levels arate groups of U.S. residents, each representing about 200 individuals per each group, was analyzed. Additionally, serum collected from 5 groups of U.S. residents in of PBDEs in people, will developmental health 2002, each representing about 10 individuals per group, were analyzed. Seven of the effects (from co-exposures to PCBs and most commonly found PBDE congeners in people and wildlife, as well as a polybromi- PBDEs) become the most sensitive endpoint nated biphenyl congener and a polychlorinated biphenyl congener, were assayed using for regulatory control of these pollutants? gas chromatography, high-resolution mass spectrometry. This figure shows that total PBDE levels in North Americans have increased substantially over the past 20 years.

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EMERGING POLLUTANTS

HUMAN CANARIES* PBDE PROFILES IN SF BAY RESIDENTS may impact fetal development and reproductive suc- KIM HOOPER 70 % cess in wildlife popula- 60 Bird Eggs tions. The health and envi- CALIFORNIA ENVIRONMENTAL Seal PROTECTION AGENCY 50 Human ronmental advantages of 40 Fish breast milk are several: to 30 promote breastfeeding; to During the past 25 years, tens of 20 monitor "body burdens"; to thousands of new chemicals (seven 10 Distribution of PBDEs identify fetal contaminants; per day) have been introduced into 0 to describe family, commu- commerce after being evaluated by 47 100 99 154 153 PBDE Profile nity, and wildlife expo- the U.S. EPA. But few (200-300) of sures; to highlight new the 85,000 chemicals presently in chemicals of concern; to commerce are regulated, despite the POP contaminants in the fetus like permit community-initiated studies; fact that many of them may adverse- PBDEs, can be most easily moni- and, in tandem with environmental ly affect human health and ecosys- tored by measuring levels in samples measurements, to provide informa- tems such as San Francisco Bay. of the mother’s breast milk collected tion on chemical levels in wildlife The persistent organic pollutants shortly after birth. The concentra- and human populations so that local (POPs) are a group of fat-loving, tions of POPs in breast milk, mater- communities can take appropriate stable, polyhalogenated industrial nal blood, or cord blood are the actions to reduce their exposures. chemicals (e.g., organochlorine pes- same when expressed on a fat- MORE ticides, PCBs, polychlorinated weight basis (e.g., pg POP/g fat) INFO [email protected] –dioxins and -furans, and poly- because POP levels equilibrate in ? brominated diphenyl ethers the fat of these three compartments. (PBDEs)) that contaminate the estu- Thus, breast milk provides us with a * The views and opinions expressed by the aries, sediments, and wildlife of San convenient window into the fetus, author are not necessarily those of the Francisco Bay. A number of these through which we can measure Department or of Cal/EPA. POPs are neurotoxic to developing chemical levels and identify new organisms, interfering with the nor- chemicals of concern. mal development of the nervous sys- The comparative ease and conven- tem in test animals, wildlife, and ience of collecting breast milk is an humans. Unfortunately, the placenta advantage. Because breast milk can is transparent to these chemicals, so be collected unprotected fetuses receive the same by mothers PBDES IN CALIFORNIA SEAL BLUBBER exposures to POPs as their mothers. and commu- Consequently, neurotoxic fetal con- nities, these 9000 taminants, such as the POPs, pose groups can significant environmental health design their 8000 hazards to wildlife and humans. studies and A relatively new group of POP have easy 7000 chemicals of concern are the access to the 6000 PBDEs, a family of persistent lab measurements. brominated flame retardants whose 5000 levels have been increasing expo- We are nentially over the past 20 years in 4000

using breast PBDE (ng/g liqid) humans and biota throughout the milk samples world. Levels of PBDEs in humans to measure 3000 and wildlife from the San Francisco adult and Bay area are among the highest in fetal "body 2000 the world. The PBDEs, like their burdens" of 1000 structural "cousins," the PCBs, are chemicals in neurodevelopmental toxicants, and human popu- easily pass through the placenta to 0 lations, and 01/01/89 01/01/91 12/31/92 12/31/94 12/30/96 12/30/98 contaminate the fetus. to flag chemicals that N=11

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STATE OF THE ESTUARY

PAHs: A THREAT other contaminants of concern, do of cardiac conduction occurs first, TO ESTUARINE FISH not show demonstrable decreases in with other common developmental the past few decades, and in many defects (such as craniofacial malfor- cases levels of these compounds are mation, neural tube alterations, bent increasing in freshwater, estuarine, spine, and kidney malformation) TRACY K. COLLIER and marine ecosystems. being secondary to cardiac effects. NORTHWEST FISHERIES SCIENCE Our results also show that PAH- Recently, technologies have been CENTER, NOAA FISHERIES exposed fish can exhibit subtle developed which allow aquatic toxi- changes in cardiac morphology, cologists to conduct sensitive devel- which may be associated with Research from our laboratories opmental toxicology studies in fish reduced fitness. Because estuaries indicates that juvenile and adult fish species, and we have been using provide important habitat for early exposed to PAHs—polycyclic aro- these methods to address the issue of life history stages of many fish matic hydrocarbons—show developmental toxicity of PAHs. species, these findings strongly sug- increased cancer risk, reduced repro- Our findings (in studies largely con- gest that strategies for reducing ductive output, and immune system ducted by Drs. John Incardona and inputs of PAHs to estuaries are suppression. Nat Scholz) suggest that PAHs have needed. PAHs are environmental contami- distinct and specific toxicities in nants that can be derived from a early life history stages of fish. MORE wide range of human activities, most Studies with 3-ring PAHs (phenan- INFO ? [email protected] notably the use of fossil fuels. threne and dibenzothiophene) indi- Levels of PAHs, in contrast to many cate that PAH-induced impairment

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restoring the estuary watershed

"We need to act sooner rather than later." PHIL WILLIAMS PHILIP WILLIAMS & ASSOCIATES, LTD. "Don’t mess with stuff too much." DENISE REED UNIVERSITY OF NEW ORLEANS

Wildcat Creek, Richmond, CA Photo: Norah Rudin 39 SOE layout 1 8/12/04 8:31 PM Page 40

STATE OF THE ESTUARY

FROM THE HILLS ects in the design stage will restore and Hamilton. In fluvial systems TO THE BAY: THE STATE sites of thousands of acres, with the the time for geomorphic evolution OF RESTORATION largest projects (in the planning and development of a mature ripari- stages) on the order of tens of thou- an canopy will be even longer than sands of acres. While fluvial for tidal wetlands. JEFFREY HALTINER restoration projects have increased • Planning: Project goals were initially PHILIP WILLIAMS in scope, their spatial scale and AND ASSOCIATES, LTD. established on a local basis, guided complexity are not as extensive as by a limited group of project stake- Restoration of aquatic habitats that of tidal systems. holders. The Goals Project provided (tidal and fluvial) in the San • Temporal: Monitoring programs a regional context for wetland Francisco Bay region is now in its and success criteria were initially restoration within the zone of Bay fourth decade. During that time, based on site characteristics in the influence. A similar level of plan- restoration has evolved from the con- initial three to five years. We now ning has not been developed for flu- struction of a few small, localized recognize that sites will continue to vial systems. However, some region- projects with minimal budgets to a evolve for decades and longer. Part al planning is occurring as a result of major element of many larger land of the shift to a longer planning watershed scale initiatives (particu- use planning processes, with involve- horizon is that people are being larly for water quality) and also in ment from numerous agencies, con- more realistic in their predictions of response to endangered species sulting firms, nonprofit organizations, site evolution. The types of sites issues (especially steelhead). Fluvial and other stakeholders. Changes have being restored now are more chal- restoration would benefit from a occurred on the following scales: lenging (the easy ones have already regional goals project to characterize been restored), and the more chal- historic changes and guide types and • Spatial: Early tidal wetland work lenging sites may take longer to extent of restoration at the county focused on single locations, while mature. They include larger or more and landscape scale. more recent projects have expanded deeply subsided sites such as Napa to hundreds of acres. Current proj-

NAPA SALT MARSH RESTORATION PREDICTED HABITAT EVOLUTION

Upland/ Transition 9000 Managed ponds 8000 Middle marsh 7000 Lower marsh

6000 Intertidalmudflat

5000

Acres Subtidal

4000 Other: nonevolving 3000

2000

1000

0 0 5 10 15 20 25 30 35 40 45 50 Years

Predicting restored marsh habitats over a multi-decade time scale, as illustrated here for the Napa River Salt Marsh restoration, helps project proponents set realistic expections about the length of time required for habitats to evolve, identify interim habitat benefits/losses, and make decisions about when to implement successive phases of multi-phase projects.

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WATERSHED

TAKE HOME • Regulatory: The regulatory role upper watershed zones have been of various government agencies degraded by 200 years of grazing; has played a significant role in often, they include eroding streams NOTES shaping some projects, especially that are supplying excessive sedi- • Opportunities to identify, expand, and those based on mitigation ment to downstream systems. recreate forgotten and neglected habi- requirements. Initially, the key Meanwhile, the mudflats fronting tats—upper watershed zones, intertidal role was the U.S. Army Corps of the shoreline play a key role in the mudflats, beaches and salt flats, and Engineers’ authority over wet- regional sediment budget, in dissi- adjacent uplands—should be pursued. lands under Section 404/Section pating energy along the shore, and 10 of the Clean Water Act. More providing valuable habitat. recently, application of endan- Acknowledgement of their role and • The S. F. Bay Habitat Goals project (and gered species laws has played a function—and restoration of these other similar documents) provided a regional perspective and guidance for major role. The broader authority areas—has lagged behind that of restoring tidal systems. We need a com- of the S.F. Bay RWQCB is cur- the more visible tidal marshes. parable regional streams/watershed rently a major influence as well, Other habitats that historically goals project. Such a project should incorporating water quality con- occurred more commonly around include a comprehensive review of his- siderations through the TMDL the Bay have been reduced or elim- toric conditions and functions provided process. inated as well, including beaches by streams and watersheds in the nine and salt flats along the east shore, Bay counties, a characterization of Despite our progress in restoring and high groundwater/saturated existing conditions, and a vision for the tidal marshes and urban streams, soils in uplands around the Bay. future. While the project would not two components of the "hilltop to specify detailed goals for very individual channel system, it would identify the Bay" ecosystems have been neg- MORE types of habitats needed most and lected: the upper watershed zones, INFO ? where they could be recreated, and mostly remaining as agricultural [email protected] would provide examples of successful lands, and, at the bottom of the sys- and [email protected] restoration projects to date. It could tem, intertidal mudflats. Many also identify specific watersheds most likely to provide suitable opportunities for restoring habitat for special status species (e.g., steelhead).

• Larger scale watershed and stream restoration projects should be pursued concurrent with tidal wetland restoration projects.

• The timeframe for wetland restoration sites to evolve to maturity is longer than we previously anticipated—more on the scale of 50 years, not five, particularly for the types of sites currently being considered for restoration. We need to better estimate the timeframes for the evolution of restored sites.

SCIENCE Restoration "success" must address issues QUESTION of site evolution, resiliency, and adaptability to future, uncertain ecological conditions. How does the time needed to characterize project success vary between ecosystems?

Alkali Heath

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STATE OF THE ESTUARY

RIPARIAN RESTORATION AROUND THE BAY

A.L.RILEY S.F. BAY REGIONAL WATER QUALITY CONTROL BOARD

Stream restoration projects around the Bay range from those that replace environmentally damaging flood control projects with more natural approaches, to rural landowner watershed management projects on rangelands and vineyards, to fisheries restoration in both rural and urban settings, including dam removal projects, to urban stream restoration as part of redevelopment, soil bioengineering/bank stabilization projects, and stream reshaping and revegetation. Programs range Riparian or stream restoration in ity is being given greater attention. from watershed partnerships to the Bay Area began with small, incre- Toxic sediments contributed by Bay watershed assessments to stream and mental rural fencing and gully repair streams and their watersheds are watershed-based hands-on education projects and small urban stream now recognized to be responsible for projects and programs. demonstration projects, but has some of the pollutants of greatest There are approximately 40 water- evolved to large projects that restore concern, including PCBs, mercury, shed partnerships in the Bay Area. significant stream systems of up to a pesticides, selenium, and dioxins. They include large-scale efforts such mile or more in length. An important The fact that the status of riparian the South Bay Watershed change is that credibility is now systems is now a topic at the State Management Initiative, the newly given to the concept that functional of the Estuary conference is indica- formed San Francisquito Watershed ecological restoration is possible tive of this new focus on streams Joint Powers Authority, and the even in difficult, degraded urban or and their fisheries and water quality Alameda Creek watershed planning rural environments, as proven by recovery. many demonstration projects. effort that focuses on ensuring water The first generation of water treat- supply, reducing flood damages, and The impact of the streams enter- ment plants were brick and mortar restoring the ecosystem and fishery. ing the Bay on the Bay’s water qual- buildings. The next generation of

EXAMPLES OF STREAM RESTORATION PROJECTS AND PROGRAMS NEW GENERATION OF FLOOD RURAL DAMAGE REDUCTION/ LANDOWNER FISHERIES HANDS-ON RESTORATION- RESTORATION PROJECTS STEWARDSHIP PROJECTS RESTORATION EDUCATION PROGRAMS

Napa River Napa Valley Vineyard Association (i.e., Lagunitas Creek STRAW program (The Bay Institute), San Pedro Creek the Rutherford Dust Restoration Team) Redwood Creek Sonoma-Marin Pinole Creek Escoot Creek Aquatic Outreach Institute (now The Alhambra Creek Marin Resource Conservation District: Stevens Creek Watershed Project), East Bay Wildcat-San Pablo Creeks Walker, Stemple, Chileno, and Olema Guadelupe Creek CYCLE, Richmond Rheem Creek Creek Watersheds Alameda Creek San Francisquito Watershed Council Coyote Creek (migration barriers removal) Guadeloupe Creek Wildcat Creek San Francisquito Creek Sausal Creek (dam removals) San Francisquito Creek Fishnet 4-C (coastal counties)

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WATERSHED

TAKE HOME water treatment plants will be the riparian systems restored along our NOTES waterways. • Information about the status of The sun has set on the era of using riparian ecosystems and planning concrete and riprap to control streams and restoration activities is lacking. and rivers and risen on a new paradigm that values balanced but • There is a crisis in restoration dynamic ecosystems. The other pro- expertise. The professional restora- found trend is the proliferation of tion community is too small to meet watershed partnerships and councils the demand, and has not organized that use interdisciplinary approaches itself to address its needs for water- to solving watershed issues and shed data, research, monitoring, and increase the transparency of govern- education. There is a dearth of ment agency work and citizen partici- apprenticeship programs, which is pation. The newly formed, statewide the way restoration skills are "California Watershed Council" has attained. taken its cue from the locally based • The restoration community also watershed partnership movement. needs a way to formalize sharing experiences because restoration is an evolving practice. One confer- MORE ence speaker decried the wide Village Creek at University Village in INFO ? [email protected] range of restoration methods being Berkeley/Albany: before daylighting (top); A Primer on Stream and River just after (bottom), and a few years later: a practiced, but this can be viewed Protection for the Regulator and functioning riparian system in an urban set- instead as a strength. One advance- Program Manager. ting (facing page). Photos: A.L. Riley. ment being made is a move away from relying on overly simplistic www.swrcb.ca.gov/rwqcb2/Agenda/ hydraulic modeling tools and a move 04-16-03/Stream%20Protection toward using a tool chest with a %20 circular.pdf large assortment of design tools that can be combined differently in different environments. • Watershed assessments are being given great attention, but they do not always meet the needs of the restoration profession. There is a split between those who study watersheds and those who actually practice restoration. A separate community of people generally present themselves to do assessments, and it is not uncommon for watershed restoration practitioners to have to perform different kinds of inventories and assessments in order to successfully address the problems that watershed councils want to have addressed. On the other hand, some restorationists act before they have acquired a reasonable amount of watershed information.

Arroyo willow, typically used in urban stream restoration projects 43 SOE layout 1 8/12/04 8:32 PM Page 44

STATE OF THE ESTUARY TAKE HOME tions in the Klamath Basin include NOTES LEARNING FROM FERC relicensing, the federal THE KLAMATH wildlife refuges, and the Endangered • Single species management is des- Species Act (ESA). tined to fail. JEFFREY MOUNT In 2001-2002, reasonable and pru- • Management needs to be adaptive U.C. DAVIS dent alternatives (RPAs) were set-up and not predictive. in the Basin to try and recover the The Klamath Basin is the second • Outside peer review works and lost river and short-nosed sucker. largest watershed—12,000 square serves us well. Those alternatives included screening miles—in California, producing • The ESA brings parties to the table and structures, dam passage facilities, extraordinary amounts of runoff. The that do not ordinarily cooperate. habitat restoration, water quality Klamath is unique. Unlike the Bay- management, coordination, and high- Delta system, it has no carryover er lake levels. That produced a sub- capacity. It’s turned upside down. • Access to and quality of the stantial crisis. The flat topography is in the upper spawning grounds is critical for watershed, where you can’t build The Klamath has one federally list- the suckers. dams and store water. The steep ed and now state-listed salmonid, the • Reductions in phosphorus from the parts—where all the runoff is—is in coho. The RPAs, which were put for- tributaries are unlikely to improve the lower watershed, where you have ward by NMFS, focused on the main water quality in Klamath Lake in no need to store water. This geogra- stem of the Klamath River, on the near future. More than 60 per- phy lies at some of the roots of the improving water quality, temperature cent of the phosphorus is from problems in the Klamath Basin. being one of the big issues, and internal loads. called for increased releases from What we can learn from the • High summer temperatures down- Iron Gate Dam. But both the suckers Klamath is that when conflicting stream of Iron Gate Dam, and lack and the coho needed high lake levels. mandates come together, you have a of quality spawning and rearing Then, in the great drought of 2001, crisis. The Klamath project was one habitat are the most significant lim- the farmers were cut off from their of the first supported by the federal iting factor for coho. Coho do not water, and the National Research Reclamation Act. It drained and rear in the main stem of the Council was invited in. reclaimed the lower Klamath and Klamath in the summer. So reoper- Tule Lake, stored water, reduced The NRC was asked to evaluate ating Iron Gate Dam to increase flooding, and promoted home- the science behind NMFS’ RPAs. releases of water that is already too steading, with a guarantee to farmers Some of theNRC’s interim findings: warm for the coho is unlikely to of water for life, something the benefit them during the summer. • Water quality is a major limiting Bureau of Reclamation doesn’t do Coho are spawning and rearing in factor for suckers in upper Klamath anymore. The project supplies irriga- the cool water tributaries. Lake. The nitrogen-fixing blue tion to about 200,000 acres. green algae that invaded upper • More water out of Iron Gate Dam Yet long before the Reclamation Klamath Lake around 50 years ago would produce considerable benefit Act, native tribal trusts were devel- is the major culprit in the decline of for the tribal trust species, the oped, in which the government guar- water quality and mass mortality of chinook salmon and the green anteed those tribes the right for water suckers in the Basin. sturgeon, which the government is for their fish. More recent complica- obligated to support. Dams have degraded water quality in this system. • How to save the suckers? SCIENCE • There is significant competition QUESTIONS A dam on Sprague River blocks 90 miles of the river; intakes need to be screened. Resource managers should focus on lake and river between hatchery and coho salmon. spawning areas. Other suggested actions include wetlands restoration, oxygenation tri- Hatchery salmon are probably sup- als (not a sustainable approach), and protection of existing populations outside of upper pressing coho production. Klamath Lake—viable populations live elsewhere in the Basin. Tule and Lower Klamath • The Klamath Basin lacks an Lakes could be re-watered and suckers re-established there, to disperse their genes. ecosystem-based approach to • How to save the coho? monitoring and research projects. We do not know enough about interactions between coho and other fish. One idea is to close one of the hatcheries for at least one full life cycle of the coho and evalu- MORE ate whether coho respond. INFO ? Emphasis must shift away from the main stem into the tributaries and sources of cold [email protected] water—the most significant limiting factor. That will involve some land-use restrictions. Iron Dam, which blocks about 10-15 kilometers of high quality habitat and access to cold water, should be removed, as should Dwinelle Dam. The Trinity River Restoration Program should be completed. 44 SOE layout 1 8/12/04 10:14 PM Page 45

WETLANDS

restoring the estuary wetlands

"Just a decade ago, we were working hard to convince the government that wetlands restoration was worthwhile. At just three bayshore sites in a little over two years, more than 12,000 people logged 36,000 volunteer hours, removed 20,000 pounds of invasive species and 15,000 pounds of trash, and planted more than 20,000 native plants to enhance 35 acres of wetland habitat." DAVID LEWIS SAVE THE BAY

Photo: David Sanger

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STATE OF THE ESTUARY

WETLAND proposed Indian gaming casino near benefit fish and wildlife species. The RESTORATION EFFORTS Sears Point Raceway has focused inventories show the spatial relation- AROUND THE BAY attention on approximately 24,000 ship between completed and planned acres of privately owned North Bay restoration/enhancement projects diked baylands that could be and existing wetland areas and iden- STUART W. SIEGEL restored. The Marin Audubon tify potentially restorable diked bay- WETLANDS AND Society acquired 630 acres that had lands, some of which may be subject WATER RESOURCES been slated for development at to development pressures. Uses of Bahia. The Department of Water these inventories include site selec- Wetland restoration has been tak- Resources acquired lands in Suisun tion for regional monitoring efforts ing place for decades throughout the for restoration. Several projects have and scientific research and identifi- San Francisco Estuary—in the South been constructed recently. cation of parcels for acquisition and restoration. Bay, Central Bay, San Pablo Bay, These inventories and maps pro- and Suisun Bay. Early projects were vide a framework to evaluate the Planned projects include about comparatively small and often were status and effects of regional efforts 19,000 acres in the North Bay mitigation projects. Recent projects to manage and restore wetlands to (13,000 acres tidal marsh and 6,000 are comparatively large and in many cases are agency- and non-profit- WETLAND RESTORATION PROGRESS: NON-TIDAL MARSH sponsored efforts to promote recov- Existing ery of the Estuary’s wetland-depend- 16 ent fish and wildlife resources. Completed Planned 14 In cooperation with PRBO Goals Target CBDA Target Conservation Science and the San 12 Francisco Estuary Institute (SFEI), we inventoried completed and pend- 10 ing tidal and non-tidal wetland restoration and enhancement proj- 8 ects within the historic margins of 6 tidal influence throughout most of Total Acres (x1000) Total the Estuary. We did not inventory 4 wetland restoration projects in Suisun Marsh. We mapped projects 2 on the EcoAtlas GIS and prepared a database providing a variety of 0 North Bay South Bay information on each project. These data are now online at www.wetlandtracker.org, maintained by SFEI. WETLAND RESTORATION PROGRESS: TIDAL MARSH This online resource contains down- loadable project information, and the Existing public is encouraged to contribute 16 Completed Planned additional content. 14 Naturally Restored Significant progress has been Goals Target CBDA Target made since the 2001 State of the 12 Estuary conference. The U.S. Fish 10 and Wildlife Service and the California Department of Fish and 8 Game acquired Cargill salt ponds and related lands (15,000 acres 6

South Bay and 1,400 acres North Acres (x1000) Total 4 Bay). The City of San Jose acquired an 850-acre South Bay salt pond. 2 The proposed San Francisco Airport runway expansion plans and wetland 0 mitigations have been put on hold. A SuisunNorth Bay South Bay

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acres non-tidal or mixed hydrology) and 18,000 acres in the South/ Central Bay (breaking down tidal and non-tidal marsh is difficult because salt pond types remain to be determined). Constructed projects include tidal marsh (4,100 acres in the North Bay; 2,700 acres in the South Bay) and non-tidal and mixed-hydrology projects (3,900 acres in the North Bay; 2,100 acres in the South Bay). Acreage sum- maries for Suisun are not available at this time; the California Bay Delta Program's Ecosystem Restoration Program established a target of restoring 6,800 acres of tidal marsh and enhancing 40,000 to 50,000 acres of seasonal wetland habitat there. The Suisun Marsh Charter Group is preparing a plan for achieving these objectives. MORE INFO ?www.swampthing.org

Warm Springs, which was opened to the tides in 1986, shown here in 1995 and 2002. Photos: Phyllis Faber

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TIDAL RESTORATION • Will perennial pepperweed evolve more salt-tolerant SCIENCE ecotypes in San Francisco Bay, increasing IN WEEDY WETLANDS: QUESTIONS PAST, PRESENT, AND its ecological range to salt marshes? • Can perennial pepperweed colonization be pre-empt- FUTURE ed by rapid establishment of dense cover by native clonal herbaceous plant species? PETER R. BAYE • Will sea level rise accelerate the invasion of Atlantic smooth cordgrass hybrids in existing salt marshes or facilitate conversion of pickleweed marsh to cordgrass vegetation? The extensive spread of pepper- • Will long-distance dispersal events increase in frequency in the North weed and Atlantic smooth cordgrass Bay and Point Reyes as the population size of the Atlantic smooth hybrids during the 1990s poses a cordgrass hybrids increases? challenge to former tenets of • What long-term effects on native Pacific cordgrass will result from restoration planning in the San introgression of smooth cordgrass hybrids, even if smooth cordgrass Francisco Bay region. Introduced phenotypes are effectively eradicated? tidal marsh plants have demonstrat- • Will hybrid smooth cordgrass undergo succession to pickleweed ed their potential to become new, marsh at threshold elevation ranges typical of Pacific cordgrass, or persistent dominant vegetation types will it persist as a dominant short-form cordgrass vegetation, as in in existing and restored tidal marsh- the native range of its Atlantic parent? es across marsh zones historically • Will geomorphic structure and tidal drainage patterns typical of occupied by native species. smooth cordgrass marshes of the Atlantic and Gulf coasts replace Only a decade ago, discussions of noxious wetland weeds in San Francisco Estuary tidal marshes, projects were novel proposals in the tions and marsh accretion. Control such as perennial pepperweed region. Until the 1990s, revegetation of wetland weeds was widely (Lepidium latifolium) and Atlantic of salt marshes was presumed to assumed to be feasible by normal smooth cordgrass (Spartina alterni- occur by natural dispersal of a few monitoring and removal of isolated flora) were marginal or lacking in dominant native plant species, fol- small infestations. Restoration most in wetland restoration and lowing orderly and predictable designs generally did not address management plans. At that time, zonation patterns and successional conservation of historic patterns of large-scale tidal marsh restoration sequences defined by tidal eleva- plant diversity, a concern that

ATLANTIC VS. PACIFIC CORDGRASS MARSH STRUCTURE

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emerged only after invasive non-native marsh plants began to dominate much of the Estuary. Records show that perennial pepperweed appeared sporadically around the edges of the Estuary in the 1950s. It now dominates extensive areas of high brackish tidal marshes in Suisun Marsh and San Pablo Bay. In the South Bay, perennial pepperweed dominates extensive brackish fringing marshes of sloughs. Effective control techniques for this species in tidal wetlands are still undeveloped. A new regional control program for four invasive nonnative Spartina species has recently been implemented, but only as the hybrid swarm of smooth cordgrass proceeds to invasion stages of exponential (or greater) growth. Smooth cordgrass hybrids have recently invaded high marsh zones in Newark. Saltmeadow cordgrass (Spartina patens) has been detected in San Pablo Bay, and has been found to be more widespread in Southhampton Marsh, Benicia, than previously known. Mature colonies of another nonnative colonial grasslike rush (Juncus sp., ten- tatively J. gerardi), have been detected in brackish high marsh at Southhampton. No regional control efforts for any other wetland weeds have been initiated. MORE INFO ? [email protected]

Pacific cordgrass

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TAKE HOME VARIABILITY IN mitment of resources. While such WETLAND RESTORATION restored lands might be "wet," they are not true estuarine or tidal wetlands and NOTES will not be resilient to natural stresses. DENISE J. REED The biological functions they provide • The concept of "pulsing" as a UNIVERSITY OF NEW ORLEANS represent a human-maintained disequi- vital dynamic in estuarine librium. If particular functions are ecosystems has been recog- Wetland restoration efforts must required or expected, lands can be nized for decades. While initial embrace the natural variability of the managed for such purposes, but the work focused on the role of estuarine system—daily tides, annual result should not be considered wet- tidal fluctuations in providing a floods, and (less frequently) land restoration. In recent years, the subsidy to estuarine ecosys- droughts—to be sustainable. creation of engineered microtidal wet- tems, more recent work has lands has been proposed for the identified energetic forcings In the San Francisco Estuary we Estuary. This approach calls for con- occurring over a variety of must consider not only the physical trolling the fundamental natural time and space scales that reg- structure and everyday dynamics of dynamics of tidal marshes, and expects ulate biological processes and restored wetlands but also how they that we can anticipate the changing control geomorphic struc- might be influenced by water manage- dynamics of the system adequately tures. ment decisions. Estuarine wetlands enough to manipulate them to our • Within the San Francisco are very resilient to natural variability, advantage. This is not working with Estuary, tidal pulsing is super- but changing that natural variability nature; this is working against nature. imposed on seasonal and inter- has consequences for estuarine wet- At the same time we have broad annual variability in freshwater lands and associated biota. There is restoration goals that point toward a flows. The geomorphology of ample evidence from ecosystems self-sustaining system. There is an the Estuary is still adjusting to throughout the world that changes in inherent disconnect between those two the huge pulse of sediment flooding, drought, or other elements approaches. "Muted" tidal wetlands is delivered as a result of of the hydrograph are likely to pro- a misnomer – they are an artificial hydraulic mining activities, and duce substantial consequences to the ecosystem not driven by the tide but by massive alterations to the ecosystem. While the wetlands them- human management of the tide. We intertidal system caused by selves may survive, the biological may get a mosaic of diverse habitats, drainage of wetlands and Delta functions they support will change. but it is very unlikely that we will get islands. While human actions However, for systems that are this natural self-sustaining systems, and it’s have altered the system struc- dynamic, diverse, and complex, no also very unlikely that the inherent nat- turally, some elements of methods are available that can define ural characteristics, the dynamic natu- freshwater flow variability still the extent to which natural flow ral characteristics of an estuary, are exist, albeit much modified, regimes can be changed without caus- going to be provided for. and the inherent tidal nature ing significant ecosystem changes. of the system is still intact. Any change to the regime is, in effect, an experiment with, at best, a hypoth- MORE • We should focus on the vari- esized outcome. INFO [email protected] ability in the Estuary, the tides and the floods, and think As we move forward with restoring about how they make the sys- the Estuary’s wetlands, we need to tem work and how important keep in mind that we have a they are to the Estuary. very complex hydrological HOW WETLANDS WORK dynamic to cope with. • If we want to restore tidal Hydrology is the lifeblood of wetlands, we need to keep tidal marshes: extremes and Structure the daily tidal variability going Abiotic and allow big flooding events disturbances are important. Biotic Wetland restoration that to influence and benefit the Estuary. depends on levees or struc- Restoration Actions tures—and their continued operation and maintenance— Process Function to modulate essential estuar- Hydrological Input (Capture) ine processes is sustainable Sedimentological Production Geochemical Cycling only with a continued com- Biological/Ecological Storage Output

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MONITORING MARSHES

PHYLLIS M. FABER PHYLLIS M. FABER & ASSOCIATES

Long-term monitoring is essential for us to gain an understanding of the evolution of tidal salt marshes in San Muzzi Marsh South Channel, 1994 Francisco Bay and to develop realistic expectations for future restoration Photo: Phyllis Faber TAKE HOME projects. Three sites around the Bay China Camp provides an excellent have been monitored annually since control marsh for Bay Area restora- NOTES 1986: the Muzzi Marsh in Corte tion projects as it is one of the very Madera in Marin County; Coyote few sites around San Francisco Bay • Getting elevations correct is very Creek Lagoon (formerly called Warm where a healthy tidal salt marsh has important if we are going to use Springs) in Fremont in Alameda its original surrounding watershed dredge spoils. County; and China Camp in San intact. Rafael in Marin County. A fourth site, • Vegetation establishes naturally Sonoma Baylands, has been moni- Monitoring included measuring making planting wasteful and tored annually since 1996. China sedimentation rates through annual unnecessary. Camp serves as a control marsh. surveys of the marsh plain, and col- • We need to be patient in allowing lecting data on annual patterns of natural processes to evolve. A portion of the 200-acre Muzzi vegetation establishment and species Marsh provided a dredge disposal site distribution. We found that vegetation • Plants species distribution is sensi- (70 acres), with overflow containing establishes itself naturally when the tive to changes in tidal prism, to fines deposited onto the landward elevations and soils are appropriate. elevational and salinity changes, and portion of the mitigation site (130 That said, a mature pickleweed marsh to seasonal rainfall patterns. acres) for the Larkspur Ferry takes 30 to 40 years to develop. • Simplicity should be a goal in Terminal. Bayward portions received Because tidal channels enhance the designing monitoring programs to no spoils. The project was completed, ingress and egress of the tidal prism assure long-term success. and dikes were breached in 1976. to more remote parts of a tidal marsh Coyote Creek Lagoon served both as well as provide habitat to an as a sediment supply site as well as a endangered species, the clapper rail, and species of fish, their evolution is mitigation site for developing an • What role does long-term of particular interest. industrial park in Fremont. In 1986, monitoring following the excavation of sediment MORE SCIENCE play in for the industrial site, leaving a mas- INFO [email protected] QUESTIONS adaptive sive 200-acre basin, dikes were management? breached from the lagoon into Coyote Slough and a little later into Mud • How do we recognize Slough. The mitigation was predicat- differences between sites ed on the refilling of the basin by around the Bay? sediment from the sloughs (and subsequent marsh development). • Can we develop realistic expectations for future restoration work without long-term monitoring?

• What should be monitored, and where do we start?

Muzzi Marsh South Channel, 2003 Photo: Phyllis Faber 51 SOE layout 1 8/12/04 8:35 PM Page 52

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TAKE HOME MIASMA REVISITED: tive attitudes both towards wetlands WILL WETLAND (the apparent ultimate cause of dis- NOTES RESTORATION ease) and foul air (the hypothesized proximal cause). • Some wetlands are more mosquito- KILL YOU? prone than others. High-risk wet- While "malaria" increasingly was lands include seasonal wetlands, used to describe the symptoms of a wetlands with dense vegetation, KARL MALAMUD-ROAM specific disease complex, rather than wetlands without good drainage or CONTRA COSTA MOSQUITO its cause, an ancient term—"mias- operations and maintenance budg- & VECTOR CONTROL DISTRICT ma"—continued to denote foul or ets, and lots of small dispersed sites unhealthy air, especially where it for which it is harder to track down The recent spread of West Nile smelled of rot, and, more broadly, the landowner. virus as a threat to humans and any polluted or noxious environ- wildlife has rekindled old public fears ment. The "miasmic theory of dis- • Good tidal flushing helps prevent about wetlands and forced wetlands ease" – that air or some matter in it mosquitoes. advocates and managers to reevaluate carried disease from rotting matter • Juvenile mosquitoes need three-plus those fears and how best to address to victims—was largely discredited days of standing water in order to them. This year—2004—is going to by the recognition in the 1880s that reproduce. be tough for California, with West cholera was spread by waterborne Nile expected to hit hard, budgets • See : www.sfbayjv.org for up-to- bacteria, but the words, and the date info on West Nile Virus. being cut, and new regulations—and aversion to wetlands, continued. created wetlands—being put into place. Wetland restoration is possible This dislike was apparently justi- for migratory waterfowl (other and compatible with mosquito con- fied some two decades later when species were recognized, but elicited trol, but it has to be done right. Ronald Ross and others finally much less public or regulatory sup- demonstrated a mechanistic link Although wetlands are widely port initially), and mosquito-borne between wetlands and diseases. diseases had declined. A tension viewed today as important natural Although the link was not a miasmic resources, they have historically been developed between natural resource mist, it was another air-borne disease management and public health per- seen as noxious and dangerous, and it vector—the mosquito. Following this is crucial for wetland advocates and sonnel, which continues to the present discovery and the subsequent success day. managers to understand the objective of some regional programs to reduce risks to public health posed by these malaria, yellow fever, and other mos- Perhaps ironically, the development landscapes, the public perceptions quito-borne diseases by reducing of DDT and other pesticides during associated with these risks, and strate- mosquito habitats, the old fears of World War II initially reduced this gies which might reconcile wetland marshes and swamps were widely tension, as these chemicals allowed restoration with public health. seen as scientifically justified, and mosquito control without drainage Environmental factors have been publicly-funded mosquito control, and with few immediately apparent postulated as causes of human or ani- often involving draining wetlands, environmental impacts. Over the fol- mal disease since at least the time of became widespread by the mid- lowing decades, however, and in par- Hippocrates, and a specific apparent 1920s. During the Great Depression, ticular after Rachel Carson published association between wet vegetated the imperative to put men to work led Silent Spring, pesticides themselves areas and ill health is still reflected in to a massive expansion of ditching in became scrutinized by resource man- the French term for malaria – palud- the name of mosquito control in the agers and the public, leading to the isme (literally "marsh fever"). United States, including in many development of more safe and selec- "Malaria" ("bad air") was itself intro- areas where mosquitoes had probably tive pesticides, and to a reevaluation duced into the English medical litera- not been prevalent. At the same time, of the role of water and/or vegetation ture in 1827 as a shorthand for the natural resource managers had management in mosquito control. earlier "paludal poison" and "marsh increasingly begun to demonstrate the These changes, together with the cul- miasma," terms which illustrate nega- significance of wetlands as habitats tivation of working relationships between resource managers and mosquito control personnel, allowed wetlands restoration to take place over the last two decades without an apparent rise in mosquito-borne diseases. MORE INFO [email protected]

52 Reproduction of an illustration in an 1888 edition of Drainage Lisa Krieshok Journal showing critters fleeing a drained swamp. SOE layout 1 8/12/04 8:35 PM Page 53

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EELGRASS: INVENTORY, well as for oceanic species that enter beds, characterizing physical param- CHARACTERIZATION, estuaries to spawn. eters within eelgrass beds, and creating a predictive model of eelgrass AND A PREDICTIVE In recent years, resource managers habitat based on physical parame- have become more interested in eel- MODEL ters. grass in San Francisco Bay, and greater concerns for this habitat type Results of the 2003 eelgrass sur- KEITH W. MERKEL have emerged. Part of this increased vey indicated that more than 1 per- MERKEL & ASSOCIATES, INC. attention was a result of the San cent of San Francisco Bay supports Francisco Bay Area Wetlands eelgrass, an order of magnitude The San Francisco Bay-Delta Ecosystem Goals Project, which greater than the amount documented Estuary is the largest estuarine system illuminated the imperiled status of in the late 1980s. In addition to the on the West Coast of North America, the Bay’s eelgrass. In addition, sev- baseline established by this survey, but relative to other major estuaries eral high profile projects, such as the eelgrass bed characterization along the Pacific Coast, it has the San Francisco-Oakland Bay Bridge through this program has provided a lowest coverage per area of eelgrass Seismic Safety Project, sought to much-needed understanding of eel- (Zostera marina), a flowering marine restore significant eelgrass beds. grass habitat requirements. These plant that provides excellent habitat Given this increased attention, data have been incorporated into a for other plants and animals. In the Caltrans, in consultation with model that can be used to predict late 1920s, eelgrass was reportedly NOAA Fisheries, funded a resource potential eelgrass habitat throughout abundant along the shores of San management program to document the Bay. Francisco Bay. However, in 1987, a National Marine Fisheries Service EELGRASS LOCATIONS EELGRASS IN WEST COAST survey indicated that only 0.1 percent CENTRAL SAN FRANCISCO BAY, 2003 ESTUARINE SYSTEMS of the total Bay bottom supported eel- SYSTEM EELGRASS PERCENT grass, and that much of the eelgrass COVERAGE (ACRES) COVERAGE was highly stressed. This eelgrass Mission Bay 1,210 54% coverage in San Francisco Bay was at San Diego Bay 1,626 14% Humboldt Bay 4,821 10% least an order of magnitude lower San Francisco Bay 2,611 1% than other bays in California; over 14 percent of the bottom of San Diego Bay is covered with eelgrass, and the bottoms of Mission Bay (San Diego) MORE and Humboldt Bay are covered by INFO [email protected] approximately 54 and 20 percent, respectively. Eelgrass occurs in shallow bays and estuaries throughout the world. It creates a unique structural and biological environment, and plays many roles eelgrass bed abundance, distribution, within estuarine systems. Eelgrass and characteristics in the Bay in clarifies water through sediment trap- order to improve the state of man- ping and stabilization, transforms agement science and policy for this nutrients, and oxygenates the water. It habitat. is a primary producer in a detritus- Work for based food web and provides physical this pro- • What is the rate of recovery of eelgrass structure for epiphytic plants and ani- SCIENCE gram QUESTIONS following disturbance? mals, which in turn are grazed upon included by other invertebrates, larval and surveying • What is the genetic relationship of eelgrass populations juvenile fish, and birds, contributing the entire within the Bay and between other bays and estuaries to the ecosystem at multiple trophic Bay for eel- on the West Coast? levels. It also serves as a nursery area grass, com- for many commercially and recre- paring the • What is the composition of faunal communities that ationally important finfish and shell- genetics of utilize eelgrass beds in the Bay? fish species, including those that are eelgrass resident within bays and estuaries, as

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TAKE HOME WILDLIFE AND NOTES PUBLIC ACCESS • Access to the Bay allows the public to discover, experience, CAITLIN SWEENEY and appreciate the Bay’s natural SAN FRANCISCO BAY resources and can foster public CONSERVATION AND DEVELOPMENT COMMISSION support for Bay resource protection, yet studies indicate that public access may have immedi- As more people take part in recre- Francisco Bay Conservation and ate effects on wildlife, including ational activities in and around the Development Commission (BCDC) flushing, increased stress, inter- Bay, and as the shoreline and wildlife embarked upon an in-depth two-year rupted foraging, or nest aban- habitat shrink as more land is devel- research and policy development donment, and may result in oped, interactions between humans process, the Public Access and adverse long-term population and wildlife are increasing. To Wildlife Compatibility Project, which and species effects. address these concerns, the San culminated in the revision of BCDC’s San Francisco Bay Plan • Because effects on wildlife are public access findings and policies. site-specific, it is important to • What are the SCIENCE The revised findings and policies accurately characterize site, habi- QUESTIONS effects on wildlife better reflect current knowledge tat, wildlife conditions, and of specific types about interactions between public human activities. of human activities at various frequencies and scales? access and wildlife, and provide • Potential adverse effects from • Do certain wildlife species more detailed policy guidance on public access may be avoided or become adapted to human providing maximum feasible public minimized through appropriate interaction, and are there other access while protecting wildlife from siting, design, and management. impacts to wildlife as a result? significant adverse effects. The relative advantages and dis- • How effective are specific site, advantages of specific strategies MORE design, and management INFO [email protected] depend on the environmental strategies in avoiding or reduc- ? characteristics and the likely ing adverse effects of human human use of the site. activities on wildlife? • Providing diverse and satisfying public access opportunities can reduce the creation of informal access routes, which will help PUBLIC ACCESS: EFFECTS ON WILDLIFE decrease interactions between humans and wildlife, trampling Human/Wildlife and erosion of vegetation, and Interactions fragmentation of habitat. Formal (recreational activity) public access also provides for more predictable human actions, which may help wildlife adjust to Direct Impacts Indirect Impacts human use. • The integration of public access early in the project design Harassment Harvest/Mortality Habitat Modification phase,and an integrated public process will increase the potential for success in balancing public access and wildlife protection. Alteration of Behavior Displacement Reproduction Level

Species Composition and Structure

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FUNDING WETLAND Estuary wetland goals have been Until a strategy is developed and RESTORATION partially detailed in the Baylands implemented to fund systematic Ecosystem Habitat Goals Report and implementation of wetland restora- in the CALFED Ecosystem tion goals, funding will remain at MARC HOLMES Restoration Plan. The establishment inadequate levels and worthy THE BAY INSTITUTE of the San Francisco Bay Habitat restoration opportunities will be lost. Joint Venture has enabled novice We also need to encourage those Many wetland restoration projects applicants to find assistance and has who are not part of the known con- ripe for implementation lie idle for encouraged veteran applicants to stituency—poets, writers, and pho- lack of funds, despite the fact that coordinate their efforts and optimize tographers like John Hart and David numerous sources of funding are chances for success, all within the Sanger, for example—to help devel- available to finance them. Part of the parameters of the existing funding op a greater sense of identity for the problem is that systematic efforts to system. These are first steps in rais- Bay, and increase funding opportu- fund regional wetland restorations are ing the importance of restoration nities to help restore it. goals from the point of view of largely absent. In their place is a sys- MORE state, national, and private funding tem of ad hoc initiatives guided more INFO [email protected] by opportunity than by plan. This sources. It is not enough, however. ? approach fails to capitalize on the The Joint Venture now should additional funding that could be work with state, federal and private tapped by highlighting the national partners to develop a restoration and international ecological signifi- funding strategy that enables attain- cance of the restoration goals. ment of restoration goals. To my One challenge for San Francisco knowledge, no such strategy has ever Bay is its lack of a strong identity in been developed. We also need a Washington, D.C. "Historic diked planned strategy to finance restora- baylands" doesn’t quite compete with tion and operations and maintenance, the poetic "river of grass" image of not merely acquisition. The Joint the Everglades. Venture should publish such a plan. Photo: David Sanger

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TAKE HOME PREDICTING even with no further human inter- THE FUTURE OF vention. Today, we are making deci- NOTES SAN FRANCISCO BAY sions about actions such as large- scale habitat restoration, or disposal • The Estuary as a geomorphic sys- of dredged sediments, that will tem is dynamic and evolving, PHILIP B. WILLIAMS affect how the mix of Bay habitats whether or not humans are on its PWA LTD, CONSULTANTS IN will evolve. periphery. Inherent, integral ero- HYDROLOGY Fortunately, we now have a variety sional and depositional processes of analytic and empirical tools that determine its physical form and Over the last 150 years we have can be used together to make projec- hence its mix of habitats. The seen major changes to the size, tions of how the Estuary’s shape will young Estuary is still a drowning shape, and habitats of San Francisco evolve. We can use these to predict river valley and has not yet Bay. The most dramatic recent the mix of habitats we will see in the achieved equilibrium between sedi- changes have been due to human future. Constructing this future "snap- ment deposition and erosion. actions—whether hydraulic mining shot" of Bay habitats in the year 2053 • We are faced with a diminishing in the Sierra or conversion of tidal will be a powerful tool for Estuary- sediment supply in the Estuary and marshes to farmland—but we also wide restoration planning. It will accelerated sea level rise. It will be understand that for the last 10,000 allow us to better assess the future easier to restore vegetated marshes years, the Bay has been changing its impact of large scale changes such as on subsided sites now than if we shape and character as sea level rose those proposed for airport runway wait until later. As sea level rises, and the Estuary expanded inland. expansion, inform the design of large we risk losing valued mudflats and We can see the Estuary as a single restoration projects to ensure we marshes. dynamic evolving system, whose achieve net gains in all types of habi- • We now have a better understand- shape at any point in time is deter- tats, and allow us to anticipate likely ing of how to predict future geo- mined by sedimentary processes future changes such as shoreline ero- morphic and habitat changes. responding to sea level rise, sediment sion or deepening tidal channels. The Relying exclusively on numerical inflows from the watershed, the pre- images and maps of past habitats models can get in the way of how vailing winds, waves, climate, tidal have powerfully influenced our think- we think about the Estuary. We flows, and the geomorphic legacy of ing about restoration goals. Equally need to use empirical or analytical the drowned valley of the pre-historic important is an understanding of what tools as well, based on monitoring Sacramento River. The San the future Bay will look like. of and research on the Bay’s Francisco Estuary Institute’s MORE restored marshes. EcoAtlas provides us with a snapshot INFO [email protected] • The challenge is not just to restore of what Bay habitats looked like on individual wetland sites but also to this evolutionary path 200 years ago. cumulatively manage and restore Human intervention has altered both the Estuary as a whole to make the estuarine landscape and the sedi- sure we maintain or increase the mentary processes that determine this extent and mix of desired habitats evolutionary trajectory. into the next century. Over the last two decades our understanding of sediment dynamics and how Bay habitats are evolving SCIENCE • How will the morphology has significantly improved. For QUESTIONS — or shape — of the example, USGS research is showing Estuary change in the next that mudflats are shrinking while century in response to rising sea level and long term monitoring is showing diminishing sediment supply? how long it takes for restored marshes to become established. With • How will these changes affect the overall accelerated sea level rise and dimin- area of mudflats and marshes? ishing sediment delivery, we can anticipate that 50 years from now, • What analytic and empirical tools can we Bay morphology and habitats will be use to predict how the physical Estuary is significantly different, with smaller likely to evolve? mudflats and eroding marshes— • Can we plan individual restoration projects to provide cumulative net habitat increases Pickleweed at the Estuary scale? 56 SOE layout 1 8/12/04 8:35 PM Page 57

SALT PONDS

restoring the estuary salt ponds

"This is the largest single habitat restoration project, the most complicated restoration project ever envisioned for the Estuary."

MIKE MONROE U.S. EPA

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PLANNING FOR SALT enhancing habitats in the North Bay restoration planning for the South POND RESTORATION ponds. The project objectives for the Bay Salt Ponds with the California Napa River Unit are: (1) to restore Department of Fish and Game and large patches of tidal habitats in a the U.S. Fish and Wildlife Service, AMY HUTZEL band along the Napa River, in a the land managers, and the Santa CALIFORNIA STATE COASTAL phased approach, to support a wide Clara Valley Water District, Alameda CONSERVANCY variety of fish, wildlife, and plants, County Flood Control District, and including special status species, and the U.S. Army Corps of Engineers. Resource managers in the San (2) to effectively manage water The agencies will engage trustee and Francisco Bay face an unprecedented depths and salinity levels of remain- regulatory agencies, local govern- opportunity to meet many of the ing ponds to benefit migratory and ments, community groups, recreation goals and objectives of the Baylands resident shorebirds and waterfowl. and access advocates, environmental organizations, and the public in this Ecosystem Habitat Goals Report by The work undertaken in the North multi-objective project that will com- restoring large areas of tidal habitats Bay provides lessons for the restora- bine habitat restoration, flood control, and enhancing the management of tion planning of the South Bay Salt and public access. former commercial salt ponds for Ponds, including the need for interim wildlife. In 1994, Cargill ceased pro- management, the need for scientific MORE duction of salt in the North San oversight and involvement, and the INFO [email protected] Francisco Bay and sold 9,850 acres, benefits of working collaboratively consisting of twelve evaporator ponds with partners and stakeholders. The and associated remnant sloughs and Conservancy will facilitate long-term fringing marsh, to the state. In 2003, California and the federal government SOUTH BAY SALT POND RESTORATION PROJECT acquired15,100 acres of salt 92 Hayward Lands Retained or Sold to Other Cargill has sold or proposes to sell to evaporator local government agencies 11 12 ponds in South 10 13 Cargill retains land for salt production 14 San Francisco 8 9 6B Cargill retains land for other purposes San Mateo Bridge 6A Meters Bay and an 8A 8 0 1,000 2,000 4,000 additional 1,400 Miles Alameda Creek 1 6 Union City 0 1 2 4 acres of crystal- 7 5 2 6C lizer ponds 4 880 4C 5C along the Napa 1C River from 1A 2C Alameda County 2A Cargill. Flood Control 3A Channel 84 The 4A Fremont California State South 5 7 8 San Francisco Bay 4B Coastal 9 6 Conservancy, d o 1 o 4 2 PP1 Newark California w d Department of e 3 R Fish and Game, 13 10 27 1 Dumbarton 12 10A and U.S. Army Bridge 101 Newark 11 26 2 Corps of 5 4 Slough Mowry Fremont SF2 8 Slough 7 Engineers have 3 6 undertaken a Redwood City S5 1 A22 5 Feasibility East 2 3 A23 Palo Alto 4 Study to evalu- Menlo A19 C o y o t e C r e e k A21 A20 ate alternatives Park Alviso Palo Slough A9 Milpitas Guadalupe A17 for reducing A14 A15 Alto Slough A18 A3N A10 salinity and A1 A11 A13 B1 restoring or A2W B2 A16 A2E A5 A7 A12 Alviso Mountain A3W View A8 San Jose A4 Sunnyvale 58 SOE layout 1 8/12/04 8:35 PM Page 59

SALT PONDS

SNOWY PLOVERS during nesting season to minimize One of the most difficult chal- human disturbance. lenges to overcome will likely be predation by species such as corvids JOY ALBERTSON Recently, more than 15,000 acres (ravens and crows) and gulls, which U.S. FISH & WILDLIFE SERVICE of south San Francisco Bay salt exploit nesting and foraging oppor- ponds were acquired by the U.S. Fish tunities provided by transmission In the near future, large-scale and Wildlife Service and the towers, landfills, and urban develop- restoration and management of South California Department of Fish and ment. Although many challenges lie Bay salt ponds will offer a challeng- Game. The ponds will be restored to ahead in plover recovery, these chal- ing and unique opportunity to con- a mosaic of tidal marsh, managed lenges can be overcome with the serve the Pacific coast population of ponds, and salt pans. The salt pan help of additional research, protec- the western snowy plover habitat to be managed for snowy tive measures, and adaptive habitat (Charadrius alexandrinus nivosus), plovers will include several managed management. which is listed as federally threat- pond complexes in different areas of ened. Current threats include habitat the South Bay. This new opportunity MORE degradation caused by human distur- for active habitat management— INFO [email protected] bance, urban development, invasive including managing pond water lev- ? plants, and expanding predator popu- els and salinities, removing problem lations. Management actions to predators, minimizing human tres- reduce these threats and to satisfy the pass and disturbance, controlling veg- biological needs of the plover must etation, and resolving conflicts with be undertaken to assure recovery. management for other special status San Francisco Bay is one of 20 species—will be crucial to the recov- remaining snowy plover breeding ery of local breeding populations and areas in California, supporting will greatly benefit the health of the approximately 10 percent of the Pacific coast population. state-wide population, underlining the potential importance of the Bay in recovery of the plover. Recovery criteria include maintaining 500 breeding adults in the San Francisco Bay unit. The current breeding population in San Francisco Bay is between 100 and 150 breeding adults, with the majority breeding on dry salt pan areas of man-made salt ponds in the southern part of the Bay. In particular, the medium-salinity salt ponds with dry pond-bottoms provide both nesting and foraging requirements for the plover. In the past, most of these salt ponds were under commercial salt production, and snowy plovers nest- ed opportunistically only when ponds happened to be dry during the breeding season. To date, management activities have focused on protection of existing plover breeding populations, but there have been few opportunities to enhance plover nesting and foraging habitat through water management. Current management activities include controlling mammalian predators, building nest Lisa Krieshok exclosures, and closing nesting areas

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TAKE HOME WATERBIRDS IN Preliminary results demonstrate that THE SOUTH BAY while restoring significant amounts of tidal marsh habitat will benefit birds NOTES that depend on tidal marshes, we need • Numbers of waterbirds using the NILS WARNOCK, ET AL. to plan carefully and develop a mosa- PRBO CONSERVATION SCIENCE restored areas of the South Bay ic of interspersed tidal marsh and will decrease dramatically if all salt shallow water habitat to reduce the ponds are restored to homoge- Millions of waterbirds (shorebirds, likely costs to waterbirds that current- neous tidal marshes. waterfowl, gulls, terns, grebes, and ly depend on salt ponds. waders) have come to depend on • Habitat modifications such as the creation of large channels and commercial salt ponds as a replace- MORE ment for tidal mudflats and other nat- ponded areas within tidal marsh INFO [email protected] areas can greatly reduce negative ural shallow water habitats, such as ? effects on waterbird popula- salt pannes and seasonal wetlands, tions. which have declined from their his- • What is the optimal toric extent around the Bay. Although SCIENCE • Leaving some salt ponds QUESTIONS mix of tidal marsh, salt within a wetland mosaic can the recent acquisition of over 6,000 pond, and other Bay hectares of salt ponds by state and mitigate or even eliminate neg- habitats that maximizes the diversity ative effects on waterbird pop- federal wildlife agencies provides an and numbers of waterbirds using ulations. unprecedented opportunity to restore the restored area? large areas of contiguous tidal wet- • Landscape setting, including lands in the South Bay, the science of proximity to urban develop- • What will happen to birds ment or the Bay/mudflat edge, tidal marsh restoration is new and displaced by the restoration evolving, and studies of tidal marsh can affect the value of salt process? Will they and can they ponds and restored marshes restoration trajectories and outcomes move to other parts of the Estuary? for birds and is an important are few, especially with respect to Conversely, how quickly will bird consideration in the design of bird and other vertebrates. populations use new habitat that is marsh restoration projects. PRBO has completed the first phase created? • The selection of which salt of a long-term effort to evaluate the ponds to retain and the salini- potential effects of salt pond restora- • Will tidal flats be affected by habitat ties and depths at which they tion on San Francisco Bay wetland restoration in the South Bay and are managed will affect use of bird communities. We used compre- how will this impact waterbirds? the restored area by waterbird hensive, standardized bird survey data populations. from salt pond and tidal marsh habitat • How will threatened and endan- to develop models that predict the gered species and other species of impact of specific restoration scenar- conservation concern respond to ios on South Bay bird species rich- habitat restoration in the Estuary? ness and abundance.

RESTORATION SCENARIO LANDSCAPE SCENARIO All Ponds Retained 80,000 70,000 All Ponds Restored to All Ponds Retained 70,000 All Restored Marsh, Minimum Open Water 60,000 High Restoration Feasibility 60,000 All Ponds Restored to Marsh, Mean Open Water 50,000 Random 50,000 All Ponds Restored to Clustered (Baumberg Marsh, Maximum Open Water 40,000 Clustered (Alviso SP) 40,000 30,000 30,000 20,000 20,000 10,000 10,000 0 0 Landbirds Small Large Dabbling Diving Fish-eaters Landbirds Small Large Dabbling Diving Fish-eaters Shorebirds Shorebirds Ducks Ducks Shorebirds Shorebirds Ducks Ducks

Restoration scenario predictions for all species groups (all ponds restored, variation in tidal marsh restoration endpoints). Landscape scenario predictions for species group numbers with varying salt pond/tidal marsh configurations, assuming mean open water habitat conditions. Numbers are total numbers over all ponds surveyed (based on sum of regression model density predictions for each pond). Error bars represent sums of standard errors for each pond prediction.

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THE DELTA

restoring the estuary the delta

"Operating aspects of the water projects at the tidal timescale could provide opportunities for managing both ecosystem function and water supply reliability and improve Delta salinities without costing more water."

JON BURAU USGS

Horsetail

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AN OVERVIEW Since 1995, ERP funds have been refining the set of Delta-specific OF DELTA RESTORATION awarded for planning, pilot, and restoration actions and targets, and full-scale implementation of protec- provide Delta-specific implementation and restoration of all of these tion guidance, program tracking, and LAUREN L. HASTINGS habitat types. The AB360 Delta guidance for performance evaluation ECOSYSTEM RESTORATION Levee Protection Program, the and adaptive management feedback. PROGRAM, CALIFORNIA Department of Fish and Game’s This first regional ERP implementa- BAY-DELTA AUTHORITY Wildlife Conservation Board, the tion plan will incorporate scientific Natural Resource Conservation evaluation of previously planned The Sacramento-San Joaquin Service, and others have also funded actions in light of current knowledge Delta is the hub of California’s two Delta habitat protection and restora- and restoration projects implemented largest water distribution systems— tion projects. Most of the large-scale to date. the federal Central Valley Project habitat restoration projects are in the (CVP) and the State Water Project MORE planning or pilot-scale implementa- (SWP), which, with other local dis- INFO [email protected] tion stages, including those in the ? tribution systems, supply drinking Yolo Bypass and Jepson Prairie- water to over 22 million Prospect Island Corridor in the Californians and irrigation water for North Delta, McCormack- over 7 million acres of productive Williamson Tract (part of the North agricultural land. The Delta’s mosaic Delta Flood Control and Ecosystem of habitats is home to over 750 plant Restoration Project), and Grizzly and animal species, and serves as Slough in the East Delta, and the migratory path for anadromous Decker Island, Central Valley fish and Pacific Frank’s Tract, and Flyway waterfowl, shorebirds, and Dutch songbirds. Slough/Marsh The California Bay-Delta Program Creek in the was established in 1995 to address Central/West Delta. the complex issues associated with Implemented proj- multiple demands for limited water ects include Barker resources. The Ecosystem Slough riparian Restoration Program (ERP) element restoration in the is designed to restore the ecological North Delta, health of the Bay-Delta ecosystem by Cosumnes flood- restoring ecological processes, plain restoration in increasing and improving aquatic and the East Delta, and terrestrial habitats, and minimizing Georgianna Slough stress on the system in order to sup- and North Fork port stable, self-sustaining popula- Mokelumne levee tions of diverse and valuable species. protection and The ERP’s vision for Delta riparian restoration restoration includes increasing natu- in the Central/West ral freshwater flow and improving Delta. channel configurations; increasing The ERP is cur- aquatic foodweb production; and rently in the process reducing stresses from land use and of developing the development, diversions, non-native Delta Regional species, and contaminants. Current Ecosystem ERP Delta habitat actions and tar- Restoration gets include increasing the amount Implementation of aquatic, slough, midchannel Plan (DRERIP), island, wetland (tidal, seasonal, and which will refine permanent), riparian, and upland the ERP planning habitat, including wildlife-friendly foundation for the agricultural land. Delta, including Arrowhead

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THE DELTA

USING TIDES TO salt due to the mixing of the tides in detailed examinations of how this MANAGE THE SYSTEM the Central Delta. Central Delta "pool" of freshwater works. However, our new findings With Frank’s Tract right in the suggest that operating aspects of the middle of the Central Delta, there JON BURAU water projects at the tidal timescale may be opportunities to work direct- U.S. GEOLOGICAL SURVEY could provide great opportunities for ly with the natural tidal processes. managing both ecosystem function Physical changes such as repairing A flooded island in the Central and water supply reliability and the northern and western section of Delta may hold the key to improving improve Delta salinities without levees, or constructing tidal gates water quality during low flood peri- costing more water. ods without additional water costs. could allow operators to manage After a four-month experiment in tidal processes that influence salt MORE Frank’s Tract in 2002, tracking tidal concentrations and other water qual- INFO ? [email protected] flows with drifters and measuring ity conditions, such as temperature salinity and bathymetry, we discov- and depth. ered hydrodynamic patterns that Much more work on fish passage may help address an age-old water and the transport of organisms in quality management problem. We this area is needed, as well as more now know that the tides transport salt through a series of narrow levee breaches into the pool of water in Frank’s Tract. Water sloshes back and forth, but channel configurations keep the salt from draining out on the outgoing tide. The result of this tidal "pumping" and "trapping" process can be a gradual buildup of salt in the Central Delta during late summer through early winter. From the results of computer modeling, we believe the Central Delta acts like a large mixing bowl. This means that freshwater inflows from the North Delta and diversion rates in the South Delta appear to only have an indirect effect on salinity in the Central Delta—and that tidal currents significantly contribute to salinity levels in Frank’s Tract. These findings suggest an opportunity to improve Delta water quality without requiring additional upstream water releases or curtail- ments of pumping by the state and federal diversions and may explain Franks Tract, fed by tides from the False River at left, and by the San Joaquin River at top, and the Old River at right. why at times salinity in the Central Delta can be slow to respond to releasing water from upstream reservoirs, lowering pumping rates by the state and federal diversions, and opening the Delta Cross Channel gates. These management tools are all located on the periphery of the Delta, and their effects are relatively small compared to the transport of

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Fremont cottonwood

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FOCUS ON FISH

restoring the estuary focus on fish

"Instead of asking whether fish can survive, now we’re asking if fish can thrive—can they grow and reproduce?"

LORETTA BARSAMIAN FORMER EXECUTIVE DIRECTOR S.F. BAY REGIONAL WATER QUALITY CONTROL BOARD

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SALMON AND Of the 278 streams we STEELHEAD IN studied, 70 percent definite- BAY TRIBUTARIES ly supported steelhead historically, with an additional nine percent having proba- GORDON BECKER, ET AL. ble or possible runs. CENTER FOR ECOSYSTEM Currently, about half of the MANAGEMENT AND RESTORATION streams have at least resident O. mykiss populations. Three Oncorhynchus species— We did not find any evi- steelhead, coho, and Chinook dence that any Bay Area salmon—are known to use or have stream did not support steel- used the Bay and its tributaries com- head in the past, whereas currently extirpated from the region. For monly. We looked at 278 streams in at least 83 streams are known not to Chinook, we noted only evidence 59 watersheds tributary to the Bay have even resident O. mykiss. We suggesting possible historical use of for evidence of their past or current noted an almost one-third decrease estuary streams. Now, though, sever- presence. We evaluated source infor- in the number of streams containing al streams are experiencing regular mation for reliability, and assigned O. mykiss over time. Streams shown runs. It is clear that some portion of one of four status designations—def- in the future to have only fish of this population is comprised of inite run or population, probable, hatchery origin will lead to a larger Central Valley hatchery strays, but it possible, or no run or population— measured decline in distribution, has yet to be determined if there is a for past (pre-1992) and current pres- since this project is intended to char- component representing a remnant ence/absence of anadromous acterize wild O. mykiss. historical population. Current infor- salmonids. In some cases, we were mation does not appear to justify We found 14 definite, probable, or managing Bay Area streams for unable to determine historical or possible historical coho runs in Bay current run status. coho or Chinook salmon restoration Area watersheds. Coho are now purposes if the associated actions

STEELHEAD STATUS, CONTRA COSTA COUNTY

Historical Information Current Information Definite Run or Population Definite Run or Population Probable Run or Population Possible Run or Population Possible Run or Population No Population Unknown/Insufficient Info. Unknown/Insufficient Info.

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TAKE HOME O. MYKISS AROUND THE BAY: RUN OR POPULATION NOTES DEFINITE PROBABLE POSSIBLE NONE UNKNOWN • Selecting a limited number of priority watersheds in which to attempt to re- Historical 194 14 11 0 59 establish steelhead populations offers the (70%) (5%) (4%) (0%) (21%) highest chance of success. The criteria Current 134 11 6 83 44 for evaluating watersheds should include (48%) (4%) (2%) (30%) (16%) where O. mykiss are reproducing now, where hydrologic conditions remain favorable, the amount of available habi- would conflict with, or detract from, San Francisco Estuary streams are tat, and cost, technology, and logistics. steelhead restoration. important to steelhead restoration by virtue of their proximity to the ocean A third of the study streams had • Restoration plans for priority watersheds and the high level of public support two or fewer surveys on record. should focus on passage and instream in the region. Selecting a limited Almost half had no quantitative flows, as well as habitat improvements number of priority watersheds offers information that we could use to based on natural stream function rather the best chance of success in re- characterize populations, such as than structural changes that have been establishing viable steelhead popula- fish size or relative density. As little shown to be ineffective. tions. Criteria for evaluating water- information was found regarding sheds should include where O. abundance, we noted instances of mykiss are reproducing now, where • Water supply represents a key restora- streams with reliable evidence of O. hydrologic conditions remain favor- tion challenge that will involve re-thinking mykiss population decrease. More able, the amount of available habitat, our approach to granting and condition- than half of the study streams quali- and issues of cost, technology, and ing diversion permits, to controls on fied for this classification. groundwater withdrawal, and to enforce- logistics. Sixty-seven streams presently ment regarding illegal diversions. Restoration plans for the water- have O. mykiss populations with no sheds should focus on passage and total passage barriers between the • We recommend monitoring every two instream flows, as well as habitat fish and the Bay. If we assume that years in priority watersheds to provide a improvements based on natural all 194 definite historical population measure of progress toward restoration stream function rather than structural streams originally supported goals and to allow strategies to be changes. Water supply represents a anadromy, we arrive at a decrease of retooled as our understanding of steel- key restoration challenge that will over two-thirds over time. Of the 59 head natural history improves. involve re-thinking our approach to studied watersheds, just over half of granting and conditioning diversion the historical steelhead systems have permits, to controls on groundwater • Too few resource dollars are going O. mykiss populations with no withdrawal, and to enforcement toward Bay Area streams. Steelhead downstream barriers. regarding illegal diversions. We rec- restoration should be integrated into Our study streams included 39 ommend monitoring every two years watershed management efforts now reservoirs with greater than 200 in priority watersheds to provide a underway. acre-feet capacity. Oncorhynchus measure of progress toward restora- mykiss populations are found in 17 tion goals and to allow strategies to • Restoring steelhead will benefit numer- watersheds that do not have dams, be retooled as our understanding of ous fish and wildlife species that use while 15 watersheds have popula- steelhead natural history improves. aquatic and riparian habitat. tions downstream from dams. Re- MORE visiting dam operations has the INFO [email protected] potential to substantially improve ? conditions for O. mykiss in both priority and non-priority watersheds SCIENCE • How does groundwater around the Estuary. On dammed QUESTIONS use affect steelhead habi- streams, the effect of flow alter- tat in Bay Area streams? ations on downstream habitat should be evaluated, and releases should be • Have studies shown that groundwater provided to maintain fisheries in pumping reduces the extent and dura- good condition. tion of pool habitat in systems limited by over-summering conditions?

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TAKE HOME RESTORING CENTRAL a moratorium is in place on new VALLEY CHINOOK water withdrawals and transfers in NOTES SALMON AND the Columbia Basin. While fish and water managers are concerned with STEELHEAD — ADVICE • Scientists need to develop the data the impacts of single water actions on and models to characterize and TO CALIFORNIA specific fish runs as urbanization and predict the effect of water policy agricultural development increase, actions on temperature as well as their real concerns are the cumulative JIM ANDERSON flow, and then link these proper- impacts of many future water with- UNIVERSITY OF WASHINGTON, SEATTLE ties to fish life history fitness drawals. But water and fish managers through their physiological and simply do not have the scientific behavioral mechanisms. Fishery scientists and managers in tools to assess these cumulative • Only with an ability to evaluate the Pacific Northwest have focused impacts, especially in the face of individual decisions in terms of on the effects of freshwater flows on global warming, and as a result, man- their cumulative impacts will man- salmon and steelhead for 40 years; agement has become largely discon- agers be able to effectively balance however, recent research indicates nected from science. Today there is the competing demands for water. that water temperature may be just as more controversy, uncertainty, and important as flows. legal action in the basin than ever determines when eggs emerge from Although my own studies comprise before. the gravel, the timing and survival of only 20 years, some of my observa- New research points to an impor- smolt migrations, and when and tions, in terms of science and policy, tant factor that would reconnect where the adults spawn. Temperature may provide a useful perspective to water management and fishery sci- also appears to be a primary factor in California in dealing with very simi- ence. In particular, the research the growth and survival of salmon lar issues. We can consider independ- shows that temperature is of much and steelhead in the ocean. ently the evolution of fish/water sci- greater importance than flow in struc- ence and management over the past turing the life-history strategies of MORE four decades. After the first decade of salmon and steelhead. Temperature INFO ? [email protected] research, culminating in seven data points relating flow and smolt sur- STREAM TEMPERATURE AND SALMON vival, fisheries scientists universally believed that increasing flows in the 1 3 4 6 7 10 1 3 4 6 7 10 2 5 8 9 2 5 8 9

system produced significant positive 15 II 15 III improvements in juvenile fish sur- IV vival. Consequently, managers estab- 15 15 lished a modest flow augmentation 15 I program of 3.5 million acre feet to 5 20 20 assist smolts on their spring migra- 20 tion. Today, after over 10,000 meas- 1111 1122 11331144 11661177 1188 1199 2200 2211 22 15 131211 10 11 12 1314 1617 18 19 20 21 22 urements of fish survival, there is no Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul clear evidence that water augmentation in the Columbia/Snake River Adults and Fry in Mill Creek system improves fish survival. 1 However, the flow augmentation program now targets up to 16 MAF, and 0.8 0.6 • Will 0.4 Adults 35mm fry SCIENCE anthropogenic 0.2 QUESTIONS and natural 0 changes in Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul stream temperature patterns shrink the window of opportu- Salmon life history strategy fits within a window of opportunity determined by seasonal nity for certain salmonid life changes of water temperature with stream elevation. The upper panel shows isotherm (°C) history strategies? contours representative of northern Sierra Nevada streams. The lower panel shows adult and fry relative abundances in Mill Creek, a tributary of the Sacramento River. Spring chinook • What changes in water opera- upstream migration occurs to the left of Line I, which depicts the 20°C isotherm that blocks migration. Line II depicts the elevation at which salmon can survive the summer warming. Area tions might expand windows III depicts 12° and 14°C isotherms, which bracket the temperature range for spawning. Area IV of opportunity for salmonid life depicts the modeled fry mergence pattern. 68 history strategies? SOE layout 1 8/12/04 8:37 PM Page 69

FOCUS ON FISH

TAKE HOME HOW FISH USE The Estuary’s tidal marshes also TIDAL MARSHES support a somewhat unique resident fish community. This includes the NOTES longjaw mudsucker, threespine stick- • We need to remember that tidal KATHRYN HIEB leback, rainwater killifish, and west- marshes are a mosaic of habitat CALIFORNIA DEPARTMENT OF FISH ern mosquitofish, which are rarely types, including pannes, vegetated AND GAME collected in the open waters of the marsh plain, emergent vegetation, Estuary. These resident species are in Tidal marshes are one of the least- and unvegetated channels, and each some respects even less studied than studied fish habitats in the Estuary. species and life stage may use these the transient species, as they occupy habitat types differently. The Estuary supports a rich fish habitat types within the marshes that fauna, including transient, resident, have been rarely sampled. Recent and migratory species, with habitats studies in San Pablo Bay marshes ranging from deep channels to eel- have shown that there is a transition grass beds, tidal flats, and tidal marsh- from resident species in the higher es. Many species found in the open elevation marsh habitat types to tran- waters of the Estuary have been col- sient species in the lower elevation lected in tidal marshes, but the role habitat types. In designing restoration and importance of these marshes to projects and monitoring plans we the Estuary’s fishes are largely need to remember that tidal marshes unknown. This is especially true for are a mosaic of habitat types, includ- many of the transient species that use ing pannes, vegetated marsh plain, the Estuary as a nursery, including the emergent vegetation, and unvegetated surfperches, silversides, and many of channels, and each species and life the gobies, sculpins, and flatfishes. stage may use these habitat types dif- The mere presence of juveniles in a ferently. tidal marsh does not mean that it is a MORE nursery. We do not know if densities, INFO [email protected] growth, or survival are higher in the ? Estuary’s tidal marshes compared to other nearby juvenile habitats or if WEST COAST THREESPINE STICKLEBACK juveniles are able to successfully emigrate from all of the Estuary’s marshes to the species’ adult habitat. In addition, we lack basic life history information for some of these transient species, such as the timing of immigration to marshes, duration of stay, and habitat types used in the marshes.

• Are densities, SCIENCE QUESTIONS growth, or survival higher in the Estuary’s tidal marshes compared to other nearby juvenile habitats?

• Are juvenile fish able to successfully emigrate from all of the Estuary’s marshes to the species’ adult habitat?

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TAKE HOME CAN WE SEPARATE and Delta smelt populations caused HUMAN FROM NATURAL by exposure to toxic pesticides from NOTES INFLUENCES ON FISH? mortality due to poor feeding success. Use of this information with estimated birth-dates of individuals • There are many complex influences WILLIAM A. BENNETT and statistical analyses of monitor- on fish populations at regional and JOHN MUIR INSTITUTE ing data is currently helping to iden- local scales. Subtle and unseen nat- OF THE ENVIRONMENT tify the relative contribution of fish ural effects can have larger influ- BODEGA MARINE LABORATORY losses in water export operations. UNIVERSITY OF CALIFORNIA, DAVIS ences than episodic and conspicu- Recent statistical analyses also show ous human effects. that larger-scale climate cycling can Although human alterations to the have direct effects on populations as Estuary are frequently promoted as well as potential indirect influences • Separating human from natural causes for declines in its fish popu- on the Estuary's capacity to main- influences on fish populations lations, little work has been done to tain fish abundances. Climate remains a challenge, and one that distinguish among a variety of cycling or "regime-shifting" has will require considerable investment before reliable management potential human and natural causes, been shown to have a dominant and restoration strategies can be or at the level of the population as influence on oceanic fish beyond determined. That said, we can now that attributed to human fishing. opposed to individuals. This prob- distinguish and measure many Under certain circumstances, the lem is scientifically challenging effects and are developing models because human and natural influ- influences of natural climate cycling to provide quantitative estimates of ences may be co-occurring and may also outweigh other human and these effects on populations. interacting in complex ways to natural influences on fish popula- cause population declines. tions within the Estuary. • It will be crucial to maintain a pop- Recently, interdisciplinary MORE ulation-level focus and an aware- research teams have been successful INFO ? [email protected] ness of how larger-scale climate at separating mortality in large num- cycles may interact with other influ- bers of individuals of striped bass ences within the Estuary to collectively determine fish abundances. STRIPED BASS • We do know that El Niños con- strict or delay spawning season and may decrease carrying capacity of the habitat. We predict that Delta smelt will do poorly under global warming.

DELTA SMELT

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POLITICS & PLUMBING

politics & plumbing

"The Estuary fits into the grand scheme of water management in California through both physical connections and political connections. We increasingly hear about how things happening on the Klamath River are tied to Southern California; how things happening on the Colorado River in San Diego are tied to the Bay- Delta system…"

TIM RAMIREZ CALIFORNIA BAY DELTA AUTHORITY

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A REGIONAL rather than by agencies in ing one that established regionally APPROACH TO Sacramento or Washington, D.C. based seats for public members of the new California Bay Delta WATER MANAGEMENT State and federal agencies, under Authority to govern CALFED. And the umbrella of the CALFED Bay perhaps most significantly, voters Delta program, continue to invest in passed Proposition 50, the largest PATRICK WRIGHT programs to meet the state's water water bond in California history, CALIFORNIA BAY DELTA AUTHORITY needs, but CALFED-directed water- largely on the promise of more fund- supply projects are focused primari- ing dedicated to reducing depend- The U.S. Department of Interior's ly on improving system-wide relia- ence on imported supplies. cutoff of California's surplus sup- bility and reducing bottlenecks in plies from the Colorado River sent the Delta. The recent emergence of None of this means that a failure shock waves through the state's strong local and regional programs in negotiations to reduce California's water system and the hallways of the marks the beginning of a historic surplus from the Colorado River will Legislature and Congress. But from shift from a decades-long era of cen- not have serious repercussions. As a statewide perspective, more tralized state and federal water plan- the success of the CALFED program revealing is the lack of panic from ning that began in the 1930s, to a demonstrates, money and water are the Metropolitan Water District regionally and market-driven more likely to flow to regional proj- (MWD) and other local water agen- approach that better reflects the ects under a comprehensive plan that cies, which have been developing state's variable hydrology, regional reduces conflict than to those under alternative supplies in an enlight- differences, and the growing sophis- a cloud of gridlock and litigation. ened shift toward regional water tication of local water districts. The CALFED and Colorado River management planning. agreements provide the framework To provide a framework for these and the stability for regional and Despite losing up to 600,000 acre- efforts, CALFED has brought the market-based water plans already feet of supply after two consecutive water and environmental interests well under way in reshaping dry years—enough to supply 3 mil- together after decades of gridlock, California's water future. lion people—MWD is saying that reducing conflicts over Delta exports shortages are at least two years away, and smoothing passage for three MORE and there's no talk of rationing. What consecutive water bonds. Billions of INFO [email protected] gives? In the past, agencies faced dollars are now flowing to local and with shortages would have demand- regional communities throughout the ed to be bailed out by a new genera- state to meet their most pressing tion of state or federal water projects. water needs. Instead, they are taking matters into Four bills promoting regional their own hands by developing efforts were enacted in 2002, includ- diverse, regionally-based plans that reduce their dependence on the Sacramento-San Joaquin Delta and WATER SUPPLY RELIABILITY the Colorado River and that are bet- WATER USE EFFICIENCY ACCOMPLISHMENTS ter tailored to each region's variable climate and hydrology. Like prudent bankers, regional 5 agencies are developing portfolios of 15 5 assets to improve the quality and 28 8 No. of Projects Awarded 10 12 reliability of their supplies. From the 5 3 Funding ($ Million) Sacramento Valley Water Bay & Delta Sacramento Valley Management Agreement to the Santa Total Reported Ana Watershed Project Authority, Yield (TAF) Local these agencies are investing in sur- 29 face and groundwater storage, con- Fed 45 servation, reclamation, desalination, 14 3 22 State 21 land retirement, water transfers, and 8 3 7 14 9 other projects to diversify their San Joaquin Valley So. California Region plans. With few exceptions, the plans are being developed locally

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AN AGRICULTURAL meet water supply needs is over and ground, everybody who participated PERSPECTIVE will not reoccur again in our life- wants to know exactly what the rules ON CALIFORNIA’S times. We cannot depend on large- are for taking it out and who gets it. scale planning or construction pro- And by doing that you have the vest- WATER MANAGEMENT grams or dollars from Washington or ed interest of each of those partici- Sacramento to make Kern County pants, motivating them to make sure BRENT WALTHALL agriculture viable. That responsibility that that groundwater is managed in KERN COUNTY WATER AGENCY lies with the Kern County Water a responsible way. The best ground- Agency and its members. So we water management plans aren’t those embarked on a very ambitious local that are mandated by Sacramento but The State Water Project (SWP) projects program focused mainly on those that are in fact are necessary to supply is very important to our water conservation and conjunctive operate groundwater basins. The agency. We have contracts for about groundwater use. Kern County is construction and operations of our a million acre feet, and that water is well known as one of the areas in the groundwater basins is expensive. We what gets us through long- and short- state that has aggressively pursued take water from the SWP. We are not term droughts. In dry years, current groundwater conjunctive use as a subsidized; the SWP contractors pay reliability curves show that about 20 way to manage water supply reliabil- 100 percent of the cost of that proj- percent of the time we can expect ity. We have built over 10,000 acres ect, and in some cases pay a little only 50 percent of that water. So of storage—groundwater percola- more. We are thus accustomed to over the long term, in 1 out of 5 tion—basins, and 60,000 acre feet paying the actual cost of water deliv- years we can expect to have only one per month can be put into the ground ery, so when it comes to building our half of our SWP supply available. In own local facilities, we have been 1991, as an agricultural contractor, willing to absorb that cost ourselves, we got zero water, which is not con- “Agriculture largely with local dollars in conjunc- ducive to farming in California. That tion with outside interests. was a difficult year for us; it was a should not be wake-up year for us. It was the first Participants in our groundwater year it had ever happened, and it the new supply banks come from throughout the made drastic changes in the way we state. The Metropolitan Water viewed our future. Since then, we of first resort.” District partners with the Semitropic have done additional studies on relia- Water District in our area, and they have a groundwater conjunctive use bility. What we examined most in years when water is available. program that they operate them- specifically was if the 1987-1992 That is a lot of water, and it can be selves. That program also includes drought recurred, how would it affect done fairly quickly. We have over Santa Clara Valley; it has included us? Under the existing environmental 124 recovery wells throughout our the City and County of San regulations and existing infrastruc- service area, many of them operated Francisco in the past, and the ture, in a repeat of that drought, we by our 13 member units. They were Environmental Water Account. Our would have about a 40 percent sup- built so that water can be taken back groundwater banks can be used not ply, not sufficient to sustain agricul- out quickly. They are large—and only for our own benefit, but for the ture over the long term in our area. quite expensive—wells. We have benefit of others as well. There are potential future reduc- over 409,000 acre feet that can be tions to our water supply: additional extracted from those basins on an MORE ESA listings, increasing urban annual basis. So we can meet a sig- INFO ? [email protected] demands. We believe that the new nificant portion of our demand from Bulletin 160 relies far too heavily on our own internal, underground stor- securing additional supplies from age reservoirs—if we can fill them. agriculture in order to meet those We have the infrastructure; we urban and environmental needs. understand the groundwater basins Agriculture should not be the new well enough; and we have imple- supply of first resort. mented groundwater management plans consistent with AB 3030. So what do we do? Our long term water supply future is not assured Our experience is that the best and is in fact threatened. The era of groundwater management plan is a large infrastructure projects built by groundwater conjunctive use pro- state and federal governments to gram. Once you put water into the

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AN URBAN PERSPECTIVE lars are being spent on ecosystem the South Delta Improvements restoration, a program begun in late Program looked like they were on the 1994 when several CUWA member way to being resolved as a result of STEVE MACAULAY agencies committed more than $30 separate discussions among these CALIFORNIA URBAN WATER million with the recognition that parties. Fishery agencies have been AGENCIES (CUWA) urban water supply reliability is heavily engaged in the issues related directly linked to a healthy aquatic to environmental features of a possi- 2003 was a year of change: A per- environment. This was a risk nine ble program. Discussions with envi- manent Bay-Delta Authority was cre- years ago, but it was followed by a ronmental organizations commenced ated, the CALFED Bay-Delta financial commitment to ecosystem immediately upon development of a Program had its third full year; restoration in three subsequent bond proposed program, and the public decades of study of the "Delta con- issues. CALFED is founded on a involvement process continues. This veyance problem" culminated in a principle that a comprehensive (more program is very much a work in Draft EIR/EIS; and appropriations balanced) approach to restoration progress. from both the state and federal gov- works best. The "CALFED way" By spring 2004, a "Delta improve- ernments came close to collapsing, makes environmental restoration and ments package" had emerged, which due to continued, serious budgetary affordable improvements in water both the Bay-Delta Authority Board problems. supply complementary actions within and the Bay-Delta Public Advisory an overall program. In 2004, the key issues remained— Committee were briefed on. The as they have been for 30 years— At the time this abstract was first "package" included water quality water supply reliability, improve- prepared (mid-August 2003), there improvement, ecosystem restoration, ments in water quality, and conflicts was cautious optimism that a suc- and other features, including propos- between water diversions and fish. cessful solution could be reached. als to address the quality of water The promise of CALFED has been Longstanding conflicts among State coming into the Delta from the San resolution of these problems and Water Project and Central Valley Joaquin River. The "package," as it developing a physical/institutional/ Project export water users, the may be modified throughout the regulatory solution that works within Department of Water Resources and summer of 2004, will be an alterna- the comprehensive CALFED frame- the U.S. Bureau of Reclamation tive in a Draft EIR/EIS to be issued work. Hundreds of millions of dol- regarding sharing of the benefits of in late 2004. Urban water agencies are particularly interested in the proposals to improve Delta water quality for drinking water purposes.

MORE INFO [email protected]

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AN ENVIRONMENTAL the CVPIA, according to the meas- only 43,000 acre-feet has been PERSPECTIVE urement system in place when the acquired for the EWA through oper- CALFED agreement was signed. ational flexibility, 152,000 acre-feet Furthermore, the Department of the less than the 195,000 acre-feet that SPRECK ROSEKRANS Interior has not yet revealed how it were projected by project operators ENVIRONMENTAL DEFENSE will implement the Appellate and fishery biologists when the Court’s ruling on the "Primary EWA was developed. The flexibility to modify water Purpose" of the B2 account. Finally, There are opportunities for these projects for the protection and Interior has offered only a token gaps to be filled, but it is unclear restoration of fish and wildlife in the allocation of water pursuant to the whether the federal and state agen- Central Valley and Bay-Delta is sig- "reoperation" provision of Section cies have the institutional and politi- nificantly less than what the B1 of the CVPIA. CALFED ROD provided when it cal will to do so. Implementation of the was signed three years ago. Both the MORE Central Valley Project Improvement Environmental Water Account has INFO been less contentious than that of ? Act’s B2 account and the Spreck_Rosekrans the CVPIA operational provisions. Environmental Water Account are @environmentaldefense.org deficient by hundreds of thousands Its long-term funding stream is of acre-feet. uncertain, however. Also, the operational flexibility that was intended to In 2003, the B2 Account used provide supplies to the EWA has only 462,000 of the 800,000 acre- fallen far short of expectations. Over feet of dedicated yield provided by three years, an annual average of

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HIGHLIGHTS OF THE CALIFORNIA THE POTENTIAL FOR of recycled water used in California WATER PLAN 2003 WATER RECYCLING from approximately 500,000 acre- feet annually to about two million KAMYAR GUIVETCHI acre-feet annually by 2030. This CALIFORNIA DEPARTMENT JONAS MINTON could free up enough fresh water to OF WATER RESOURCES CALIFORNIA DEPARTMENT OF meet the household water needs of WATER RESOURCES 30 to 50 percent of the additional 17 New Planning Framework: million new Californians expected • Uses input from a 65-member public California is able to meet many, by 2030. An investment of $11 bil- advisory committee but not all, of its water demands lion (approximately $400 million • Develops water "portfolios" using 1998, most years. Except in multi-year annually) would be needed to 2000, 2001 data droughts, most urban areas have suf- achieve this goal. • Develops regional reports reflecting ficient supplies. However, even in The task force identified 26 issues regional goals and plans average years, some agricultural and and made recommendations for • Uses multiple scenarios to account for environmental needs are not fully addressing obstacles, impediments, future uncertainties and risks met. In addition, California contin- and opportunities for California to ues to overdraft some of its ground- • Uses many strategies to help meet future expand recycled water use. Among demands water basins and surface reservoirs. the recommendations were: By the year 2030, California’s population is projected to increase by • Expand funding for health Issues and Challenges: about 50 percent—17 million more research, recycling projects, • There are gaps in data and information Californians needing water for public awareness, and • Modeling tools not fully developed academic programs domestic use and for the commerce, • Revising the process impacted schedule industry, and agriculture that will • Engage the public in an active • Staff and budget are reduced employ them. If this is not formida- dialogue in the media, communi- ble enough, we must also reduce our ties, and schools across California • There is a lack of consensus whether use of Colorado River water. For new surface storage should be included • Adopt uniform state-wide regula- as a future strategy many years, we have been using tions for dual plumbing and indoor more than our 4.4 million acre-feet use of recycled water per year allocation. Recommendations • Include conservation, improved for the Future: In order to balance our demands storage, desalination, and volun- for water with other values, such as • Promote and assist regionally based, inte- tary water exchanges between grated, multi-resource planning protection of our environment and California communities and indus- public health, we must seek a port- tries as part of the solution. • Improve coordination of land use plan- folio of new water supplies and ning and water management Most recycled water projects now water management options— • Diversify regional portfolios using 25 occur in urban areas. Yet other increased water conservation, con- resource management strategies potential uses of recycled water junctive use of surface and ground might include wetlands restoration, • Reduce uncertainty (fill in data and tool water, desalination, storage in sur- stream flow augmentation, or gaps) face and groundwater basins, and Estuary enhancements. water recycling. Estimates for Additional MORE A 40-member Recycled Water Demand by 2030: INFO [email protected] Task Force, including federal, state, ? • To accommodate 17 million more and local governmental and private Californians: need an additional 2-3 mil- sector entities, environmental organ- lion acre-feet izations, public health professionals, • To recover groundwater overdraft: need world-renowned researchers, water an additional 1-2 million acre-feet managers, and community activists • To restore the environment: more is was established pursuant to required (range being estimated) Assembly Bill No. 331. That bill, authored by Assembly Member • To maintain irrigated agriculture (about Goldberg and signed by Governor the same as now) Davis in 2001, found that the poten- MORE tial exists for increasing the amount INFO [email protected]

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DEVELOPING to reduce supply uncertainty. MWD MWD also supports increasing the A RELIABLE WATER supports the following programs, to supply of water, within the constraint SUPPLY PORTFOLIO reduce uncertainty over the needs of of financial affordability, through the the environment: following actions:

TIMOTHY H. QUINN • The CALFED Science Program, to • Implementing the Sacramento METROPOLITAN WATER DISTRICT better understand the environment’s Valley Water Management OF SOUTHERN CALIFORNIA needs and possible resolutions to Agreement, which develops water water shortages; through conjunctive use programs • CALFED’s Ecosystem Restoration to help meet Delta water quality Coping with uncertainty in water objectives and implements supply is the biggest concern of urban Program, to recover endangered species; and improvements in infrastructure, water agen-cies. Even a threat of which will reduce gross river diver- shortage creates concern for the econ- • The Environmental Water Account, sions, leaving additional water in omy. About a third of Southern to give fishery managers the water critical reaches of the Sacramento California’s water supply comes from they need to take action when most River and tributaries. the State Water Project (SWP). As needed. • Negotiating agreements with will- originally envisioned, the SWP was Recognizing the variable nature of to be a nearly 100% reliable source. It ing sellers to transfer water during precipitation, MWD plans to survive dry years. would capture water in the wettest droughts by storing water, made pos- portion of the state, the north coast sible by the following actions: None of these programs in isolation mountains, and deliver it to urban provides the needed reliability. Yet, water users in the Bay Area, Central • CALFED’s South Delta together they can work synergistically Coast, and Southern California, and Improvement Program, including to meet the needs of the Estuary and to agricultural water users in the increasing the peak capacity at the the economy of California. Central Valley. However, changing Banks Pumping Plant, to capture environmental and financial priorities more water when it is available; MORE kept the SWP from building its full • Investments in demand manage- INFO [email protected] vision. As a result, the ability of the ment, to have water to store in wet ? SWP to deliver water depends greatly years; and on precipitation. • Investments in regional storage In response, the Metropolitan Water capacity, to provide a location to District (MWD) works in many ways place any extra water captured.

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TAKE HOME CALIFORNIA’S ECONOMY and other human-capital intensive CAN GROW WITH techniques. In many cases, water use NOTES A NEW APPROACH TO efficiency is a profitable investment. Cost-effective conservation tech- MANAGING THE ESTUARY • Additional baseline withdrawals niques for homes and businesses are from waterways aren’t neces- available now. The Institute’s recent sary in future decades, and GARY WOLFF report, Waste Not, Want Not: The baseline withdrawals can be THE PACIFIC INSTITUTE FOR STUDIES Potential for Urban Water Use reduced if conservation and effi- IN DEVELOPMENT, ENVIRONMENT, Efficiency in California presents data ciency are pursued more AND SECURITY supporting a softer path. aggressively. We must keep in MORE mind that baseline withdrawals In California and most modern INFO [email protected] (those made to satisfy average economies today, economic growth www.pacinst.org/reports/urban_ annual consumption needs) are does not require more water. Statistics usage/waste_not_want_not_full_ different in concept than with- for the United States and other coun- report.pdf drawals made to fill storage tries show a sustained and (surface or subsurface). In other clear "de-coupling" of eco- words, our findings do not rule THE LINK BETWEEN WATER USE out additional withdrawals to nomic growth and water AND ECONOMIC GROWTH CAN BE BROKEN extracted from the environ- 8000 1000 support new storage projects. ment beginning several Presumably these withdrawals 7000 900 /yr) decades ago. 800 3 could take place in wet years, 6000 with minimal environmental California rivers and 700 5000 impacts. groundwater basins are nearly 600 all over-allocated. New water 4000 500 • We need to think more clearly is simply not available. The 3000 400 and "separately" about with- $1996 US GNP 300 drawals for storage versus with- health of our ecosystems, the 2000

strength of segments of our 200 Withdrawals (km Water drawals to meet baseline needs. economy that depend on 1000 100 These categories have been healthy aquatic systems (e.g., 0 0 blurred historically, which is fishing, recreation, tourism), 1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 politically advantageous for and the quality of our chil- those who advocate more with- dren’s lives would be signifi- CALIFORNIA’S INDOOR RESIDENTIAL WATER USE drawals—because they can jus- cantly improved if we took tify everything as a response to 6000 less water from natural sys- No Efficiency Improvements drought. But we need to stop tems, at least some of the time Current Use doing that, and justify with- 5000 Cost-Effective Efficiency* (e.g., dry years, when margin- drawals for storage based on al flows may have higher eco- 4000 drought needs and withdrawals logical value). for baseline based on baseline 3000 needs. Certainly, these are relat- The good news is that ed (a growing baseline means 2000 California’s economy can the percentage of years that are grow for decades to come

Million Cubic Meters/Year 1000 drought years will grow as well), without taking more water but they can and should be sep- from the environment. The 0 arated analytically. "hard path" of centralized cap- 1980 1985 1990 1995 2000 2005 2010 2015 2020 ital investments in concrete and steel is slowly being con- • How much more than baseline needs can we withdraw in wet verted to a "soft path" that SCIENCE years for storage purposes? supplements existing infra- QUESTIONS structure with decentralized Recent studies suggest that periodic pulse flows are very important for ecological rea- investments in efficient appli- sons; that is, that the economic notion of diminishing marginal utility is at least par- ances, public education and tially wrong when it comes to instream flows in some streams. Maybe higher annual behavioral changes, water flows have diminishing utility some years but strongly increasing utility once every recycling and dual piping sys- three-five years or so. The three-five years is an example, which we need science to tems, land use practices that estimate, and similarly we need science to estimate the size of the pulses that are recharge groundwater aquifers, beneficial.

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TAKE HOME CAN WE PUMP MORE • Are there other ways of providing WATER AND PROTECT water to people than the freshwa- NOTES THE ENVIRONMENT? ter sources to the Estuary? Such questions raise still more • We need to know more about the questions, for example, how do we biology of at-risk species in the Delta, DIANA JACOBS define "need"? Do we aim for just especially population-level effects of CALIFORNIA DEPARTMENT OF FISH barely getting enough or for getting water management actions. We must AND GAME the most we can get? With regard to continue to invest in science. We ecosystem needs, we have the scien- must continue to collaborate, have The major freshwater sources to tific challenges of not knowing all patience, and acquire more knowl- the Estuary are the rivers of the the major determinants of ecosystem edge. Central Valley. These rivers are also health and not knowing the relative the source of drinking water for two- importance of those factors we can • Will proposed thirds of the state’s population and manage. For example, we may SCIENCE QUESTIONS flow changes cause provide irrigation for millions of assume that freshwater inflow is one detectable effects acres of farmland. Providing water management knob we can adjust. in the ecosystem? for people and farms at this large However, as we study the Estuary scale requires massive infrastructure we find that detecting the effects • Will proposed flow changes add and substantial control of water of flow changes in the context of to cumulative impacts on the ("operations"). Large-scale struc- everything else which influences ecosystem? tures and operations such as the the system—whether natural or State Water Project and the federal anthropogenic—can be difficult. Central Valley Project have large heavily on scientific research target- and long-lasting effects on the ed to key uncertainties. The ecosystems of rivers and the Bay- “The stakes are CALFED Record of Decision Delta Estuary. In the future, we will (ROD) proposes increasing pumping likely see big changes in operations high for people from the Delta to 8,500 cfs, under but not necessarily to infrastructure. the South Delta Improvements What will operations changes mean and ecosystems.” Program. The ROD also requires to the environment? The way we that this apparently incremental manage water may create conflicts change in diversion be conditioned among competing human uses of upon avoiding adverse impacts to Different policy perspectives will water: the stakes are high for people fishery protection and in-Delta water lead down different paths in the face and ecosystems. interests. of incomplete knowledge. Using the The premise of the California CALFED approach means that our MORE Bay-Delta Program, CALFED, is management decisions should be INFO [email protected] that resolving conflicts among and incremental and balanced, and rely between human water uses and ecosystems requires a solution commensurate with the problems—one that is large and comprehensive. The CALFED program strives to resolve conflicts over water by taking a balanced, comprehensive approach. Some of the major challenges facing the CALFED program can be restated in several questions: • How much freshwater does the Estuary need? • How much water can we remove from the Estuary and have a sustainable estuarine ecosystem? • How much freshwater do people need?

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WHERE TO FROM HERE? coordinated those actions upstream the economy of the county from on the Yuba and Merced, and we’ve which the water is transferred. The done some power bypasses on the question is, do we continue the JERRY JOHNS American to better protect upstream EWA or not? Who benefits? What CALIFORNIA DEPARTMENT OF resources when moving water south. size should it be? How do we split WATER RESOURCES Over these last three years, 918,000 the costs between the water uses and acre-feet of water has been used for the public in a reasonable and effec- For the first time in recent history, fishery actions at a cost of about tive manner? both agricultural and urban water $120 million. For perspective, when Large problems are best addressed users are supporting the continuation New Melones, the last major on- in pieces; you have to take things of the Environmental Water Account stream reservoir was built, when it apart, figure out how to best inte- (EWA) and maybe even paying for had yield, it had yield of 200,000 grate the problems—figure out what it. The EWA was the glue that put acre feet. Over the last three years, to do with EWA, Delta water quali- CALFED together. We had the envi- we’ve been able to provide that kind ty—and then put it all back together ronmental community and fishery of yield to the system without build- again in a reasonable fashion. The agencies looking for additional envi- ing a new on-stream reservoir. This is key is getting to an integrated solu- ronmental protection. And we had a big benefit to the system. It’s not tion that works. Adaptive solutions water contractors that felt they had cheap, and we have to figure out how are a better way to handle additional already given enough, and wanted to finance it as we move down the environmental protection. We need more supply. The EWA provided road. What price peace? We have, for to have a regulatory floor; a base- both water supply reliability and a the first time in a long time, the envi- line. But if we’re looking for water trajectory for recovery for the fish ronmental and the water folks getting supply assurances or a trajectory for and environmental folks. along with Delta actions. recovery, we can do that better in an The EWA is the piece that pro- We are moving more to a north- adaptive mode that incorporates sci- vides the environmental protection south strategy of moving water for ence as we’re making decisions. As that allows us to move forward in a EWA; it provides upstream benefits we try to put these things together, productive way. The ROD says that and takes advantage of capacity that we need to remember that every- the EWA is to provide protection for becomes available to EWA. We’ve thing that counts can’t be counted. fish in the Bay-Delta system with no taken actions on both the state and We are going to have to move for- changes in the operations of the federal sides of the system to pro- ward sometimes when we don’t CVP and SWP in an uncompensated vide assurances to both projects. We have all of the answers to all of the manner. It was a four-year program, need to coordinate this program with problems. We can’t count all the fish a test, to see if we could make other types of transfer programs in species we’re worried about. We things work—get the water to pro- the Estuary. In terms of transfers, we can’t do everything. We have to vide environmental benefits. need to remember three things. You move forward with the best knowl- Management of the EWA is done can have no injury to legal users of edge we have. water. You can have no unreasonable by the three state and federal fisheries MORE effects to fish or wildlife and no agencies and the two state and feder- INFO ? (916)653-8045 al water agencies. Operators and fish unreasonable economic impacts to folks sit down in the room at the same time and make decisions about EWA EXPENDITURES OCTOBER 2000 THRU SEPTEMBER 2003 how to operate the SWP and provide 208 200 additional protection for fish. Salmon/Steelhead 26 Salmon/Steelhead/Delta Smelt The EWA is working. We’ve had Delta(Conversion) VAMP 149 two dry years and an above-normal 150 Salmon/Delta Smelt year, with no big environmental or Salmon/Delta Smelt(CVP) water fights, nothing like we saw in 69 the mid-1990s. The fisheries benefit- 100 ed—we have taken actions way 169 before you could have done them 69 69 65 66 under the ESA—and water supply 50 49 reliability has been there. In 2002, we 52 18 38 62 89 had a 70 percent supply to the CVP 29 28 Amount Of Water (Thousand Acre-feet) Amount Of Water 31 32 and the SWP. We’ve focused princi- 20 9 5 2 19 17 17 3 13 pally on Delta actions, but we’ve 0 JFMAMJJASONDJFMAMJJASONDJFMAMJJAS 2001 2002 2003 80 SOE layout 1 8/12/04 8:38 PM Page 81

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KEY ON P. 88 Hieb, Kathryn, Cal Fish & Game. McKee, Lester, Jon Leatherbarrow, Robin PRESENTATIONS* Understanding How Fishes Use the Estuary’s Tidal Marshes. Grossinger, Sarah Pearce, S.F. Estuary Institute. Our Changing Albertson, Joy, S.F. Bay National Holmes, Marc, The Bay Institute. Understanding of the Importance of Wildlife Refuge. Snowy Plover Funding Wetland Restoration Tributary Stormwater Loads to Management Challenges in San Projects in the Estuary. Contamination of San Francisco Bay. Francisco Bay. Hooper, Kim, Cal EPA. Lessons Merkel, Keith W., Merkel & Anderson, Jim, University of from the PBDEs – The Value of Associates. Eelgrass Inventory, Washington. The Restoration of Monitoring Community Body Management, and Restoration in San Central Valley Chinook Salmon and Burdens Using Breast Milk. Francisco Bay. Steelhead – Advice to California. Hutzel, Amy, California State Minton, Jonas, California Baye, Peter R., Wetlands and Coastal Conservancy. San Francisco Department of Water Resources. Water Resources. Tidal Restoration Bay Salt Ponds: Long-Term California and the Potential for in Weedy Wetlands: Past, Present, Restoration Planning. Water Recycling. and Future. Jacobs, Diana F., Cal Fish & Game. Monroe, Michael W., U.S. EPA. Habitat Restoration and Becker, Gordon. See Leidy, Rob. Can We Pump More Water from Enhancement: Accomplishments and the Estuary and Still Protect the Bennett, William A., John Muir New Science – An Overview. Institute of the Environment, Environment? Bodega Marine Laboratory. Can We Mount, Jeffrey F., U.C. Davis. Leidy, Robert, U.S. EPA, Gordon Wasted Waters: Do Floods in the Separate Human from Natural Becker, Brett Harvey, Andrew Central Valley Constitute Beneficial Influences on Fish Populations in the Gunther, Center for Ecosystem Use of Water? Estuary? Management and Restoration. Past and Present Status of Steelhead in Pawley, Anitra, The Bay Institute, Collier, Tracy K., NOAA Fisheries. and Bruce Thompson, S.F. Estuary San Francisco Estuary Streams: Developmental Toxicity of PAHs: An Institute. Establishing Indicators of Implications for Restoration. Increasing Concern for Estuarine Estuarine Health: Progress and Fish. Lewis, David, Save the Bay. Citizen Challenges. Davis, J.A., B.K. Greenfield, J.E. Involvement and Benefits to Quinn, Timothy H., Metropolitan Leatherbarrow, N. David, D.R. Restoration. Water District of Southern Oros, D. Yee, M.S. Connor, S.F. Lichten, Keith H., S.F. Bay Regional California. The Estuary and Estuary Institute. Choosing a Future: Water Quality Control Board. Southern California; Developing a The Long-Term Fate of Persistent Stormwater Contamination: Simple Reliable Water Supply Portfolio. Chemicals in San Francisco Bay. Things That Work. Reed, Denise J., University of New Orleans. Sustainability in Wetland Faber, Phyllis M., Phyllis M. Faber Luoma, Samuel N., CALFED & & Associates. What Are We Restoration: The Importance of U.S. Geological Survey. Will Variability. Learning from Long-Term Improved Environmental Monitoring? Management Come from Better Riley, A.L., S.F. Bay Regional Water Quality Control Board. Riparian Flegal, A. Russell, U.C. Santa Understanding Ecosystem Processes Restoration Around the Bay. Cruz. Decadal Variations in Metal in the San Francisco Bay-Delta and Contamination in San Francisco Bay. Its Watershed? Rosekrans, Spreck, Environmental Defense. Managing Project Macaulay, Steve, California Urban Haltiner, P.E., Jeffrey and Michelle Operations with the Environmental Water Agencies (CUWA). An Urban Orr, PWA. Hills to the Bay: Lessons Water Provided by the Central Learned from Restoration. Perspective. Valley Project Improvement Act and Hart, John and David Sanger. The Malamud-Roam, Karl, Contra CALFED’s Environmental Water Account. News from the San Francisco Costa Mosquito & Vector Control Estuary: A Writer and Photographer District. Miasma Revisited: Will Schwarzbach, Steven, Western Reflect. Wetland Restoration Kill You? Ecological Research Center, USGS BRD, and Terry Adelsbach, Hastings, Lauren L., California McDonald, Thomas A., Office of Environmental Health Hazard Sacramento Fish and Wildlife Office, Bay-Delta Authority. Habitats in the USFWS. The Biological Legacy of Assessment. The Risk Posed by the Hub: An Overview of Delta Mercury Contamination: Restoration. PBDEs, a Class of Flame Retardants. Implications of Methylmercury Bioaccumulation for Estuarine Birds in San Francisco Bay.

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Siegel, Stuart W., Wetlands and POSTERS* Ayres, Debra and Donald Strong, Water Resources. The Status of U.C. Davis. Hybrid Cordgrass Wetland Restoration Efforts in the Abbott, Robert, Strategic (Spartina) and Tidal Marsh Baylands. Environmental Consulting. Impact of Restoration in San Francisco Bay: If Intense Anthropogenic You Build It, They Will Come. Sweeney, Caitlin, S.F. Bay Hydroacoustic Noise on San Conservation and Development Bach, Eve and Ruth Gravanis, Francisco Bay Aquatic Life. Commission. Public Access and The Public Trust Group. The Role of Wildlife Compatibility. Adams, Peter B., National Marine the Public Trust Doctrine in Fisheries Service. Population Status Protecting the Estuary. Travis, Will, S.F. Bay Conservation of North American Green Sturgeon, and Development Commission. Bergendorf, David, U.S. Fish & Acipenser medirostris. Celebrating the San Francisco Wildlife Service. Chinese Mitten Estuary Project and the Tenth Adelsbach, Terry, U.S. Fish & Crab (Eriocheir sinensis) Reporting Anniversary of the Comprehensive Wildlife Service, Cheryl Strong, S.F. System and Monitoring Program in Conservation and Management Plan. Bay Bird Observatory, Steven E. California. Schwarzbach, U.S. Geological Warnock, Nils, Diana Stralberg, Berthelsen, Martha, Sharon Survey. Mercury, PCBs, and Dioxin- Nadav Nur, Gary Page, PRBO Farrell, Apple Szostak, Aquatic Equivalents in Piscivorous Seabirds Conservation Science. South San Outreach Institute. Developing Breeding in San Francisco Bay. Francisco Bay Restoration Effects on Watershed Stewardship: Linking Shorebirds and Waterfowl. Adelsbach, Terry, U.S. Fish & Community-Based Restoration and Wildlife Service, Jianwen She, the Home Landscape. Whitehead, J.A., S.L. Anderson, Department of Toxic Substances Bodega Marine Laboratory, U.C. Bias, Michael A., Ecosystem Control, Steven E. Schwarzbach, Davis; K. Kuivela, U.S. Geological Restoration Sciences; Thomas U.S. Geological Survey, Survey, B.W. Wilson, U.C. Davis. Keegan, ECORP Consulting; Isa Christopher W. Thompson, Biomarker Responses in Fish Woo, Scott Demers, John Washington Department of Fish & Exposed to Pesticide Runoff in the Takekawa, U.S. Geological Survey; Wildlife. Brominated Fire Retardants Field and Laboratory. Giselle Downard, U.S. Fish & (PBDEs) in Tern Eggs from the San Wildlife Service; Fritz Reid, Ducks Whyte, Dyan C., S.F. Bay Regional Francisco Bay and Washington State. Unlimited. Monitoring Fish Water Quality Control Board. Allen, Peter, Joseph J. Cech, Jr., Assemblages Among Tidal Marsh TMDLs: Water Quality Solutions for Mary Nicholl, Stephanie Cole, Restoration Projects in San Pablo San Francisco Bay. U.C. Davis. Post Yolk-Sac Larval to Bay. Williams, Philip B., PWA. Early Juvenile Green Sturgeon Breaux, A., M. Martindale, S. Predicting the Future of San (Acipenser medirostris) Growth in Cochrane, J. Evans, B. Pavlik, L. Francisco Bay. Elevated and Cycling Temperature Suer, D. Benner. Assessing Regimes. Wise, John, U.S. EPA (retired). The Wetland Restoration Projects in the Challenge of Garnering Public Allen, Peter, Joseph J. Cech, Jr., San Francisco Bay Region. Support. Stephanie Cole, Mary Nicholl, Brosnan, John, S.F. Bay Area Brian Hodge, U.C. Davis. Salinity Wolff, Gary, The Pacific Institute. Wetlands Restoration Program. Tolerance and Acclimation in The Estuary and California Water Increasing Interagency Coordination Developing Juvenile Green Sturgeon Management: Can We Support on Wetlands Restoration: The San (Acipenser medirostris). California’s Growing Economy With Francisco Bay Area Wetlands a New Approach to Water Arce, Ruth E., City College of San Restoration Program. Management? Francisco, and C. E. Crocker, Brown, Kurtis, U.S. Fish & Wildlife Romberg Tiburon Center for Wright, Patrick, California Bay- Service. Spawning Areas of Green Environmental Studies. Specific Delta Authority. The Estuary’s Sturgeon (Acipenser medirostris) in Growth Rates of Age-0 Green Connection to the Colorado River the Upper Sacramento River, Sturgeon (Acipenser medirostris); and the Significance of Taking a California. Effects of Moderate Salinity: Regional Approach to Water Preliminary Data. Management. Arp, Alissa. The Romberg Tiburon Center for Environmental Studies, San Francisco State University.

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STATE OF THE ESTUARY

Teh, Swee J., Guo Hua Zhang, Word, Jack Q. and Scott Dong-Fang Deng, Foo-Ching Bodensteiner, MEC Analytical ACRONYM KEY Teh, Philipp Rosenkranz, Teresa Systems. Use of a Forensic Sediment W.–M. Fan, U.C. Davis. Effects of Data Evaluation Tool for Assessing CALFED: CALFED Bay-Delta Program Dietary Selenium on Reproduction Potential Sources of Mercury DFG: California Department of Fish and of Medaka. Contamination in Oakland Harbor. Game Teh, Swee, J. Lesa Erecius, Wunderlich, Veronica and Carlos DHS: California Department of Health Matthew Bartosiewicz, Crocker, Romberg Tiburon Center Services U.C. Davis. Expression Profiling of for Environmental Studies. The DWR: California Department of Water Selenium Using a Japanese Medaka Effects of Elevated Temperature and Resources cDNA Microarray. Hypoxia on Growth of Age-0 Green Sturgeon, Acipenser medirostris. GGNRA: Golden Gate National Topping, Brent R., James S. Recreation Area Kuwabara, Mark Marvin- Zaremba, K., P.R. Olofson, E.K. DiPasquale, Jennifer L. Agee, Grijalva, S.F. Estuary Invasive MWD: Metropolitan Water District of Southern California U.S. Geological Survey. Sediment Spartina Project. Challenges of Remobilization of Mercury in South Restoring Native Habitat in a Non- NMFS: National Marine Fisheries Service San Francisco Bay. Native Hybrid Spartina Invaded NOAA: National Oceanic and Ecosystem. Van Eenennaam, Joel P., Javier Atmospheric Administration Linares-Casenave, Serge I. Zemitis, C.R., C. Schmutte, K. NOS: National Ocean Service Doroshov, U.C. Davis. Nelson, T. Hall, California PRBO: Point Reyes Bird Observatory Reproduction and Early Life Stages Department of Water Resources. of Green Sturgeon (Acipenser Four Major Sacramento-San Joaquin RCD: Resource Conservation District medirostris). Delta Restoration Projects. SFBBO: San Francisco Bay Bird Van Keuren, Neal P., James W. Zemitis, C.R., C. Schmutte, G. Observatory Downing, City of San Jose; Eric Knittweis, California Department SFBCDC: San Francisco Bay Webb, Ron Duke, H.T. Harvey and of Water Resources; Jeff Mount, Conservation and Development Associates; Bob Battaglio, PWA. Chris Hammersmark, Geoff Commission South San Francisco Bay Marsh Schladow, Bill Fleenor, U.C. SFBRWQCB: San Francisco Bay Regional Ecology: Tidal & Edaphic Davis; Keith Whitener, The Water Quality Control Board Characteristics. Nature Conservancy, Cosumnes SFEI: San Francisco Estuary Institute River Preserve. McCormack- Van Keuren, Neal P., James W. Williamson Tract Adaptive Planning SFEP: San Francisco Estuary Project Downing, City of San Jose; Eric and Restoration. Webb, Ron Duke, H.T. Harvey and SWRQB: State Water Resources Control Associates. Marsh Plant Associations Board of South San Francisco Bay. *Titles within the Presentations and Posters USACOE: United States Army Corps of Engineers Werner, Inge, Swee J. Teh, sections based on abstracts submitted prior to the conference. Some details may have USBR: United States Bureau of Seema Datta, Lu X. Q., Tom changed since then. Young, U.C. Davis. Biomarker Reclamation Responses in Macoma nasuta USDA: United States Department of (Bivalvia) Exposed to Sediments Agriculture from Northern San Francisco Bay. USEPA: United States Environmental Werner, Inge, Javier Linares, Protection Agency Gina Lee, Joel Van Eenennaam, USFWS: United States Fish and Wildlife Serge I. Doroshov, U.C. Davis. Service Tolerance and the Heat-Shock Protein Response in Larval Green USGS: United States Geological Survey Sturgeon (Acipenser medirostris). Weston, Donald P., U.C. Berkeley, and Michael J. Lydy, Southern Illinois University. Pyrethroid and Organochlorine Pesticides in Agriculture-Dominated Streams of the Central Valley.