State of the Estuary 2006 Science & Stewardship STATE of the ESTUARY 2006 OPENING REMARKS BIG PICTURE, WARNING BELLS

State of the Estuary 2006 Science & Stewardship STATE OF THE ESTUARY 2006 OPENING REMARKS BIG PICTURE, WARNING BELLS

Opening Remarks

This Report describes the current total runoff), provides drinking water restoring the Estuary. The S.F. Estu- state of the San Francisco Bay- Sac- to 22 million Californians (two-thirds ary Project’s CCMP is a consensus ramento-San Joaquin Delta Estuary’s of the state’s population), and irrigates plan developed cooperatively by over environment — waters, wetlands, 4.5 million acres of farmland. The 100 government, private and commu- wildlife, and watersheds. It also high- Estuary also enables the nation’s fi fth nity interests over a fi ve-year period lights restoration activities, research largest metropolitan region to pursue and completed in 1993. The project needs, and pressing issues we need diverse activities, including shipping, is one of 28 such projects working to address if we are going to protect fi shing, recreation, and commerce. to protect the water quality, natural water quality, supply, and habitat. Finally, the Estuary hosts a rich di- resources and economic vitality of versity of fl ora and fauna. Two-thirds estuaries across the nation under San Francisco Bay and the Delta of the state’s salmon and at least the U.S. Environmental Protection combine to form the West Coast’s half of the birds migrating along the Agency’s National Estuary Program, largest estuary, where fresh water Pacifi c Flyway pass through the Bay which was established in 1987 through from the Sacramento and San Joaquin and Delta. Many government, busi- Section 320 of the amended Clean rivers and watersheds fl ows out ness, environmental, and community Water Act. Since its creation in 1987, 1 through the Bay and into the Pacifi c interests now agree that benefi cial use the Project has held seven State of the Ocean. In the early 1800s, the Bay of the Estuary’s resources cannot be Estuary Conferences and provided covered almost 700 square miles, and sustained without large-scale envi- numerous publications and forums the Delta’s rivers swirled through a ronmental restoration. There is also a on topics concerning the Bay-Delta vast Byzantine network of 80 atoll- greater need than ever for increasing environment. In 2001, CALFED like islands and hundreds of miles of public awareness about the Estuary. joined the Estuary Project as a major braided channels and marshes. Back sponsor of the conference. CALFED then, almost a million fi sh passed This 2006 State of the Estuary is a cooperative state-federal effort, of through the Estuary each year and Report summarizes advocacy and which U.S. EPA is a part, to balance 69 million acre-feet of water crashed stewardship efforts, and restoration efforts to provide water supplies and down from mountain headwaters and science recommendations drawn restore the Bay-Delta watershed. toward the sea. But in 1848 the Gold from the 44 presentations and 195 Rush began and hydraulic mining posters of the October 2005 State of plugged the rivers and bays with more the Estuary Conference and related than one billion cubic yards of sedi- research. The report also provides ments. Over time, farmers and city some vital statistics about changes in TABLE OF CONTENTS builders fi lled up more than 750 square the Estuary’s fi sh and wildlife popula- miles of tidal marsh, and engineers tions, pollution levels, and fl ows over Executive Summary ...... 2 built dams to block and store the rush the past two years, since the last State Vital Stats ...... 11 of water from the mountains into of the Estuary report was published. Big Picture; the Estuary and massive pumps and Warning Bells...... 27 The report and conference are canals to convey this water to thirsty The Role Of Science ...... 37 all part of the San Francisco Estuary cities and farms throughout the state. Works In Progress ...... 47 Project’s ongoing efforts to implement Science, Learned Today’s Estuary encompasses its Comprehensive Conservation and & Needed...... 55 roughly 1,600 square miles, drains Management Plan (CCMP) for the Work To Be Done ...... 67 more than 40% of the state (60,000 Bay and Delta and to educate and Bibliography...... 85 square miles and 47% of the state’s involve the public in protecting and STATE OF THE ESTUARY 2006 BIG PICTURE, WARNING BELLS

get involved in making decisions about the Bay-Delta Executive Estuary, said Schubel. “If you’re not at the table,” he Summary quipped, “you’re on the menu.”

Reprint of a December 2005 ESTUARY Newsletter article. Lack of scientifi c understanding isn’t the problem at this point, said Schubel, who called for a “compelling vision” and new approaches for managing Bay-Delta Amid the metaphorical popping of champagne corks resources, including better communication with the at this year’s “Celebrating Science and Stewardship” public. “We spend $100 million per year explaining why State of the Estuary Conference in Oakland’s Henry J. agriculture is important,” he added. “But we spend less Kaiser Convention Center, scientists and policymakers than 10 percent of that telling people why oceans and sounded a series of SOS calls to an audience of more estuaries are valuable.” Schubel also advised the crowd than 700. The loudest cries for attention were over the that we need to be fl exible in managing water resourc- Delta and the ways it is changing physically, politically, es. But the bottom line, he said, is that we must build and ecologically, and how the future of the Central Val- better collaborations among researchers, decisionmak- ley—as ag land or urban sprawl—will affect the Bay- ers, and stewards. Delta Estuary. The S.F. Regional Board’s Larry Kolb kicked things “To protect the Delta, off by asking whether Californians are as “clueless” in we need a new Sylvia managing our water systems—and the Delta—as those who channelized the Mississippi River, cutting it off McLaughlin, Kaye Kerr, from its fl oodplains and depriving the wetlands at its and Esther Gulick.” 2 mouth of sediment, thereby contributing to the damage from Hurricane Katrina. In both places, said Kolb, Joe Bodovitz, former executive director, BCDC we are mismanaging water and marshes, building on and California Coastal Commission subsided marshy soils—on fl oodplains—and then, in a vicious cycle, building ever bigger levees and dams to Stewards were also on the mind of Joe Bodovitz, protect the homes and infrastructure behind them. the former—and fi rst—executive director of both BCDC and the Coastal Commission, who began his talk by chronicling the sometimes-volatile political pro- “We spend $100 million per cess that led to the creation of CALFED. Under former year explaining why agricul- governor Pat Brown’s reign—which Bodovitz termed the “golden era of California”—the State Water Proj- ture is important. But we ect and lots of other infrastructure we benefi t from spend less than 10 percent of today got built. But things are changing, he warned, that telling people why oceans stressing that as the state’s population burgeons, the and estuaries are valuable.” Central Valley will need more water and will play a more prominent role in water plumbing and politics. Jerry Schubel, Aquarium of the Pacifi c The most critical issue facing the Bay-Delta, said Bodo- vitz, is how much water Central Valley agriculture will Other speakers following Kolb the fi rst morning keep or sell to urban areas. sounded more alarms—and called for action. Jerry Echoing Schubel, Bodovitz said another critical Schubel, from the Long Beach Aquarium of the Pacifi c, issue is stewardship. To protect the Delta, he said, we told the crowd that while we’ve made huge strides with need a new Sylvia McLaughlin, Kaye Kerr, and Esther science, we need to make sure stewardship keeps pace. Gulick, the three Berkeley women who kept the Bay “Both scientists and citizens need to be keepers of the from becoming a parking lot. Saving the Delta is a Estuary,” said Schubel. Everyone—“all sizes, shapes, much trickier proposition, said Bodovitz. Recalling how races, NGOs, scientists, and politicians”—needs to the three women got people to send bags of sand to STATE OF THE ESTUARY 2006 EXECUTIVE SUMMARY BIG PICTURE, WARNING BELLS

their legislators, he said, “People could understand that is going to happen has already happened. “The pace of if we fi lled the Bay, things would be greatly changed. [physical] change is rapid, yet we’ve got four CALFED People got it—it was either going to be water or dry programs wrapped around a static Delta,” said Mount. land.” But the Delta, he said, is “light-years more Today’s engineering is based on 1980s hydrology, he complex” and gets approached as a plumbing problem warned, predicting that South Delta improvement instead of as a landscape. projects will adapt poorly to changing conditions. The Delta is warming up, and its hydrology and ecosystems are changing, he said. “If you raise sea level by three “People could understand feet, the Delta ecosystem is going to be more like a that if we fi lled the Bay, things Chesapeake Bay. In 15 to 20 years, we’ll have a whole would be greatly changed. different food web.” Mount said we need to defi ne future probable states and take the long view, recognizing People got it—it was either that some ecosystem services cannot be sustained over going to be water or dry land. the long term. In response to moderator Tim Ramirez But the Delta is light-years asking which ecosystem service will “get voted off the more complex.” island,” Mount predicted that the loser will be farming. The Department of Water Resource’s Jerry Johns Joe Bodovitz followed Mount, taking more of a crime-scene approach. We need to act now to protect the infra- One of the morning’s highlights—a preview of Ron structure—high-pressure gas lines, water lines, and Blatman’s upcoming four-part television documentary, roads, among others—that crisscrosses the Delta, said “Saving the Bay”—showed exactly what stewardship Johns. “We need to take a comprehensive view and 3 can do. With historical and current images of the Bay make ‘no-regrets’ decisions that improve fl exibility.” and interviews with then-legislators and key environ- But Johns also asked whether it is possible to “move mental activists, the fi lm chronicles how by the 1960s, forward” with pumping more water from the Delta almost one-third of the Bay had been fi lled, and how when we don’t understand the recent decline in pelagic a 1959 Army Corps of Engineers report predicted organisms. “Do we put off decisions on [water project] that by 2020, 70 percent of the Bay would be fi lled for operations until we have more data, a new ROD?” development. But then the three women who founded Save the Bay stepped in and stopped the fi ll. “The Delta is the number-one On the conference’s second day, speakers focused on the disconnect between the Delta’s geomorphology most-subsided landscape in and the state’s land use policies: As the Delta contin- the world relative to its size… ues to subside, we continue to build more houses and Once you start putting homes other structures behind levees, partly in response to in the Delta, all bets are off.” the Bay Area’s expensive housing stock. “The Delta is the number-one most-subsided landscape in the world Jeff Mount, UC Davis relative to its size,” announced U.C. Davis’ Jeff Mount. Mount predicted that as urbanization continues to Whatever we do, said the Central Delta Water encroach upon the Delta—30,000 homes were ap- Agency’s Tom Zuckerman, the solution needs to be proved in fl ood-prone areas in Stockton and another “Delta-centric” and come from the people who live 8,500 in Lathrop—some of the ecosystem services the in the Delta. Zuckerman added to Mount’s concerns Delta has provided in the past will have to give, par- about the onslaught of urbanization. “We need to ticularly if we continue our practice of serial engineer- avoid making stupid, thoughtless decisions, such as ing and particularly if we continue sprawling. “Once putting people behind levees in tract houses,” said you start putting homes in the Delta, all bets are off,” Zuckerman. “But how do we get politicians—the state declared Mount. Mount said we are mistakenly treat- government and the federal government—to focus on ing the Delta like a crime scene, where everything that STATE OF THE ESTUARY 2006 BIG PICTURE, WARNING BELLS

the Delta? It really is entitled to priority. It’s an environ- It takes scientists—not politicians—to delineate mental and recreational treasure.” Zuckerman told the fl oodplains. Yet one conference speaker, MWD’s Tim audience that we have a once-in-a-lifetime opportunity Quinn, said scientists should not be making policy. “Too to preserve the standard of living and way of life in the often in California water, you have people sitting at Delta—an opportunity that will soon be lost. the table crossing the line,” said Quinn. “We also have scientists crossing the line. The San Francisco Chronicle, Former Rio Vista mayor Marci Coglianese reiter- Contra Costa Times, and Sacramento Bee are not good ated Zuckerman’s concerns and added to them. “The places to publish your science.” Quinn’s comments Delta is no longer a remotely populated area,” she aside, most conference speakers said there was an said. “It’s no longer a backwater fi lled with fi sh and ever-increasing and more urgent need to communicate stubborn farmers.” Since 1993, said Coglianese, more science to the public. than 94,000 residential units have been built in the Delta’s secondary zone. “Every day, the Delta is being The science behind the recent decline in pelagic infl uenced by a Tower of Babel of governmental agen- organisms in the Delta was a popular topic. Ted Som- cies,” said Coglianese. “But there is no shared vision mer outlined the Interagency Ecological Program’s ef- or acknowledgment of impacts. The time is ripe for a forts to identify all possible causes of the decline, from broader examination of all state policies affecting the toxic algal blooms and new pesticides to the timing Delta; we need a serious discussion of how state and and amount of Delta pumping to impacts from exotic local growth policies are putting development behind species. Posing another possible cause, Sommer cited levees and in fl oodplains.” problems with two species of zooplankton—Pseudodi- aptomus forbesi and Limnoithona tetraspina. Pseudodi- aptomus, which crashed in 2004, is a major food source “...we need a serious for larval fi sh, said Sommer, while Limnoithona, which 4 discussion of how state and was relatively abundant in 2004, is a poor food source local growth policies are and possible predator of Pseudodiaptomus. The next day, S.F. State University’s Wim Kimmerer explained putting development behind that the Pseudodiaptomus population had a recruitment levees and in fl oodplains.” failure in recent years, which meant the loss of later life stages that would grow to adult organisms—and said Marci Coglianese, former mayor, Rio Vista there is no evidence that Limnoithona feeds on other copepods. He is trying to fi gure out why copepods Although the Delta Protection Commission has crashed but not phytoplankton. Another culprit could made a laudable attempt to protect the inner core, said be the invasive overbite clam, which may have deci- Coglianese, the legislature has not given it any real au- mated Pseudodiaptomus larval stages. thority, and new confl icts are cropping up even there. Like Zuckerman, Coglianese thinks we have a “teach- able moment” right now, after Katrina, in which we “The fundamental problem have the public’s attention. Yet, she concluded, “The in the Delta is that the state fundamental problem in the Delta is that the state government is not supplying the leadership needed to deal government is not supplying with hard problems. I urge the governor as he tries to the leadership needed to deal refocus CALFED to bring together local governments, with hard problems.” legislators, and interests who are talking to themselves right now.” Solutions to the Delta’s problems cannot be Marci Coglianese, former mayor, Rio Vista imposed on the Delta, said Coglianese. “But we need some unifying force to bring us together. Right now, Many speakers suggested that poor water quality— we’re a region without leadership. We need the state particularly as a result of the huge increase in the use of to help us out. Most of us don’t even know where the pyrethroids by farmers—may have decimated pelagic fl oodplains are.” organisms. If we are going to improve water quality STATE OF THE ESTUARY 2006 EXECUTIVE SUMMARY BIG PICTURE, WARNING BELLS

in the Delta, many folks think we can’t do it without housing in the Bay Area and coastal regions gets less addressing water quality in the San Joaquin River. “It’s affordable, people continue to pour into the Central not if, but when we restore the San Joaquin,” pro- Valley.” Plus, said Whiteside, there is a high rate of claimed the Bay Institute’s Gary Bobker. When Friant immigration from other countries—and a high fertil- Dam was put in, the river was fl at-lined, said Bobker, ity rate among Central Valley residents. Whiteside and the main stem cut off from the Delta. This has wondered why farmers and environmentalists are not resulted in saltwater intrusion and poor water quality in partnering to save open space and ag land in the valley. the Delta, said Bobker. But when a developer offers a farmer a million dollars for an acre, she lamented, ag land disappears. “I urge Low fl ows in the San Joaquin have contributed you to help us,” she implored the crowd. “We have a to the problem of low dissolved oxygen in the water, chance right now to develop a strategic long-term view particularly in the Stockton Ship Channel, the topic of the valley.” of U.C. Davis’ Alan Jassby, who explained that other contributing factors include dredging of the channel, its A panel discussion on CALFED and its role in the geometry, and inputs of oxygen-devouring nutrients, Delta wound up the talks on Day Two, with moderator such as nitrogen and phosphorus. Lawrence Berkeley Steve Ritchie questioning whether the state and federal Laboratory’s Tryg Lundquist explained how real-time agencies that make up CALFED are capable of resolv- management of water quality in the San Joaquin could ing the thorny issues looming ahead. CALFED’s new allow resource managers and farmers to take advan- interim director, Joe Grindstaff, said he thinks people tage of windows of opportunity for improving water have forgotten how important it is to work together as quality by holding back polluted water and releasing an institution. “If we didn’t have [CALFED], we’d have it at times when there is less pollution in the river. to invent it again,” said Grindstaff. The other panel- USGS’s Larry Brown described the river as the “most- ists—the Department of Water Resources’ Les Harder, 5 invaded major river in the West,” but said a surprising Gary Bobker, and the State Water Contractors’ Laura number of native fi sh species are surviving in it anyway. King Moon—agreed, although Bobker suggested that maybe CALFED’s structure needs to evolve. “Any pro- U.C. Berkeley’s John Dracup warned that global gram is about achieving your ends,” said Bobker. “If we climate change could affect the river—and Northern don’t have clear and measurable goals, we don’t know California rivers overall—by putting more water in where we are.” Bobker argued for a more independent them earlier in the spring (which might tempt water science program than we’ve had in the past under purveyors to build more dams), and less later in the CALFED, while King Moon said the program might year when we need it more. The Friant Water Author- need to become more strategic in its focus. Harder ity’s Ron Jacobsma said that this year, more water was pointed out that under the current science program, released from dams on the San Joaquin than “would our level of scientifi c understanding has increased have occurred in nature.” Scott McBain, of McBain and exponentially. Trush, delved into restoration challenges, describing the river’s variable underlying geology and geomorphol- And the science at the conference was extensive, ogy. The river’s slope and gravel pits are constraints, al- both big picture and detail-oriented. The fi rst day’s though not insurmountable ones, said McBain. His fi rm speakers discussed how science will guide restoration has restored other rivers that had been gravel-mined, around the Bay. U.C. Berkeley’s Maggi Kelly told the he said, adding that some solutions—such as removing crowd that by taking a landscape ecology approach— dikes and berms and allowing the river to re-establish and applying a variety of spatial scales—we can decide a channel and fl oodplain in certain areas—would be which functions we are interested in maintaining and simple. restoring in Bay wetlands.

The river’s valley was the topic of the Great Valley One of the largest such projects—the South Bay Center’s Carol Whiteside, who painted a picture of a salt ponds—was the topic of San Jose State Universi- rapidly disappearing landscape. The Central Valley’s ty’s Lynne Trulio, who explained how science is helping population is growing faster than California, the United deﬁ ne goals and pin down uncertainties. “How much States overall, and even Mexico, said Whiteside. “As tidal marsh should we restore?” asked Trulio. “Adaptive STATE OF THE ESTUARY 2006 BIG PICTURE, WARNING BELLS

management will tell us how far we can go along the know that the Delta is the “detritus mill” for the Bay, way. We will learn as we go—it’s not trial and error, but said Simenstad, with 30 percent to 40 percent of the it’s based on an understanding of the system.” Science organic matter it exports out of the system going to will also guide how we monitor projects, said Trulio. downstream food webs. Simenstad said we also know, from studying Suisun Marsh, that tidal marshes are Stuart Siegel, next on stage, set forth several needs highly productive, are critical rearing areas for fi sh and related to monitoring, which is often seen as not that invertebrates, and provide refuge for native species. important. In monitoring, said Siegel, we need to look for change, try to detect the outcomes of our actions Tidal marsh restoration is also important for non- by analyzing data, and convert that analysis to knowl- aquatic species. PRBO researchers are studying how edge. We need to make information widely available, birds like song sparrows and common yellowthroats are develop “lessons learned” and reference conditions, responding to marsh restoration—and how landscape- and solve problems related to wetland restoration—like level factors, vegetation, and hydrological and geomor- mercury methylation, contaminants, and sediment phic processes limit their numbers and reproductive supply, to name just a few, said Siegel. We also need to success. We also know that birds—songbirds in par- come up with science-based strategies for regional and ticular—respond rapidly to riparian habitat restoration. sub-regional monitoring efforts, he suggested. PRBO’s Geoff Guepel showed a graphic illustrating the immediate and steady upward climb of bird density on Thirty years of monitoring of 45 tidal marsh resto- the Sacramento River after restoration, and described ration projects (2,800 acres) implemented around the how this year, the endangered least Bell’s vireo and the Bay since the 1970s gives us suffi cient information to locally extirpated yellow warbler returned to a newly restore the 20,000 acres now in planning and design restored site on the San Joaquin River. “Revegetation stages, said Phyllis Faber. The lessons learned on those is working,” said Guepel, who added that planting a 6 projects helped form the basis of the Design Guidelines habitat mosaic and a diverse understory is critical to for Tidal Wetland Restoration in San Francisco Bay, restoring bird diversity. But he cautioned that without published by Phil Williams and Associates and the Bay Institute with funding from the Coastal Conservancy. restoring fl oodplain dynamics and taking other con- Faber said one thing we know for sure is that if we servation actions, nest success—especially in remnant get the elevations right, “it is wasteful and costly to forests—may remain low. plant. Natural processes have fared better than highly engineered projects. We need to be more patient, to “The ecological value in in- measure time for restoration in decades, not years.” termediate-stage restoration PWA’s Michelle Orr spoke of lessons learned in South Bay restoration projects. We now know that sites is very high.” we do have enough sediment in the South Bay for tidal Nadav Nur, PRBO Conservation Science marsh restoration, said Orr, but we do not yet understand the sediment demands of mudfl ats. For some species, like chinook salmon and steelhead The University of San Francisco’s John Callaway in the Central Valley, restoration measures will need talked marsh and mudfl at too, examining whether to be more drastic. NOAA’s Steve Lindley described elevation is a good predictor of tidal salt marsh plant how his agency is developing viability goals for popula- distribution and concluding that while elevation is im- tions and evolutionarily signifi cant units (ESUs) for portant, so are inundation by the tides and creeks and each species. But he cautioned that without access to competition from other plants. their prime spawning habitat—much of which is behind impassable dams—these fi sh will remain at risk of Another area we don’t completely understand is the extinction. extent to which restoring tidal wetlands will benefi t Bay food webs. The interactions between tidal wet- Restoring habitat by removing dams is politically lands and pelagic areas are not well understood, said tricky but pretty straightforward from a fi sh’s per- the University of Washington’s Si Simenstad. We do spective—suddenly you have access to habitat that STATE OF THE ESTUARY 2006 EXECUTIVE SUMMARY BIG PICTURE, WARNING BELLS

you didn’t before. But for other types of restoration sessed with performance measures,” said Pawley. With projects, said PRBO’s Nadav Nur, we need to develop a simple conceptual framework, the scorecard asks, in success criteria that focus on evaluating young restora- general, if we can fi sh from, swim in, and drink Bay-Del- tion sites, so we can enhance the values of those sites ta water, explained Pawley. While there is an incremen- for the critters we are targeting for recovery and so tal upward trend in these criteria for the Central and we can take corrective steps if necessary. We do know South bays, said Pawley, the upper parts of the Bay— that a site doesn’t have to be mature to be valuable as San Pablo and Suisun bays—are in serious trouble, with habitat, said Nur. “The ecological value in intermedi- fi sh and other organisms declining and invasive species ate-stage restoration sites is very high.” increasing. “We’ve done a lot of damage to the Bay, and it will take a while to reverse,” she predicted. It is also important to evaluate restoration from the perspective of the most dominant species, cautioned What’s really needed in monitoring the health of the the South Bay Salt Pond Restoration Project’s Steve Estuary is an approach linking ecology and toxicology, Ritchie. “We can’t let endangered species run the said Susan Anderson of U.C. Davis’ Bodega Marine show. We need to use every opportunity to educate Laboratory. She described how she has measured the folks and to monitor changes in community values and exposure of mudsuckers, a sediment-dwelling fi sh, to interests as well. We need to make sure restoration contaminated sediments in Stege Marsh. “They’re not works for humans, as well as animals.” sexy, but they live in salt marsh mud and are directly exposed to the sediments being regulated. We can The S.F. Bay Joint Venture, by pulling in as many measure a lot of things in an effi cient and humane human stakeholders as possible, is trying to make way—we use every part of the fi sh.” Anderson pointed sure that happens. The Joint Venture’s Beth Huning out that just because we don’t always measure the gave an overview of wetland and riparian acquisition, effects of contaminants on fi sh and invertebrates, that 7 restoration, and enhancement projects around the Bay, doesn’t mean impacts aren’t there. “Our contention is describing how building partnerships among businesses, that it’s not enough to go out and see marsh birds—we private individuals, and nonprofi ts has been critical to need to know their health.” the projects that have taken place so far. Huning em- phasized the importance of acquisition. “Before we can restore, we need to protect,” she said. “Our challenge is to put the

And to acquire more land for restoration, we need Bay, Baylands, and water- to convince the public of the value of restoration. Sci- sheds back together again” ence alone isn’t enough, said the S.F. Regional Board’s Bruce Wolfe, echoing earlier speakers. We must also Josh Collins, San Francisco Estuary Institute be able to report on our actions to the public in ways they can understand, said Wolfe. “Decisionmakers The health of the food web also affects humans, of and the public want to know how we’re doing, they course, particularly those who eat fi sh from the Bay want to know what we’ve done, and they want to and Delta. Cal EPA-OEHHA’s Bob Brodberg chroni- hear the message in easy-to-understand terms. “‘Re- cled the history of fi sh consumption advisories for the storing creeks’ resonates better than ‘minimizing the Bay-Delta and said that as new chemicals are found, hydrogeomorphic impacts to riverine functions,’” said they will be monitored extensively. Consumption advi- Wolfe, who added that his agency is committed to sories not only provide the public with information and working with Bay nonprofi ts and scientists to identify choices, said Brodberg, but could also be used in setting cleanup and restoration goals. The current advisory what enhancement and restoration the Estuary needs, for the Bay-Delta Estuary, said Brodberg, is that adults the performance standards needed to do that, and how should eat no more than two meals per month of Bay best to track our progress as we move forward. sport fi sh, including sturgeon and striped bass caught in The Bay Institute’s Anitra Pawley described her the Delta. Adults should not eat any striped bass over agency’s attempts to track progress with its just-re- 36 inches, said Brodberg, and women who are preg- leased second Ecological Scorecard. “Society is ob- nant, may become pregnant, or are nursing should not STATE OF THE ESTUARY 2006 BIG PICTURE, WARNING BELLS

eat more than one meal of fi sh per month—nor should With help from volunteers—and from federal and children under the age of six. state agencies, nonprofi ts, and local governments and businesses—we’re making progress. The largest resto- Another restoration and monitoring link we need ration projects ever undertaken on the Bay are under- to make is that of watersheds to wetlands, said SFEI’s way. The Coastal Conservancy’s Amy Hutzel gave a Josh Collins “We have to embrace the idea that the progress report on two large tidal marsh restoration Baylands really are the edge of the Bay,” he said, add- projects in the North Bay—the Napa salt ponds, which ing that those places where streams and rivers meet began in Fall 2005, and the Hamilton Airfi eld. Napa is the Bay have become a sort of no-man’s land, falling less subsided than Hamilton, said Hutzel, and will be somewhere between watershed science and Bay sci- restored primarily by breaching and lowering exist- ence. “Our challenge is to put the Bay, Baylands, and watersheds back together again,” said Collins. “We ing levees. Hamilton, which has subsided by about 10 need to reconnect with our watersheds.” Yet this year’s feet, presents more of a challenge and will need seven conference had little focus on the streams that fl ow to million cubic yards of dredge material deposited on it to the Bay or their watersheds. Collins’ take-home point achieve a restorable elevation. was that we need to set riparian habitat goals—“force The South Bay is also gearing up, said Cal Fish & ourselves to just do it!”—as we have already done for Game’s Carl Wilcox, with restoration projects at Bair wetlands. Island (1,700 acres of diked Baylands to tidal marsh), The only other discussion of streams and water- Eden Landing (650 acres of former crystallizers and sheds occurred in a panel presentation about steward- salt ponds to tidal marsh, plus enhancing another 200 ship around the Bay—a fi rst for the State of the Estu- acres of managed ponds and restoring some sloughs), ary Conference. Four people working and volunteering and the former salt ponds (15,100 acres acquired from 8 to improve habitat and water quality in and around the Cargill in 2003), which are being managed under an Bay described just how essential volunteers have be- initial stewardship plan. come to maintaining and restoring wetlands, uplands, and streams. The Golden Gate National Parks Con- servancy’s Mike Lee calculated that more than 16,000 “We have groundwater volunteers contribute 382,000 hours of support each overdraft of one to two year to his agency, dealing with visitors, working in million acre-feet statewide. native plant nurseries, maintaining trails, counting and banding birds, and handling other tasks. Mondy Lariz, We cannot keep doing that with the Stevens and Permanente Creeks Watershed kind of defi cit spending.” Council, said his organization has at least 80 full-time volunteers engaged in watershed stewardship, including Kamyar Guivetchi, Department of Water Resources water quality monitoring. And recently, 1,460 volunteers helped clean up 46 miles of creeks in Santa Clara Progress is being made not only on the ground but County, said Lariz, removing 40,000 pounds of trash. also at the policy level. The Department of Water U.S. Fish & Wildlife’s Mendel Stewart said volunteers Resources’ Kamyar Guivetchi unveiled the California at the S.F. Bay National Wildlife Refuge complex are Water Plan 2005, which, for the fi rst time, includes an the equivalent of 19 full-time staff people, at a dollar implementation plan for using water effi ciently, pro- value of $470,000. And Save the Bay’s Marilyn Latta tecting water quality, and supporting environmental concluded that nearly 30,000 volunteers have contrib- stewardship. “We have to wring every drop of water uted 150,000 hours to work on habitat restoration with out of our water supply system,” said Guivetchi. “We her organization over the past fi ve years. “Without have groundwater overdraft of one to two million public education and community support, we will never acre-feet statewide. We cannot keep doing that kind be able to truly save the Bay,” she said. “Stewardship of defi cit spending.” Guivetchi proclaimed that in the is one piece of the solution.” Volunteers cannot replace future, we must have a better link between land use “large-scale construction” efforts in restoration, she planning and water management, and that planning added, but they can supplement and enhance it. should be more inclusive of tribal and disadvantaged STATE OF THE ESTUARY 2006 EXECUTIVE SUMMARY BIG PICTURE, WARNING BELLS

communities. Another sea change for this plan, he told stacle for nonpoint source pollution control efforts, said the crowd, is that key decisions about water are going Hanak. Yet despite the woeful state of the state’s pig- to have to be made at the regional level—although not gybank, most Californians are quite concerned about as islands unto themselves. coastal pollution, toxics in soil and water, and polluted runoff in our rivers and lakes, according to an Institute Amid the progress, new and old challenges lurk. survey. And most people surveyed agreed that even Maurya Falkner with the State Lands Commission with the large state budget defi cit, we should continue reported on the 2003 reauthorization of a statewide to fund environmental programs at the current level. mandatory ballast water management law designed to reduce or prevent invasive aquatic species from enter- Adding to the doom side, the Coastal Conser- ing the state’s waters. Falkner said vessels have exceed- vancy’s Nadine Hitchcock warned that although the ed compliance requirements by 90 percent, but fouled Conservancy and the Wildlife Conservation Board ship hulls are still introducing invasives. SFEI’s Andrew have acquired more than 100,000 acres around the Bay, Cohen said that while the reports about compliance there is almost no money left for new projects. Politi- are reassuring, if you read the fi ne print, many ships are cians frequently see funding for ecosystem restoration exempted and there is no good method of testing ships’ as competing with funding for traditional engineer- ballast water at the end of a voyage. Cohen estimates ing projects, said Hitchcock. Despite these setbacks, that even when ballast water exchange does occur— Hitchcock said, we need to do more restoration more than 200 miles from shore as required—only 70 projects in disadvantaged communities, like the Con- percent to 85 percent of the organisms are removed. servancy-funded restoration of Yosemite Slough in San Cohen agreed that fouled hulls are one of the biggest Francisco’s Hunter’s Point. “We have many more com- problems and added aquaculture to the list: “It’s good peting needs with limited funds,” concluded Hitchcock. at moving diseases and parasites and pests.” “We need to develop a regional vision for the landscape 9 Another pest—of the vegetative kind—was the and pursue local and regional funding. There’s a horse topic of the S.F. Estuary Invasive Spartina Project’s race between people acquiring land for preservation Erik Grijalva, who reported on the most recent effort and people acquiring it for development.” to control invasive spartina species. Between 2001 and 2003, said Grijalva, there was a 260 percent increase “We need to develop a in non-native spartina hybrids with diverse genotypes that can start new colonies anywhere. “The greatest regional vision for the land- threats are to mudfl ats and restored tidal marshes,” scape and pursue local and said Grijalva. “If we do something right now, we have regional funding. There’s a a chance to control it.” This year’s treatment, after the marshes were surveyed for the presence of clapper horse race between people rails, tackled 70 percent to 80 percent of the infesta- acquiring land for preservation, said Grijalva. tion and people acquiring it But the biggest challenges for the Estuary—and for development.” for restoration projects—will likely be meeting the economic and environmental challenges of the state’s Nadine Hitchcock, California Coastal Conservancy increasing population, said the Public Policy Institute of California’s Ellen Hanak. The state’s reliance on bonds The Department of Water Resources and the to pay for public investments in infrastructure, land ac- Coastal Conservancy recently acquired the former quisition, park lands, restoration—and a host of other Dutch Slough dairy farm in eastern Contra Costa public benefi ts—is not sustainable, said Hanak, since County—at the center of the “horse race.” That site the ratio of general fund debt to revenue may limit our will be restored to tidal marsh instead of being covered capacity for new bonds in the near future. That bodes with 4,500 houses. “All of our restoration efforts will ill for restoration—state bonds have been its main fund- be relatively futile if we are unable to stem the tide of ing source for several years. Funding will also be an ob- urbanization in the Delta,” said the Natural Heritage STATE OF THE ESTUARY 2006 BIG PICTURE, WARNING BELLS

Institute’s John Cain, one of the project’s managers, there can be too much science—that she saved the Bay sounding again the warnings from earlier in the confer- because she had “never seen anything so beautiful.” ence. The most important thing we can do now, said We need to remember those reasons, said Travis, when Cain, is to acquire land. “Restoration can wait, but communicating with the public. the time for acquisition and preservation is now,” said Dismayed at the lack of discussion of the environ- Cain, who thinks we should expand the Delta Protec- ment and the Bay at a recent Bay Area Council dinner tion Commission to protect the secondary zone in the he attended, Travis told the Estuary conference crowd, Delta. “We need to make the case for the Bay in the language most people understand—that of economics.” If we sit “Restoration can wait, but around speaking science among ourselves, he warned, we will fail to play the role we need to play in political the time for acquisition and decisions about where the predicted one million new preservation is now” California residents will live and work, how to develop affordable housing for those residents, and how they John Cain, Natural Heritage Institute can avoid spending most of their lives in traffi c jams. “We need to better explain, in economic terms, why There is a lot of work to be done, especially around protecting the natural environment is important to land use issues—the ghost in the cellar we’ve never solving these other problems,” said Travis. quite faced. Yet it is not too late for the Bay Area to lead the way to a more sustainable future, said Rain- According to the Joint Venture Silicon Valley’s forest Action Network founder Randy Hayes, now Russell Hancock, the Silicon Valley is starting to think with the City of Oakland. “San Francisco, Berkeley, about how the environment benefi ts its economy, 10 and Oakland were named as among the top 10 ‘green which, he said, is slowly improving in a more sustain- cities’ in the country,” he told the audience. “But we’re able way, without another fl ash-in-the-pan dot-com at best light green. We can work toward medium and boom and bust. “The best way to compete [with deep green. We need to work toward an ecological U- other regions] is to provide a fabulous place to live,” turn, to start a paradigm shift that sets the tone for the said Hancock. As Travis put it, with the Bay, we have entire country.” the “equivalent of a national park in our front yards,” where we can swim, fi sh, sail, and enjoy wildlife. “The decision to save the Bay in 1965 is responsible for “We need to better explain, our economic prosperity today,” Travis reminded the in economic terms, why crowd. “[The Bay] is probably the best fringe benefi t any Bay Area employer can offer. We need to keep protecting the natural envi- reminding them of how much it’s worth.” ronment is important to solving other problems.” “With the Bay, we have the Will Travis, BCDC equivalent of a national park in our front yards, where we Not only did there seem to be a general consensus can swim, fi sh, sail, and enjoy among conference speakers that we need better land use policies and communication with the public, but wildlife.” there was also a consensus that we cannot rest on Will Travis, BCDC past accomplishments. We need to keep on saving the Bay, as Save the Bay founder Sylvia McLaughlin said in a recent interview in the San Francisco Chronicle. In his rousing conference wrap-up, BCDC’s Will Travis described how McLaughlin told him that sometimes RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP VITAL STATISTICS

V 11

Photo courtesy of David Hart and John Sanger STATE OF THE ESTUARY 2006 VITAL STATISTICS PERCENT OF INFLOW DIVERTED with the design, construction Flows 50 and operation of water recycling projects. For example, the Dub- lin San Ramon Services District Recent Infl ows 40 (DSRSD) recycling facility’s cur- Normal or above normal rainfall rent treatment capacity is 3 million gallons per day (mgd), with has meant improved Delta infl ows in 30 recent years. Infl ows to the Delta and 10 miles of distribution installed. Estuary were 21.6 million acre-feet Planned capacity for this facility is 9.6 mgd. DSRSD and the East (MAF) in water-year 2004 (October 20 1, 2003–September 30, 2004) and Bay Municipal Utility District 21.8 million acre-feet (MAF) in water- (EBMUD) are jointly developing the San Ramon Valley Recycled year 2005 (October 1, 2004–Septem- 10 ‘97 ‘98 ‘99 ‘00 ‘01 ‘02 ‘03 ‘04 ‘05 ber 30, 2005). Delta outfl ows were Water Program (SRVRWP), 15 MAF in 2004 and 15 MAF in 2005. S DWR E TOT which will serve areas of Black- Source: DWR, Exports TOT (Interagency Ecological Program, hawk, Danville, Dublin, and San 2005) Water Use Effi ciency Ramon. When complete, this multi-phased 6.7-mgd project is ex- Water use effi ciency, conserva- pected to deliver 3.3 mgd to DSRSD’s Diversions for tion, and recycling projects within service area and 2.4 mgd to EBMUD’s Benefi cial Use the Bay-Delta region aim to provide a service area with 1 mgd available to “drought-proof ” source of water to either. DSRSD has been delivering Water is diverted both within the help meet the needs of cities, indus- recycled water since November 2005. EBMUD customers including the 12 Delta and upstream in the Estuary’s tries, and agriculture. As of 2004, watersheds to irrigate farmland and CALFED’s water use effi ciency City of San Ramon, the San Ramon supply cities. In-Delta exports have program had provided $43 million in Valley Unifi ed School District, and largely remained within the range of 4 water recycling grants, with additional Chevron’s world headquarters began to 6 MAF per year since 1974, but the funding provided by propositions 13 receiving recycled irrigation water in percentage of Delta infl ow diverted and 50. CALFED expects that these February 2006. Meanwhile, EBMUD can vary widely from year to year. projects will make a signifi cant contri- currently produces almost 6 mgd of In water-year 2004, 6.1 MAF was bution toward meeting its water use recycled water. In addition to its joint diverted, and in 2005, 6.4 MAF. The effi ciency goals. project with DSRSD, EBMUD’s multi- average percentages of total Delta phased East Bayshore Recycled Water At the local level, the Bay Area infl ow diverted were 36.9 in 2004 and Project (EBRWP) is currently under Water Recycling Program’s (BAR- 36.7 in 2005. (Interagency Ecological construction and is expected to begin WRP) Master Plan, now complete, Program, 2005) delivery to Oakland customers in the calls for recycling 125,000 acre-feet/ late summer or fall of 2006, expanding MORE year in the Bay Area by 2010, and to Albany, Berkeley, and Emeryville INFO? [email protected] about 240,000 af/year by 2025. Many in 2007. The EBRWP will ultimately Bay Area agencies are forging ahead include nearly 30 miles of pipeline through parts of Alameda, Albany, FRESHWATER FLOWS TO THE SAN FRANCISCO ESTUARY, 1980-2005 Berkeley, Emeryville, and Oakland and IN MILLIONS OF ACRE FEET will save 2.5 mgd (2,800 acre-feet/ 70 Total Delta Inflow year) once all recycled-water custom- Net Delta Outflow ers are hooked up to the system. The 60 (after export and in-Delta use) 50 fi rst phase will supply up to 0.7 mgd. Eventually, EBWRP water may be 40 used in wetlands restoration. 30 MORE 20 INFO? [email protected] 10

0 '80'82 '84 '86 '88 '90 '92 '94 '96 '98 '00 '02 '04

Source: DWR, Dayflow QTOT RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP VITAL STATISTICS

Steelhead

Chinook Salmon Illustrations: Bill Crary

ing to spawn each year (“adult escape- 2001, for example, changing the need Fish ment”). The latter number—based to reduce pumping and use EWA on how many fi sh passed through the resources to protect fi sh. The winter- 13 Central Valley Salmon Red Bluff Dam fi sh ladders—became run population was 8,218 in 2003 and questionable in recent years as the 7,785 in 2004. The 2005 winter run Most populations of Central Valley dam gates remained open for longer was estimated by the Department of chinook salmon seem to be holding rel- periods and fewer fi sh had to use the Fish and Game as 15,000, of which 18 atively steady. Central Valley chinook ladders. An alternative method, counts percent were hatchery fi sh—higher salmon occur in four discrete runs— of spawned female carcasses upstream, than the usual 5 to 10 percent. (Sacra- winter-run, spring-run, fall-run, and backed up by earlier surveys, revealed a mento Bee, November 21, 2005) late fall-run (run refers to the season variation of up to a factor of fi ve in the in which adults return to their native The next most sensitive stock, the total estimates of spawning adults. The streams to spawn). The winter-run chi- spring-run, was state listed as threat- new higher estimates of adult escape- nook salmon, with the lowest popula- ened in 1998 and federally listed in ment translated into a higher estimate tion, has been listed as both a state and 1999. The spring-run population was of juvenile production and meant that federal endangered species since 1994. 17,564 in 2003 and 13,907 in 2004. the take limit was never reached in As a result of more regular interagency Sacramento fall-run are the most scrutiny of operations, a new counting method for chinook SALMON RUNS OF CONCERN winter-run salmon critical IN THOUSANDS OF ADULT FISH RETURNING TO SPAWN to assessing “incidental take limits” is now in place. Fed- 70 WINTER-RUN TO UPPER SACRAMENTO RIVER eral incidental take limits for 60 FALL-RUN TO SAN JOAQUIN RIVER winter-run allow up to two 50 SPRING-RUN TO UPPER SACRAMENTO RIVER percent of “juvenile produc- 40 tion” to be lost at the pumps. The formula for setting take 30 limits combines the number 20 of offspring produced (“ju- 10 venile production”) with the 0 number of adult fi sh return- '80'82 '84 '86 '88 '90 '92 '94 '96 '98 '00 '02 '04 STATE OF THE ESTUARY 2006 VITAL STATISTICS

abundant chinook stock. Their popula- year abundance were very low the Delta smelt environmentally sensitive. tion fl uctuated from 569,976 return- years these fi sh were spawned. This Possible reasons for the decline of ing in 2001 to 839,956 in 2002 (the relationship is the subject of on-going Delta smelt include reductions in Delta estimated population for Battle Creek investigation. outfl ow, extreme high fl ows (which was the highest on record), dropping to MORE displace them away from suitable 579,293 in 2003 and 346,277 in 2004. INFO? [email protected] rearing habitat), entrainment losses Returns of the San Joaquin fall-run at major water diversions and power in 2003, at 25,348, and in 2004, at plants, prey item changes, competition, 22,654, were both above the 1967– Delta Smelt toxicants, disease, changes in salinity, 1999 average annual return of 20,470. and predation. The late fall-run (distinct from fall-run) The Delta smelt (Hypomesus trans- Delta smelt abundance generally population was 8,322 in 2003, increas- pacifi cus), a 55–70 mm long osmerid, increased during the 1990s, which ing to 13,922 in 2004. is endemic to the upper San Francisco Estuary. It was once quite common, may have been due to above-normal MORE outfl ow conditions and reduced pump- INFO? [email protected] but a dramatic decline in the 1980s led to the federal and state listing of this ing exports, aiding in the transport of fi sh as a threatened species in 1993. larval/juvenile fi sh from the Delta to Striped Bass It is the annual life cycle, limited diet, their rearing grounds in the Suisun Bay low fecundity, and restricted distribu- area. To reduce the impact of Delta Native to eastern North America, tion within the Estuary that make pumping operations on smelt, CAL- the striped bass (Morone saxatilis) was introduced to California in 1879, when fi sh from New Jersey’s Navasink River STRIPED BASS INDEX 1961-2005 were released in the San Francisco 14 Estuary. The species did well in its FMWT Index new environment, supporting a com- 20000 mercial fi shery from 1888–1935, and is still the basis for an important sport fi shery. However, the population be- 15000 gan to decline in the 1930s, prompting tighter regulation of sport fi shing and 10000 intensive research.

Abundance indices of striped bass in their ﬁ rst year of life (young-of- 5000 the-year or YOY) remain at very low levels. Where the peak Midsummer 0 Townet Survey (TNS) index was 117 61 63 65 67 69 71 73 75 77 79 81 83 85 87 89 91 93 95 97 99 01 03 05 in 1965, the 2005 index was 0.9. The TNS index of 0.8 in 2004 was the TNS Index lowest in the 45-year history of the 120 survey. Where the peak Fall Midwater Trawl Survey (FMWT) index was 100 20,038 in 1967, the 2005 index was 121, up from 53 in 2004. 80

Calculations of recent adult striped 60 bass numbers have not been completed, but catch-per-unit-effort and 40 length-frequencies during 2005 spring tagging for the adult population study 20 show recruitment has been substantial even though indices of young-of-the- 0 61 63 65 67 69 71 7375 77 79 81 83 85 87 89 91 93 95 97 99 01 03 05 RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP VITAL STATISTICS

FED developed the Environmental through 2005, and so has the abun- and their recruitment appears most Water Account (2000), which helps to dance of longfi n smelt, as measured strongly associated with the mag- reduce Delta smelt take by shifting the by Cal Fish & Game’s Fall Midwater nitude and duration of fl oodplain timing of pumping. It is still diffi cult to Trawl Survey. Since 2003, the abun- inundation during the spawning period determine whether or not this effort is dance index for longfi n smelt has been (Sommer et al. 1997, Moyle et al. benefi ting Delta smelt on a population below 200, and in 2005 it dropped to 2004). In September 2003, US Fish & level. 129. These indices are close to the Wildlife removed splittail from the list record low indices recorded at the end of threatened species. The silvery- More recently, as of 2001, Delta of the 1987–1992 drought (http:// gold minnow, found only in tributaries smelt abundance indices have reached www.Delta.dfg.ca.gov/data/mwt/), to the S.F. Estuary and the Delta, is all-time lows for two of California and probably refl ect poor early sur- the only fi sh species to be de-listed Department of Fish and Game’s (DFG) vival conditions resulting from recent for reasons other than extinction. long-term monitoring surveys, Summer low winter outfl ow years and changes Although splittail was de-listed, it re- Townet Survey (TNS, since 1959) and in food web dynamics brought about mains a species of concern because of the Fall Midwater Trawl (MWT, since by the introduced Asian clam, Corbula its limited access to spawning habitat 1967), despite respectable water years. amurensis (Kimmerer 2002). On a pos- during low fl ow years and the po- For example, TNS indices from 2003– itive note, for several years Cal Fish & tential for future water management 2005 are 1.6, 2.9, and 0.3 respectively Game has continued to collect 115–40 decisions to exacerbate its situation. (compared to the 2002 TNS of 4.7), mm spawners (about three years old) MORE while MWT indices for the same years in trawl sampling. These age-three fe- INFO? [email protected] are 210, 74, and 26 (compared to the males can produce over twice as many MWT 36-year average of 556). Such eggs as age-two females, and such Pacifi c Herring abrupt decreases in Delta smelt and spawners can help buffer against poor other pelagic fi shes have prompted a year-classes. (Baxter, Pers. Comm., Until 2005, the spawning biomass 15 special task force to address this Pelagic 2006) of Pacifi c herring (Clupea pallasi), Organism Decline (POD). which supports the Bay’s largest com- MORE Just recently (2005) a new moni- INFO? [email protected] mercial fi shery, has remained below toring survey called the Delta Smelt the long-term (since 1978) average of Larval Survey (DSLS) began, which 52,234 short tons. In response to this targets larval Delta smelt. Information Splittail decline, the Fish and Game Com- from the DSLS along with the 20 mm mission, which manages the fi shery, Abundance of young Sacramento survey may aid in water management lowered catch quotas. Although splittail (Pogonichthys macrolepidotus) decisions in order to maintain a bal- ocean productivity has been favor- has been low from 2002 to 2005 ance between preserving Delta smelt able for herring over the last several based upon results from the Cal years, a large recruitment of young and providing California’s water. Fish and Game Fall Midwater Trawl fi sh to the spawning population has MORE (http://www.Delta.dfg.ca.gov/data/ yet to occur, and older age classes INFO? rmayfi [email protected] mwt/). For most of these years low have been declining. Following record abundance resulted from low river high biomass levels of 99,050 short Longfi n Smelt fl ow and lack of fl oodplain inundation tons in 1995–1996 and 89,570 short during the splittail spawning period in tons in 1996–1997, spawning biomass Longfi n smelt (Spirinchus thaleich- late February–May. However, spring plunged to 20,000 short tons fol- thys) in the Estuary represent the fl ows in 2005 appeared good and lowing the 1997 El Niño. Since then, southernmost spawning population in some recruitment was detected by spawning biomass estimates have North America, and their abundance US Fish and Wildlife beach seining been 39,500 short tons for 1998–1999, continues to be positively corre- and trawling surveys (www.Delta.dfg. 27,400 short tons for 1999-2000, lated with Delta outfl ow during their ca.gov/data/rtm2005/), so low Fall 37,300 short tons for 2000–2001, December-May larval period (Baxter Midwater Trawl abundance was not 35,400 short tons for 2001–2002, and 1999). Since the extremely wet winter expected and remains to be investi- 34,400 short tons for 2003–2004 (a of 1998, Delta outfl ow for the Decem- gated. Splittail are known to spawn biomass number was not fi nalized for ber-May period has generally declined on inundated terrestrial vegetation, 2002–2003 because of discrepancies STATE OF THE ESTUARY 2006 VITAL STATISTICS

between spawn deposition survey tion Center and a March 2004 court nonpredatory species spend their data and hydroacoustic survey data). decision remanding the determination, entire lives in their natal streams. The The 2004–2005 spawning biomass es- NMFS proposed listing the southern larvae subsist on algae and detritus; timate was 58,934 short tons, a 71% population segment as threatened in after metamorphosing in the fall, increase from the previous season and April 2005. The agency’s supporting adults spawn in spring in gravelly riffl es the fi rst estimate to exceed the long- rationale included the concentration and die without feeding. term average of 51,825 tons used to of spawning adults in a single river, First collected from the Fri- set fi shery quotas since the 1996–1997 loss of spawning habitat in the upper ant-Kern Canal in 1976, Kern brook season. Sacramento and Feather Rivers, and lampreys were later found in the negative trends in commercial bycatch MORE lower Merced, Kaweah, Kings, and INFO? [email protected] and juvenile entrainment data since San Joaquin Rivers. As larvae, they occupy silty backwaters of foothill Green Sturgeon streams, preferring cool, shallow pools and other low-fl ow environments with Limited evidence sug- sandy or muddy substrates. Many gests that overall, the popu- such habitats have been eliminated by lation of the anadromous channelization. Known populations 1986. NMFS also noted that green green sturgeon (Acipenser medirostris) are scattered through the San Joaquin sturgeons may be feeding on the may be declining in California. It is drainage and isolated from each exotic overbite clam which is known known to spawn in the Klamath, Trin- other. With one exception, all popula- to bioaccumulate toxic selenium. A ity, and Sacramento rivers, as well as tions are below dams where sudden public hearing on the proposed listing the Rogue River in Oregon. Little is changes in fl ow may strand the larvae. has been held, and a fi nal determina- known about its historic or current Larvae have also been drawn into the tion is pending. Meanwhile, scientists 16 distribution and movement through- siphons of canals from which they are studying parameters infl uencing out the Estuary, but abundance esti- are unable to return to the spawning sturgeon movement within the Estu- mates do not suggest that the popula- grounds. ary, preferred spawning locations and tion has declined in the Estuary (Kelly environments, and residence time A California species of special & Klimley 2004, Cal Fish & Game within the river and Estuary system concern, the Kern brook lamprey was 2001). While green sturgeon are (Kelly & Klimley, 2004). The results denied federal protection in a US Fish long-lived (up to 70 years), delayed of such studies could inform improved & Wildlife Service decision in January reproduction, combined with habitat natural resource management and 2005. A listing petition for four west- destruction and pressure from fi shing, protection efforts for the species. ern lamprey species had been submit- makes it diffi cult for them to replenish ted two years earlier by the Center their populations quickly. In 2001, a MORE INFO? [email protected] for Biological Diversity and 10 other coalition of environmental groups pe- conservation groups. FWS claimed titioned NMFS to list the green stur- the petitioners had not provided geon as either endangered or threat- Kern Brook Lamprey specifi c information on threats to the ened. As part of its review, NMFS Kern brook lamprey and another non- identifi ed two distinct population Endemic to the San Joaquin Val- migratory species, the western brook segments: the northern population ley, the Kern brook lamprey (Lampe- lamprey. (found north of the Eel River along tra hubbsi) is a primitive eel-shaped the coast) and the southern popula- vertebrate with an unusual life cycle. MORE tion (includes any coastal or Central Typical lampreys are predators, at- INFO? [email protected] Valley populations south of the Eel taching to fi sh with suckerlike mouths, River, with the only known popula- rasping a hole with a tongue covered tion in the Sacramento River). NMFS with sharp plates, and feeding on the declined to list the green sturgeon in victim’s blood and body fl uids. How- 2003, but placed both population seg- ever, several species have evolved ments on its list of species of special a nonpredatory lifestyle. Instead of concern. Following litigation by the migrating to sea as larvae (ammocoe- Environmental Protection Informa- tes), Kern brook lampreys and other RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP VITAL STATISTICS

and is now much more abundant than ten crab’s major impact is stealing bait Invasive Species it has been in past decades. While from sport anglers at some locations eradication is not possible at this point, in the Delta and Suisun and San Pablo Green Crab the National Green Crab Management bays. Plan includes several recommendations What controls mitten crab popula- The European green crab (Carci- for local population control strategies. tion in the Estuary is not understood, nus maenas) is now established in every These include early warning methods although winter temperatures and signifi cant bay and estuary between for new range expansions, prevention outfl ow are hypothesized to control Monterey, California and Gray’s measures against new introductions, larval survival and settlement time. Harbor, Washington. It appeared in and coordinated monitoring of popula- A “boom-and-bust” cycle has been South S.F. Bay in the early 1990s and tion trends, new outbreaks, and losses reported for some introduced species, has spread north at least as far as the to commercial fi sheries. although this may not be universally Carquinez Strait. Salinity limits the MORE true for all introductions. crab’s distribution: crabs have been INFO? [email protected] collected from water MORE INFO? [email protected] ranging from 5–31 parts Chinese Mitten per thousand (ppt) salt Crab to water, but few have Northern Pike been collected from The Chinese mitten water with less than 10 crab (Eriocheir sinensis) The voracious Northern pike ppt. A 10-year study population has increased (Esox lucius), native to Canada and in Bodega Bay found that in contrast rapidly since it was fi rst reported in the Midwest, was illegally planted to their slow growth rates in Europe, the S.F. Estuary in the early 1990s. in the 85,000-acre-foot Lake Davis green crabs here grew rapidly and Numbers of downstream migrat- reservoir in the early 1990s. In 1997, 17 reached sexual maturity in their fi rst ing adults peaked at the BurRec fi sh the California Department of Fish and year. Over the course of the study, the facility in 1998, while adult numbers Game treated the lake with Rotenone green crab severely reduced the abun- in northern S.F. Bay peaked in 1998 to eradicate pike from the lake. The dance of three common invertebrate and 2001. All data sources support a pike were signifi cant predators on the species, but did not impact the shore- population decline from 2002 through rainbow trout and also presented a bird food web (Grosholz et al. 2000). 2004, with the 2004 count the low- potential threat to the Delta ecosys- Another consequence of green crab est since 1996. No adult crabs were tem. The treatment temporarily shut predation is the accelerated invasion of detected in Suisun Marsh in 2004, and the lake to all recreational uses and another invasive species, the eastern only four public reports of sightings compromised local water supplies. In gem clam, which was introduced into were made to the toll-free reporting May 1999, about a year after more Bodega Harbor nearly 50 years ago line. When numbers are low, the mit- than a million trout were planted and the lake had reopened, the pike MITTEN CRAB STATUS reappeared, possibly intentionally reintroduced. Biologists have pulled 1000000 6 USBR approximately 55,000 pike from the 100000 CDFG 5 lake since 2000. In September 2005

10000 4 DFG announced a new preferred pike-eradication proposal in which the 1000 3 lake’s volume would be drawn down CDFG CPUE USBR Catch (thousands) 100 2 by 75 percent and another Rotenone treatment would be applied. This 10 1 would not affect drinking water for 1 0 the city of Portola, which now uses 96 97 98 99 00 01 0203 04 05 wells and springs. A joint EIR/EIS will Year be prepared by DFG and the Plumas

Total catch of adult mitten crabs at BurRec’s fish facility (bars) and catch per unit effort (CPUE) of National Forest. DFG is also working adult mitten crabs from Cal Fish & Game’s S.F. Bay Study otter trawl survey (line), 1996-2005. with community leaders to prevent STATE OF THE ESTUARY 2006 VITAL STATISTICS

another reintroduction, a criminal native Spartina foliosa, regional loss of expects to control the invasive Spartina offense with penalties including a fi ne unvegetated tidal fl at habitat, elimina- by 2010. of up to $50,000 and up to a year in tion of small tidal channels, and loss MORE jail. For current status, visit www.dfg. of pickleweed habitat essential to the INFO? [email protected] ca.gov/northernpike/index.html. endangered salt marsh harvest mouse. MORE Infested acreage increased by 280 INFO? [email protected] percent from 2001 to 2003, affecting Gobies both established and newly restored marshes—11,500 acres altogether.The Four species Asian Clam rate of spread is greatest on mudfl ats of non-native and restored tidal marsh. gobies inhabit The Asian clam (Corbula amuren- the San Francisco Estuary, all be- sis) continues to be the dominant ben- The invasion no longer consists of lieved to have been introduced via thic organism in the North Bay. The the pure parent genotype; many hybrid ballast water release. The California seasonal decline of the bivalve contin- morphologies have been observed. Department of Fish and Game’s San ues to occur throughout the North Bay Hybrids are more vigorous and repro- Francisco Bay Study (Bay Study) in winter of most years, and is followed ductively fi t than either of the parent catch-per unit-effort (CPUE) of the species. Control efforts by the Inva- by peaks in density after reproduction chameleon goby (Tridentiger trigono- sive Spartina Project in 2005 targeted in spring and fall. There have been cephalus), shimofuri goby (T. bifascia- 132 subareas, with a goal of treating some short-duration phytoplankton tus), and shokihaze goby (T. barbatus) 70 to 80 percent of the infestation. blooms in the North Bay for the last have been relatively stable since 2001. Permits and funding are in place for several years during early spring, when The yellowfi n goby (Acanthogobius 2006–2007. In the 2005 season, the Corbula biomass is at an annual mini- fl avimanus) has historically been the previously used herbicide glyphosate mum. These blooms have been earlier most abundant and widespread of the 18 (Aquamaster®, the aquatic version of and shorter in duration than historic introduced gobies. Yet in 2002 and Roundup®) was largely replaced by a blooms. Corbula was fi rst seen in the 2003, Bay Study shokihaze goby catch new agent, imazapyr (Habitat®), only South Bay in 1988 and had become a exceeded yellowfi n goby catch. recently registered for use in Cali- dominant bivalve by 1990. Unlike in the fornia. Unlike glyphosate, treatment The shokihaze goby was fi rst North Bay, however, the South Bay with imazapyr does not require a 6- to discovered near the Antioch Bridge phytoplankton bloom has not been de- 12-hour post-application period within November 1997; it has since pleted by Corbula fi lter-feeding. This is out tidal inundation. Also, glyphosate become one of the most abundant due to the seasonal cycle of Corbula in tends to bind to sediment and become demersal fi shes in Suisun Bay and the that part of the Bay—during the spring inactivated, and requires coating of the lower Sacramento River. The diet of bloom period, clam biomass is very low entire plant. Human health risks from juvenile and adult shokihaze gobies and thus the clam’s grazing pressure imazapyr are reported to be low, and in the upper Estuary is dominated by is too low to restrict phytoplankton the herbicide is less toxic to aquatic gammarid amphipods, with isopods, bloom formation. organisms than glyphosate; however, clam siphons, copepods, barnacle cirri, MORE there is a high risk of damage to non- polychaetes, mysids, and hydroids INFO? [email protected] target plants if inadvertently applied. also contributing to a large part of the One complication in the campaign diet. The shokihaze goby is capable of Cordgrass against invasive Spartina has been the killing and consuming fi sh, as observed presence of high densities of the endan- in aquaria, yet fi sh are rarely found gered California clapper rail (Rallus Species of Spartina (cordgrasses), as a prey item. The impact of the longirostris obsoletus) in some infested introduced into the Estuary in the shokihaze goby on native fi shes in the areas, including Arrowhead Marsh and 1970s, have spread rapidly and pose a Estuary by predation is believed to be Colma Creek. The presence of the rails serious threat to the success of future minimal, yet its consumption of inver- will require treatment outside the birds’ tidal marsh restoration throughout tebrates and aggressive behavior could February-through-August breeding the Estuary. The impacts associated result in competition for resources season and a phased approach involving with the spread of Atlantic cordgrass with other fi shes. revegetation with native species. With (Spartina alternifl ora) include hybridiza- adequate funding, the Spartina Project tion with and likely local extinction of RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP VITAL STATISTICS

Shokihaze goby distribution has its presence was confi rmed in 2001, project tracking system. While water- expanded downstream from the upper and Drake’s Estero. On the seabed, fowl habitat will remain a key focus for Estuary to the South Bay. Shoki- Didemnum smothers burrowing both joint ventures, updated plans will haze gobies were collected near the bivalves by growing over their siphons. also include specifi c goals for breeding Dumbarton Bridge in February 2002 It has been found covering more than and wintering waterfowl, shorebirds, and also in November and December 60 square miles of North Atlantic grassland and riparian birds, and other 2004. Shokihaze gobies have been col- seafl oor with a slimy monoculture wetlands-associated birds, and will lected in salinities ranging from 0.09 at Georges Bank, and biologists fear address agricultural practices and to 28.81 parts per thousand in the it may become established on the protection. Central Valley partner- Estuary. The potential exists for their Cordell Bank. ships have resulted in three North range to continue to expand within American Wetland Conservation Act MORE the Estuary and also into other bodies INFO? [email protected] (NAWCA) grants totaling nearly $3 of water within California. million for wetland conservation ac- MORE tivities in Suisun Marsh and in the Yolo INFO? [email protected] Wetlands and Delta basins. Meanwhile, regional interests continued with wetlands-re- & Wildlife lated planning, partnerships, and fund- European Sea Squirt raising. CALFED completed a draft regional implementation plan that A relative newcomer to San Fran- Wetlands includes eight restoration priorities cisco Bay, the European ascidian or and continued to provide signifi cant sea squirt Didemnum cf. lahillei forms San Francisco Bay Joint Venture funding for restoration projects and amorphous masses on docks, piers, partners completed several major ecosystem planning and processes. As rocks, gravel, and other hard surfaces. acquisitions around the Bay, including of 2004, CALFED had provided $177 Taxonomy is controversial, and mul- Cargill properties in the South Bay 19 million for restoration projects in San tiple species may be involved. (16,000 acres) and the Bahia wetlands in the North Bay(600 acres). Current Francisco Bay, with additional funding Ascidians, distant relatives of efforts include restoration planning for under the Delta Regional Ecosystem vertebrates, metamorphose from a Restoration Implementation Plan the South Bay salt ponds and restora- tadpole-like larval stage into sessile (DRERIP). The San Francisco Bay tion projects on Petaluma and Triangle fi lter-feeders. Didemnum is a colonial Area Wetlands Restoration Program marshes, Simmons Slough, Pacheco form and potentially one of the most (WRP), a partnership of 18 federal, Marsh, Hamilton Air Force Base–Bel signifi cant fouling organisms in the state, and local public agencies, is Marin Keys, Napa-Sonoma Marshes, Bay. Since its larval form is unable to working to implement the CCMP’s Cullinan Ranch, Napa River Flood survive long in ballast water, it most wetlands action items and the broad Control Project, American Canyon, likely arrived on a ship’s hull sometime recommendations of the Baylands Dutch Slough, Eden Landing Eco- prior to 1993 when it was fi rst de- Ecosystem Habitat Goals Report. logical Reserve, West Stege Marsh, tected. It reproduces rapidly, tolerates and Sears Point. In the North Bay, For a comprehensive list of wet- a wide range of depths, and, like many efforts are underway to acquire and land restoration projects that have exotics, has no known predators in permanently protect privately owned been implemented around the Bay, local waters. Its spread appears to be tidal wetlands and diked baylands. see the database and maps compiled limited only by salinity and substrate Nearly 300 other projects to protect by Wetlands and Water Resources requirements. and restore wetlands and riparian (www.swampthing.org). For wetlands Didemnum has already been habitats are also in progress. Both creation, restoration, mitigation, and identifi ed as a problem on the Atlantic the Central Valley and San Francisco enhancement projects, see the San Coast, in Puget Sound, and in New Bay Joint Ventures are updating their Francisco Estuary Institute’s Wetland Zealand and Japanese waters. Of implementation plans, and the Central Project Tracker (www.wrmp.org/proj- particular concern to aquaculturists, it Valley Joint Venture has identifi ed ectsintro.html), San Francisco Bay overgrows rafts and other structures the Delta as a high priority area for Joint Venture (www.sfbayjv.org), and on which mussels and oysters are habitat work. In collaboration with Central Valley Joint Venture (www. grown. It poses a potential threat to Ducks Unlimited, the San Francisco cvjv.org). For detailed information oyster farms in Tomales Bay, where Bay Joint Venture has created a new about CALFED’s extensive ac- STATE OF THE ESTUARY 2006 VITAL STATISTICS

tivities and accomplishments, see the San Bruno Marsh, there appears to be San Pablo Bay system and a similar CALFED Bay-Delta Program Annual strong association between increase in number in Suisun Bay and Carquinez Report 2004 (http://calwater.ca.gov/ vegetation cover provided by Spartina Strait, but the true number may be AboutCalfed/AnnualReport2004). alternifl ora and increase in clapper rail higher or lower (Evens & Nur 2002); For information about restoration of densities (S. Bobzien, Pers. Comm., new population studies are currently the Cargill property, see www.south- 2005). Studies by the Invasive Spar- underway. Key predictive factors in bayrestoration.org. tina Project suggest that rails have black rail distribution are vegetation colonized Spartina-invaded sites in height, absence of amphipods (indica- the South Bay that would otherwise tors of lower elevation marsh), and, in California have been too small to support them San Pablo Bay, presence of Frankenia Clapper Rail (H. Spautz, Pers. Comm., 2005). (an indicator of high-elevation marsh Whether this association is positive habitat) (Evens et al. 1986). According Current or negative in terms of clapper rail to the 2002 study, other variables may Bay-wide popula- population viability is an open ques- include marsh size (rail abundance tion estimates of tion. Further surveys in 2006 should tended to increase as the size of the the endangered provide a clearer picture of clapper rail marsh increased), marsh distribution California clap- distribution and population dynamics (the distributional relationship of each per rail (Rallus throughout the Bay. marsh to other marshes likely infl u- longirostris obsoletus) are not available, MORE ences rail presence and abundance), but surveys in the 1990s estimated INFO? [email protected] marsh confi guration (broader marshes their numbers at 1,040 to 1,264, with tended to support rails in higher abun- up to 564 in Suisun and San Pablo dance than linear marshes), predator Bays (1992–93 data) and up to 700 Black Rail populations (sites bound by levees or in South San Francisco Bay (1997-98 riprap provide access and habitat to 20 Tidal data). This represented an increase mammalian predators), hydrological marshlands of from a low of 300 to 500 individuals cycles (tidal marshes with full tidal the S.F. Bay in the 1980s. A new Bay-wide survey infl uence provide the best habitat for region sup- began in January 2005. Results from rails), and fl uctuations in water level port most of the California black rail the fi rst year indicate the species has (inundation above a certain depth may (Laterallus jamaicensis coturniculus) declined or been extirpated in some exclude habitat to black rails) (Evens population in the western United areas of the North Bay since the early et al. 1989, Flores & Eddleman 1993, States (Manolis 1978, Evens et al. 1990s. No clapper rails were detected Evens et al. 1991). 1991). For the most part, the breeding at any of the nine Suisun Bay sites, or distribution of black rails, state listed MORE at the mouth of Sonoma Creek where INFO? [email protected] as threatened, is confi ned to remnants the previous survey found approxi- of historic tidal marshlands in the mately 25 individuals. Two former Estuary’s northern reaches, primarily low-density sites, Richardson Bay and Least Tern those associated with San Pablo and Point Pinole, also had no detectable Suisun bays (Manolis 1979, Evens Califor- rails in 2005. The population at White et al. 1989, Evens et al. 1991). Black nia least terns Slough near Vallejo also showed a rails occur in the South Bay as well, (Sterna antillarum browni), state and sharp decline. It is unclear whether but mostly during winter, and with federally listed as endangered, contin- such small satellite populations are breeding limited to very few loca- ue to nest at Alameda Point, formerly succumbing to predation or emigrat- tions (e.g., Dumbarton Marsh). Small the Alameda Naval Air Station. While ing to other marshes. On the other numbers have also been discovered disturbances from gulls and raptors hand, counts at Heerdt Marsh and recently in small wetlands in the have increased, human disturbance Muzzi Marsh in South Marin were Sierra foothills and at a few isolated from trespassers has decreased to higher, and it is generally believed marshes in the Delta. A 1996 study almost none. Although the number that numbers have increased in San estimated approximately 14,500 black of tern pairs using the base increases Francisco Bay, especially the South rails in the entire S.F. Bay system, with each year, the number of successful Bay. In some San Francisco Bay loca- approximately 7,200 black rails in the fl edglings continues to fl uctuate. In tions such as Arrowhead Marsh and RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP VITAL STATISTICS

2005, 424 breeding pairs produced however, densities observed were the level necessary to ensure a stable 260 fl edglings, down from a previous quite high (10-fold higher than in San population. Reproductive success all-time high of 320 in 2001. Those Pablo Bay); Point Reyes Bird Obser- varies among marshes, with landscape fl edglings represented between 8 and vatory scientists estimate 10,000 to characteristics (such as proximity to 18 percent of the state’s total fl edgling 15,000 breeding individuals in Suisun the water’s edge) being good predic- population. Bay. An additional unknown number tors of nest survival. Success is lowest are present in brackish and freshwater in Suisun Bay. The greatest cause of Farther north, the number of terns marshes, which may be their primary nest failure is predation by both native at the Southern Power (formerly habitat. Point count surveys in 2004 (common raven, American crow, PG&E) cooling ponds in Pittsburg de- yielded results consistent with earlier raccoon) and non-native (house cat, creased from 13 pairs in 2001 to four in fi ndings: highest densities in Suisun red fox, Norway rat) species; rodents 2005, none of which bred successfully. Bay, lowest in San Francisco Bay. are likely the most common predator Southern Power is continuing PG&E’s Based on a small sample, nest success voluntary monitoring program at in most marshes. In addition, about 10 rate in the 2004 study was a relatively the site. A colony site was started in percent of nests fail each year due to low 21.9 percent. Salt marsh yellow- 2000 on Caltrans property in Albany, fl ooding during the highest tides. Nest throats appear to respond to specifi c with somewhere between eight and survival rates in a 2004 study were vegetation composition and are more 12 pairs in 2000; however, it has not similar to long-term averages. Estimat- abundant where there is a greater been used since 2001. The East Bay ed numbers of breeding Alameda song amount of alkali bulrush (Scirpus mari- Regional Park District recently estab- sparrows (Melospiza melodia pusillula), timus). In Suisun and San Pablo Bay, lished a least tern breeding site on the restricted to Central and South S.F. yellowthroats, unlike other salt marsh Hayward Regional Shoreline. Terns bays, range from 13,400 to 20,000 birds, show a positive association with nested at this site for the fi rst time in individuals; of Suisun song sparrows the invasive perennial peppergrass 2005, but all 8 nests failed due to dis- (Melospiza melodia maxillaris), found (Lepidium latifolium). In addition, turbance and trampling by gulls. Least in Suisun Bay, from 43,000 to 66,000; 21 they are more abundant where the terns have abandoned the Oakland and of San Pablo or Samuel’s song vegetation structure is more complex; Airport as a breeding site probably sparrows (Melospiza melodia samuelis), for example, where there is more due to predation by feral cats and found in San Pablo Bay, from 81,000 to diversity in the height of herbs. Finally, the non-native red fox (last reported 90,000. Population densities of the Al- salt marsh yellowthroats are more nu- breeding attempt in 1995). ameda subspecies have increased since merous in marshes that are more com- 1996, while densities of the Suisun and MORE pact in shape, rather than elongated or INFO? [email protected] San Pablo subspecies appear stable. irregular in shape. or joelle_buff [email protected] The presence of salt marsh song MORE sparrows is not strongly linked to any INFO? [email protected] Salt Marsh one, or even several, species of plants, Common though the three subspecies of song Yellow- Salt Marsh Song Sparrow sparrows do appear to respond posi- throat tively to gumplant and coyote brush Reproduc- and negatively to rush. Nevertheless, Surveys of tid- tive success of the population density of song spar- al marshes in 2000 salt marsh song rows is well correlated with landscape detected few yellowthroats (Geoth- sparrows has features. Density is greatest where lypis trichas sinuosa), a state species of been increas- land adjacent to the marsh contains special concern, in S.F. Bay itself; likely ing slowly since less urbanized areas and less agricul- only a few hundred are present. In 1998, which ture and a greater extent of natural up- San Pablo Bay, the estimated density was the poorest lands. Conversely, density is lowest in was also low, with an estimated total year recorded to small, isolated marshes. All three song population of 3,000 or fewer breed- date. Despite this increase, the overall sparrow subspecies are state species of ing individuals. In many marshes in success observed at most marshes special concern. San Pablo Bay, yellowthroats were (usually between 15 percent and 20 MORE completely absent. In Suisun Bay, percent of nesting attempts result in INFO? [email protected] any fl edged young at all) may be below or [email protected] STATE OF THE ESTUARY 2006 VITAL STATISTICS

Least Bell’s second brood attempt), discovered by leased at a second site, on a privately Vireo PRBO CS fi eld biologist Julian Wood, owned ranch near Vernalis. The rab- was in an arroyo willow screened by bits are not released into the wild until A small grayish mugwort. they are large enough to successfully neotropical migrant survive the translocation. All rabbits The CALFED grant for the songbird, the least are screened by a veterinarian before restoration expired in 2005. Refuge Bell’s vireo (Vireo being released. personnel and biologists are hoping for bellii pusillus) made national headlines additional funding to monitor possible The numbers in Caswell were in 2005 when a pair nested at the nesting attempts in the next breeding extremely low in 2001, but rebounded San Joaquin River National Wild- season, if the vireos return from their slightly in 2002 and 2003. The life Refuge, apparently rearing two Mexican wintering grounds. population remains too small to allow broods. The birds were fi rst detected population size estimation tools to by PRBO Conservation Science biolo- MORE INFO? [email protected] function properly, so the exact size of gist Linette Luna, who recognized the the Caswell population is not known. male’s distinctive song. This was the Efforts are underway in the park to fi rst confi rmed breeding record for the Riparian Brush improve the habitat for rabbits, as well San Joaquin Valley since 1919, and an Rabbit as for federally listed (endangered) encouraging sign of the effectiveness riparian wood rats (Neotoma fuscipes of riparian restoration. Populations riparia). of the federally Once common in riparian areas listed (endan- MORE throughout the Central Valley, the en- INFO? [email protected] gered) riparian dangered subspecies has suffered from brush rabbit loss of habitat and from brood parasit- (Sylvilagus bachmani riparius) are 22 ism by the brown-headed cowbird, Harbor Seal largely restricted to riparian habitat a relative newcomer to California. along the Stanislaus River in Caswell San Francisco Unlike songbirds that co-evolved with Memorial State Park, the San Joa- Bay harbor seal cowbirds, the vireo lacks an effec- quin River National Wildlife Refuge, (Phoca vitulina) tive nest defense. Female cowbirds and two small parcels of private land numbers have destroy or eject the hosts’ own eggs along the San Joaquin River. The remained fairly and replace them with their own, rabbits were thought to be restricted stable over the leaving the victims to raise a clutch of to the habitat in Caswell until surveys past decade, and are estimated to be cowbirds rather than vireos. By the discovered the two additional popu- over 600. Although approximately 12 time the least Bell’s vireo was federally lations (one of which was recently haul-out sites are known in the Bay, listed in 1986, the California popula- found to be more extensive than fi rst harbor seals are found in the great- tion had fallen to 300 breeding pairs, thought), and a cooperative state/fed- est numbers throughout the year at mostly in San Diego County. eral effort began a breed-and-release three sites: Mowry Slough, Yerba With effective cowbird control program on the refuge. The captive Buena Island, and Castro Rocks. and riparian restoration, the vireo breeding program was begun in early Mowry Slough, the largest pupping began to regain portions of its lost 2002, with three male and three fe- site in the Bay, is used predominantly range. Appropriate nesting habitat had male rabbits released into an enclosed during the pupping (mid-March–May) been created at the San Joaquin River pen during the winter. The rabbits and molting (June–mid-August) refuge in a project coordinated by the successfully bred, and 49 young rab- seasons. Since 2000, approximately US Fish & Wildlife Service, involving bits were later released into natural 300 harbor seals and over 100 pups PRBO Conservation Science and Riv- riparian habitat at the refuge. The have been counted at Mowry Slough er Partners. In addition to willows and program was expanded in 2003, with each pupping season. In the winter other streamside trees, River Partners two additional enclosures and 194 (mid-November–mid-March) months, planted a herbaceous understory of young rabbits released into the refuge. when Pacifi c herring (Clupea pallasi) mugwort and other species to attract As of December 2005, 100 more were spawn in the Bay, the number of seals songbirds such as the yellow warbler. waiting for release (M. Kinsey, Pers. at Yerba Buena Island increases to The second vireo nest (a presumed Comm. 2005), and 30 had been re- 200 to 300 harbor seals (1998–2004). RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP VITAL STATISTICS

Additionally, the number of seals using that could impact mouse populations almost all critical habitat in eastern Castro Rocks, a chain of rock clusters are underway in the North Bay, and Contra Costa County based on a just south of the Richmond Bridge large scale salt pond restoration has habitat conservation plan. The revi- and the second-largest pupping site in begun in the South Bay, but it will take sion also exempts routine ranching the Bay, has increased greatly during years to decades for new marshes activities on private land from federal the winter season since 2000, with a to be produced and hence increase coverage. In 2005, a court decision maximum of 300 to 600 seals record- mouse populations. Meanwhile, required the Environmental Protec- ed during recent years. The increase recent surveys document that there is tion Agency to consult with FWS on in seals hauling out at Castro Rocks in very little mouse escape cover left in the registration of 66 pesticides with the winter may be related to shifts or the South Bay, where what was once potential impacts on the frog. increases in herring spawning closer miles of high marsh vegetation has MORE to Castro Rocks. Castro Rocks is used been reduced to a maximum width of INFO? by an average of 100 seals year-round 8 to 9 feet or eliminated completely. [email protected] (2000–2004). Seismic retrofi t work (Shellhammer, Pers. Comm., 2005) began on the Richmond Bridge in MORE early 2001, and researchers from San INFO? [email protected] Western Francisco State University monitored Snowy what effect the construction had on Plover seal numbers and behavior. Despite California In the Bay Area, the federally an early shift in site use to rocks Red-Legged threatened Pacifi c Coast western located farther from the bridge when Frog snowy plover (Charadrius alexand- construction was underway in the The once-abun- rinus nivosus) is primarily associated immediate area, and an increase in dis- dant California red- with commercial salt evaporation turbances due to construction activity, legged frog (Rana ponds and levees, which means that 23 seals maintained use of the Castro aurora draytonii), land managers have not to date been Rocks haul-out site for the duration federally listed as able to actively manage habitat or of construction work (2001–2005). threatened, has resources for this species. However, (Green, Pers. Comm., 2006) disappeared from approximately 70 the recent purchase of more than MORE percent of its historical range. It is now 15,000 acres of salt ponds in south S.F. INFO? [email protected] found only in coastal wetland areas Bay by Fish & Wildlife and Cal Fish and freshwater streams from Marin & Game could aid in plover recovery. Salt Marsh County south to Ventura and in scat- Future pond management will include Harvest tered streams in the Sierra Nevada. managing several of these ponds as Mouse Range-wide, only four populations plover nesting and foraging habitat, as contain more than 350 adults. Habitat well as conducting predator control It is not loss, stream sedimentation, pesticides, and minimizing human disturbance. known whether and predation all threaten the frog, the These actions are outlined in Fish & the population of the Bay’s endan- largest native to the western United Wildlife’s draft recovery plan for the gered salt marsh harvest mouse (Re- States. In spring 2004, the US Fish & plover, which calls for increasing the ithrodontomys raviventris) has changed Wildlife Service renewed a proposal S.F. Bay breeding population from its signifi cantly over the past fi ve years. to declare 4.1 million acres across current level of 150 to 200 individuals Population studies are conducted only California, including parts of the Bay to 500. While the Bay did not his- when development projects or chang- Area, as critical habitat for the frog. torically support 500 snowy plovers, es in land use threaten the mice, and Following litigation, FWS issued a managing salt evaporation ponds for few such studies have been required revised proposal in November 2005 plovers is an opportunity for it to play during this time. When such studies which eliminated 82 percent of the a signifi cant role in the recovery of are conducted, their piecemeal nature area in the original proposal, includ- this species, especially because many makes it diffi cult for scientists to get ing many of the core areas delineated of the plover’s historic coastal breed- a take on overall population trends. in the 2002 recovery plan. In the Bay ing and wintering sites have been Several marsh restoration projects Area, the new proposal eliminates degraded by human disturbance and STATE OF THE ESTUARY 2006 VITAL STATISTICS

urban development. Off-leash dogs The diminuitive, long-legged west- fences, collisions with wind turbines, also pose a signifi cant threat to snowy ern burrowing owl (Athene cunicularia shooting, and vandalism of nests. The plovers at coastal breeding sites. hypugaea) was state-approved practice of relocating Breeding season surveys conducted once common owls from development sites is accel- in 2004 by the S.F. Bay Bird Observa- throughout erating local extirpations from rapidly tory and the Don Edwards National the West but urbanizing areas. Owls typically nest Wildlife Refuge indicate that approxi- has declined in the same burrow year after year mately 113 plovers used Bay salt precipitously and often try to return to their former ponds during the breeding season, an in California homes. One study found that only one increase from 2003, with the highest in the last sev- relocation in eight resulted in success- concentration in DFG’s Eden Landing eral decades— ful nesting at the new site. The owl Nature Reserve. In that year 59 nests breeding owls was listed as a state species of special were found and followed through to have been concern in 1994. In December 2003, completion to determine hatching suc- eliminated from at least 8 percent to the California Fish & Game Commis- cess. Due to late rains in 2005, plover 10 percent of their former range in the sion denied a petition seeking threat- breeding habitat was severely reduced state and are trending toward extinc- ened or endangered status for the owl as many of the ponds were fl ooded tion in another 25 percent. Currently, under the state Endangered Species until midsummer. Twenty nests were estimates are that more than 70 Act. A statewide census is planned for found in 2005. Many were on Refuge percent of California’s breeding owls 2006, and a new petition may be fi led property, since much of Eden Land- live in the margins of agricultural land if continuing decline is documented. in the Imperial Valley. Locally, burrowing was fl ooded. The breeding season MORE window survey conducted in May ing owl population declined 50 percent INFO? 2005 found 124 plovers mostly in salt from the 1980s to the 1990s. The owl [email protected] has been extirpated as a breeding 24 pond habitats around the Bay (Strong bird from San Francisco and Marin Pers. Comm., 2006). Avian preda- Soft Bird’s-Beak tor surveys were conducted in 2004 counties and from most of San Mateo and Sonoma counties. Breeding owls and 2005 to determine which preda- Soft bird’s-beak (Cordylanthus can still be found in scattered spots tors may be posing the highest risk to mollis ssp. mollis), state and feder- in the East Bay, primarily in eastern plover success. Common ravens were ally listed as endangered, survives in Alameda and Contra Costa Counties, found to be the primary avian predator and in Santa Clara County, where a only 19 widely scattered sites in the of concern in both years, but Califor- census seven years ago estimated only coastal salt and brackish tidal marshes nia gulls may also become a problem 120 to 141 pairs remained. Burrowing around San Pablo and Suisun bays and due to the exponential growth of their owls nest in the burrows of ground in Contra Costa, Napa, and Solano colony in salt pond A6. The US Fish squirrels and other mammals. They counties, with individual populations & Wildlife Service’s fi nal determina- require open fi elds with adequate fl uctuating from year to year. tion of critical habitat for the plover, food supply for foraging, low vegeta- issued in 2005, eliminated half of the The hemiparasitic bird’s-beak is tive cover (to watch for predators), area originally proposed, including all photosynthetic and can fi x its own and adequate roosting sites. Burrow- Bay Area habitat: the South Bay salt carbon for growth requirements. It ing owls are threatened primarily by pond restoration area was excluded also attaches to a variety of hosts, habitat loss due to urban development because it must also provide habitat including pickleweed, saltgrass, and and by the corresponding eradication for least terns, clapper rails, harvest exotic forbs and grasses. In turn, it of ground squirrels and other burrow- mice, and waterfowl, and resource supports native bee pollinators and ing rodents. Other factors contribut- managers will therefore need fl exibility moth species whose larvae eat its ing to the decline of owls statewide in managing the site. Concurrently, a seeds. Ninety percent of its historic include burrow destruction through petition to de-list the plover is under habitat has been lost with conversion disking and grading, pesticide impacts, of tidal marsh to farmland. Water agency review. increased predation by non-native or pollution, muted tidal hydrology, host MORE feral species, habitat fragmentation, association with exotic winter annual INFO? [email protected] or and other human-caused mortal- [email protected] plants, competition with invasive ity from vehicle strikes, electrifi ed Western Burrowing Owl plants, habitat fragmentation, exces- RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP VITAL STATISTICS

proportion of samples tested over the Water past ten years.

& Sediments There are indications that the current levels of contamination may Bay Contaminants be harming the health of some wildlife species. Mercury concentrations Water and sediment of the Estu- appear to be high enough to cause ary meet cleanliness guidelines for embryo mortality in clapper rails, an most pollutants. However, a few endangered species found in Bay tidal problem pollutants are widespread marshes. PCB concentrations may be in the Estuary, making it rare to fi nd high enough to also cause low rates water or sediment in the Estuary that of embryo mortality in Bay birds and sive seed predation associated with is completely clean. Several pollutants to affect immune response in harbor reduced tidal hydrology, mosquito are present at levels of concern. A fi sh seals. Selenium concentrations appear abatement activities, trampling by consumption advisory remains in ef- to be high enough to cause abnormali- over-grazing or human activity in sen- fect due to concentrations of mercury, ties in early life stages of Sacramento sitive marshes, and naturally occurring PCBs, dioxins, and organochlorine splittail and white sturgeon. Pollutant events also threaten the plant. pesticides of potential human health mixtures appear to similarly affect Researchers planted soft bird’s- concern in Bay sport fi sh. A duck early life stages of striped bass. As- beak seeds in test plots at Rush Ranch consumption advisory is also in effect sessments of benthic communities in 2000. They found that the plant due to selenium concentrations of in the marine and estuarine regions does best in patchy habitat, with gaps potential human health concern. of the Bay indicate that some areas to provide sunlight for seedlings, and may be impacted by pollutants. The Over the long term, the Estuary 25 that clipping back the vegetative can- frequent occurrence of sediment tox- has shown signifi cant improvements in opy gives the parasites a crucial boost, icity is another indicator of pollutant basic water quality conditions, such as although exotic plants take advantage impacts in Estuary sediments. oxygen content, due to investments of the gaps. High seedling mortality at in wastewater treatment. Contamina- During the past two years con- the reintroduced and natural population due to toxic chemicals has also siderable progress has been made on tion sites was linked to host associa- generally declined since the 1950s and several cleanup plans (“TMDLs”) for tion with non-native plants. The Rush 1960s. Long-term trends for pollutants pollutants of concern. The San Fran- Ranch population is expanding by of current concern vary from pollut- cisco Bay Regional Water Board is natural dispersal, and many seedlings nearing completion of TMDL projects have established outside the experi- ant to pollutant. Mercury concentra- addressing mercury, PCBs, diazinon, mental plots. However, other populations in striped bass, a key mercury pathogens, and sediment. There are tions have been displaced by invasive indicator species for the Estuary, have currently 270 San Francisco Bay plants within the last two years. shown little change in 30 years. PCB Region listings on the State’s 303(d) (B. Grewell, Pers. Comm. 2005) concentrations appear to be gradually declining. Concentrations of DDT, list of impaired waters. Upon comple- MORE tion of these TMDL projects that are INFO? [email protected] chlordane, and other legacy pesticides have declined more rapidly and may scheduled for Water Board action by soon generally be below levels of con- June 2006, we will have resolved over cern. On the other hand, concentra- 100 impairment listings in the Region. tions of chemicals in current use, such Other projects in the works include as pyrethroid insecticides and polybro- TMDLs for mercury in the Guadalupe minated diphenyl ethers (PBDEs) are River Watershed, and sediment in on the increase. Aquatic toxicity has San Francisquito Creek and Sonoma declined in the past few years, pos- Creek. sibly associated with reduced usage of MORE organophosphate pesticides. Sedi- INFO? www.waterboards.ca.gov/ sanfranciscobay/tmdlmain.htm ment toxicity, on the other hand, has consistently been observed in a large STATE OF THE ESTUARY 2006 VITAL STATISTICS

Delta & Upstream In 2004–2005, the Board ad- In the Sacramento basin in 2005, Contaminants opted amendments to its Basin Plan the Regional Board adopted Basin to address water quality problems in Plan amendments to control methyl The freshwater side of the Estuary the Delta associated with elevated mercury in Harley Gulch and Cache does not have a systematic monitor- levels of diazinon and chlorpyrifos, Creek. An amendment to control ing program to evaluate contaminant and low dissolved oxygen levels in the methyl mercury levels in fi sh in the levels in water, sediment, or biota. Stockton Deepwater Ship Channel. lower American River is scheduled for However, contaminants documented The Basin Plan amendments for each 2006–2007. to exceed either water quality ob- include an implementation plan with In the San Joaquin basin, the jectives or concentrations toxic to a schedule, and monitoring to assess Board adopted amendments for chlor- aquatic organisms in the Delta have compliance. Each plan contains a pyrifos, diazinon, boron, and salt in been given the highest priority by the reopener clause after about fi ve years 2005. The pesticide basin plan amend- Central Valley Regional Water Quality to ensure that monitoring results and ment included a formula for additivity Control Board for development of new scientifi c fi ndings are incorpo- when multiple insecticides were simul- regional load reduction and control rated into the revised implementation taneously present in water. Ongoing programs (TMDLs) under the Clean plans. A methyl mercury basin plan monitoring shows that concentrations Water Act. amendment is scheduled for Board of diazinon and chlorpyrifos continue adoption in the summer of 2006. to fall throughout both the Sacramen- to and San Joaquin watersheds, most likely because of decreased agricultural use. MORE INFO? www.swrcb.ca.gov/rwqcb5/ 26

Photo courtesy of PWA. RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP BIG PICTURE; WARNING BELLS

“The Delta is the most subsided landscape in the world relative to its total size. Once we put homes in the Delta, all bets are oﬀ : public safety trumps everything.”

— Jeﬀ Mount, UC Davis

“All of our restoration eﬀ orts will be futile if we are unable to stem the tide of urbanization in the Delta. Restoration can 27 wait—but the time for acquisition is now.”

— John Cain Natural Heritage Institute

“Funding for restoration and environmental programs will increasingly become a challenge as bond monies dry up.”

— Ellen Hanak Public Policy Institute of California

Photo courtesy of David Hart and John Sanger STATE OF THE ESTUARY 2006 BIG PICTURE; WARNING BELLS

economic growth; patterns of infra- 45 percent of U.S. residents—strongly California 2025: structure fi nancing; current estimates support protecting the environment, the Estuary in of infrastructure needs; governance even if it curbs economic growth. and institutional challenges for plan- That same survey showed that water the Big Picture ning; issues of equity; and the public’s quality issues are a big concern of perceptions of the future; prefer- more than half of the Californians HANAK, ELLEN ences regarding schools, water, and surveyed. PUBLIC POLICY INSTITUTE OF CALIFORNIA transportation; and willingness to MORE pay higher taxes or fees to fund those INFO? [email protected]; www.ca2025.org In the near future, money for preferences. restoring the Estuary—and for envi- Findings relevant to the Estuary ronmental programs in general—will concern the overall picture for public be harder to fi nd, as existing bond investment and the specifi c picture for money runs out. California 2025: Tak- TAKE water resources. Overall, California’s HOME ing on the Future, a study published by levels of public investments are largely POINTS our institute in June 2005, provides on par with those elsewhere in the context for thinking about the funding • Funding for restoration and nation. In recent years, however, the challenges and strategies in support of environmental programs will state’s contribution to this spend- the San Francisco Estuary. The study increasingly become a challenge ing has been predominantly funded considers whether the state is facing as bond monies dry up. through general obligation bonds. a growth and infrastructure crisis and High projected debt ratios suggest how to best think about planning for • Despite funding challenges, a that alternative sources may be the future. It looks at population and majority of Californians sur- needed over the years ahead. veyed support environmental 28 protection and are concerned STATE RELIES INCREASINGLY In the area of water supply and ON BONDS TO PAY FOR about water quality. PUBLIC INVESTMENTS quality, the study fi nds that the state’s numerous water and wastewater • Californians strongly support 1965-66: $307/capita utilities are largely on track to fund protecting wetlands, improving anticipated capital needs. Moreover, water quality, restricting private utilities have a straightforward way development of coastal land, to raise revenues through user fees, creating more marine reserves, which are still low relative to me- and selling environmentally safe dian income. Although the state’s fi sh or seafood. population continues to grow, demand management and water markets can • Although the state’s population lessen demand for new water, and continues to grow, demand man- there are many options available for 2002-03: $299/capita agement and water markets can generating new supplies. The thorni- lessen water demand growth. est challenges relate to environmental programs, including the restoration of the San Francisco Estuary and nonpoint source pollution programs. To date, restoration and non-point source programs have largely been funded with state bonds. As existing bond monies dry up, the question of appropriate contributions from water users General Fund will become increasingly important. Special Funds Despite funding challenges, a survey Bonds we conducted in 2003 showed that 65 Federal Funds percent of Californians—compared to RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP BIG PICTURE; WARNING BELLS Changing Bay Area Economics and the Estuary RUSSELL HANCOCK JOINT VENTURE: PROTECTED OPEN SPACE IN SILICON VALLEY SILICON VALLEY NETWORK

It is important for people who Permanently Protected care about the environment to care 30 Share of Land that is Protected about the economy too. The Estuary and Publicly Accessible Conference focuses on a number of 25 environmental performance indicators for San Francisco Bay. How- ever, these indicators—as well as our 20 ability to infl uence them—are shaped in important ways by some larger 15 considerations, including the region’s job growth, economic performance, and the ability of our public bodies to 10 Percent of the Region Percent balance economic and environmental stewardship. 5 The Silicon Valley has a huge infl uence on the Bay Area economy. 0 29 At the height of its boom, the “dot 1998 1999 2000 2001 2002 2003 2004 com” industry created 350,000 jobs. Since then, we have lost 220,000 jobs—the Internet bubble wasn’t real commerce was a real revolution, and other regions of the country, the best or sustainable, with its never-ending important companies came out of way for us to do that is to provide a spiral of prosperity. Yet Internet-based it—Google, Yahoo, EBay, to name a fabulous place to live, and that means few, and we tend to forget the net continuing to steward the Bay. gain of 130,000 jobs. A newly emerg- That commitment can be seen in TAKE ing paradigm for the region in a global- the increase in the amount of open HOME izing economy is that of small start-up space that has been protected since POINTS companies—those with seven people 1998 — from 22 to 26 percent of the or less. There are 7,000 of them in • The new economy in the Silicon region. Valley is better from a sustain- the Silicon Valley. But while Valley productivity is 2.5 times the national MORE ability standpoint. We are no INFO? [email protected] longer talking about growth average, that is not translating into job management strategies. growth or payroll increases, in large part due to intense competition from • Silicon Valley businesses and India and Asia where we are out- community leaders show a high sourcing many of our jobs, including commitment to environmental white collar jobs. Yet our new, scaled- stewardship. back economy is more viable from a sustainability standpoint, and the • A high-end workforce is often Valley will compete with its high-end characterized by heightened work force. The Silicon Valley is com- environmental sensibilities. mitted to sustainability issues such as open space and quality of living. If • Environmental stewardship is we are serious about competing with our best competitive strategy. STATE OF THE ESTUARY 2006 BIG PICTURE; WARNING BELLS Can Serial Engineering ity, and successive waves of non- native invaders, makes the Delta a of the Delta be Stopped? rapidly moving target, with prospects for even more dynamic conditions JEFF MOUNT fi shing, hunting and messing around in the future. Institutional viscosity, CENTER FOR WATERSHED in boats—has its own unique suite of limited resources, and relying on the SCIENCES past as a predictor of the future limits UNIVERSITY OF CALIFORNIA, DAVIS engineering efforts and unintended consequences. our ability to keep up with the pace The Sacramento-San Joaquin Del- of change. The grand plans of today Rather than waning due to its lack ta has become one of the most highly- will be obsolete within a generation or of success, the interventionist culture engineered estuaries of the Americas. two, demanding new, more fantastic of Delta management is only growing, For the past 150 years, intervention- engineering fi xes. Breaking out of the with new, more elaborate, and more ist approaches have dominated the cycle of serial engineering may involve expensive proposals. This engineering extraction of ecosystem services from making politically unpalatable deci- approach is predicated on the assump- the Delta and its tributary watersheds. sions about which ecosystem services tion that conditions will remain the The over-dependence on structural can be provided by the Delta and same. That is, historic imperfections in and technological “fi xes” to enhance which will have to be curtailed. ecosystem services can be engineered ecosystem services has locked man- out of the system in the future. Yet MORE agement into a cycle of serial engi- INFO? [email protected] landscape change, including funda- neering. Every engineered interven- mental shifts in hydrologic conditions, tion appears plagued by the law of subsidence, changes in land use activ- unintended consequences, creating an ever-escalating demand for more 30 engineering fi xes. With CALFED at TAKE • We could also see punctuated a political and economic crossroad, it HOME change versus gradual change, is reasonable to question whether this POINTS meaning that change could take approach is sustainable. • The Delta is the most subsided place abruptly. Gradual change is a certainty. Punctuated change is The Delta is the regional ar- landscape in the world relative to likely. chetype for serial engineering. The its total size. reclamation of more than 500,000 • Once we put homes in the Delta, • We will have a physical collapse of acres of tidal marsh involved the engi- the Delta. neering of 1,100 miles of levees, 1,800 all bets are off : public safety trumps everything. water diversions, and 250 agricultural • The Delta was designed based on drain returns. The serial engineering • We have enough science to esti- hydrology 20 years old, with no challenges associated with this effort mate the probable state of the consideration of the future. are well known, including managing Delta for the next 50 years—to the most subsided landscape in the • South Delta improvements and predict critically dry years and world at the juncture of two large, barriers will adapt poorly to how to save fi sh. fl ood-prone river systems. The second changes in the Delta. great ecosystem service engineered in • The Delta is warming up. It will • Serial engineering of ecosystem the Delta—the CVP and SWP water be a vastly changed place over services is not working and won’t supply pumps—created a cascade of the next 100 years; we will see work in the future. serial engineering projects through- changes within the next 15-20 out the watershed. Use of the Delta years. • Some of the Delta’s ecosystem for shipping, fl ood control, disposal services cannot be sustained over of urban and agricultural runoff, and • Working hard on today isn’t going the long term. as a thermal dump for power plants to change things for tomorrow. has spawned demand for multiple • A peripheral canal will create its fi xes, both within and outside of the own cascade of ecosystem eff ects. Delta. Even recreation—including RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP BIG PICTURE; WARNING BELLS A Delta Perspective on the Delta Improvement Package

TOM ZUCKERMAN • Upstream water quality and fl ow CENTRAL DELTA WATER AGENCY in the San Joaquin River below the TAKE mouth of the HOME The Delta Improvement Pack- POINTS Merced River age, or “DIP,” is a CALFED proposal • The problems in the Delta based upon an integrated regional • Drainage regulation from farmlands aren’t going to change that management plan that grew out of the and wildlife refuges in the San much. The issue is how to get stakeholder negotiations that formed Joaquin Valley the federal and state govern- the basis of HR 2828, the federal • Levee protection in the Delta ments to focus on them. reauthorization bill for CALFED. Environmental interests were notably Correction of these existing • We need to avoid making poor absent in the negotiations, and the problems, and avoidance of any decisions such as putting people whole process preceded recognition of aggravation, are conditions of any behind levees in tract homes. the precipitous decline of the pelagic increase in allowable export levels. fi shery in the Bay-Delta system. Similar protections for fi sh and wildlife • We have an opportunity to resources must be developed through preserve the standard of living Nevertheless, the DIP recognizes the NEPA-CEQA process applicable and way of life in the Delta, but and includes topics that must be ad- to the DIP, recognizing that much of we need to give the Delta prior- dressed to improve water supply and the burden of addressing these issues ity. It is an environmental and quality issues in the Delta and in the falls upon the exporters as mitigation recreational treasure. Lower San Joaquin River. Those is- 31 for problems created or aggravated by sues, which have resulted largely from the exports. • We cannot go on thinking of the water export operations, include: MORE Delta as an inexhaustible water • Water quality at sensitive diversion INFO? [email protected] supply for southern California. points in the Delta • We need to fi gure out how to • Water supply and channel level suf- maintain Delta water quality, fi ciency at sensitive diversion points keep enough water in its chan- in the Delta nels, and how to restore the lower San Joaquin River, where water quality is critical for the river and for its users and exporters.

• The emphasis always seems to be on exports. We need to focus instead of restoring pelagic ﬁ sh, salmon, and striped bass to the Delta.

• Solutions need to be Delta-centric.

Photo courtesy of USGS STATE OF THE ESTUARY 2006 BIG PICTURE; WARNING BELLS Challenges Facing the San Joaquin Valley

CAROL WHITESIDE GREAT VALLEY CENTER TAKE • We have a chance to develop a HOME strategic long-term view of the The San Joaquin River runs POINTS valley—we urge Bay-Delta Estuary through a valley 450 miles long and • Habitat Conservation Plans have folks to help us. Otherwise, the 50 miles wide—an area the size of met with very mixed results in future of the valley environment the state of Kentucky—and it is a the valley. There is a belief that if looks very shaky. region that is rapidly changing, with people just wait long enough, the implications for the entire state and • Why are farmers and environ- Endangered Species Act will go the Bay-Delta Estuary. Within the last mentalists not partners? Some away. 150 years, the valley has been trans- farmers fear costly environmen- formed from a place characterized by • The focus of the region is on tal regulations that make them seasonal wetlands, deep tules, and jobs and economic development. feel vulnerable, plus it is hard to roaming grizzly bears into one of the The environment is not seen as a turn down $1 million an acre from richest agricultural areas in the world. Republican issue. developers. Now changes are ﬂ owing again, this time from different sources. Waves • Public concern about the “envi- • We need to put some certainty of new residents—immigrants from ronment” is limited to issues with back into farming and create buf- faraway places and migrants from the immediate impacts on people, fers between farmland and urban coastal parts of California—plus a high such as air quality and asthma areas. birth rate in the valley are swelling and water quality and taste. the population at a growth rate that 32 exceeds that of Mexico. People come • We need to frame environmental to the valley to seek affordable hous- and resource/watershed conser- ing and new opportunities, prompted vation in terms of their economic in part by high housing costs in coastal payback. areas. The impacts of the valley’s

growth are evident in CENTRAL VALLEY POPULATION GROWTH trafﬁ c delays—up 52 percent in the north San 6,000,000 Joaquin Valley and 577 percent in the southern San Joaquin Valley since 5,000,000 1998.

Some people have 4,000,000 created a false dichoto- my between protecting 3,000,000 the environment and economic well being. The short-term re- 2,000,000 sponse most often opts for the economy over the environment. The 1,000,000 environmental health of the entire San Joaquin 0 Valley will depend in 1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 part on local politics as RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP BIG PICTURE; WARNING BELLS

CENTRAL VALLEY’S PROJECTED GROWTH RATE

450 CENTRAL VALLEY well as on the engagement and 400 MEXICO attention of the rest of the state. REST OF CALIFORNIA People who live in the region 350 REST OF US see resources in abundance and don’t understand the value of 300 those resources to the world. Those who are often in the best 250 position to protect and conserve resources are often resentful of 200 having to make economic sacri- ﬁ ces for others, whose economic 150 well being is already secure and is 100 not limited by the environment. (100’S) AREA IN 1970 IN EACH POPULATION Finding fair and balanced ways to meet all the legitimate needs of 50 this growing and changing region 0 is not impossible, but it will be 1970 1980 1990 2000 2010 2020 2030 2040 darn hard. MORE INFO? [email protected] 33

CENTRAL VALLEY STATS • By 2040, there will be the equivalent of 10 new Fresnos. • The valley produces more than 300 • By 2050, the population will be up by crops, 57 percent of the state’s $30 131 percent. billion agricultural output. If the valley were a state, it would rank ﬁ rst in • Despite the rapid growth rate, agricultural production in the nation. regional per capita income relative to the state has dropped: the San Joa- • Twenty percent of valley jobs depend quin Valley has the highest percent of directly or indirectly on agriculture. children under 18 living in poverty: 26 • The valley’s population has doubled percent, compared to 20 percent U.S. every 30 years since 1900 and now and 17 percent California overall. stands at 6.3 million. Its projected growth rate outpaces Mexico, Califor- nia overall, and the U.S.

• By 2020, more people will live in the Central Valley than the San Francisco Bay Area. STATE OF THE ESTUARY 2006 BIG PICTURE; WARNING BELLS Where Have All of the Pelagic Fishes Gone?

TED SOMMER, ET AL. DEPARTMENT OF WATER RESOURCES SUMMER TOW-NET SURVEY – DELTA SMELT 1959-2004 INTERAGENCY ECOLOGICAL PROGRAM 70 Abundance indices calculated by 60 the Interagency Ecological Program (IEP) suggest recent marked declines 50 in numerous pelagic fi shes (Delta 40 smelt, longfi n smelt, threadfi n shad, and striped bass) in the Delta and 30 Suisun Bay through 2004. Initial sta-

ABUNDANCE INDEX ABUNDANCE 20 tistical analyses of the data for these pelagic species indicate that there 10 are statistically signiﬁ cant long-term 0 * * * declines in the Delta/Suisun Bay, and ‘59 ‘64 ‘69 ‘74 ‘79 ‘84 ‘89 ‘94 ‘99 ‘04 evidence of a recent step-change—a very rapid decrease in population. conceptual model includes at least and to assign priorities to projects on Similar analyses for the ﬁ shes of the three general factors that may be the basis of where funds and resourc- San Francisco Bay showed no clear acting individually or in concert to es can be best used. The proposed 34 decline. Recent abundance estimates lower pelagic productivity. Those work falls into four general types: an for the summer tow-net survey sug- include toxins, invasive species, and expansion of existing monitoring (four gest that low Delta smelt abundance water project operations. IEP has expanded surveys); analyses of exist- continued in 2005. undertaken an interdisciplinary, multi- ing data (nine studies); new studies The low levels of Delta/Suisun agency study effort to evaluate these (six studies); and ongoing studies (four Bay pelagic species are unexpected stressors. The overall approach is studies). given the relatively moderate hydrol- based on a “triage”model to identify MORE ogy over the past three years. Our the most likely causes of the decline, INFO? [email protected]

INITIAL CLUES FROM 2005 20MM-DELTA SMELT SURVEY TAKE GREAT HYDROLOGY, LITTLE IMPROVEMENT HOME POINTS 7000 • Abundance of pelagic ﬁ shes 6000 still hasn’t improved much, despite favorable hydrology in 5000 2005 and relatively moderate hydrology during 2002-2003. 4000 • The IEP is investigating three 3000 stressors—contaminants, SUMMED CPUE SUMMED 2000 water exports, and invasive species—as major causes. 1000

0 2000 2001 2002 2003 2004 2005 RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP BIG PICTURE; WARNING BELLS Clues to the Delta Pelagic Food Web Decline WIM KIMMERER of fi sh. P. forbesi is important food for AND JOHN DURAND at least some of these fi sh during sum- SAN FRANCISCO STATE UNIVERSITY mer, implying a causal link. Chloro- phyll concentration, used to indicate The recent decline in abun- the availability of food for copepods, dance of several species of fi sh in the Illustration: Joe Eaton has not changed over the same pe- Sacramento-San Joaquin Delta has riod. The lack of decline in chlorophyll prompted an unprecedented coopera- Figuring all this out will take more would indicate that the breakdown is tive effort aimed at identifying the than expanded monitoring, although occurring in the population dynamics causes. Public and media attention to there are some key system elements of the copepods, but phytoplankton this decline has been great: pictures of not being monitored. Measuring species composition has also changed. copepods are appearing on the front processes such as growth, fecundity, P. forbesi seems to have a very low pages of newspapers! and sensitivity to contaminants will be reproductive rate, so a small decrease required if we are to go beyond status Determining the cause or causes in food consumption could have a big and trends. These efforts are begin- of the decline is an extraordinarily impact on abundance. Our ongoing ning, but must be adaptive if results diffi cult problem, exacerbated by the work on population dynamics may are to be achieved soon. intense pressure on agency scientists shed some light on these issues. MORE and their university colleagues to fi nd The next dimension is “stressors,” INFO? [email protected] “the answer.” One way to begin de- i.e., factors that might have negative limiting the problem is to investigate impacts on popula- where changes have occurred across 3535 tions. Although there each of several dimensions. The most PLANKTON PATTERNS - is a strong tendency GLIMPSES INTO THE FOODWEB obvious of these are space and time, to point fi ngers at re- and these give clues: the declines have Delta cent changes in water occurred generally in fresh to brackish export patterns in the Suisun water; since 2001, more in Suisun Bay south Delta, tempo- Copepods and the Delta than in Suisun Marsh. ral changes in actual -3 Another key dimension is species: 1000 volume exported do only some of the species present not correspond with within the spatial-temporal box of the observed popula- concern have declined, while others tion changes. Other have not. Contrasting life histories m ABUNDANCE potential stressors 100 may give a clue to why some have include anthropogenic declined and others not. 10 contaminants and

An additional dimension is trophic toxic releases from -1 position. The species that have the cyanobacteria Mi- 5 declined include the copepod Pseudo- crocystis aeruginosa, diaptomus forbesi and several species which has bloomed in the Delta since TAKE 1999. These stressors Phytoplankton

HOME have their own suite gL CHLOROPHYLL POINTS 1 of dimensions, and 1990 1995 2000 2005 • Possible infl uences on the pe- the extent of their lagic organism decline include potential effects on water project eff ects, climate the foodweb may be diffi cult to deter- eff ects, contaminants, toxic mine, especially in retrospect. algae, and introduced species. STATE OF THE ESTUARY 2006 BIG PICTURE; WARNING BELLS The Delta: A Case Study in Management Adaptability

JERRY JOHNS to the CALFED Programs so that it The environment in which we fi nd CALIFORNIA DEPARTMENT OF has sustainable funding. ourselves is changing rapidly. It will WATER RESOURCES test our water management adaptabil- In the past three years there has ity. Our ability to pass these tests will The concept of adaptive manage- been a decline in the relationships determine our future. ment has worked its way into the between the abundance of many interface between water and biologi- open water fi sh inhabiting the upper MORE INFO? [email protected] cal sciences. Adaptive management Bay-Delta Estuary and the ecological allows water and biological managers factors that have historically affected to modify environmental conditions, their abundance. This unexpected de- develop data on the effects of these crease in abundance of these pelagic TAKE changes, and then adapt operations organisms has sparked an intensive ef- HOME or standards to refl ect the knowl- fort by agency, university, and outside POINTS edge gained. This works well when scientists to determine the cause or • Adaptive management works the system being evaluated is staying causes. Making water management when the ecosystem is relative- relatively constant. However, recent decisions in light of this uncertainty ly stable. events in the Bay-Delta Estuary requires us to be pragmatic and cau- have shown us that this system has tious. In addition, the sustainability of • The Delta ecosystem is chang- changed markedly in the last few the current Delta levees infrastructure ing rapidly. Salmon numbers are years, both from an ecological point has been brought into question by the up, but pelagic organisms have 36 of view and a funding and institutional 2004 Jones Tract levee failure, funding declined. perspective. The issue now is not issues, and by scientists studying the so much adaptive management but long-term subsidence, earthquake • The state’s new water plan management adaptability to respond probability, and prospects for sea level encourages environmental to these changes. Can water and rise due to global warming. Given stewardship. That concept fi shery managers change directions these questions, the state needs to hasn’t been discussed in past as fast as the political and ecological reevaluate what the Delta will look water plans but will be—more changes around them and adapt their like in the next 50 to 100 years and so—in the future. approaches to problem solving fast develop a strategic plan towards that • It may be that we should put off enough to resolve confl icts? vision. decisions about water export CALFED has been the institu- Water planning in general in operations in the Delta until tional pillar upon which we have built California has taken a new shift with we have more data and a new today’s relationships between agencies the release of the latest California Record of Decision. and programs to protect and enhance Water Plan in spring 2005. Two new both environmental conditions in the initiatives, Integrated Regional Water • We need to make “no regrets” Bay-Delta Estuary and to provide Management and Improving the State’s decisions that improve fl exibil- the water for those who rely on the Water Management System, build ity. Bay-Delta watershed. However, the upon the principles of increased water funding for the CALFED programs use effi ciency, improved water qual- • In 50 to 100 years, the Delta has been less than expected, and ity, and environmental stewardship. will be a diff erent place. We this program is undergoing extensive A water resource investment fund is probably can’t have everyone review and possible “refocusing” to needed to help meet California’s water on the island. How are we going evaluate its successes and to hone investment strategies for the future. to protect all of the infrastruc- its mission to concentrate on resolu- A partnership with funding is needed ture that crosses the Delta? We tion of Bay-Delta confl icts. Most between local and regional entities and need to take a comprehensive importantly, CALFED will attempt to the state to meet California’s growing view. develop appropriate user contributions water needs. RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP THE ROLE OF SCIENCE

“The interactions between tidal wetlands and pelagic areas are still not well understood.”

—Charles Simenstad University of Washington

“Eighty percent of our stream reaches are now behind 37 impassable barriers. Only tiny remnant [chinook and steelhead] populations are left. We are going to have to do some creative thinking about how to preserve ESUs.”

—Steve Lindley, NOAA

Photo courtesy of David Hart and John Sanger STATE OF THE ESTUARY 2006 THE ROLE OF SCIENCE Why Track Environmental Performance?

BRUCE WOLFE plans, and the like, but the staff car- ward in terms of what we need to do, S.F. BAY REGIONAL WATER QUALITY ries out the mission by learning and and how to measure progress, let alone CONTROL BOARD understanding the impacts to our success. region’s waters, determining whether The water board’s mission is On the other hand, we have far those impacts are related to waste to preserve, protect, enhance, and better tools to assess the state of our discharges, and, if the answer is “yes,” restore the waters of the state for all. waters. The restoration of Peyton recommending that the Board take But it’s clear we can’t just say we’re Slough by Rhodia is a case in point. the appropriate regulatory action. It is going to keep working to protect the Peyton Slough was identifi ed some our job to assess whether the action Bay and expect to get all the funding years back as a toxic hot spot, due to taken gets the desired results. we need to do it. Decision-makers and extensive cooper and zinc-impreg- the public want to know how we’re This used to be a fairly straightfor- nated sediments in and adjacent to doing, they want to know what we’ve ward task. For example, in the 1960s the slough. Rhodia, as successor to done, and they want to hear the mes- and 1970s, when the water board be- the parties responsible for the waste, sage in easy-to-understand terms. came aware that parts of the Bay had responded to our requirements for “Restoring creeks” resonates better high bacterial counts, we responded cleanup with the innovative approach than “minimizing the hydrogeomor- by requiring the waste dischargers to of moving the slough away from the phic impacts to riverine functions”— disinfect their effl uents. In this instance contamination, rather than the other indeed, Los Angeles passed a $500 the cost of compliance or environmen- way around. In so doing, they’re im- million bond last year when it was tal performance was relatively modest, mobilizing the contamination, creat- pitched as restoration of the LA River and the results of that performance ing new wetlands, restoring other 38 rather than as controlling the impacts were clear and easy to track. Levels of wetlands, improving circulation to of stormwater runoff. coliform bacteria in the Bay dropped McNabney Marsh, and a host of other dramatically. We had a nice link be- benefi ts. It’s an approach we probably At the S.F. Bay Regional Water tween the environmental problem, the wouldn’t have accepted ten years ago, Quality Control Board, the Board environmental performance required, but their ability to demonstrate the members themselves make all the big and a measurable water quality result. anticipated environmental performance decisions on permits, TMDLs, cleanup and how that would be tracked sealed Another example is dissolved oxy- the deal for us. gen in South San Francisco Bay below TAKE the Dumbarton Bridge. The water The Regional Monitoring Program, HOME POINTS board found that dissolved oxygen was which is funded by the public, private at times well below what fi sh needed waste dischargers, and dredgers and • In most cases we will not have to survive, and studies indicated that implemented by the San Francisco certainty as to problem cause the culprit was ammonia in sewage ef- Estuary Institute, involves not only and will have to use a weight of fl uents from the three treatment plants monitoring for compliance with water evidence approach. Nonetheless, in the area. Fish kills were a straight- quality standards, but also interpret- we need to track performance forward problem, as was the environ- ing the results in ways people can to move forward, changing our mental performance needed: the Board understand. But even with a tool like actions when needed. required that those effl uents receive the RMP, there will always be issues additional biological treatment to that resist easy answers. An obvious • We must start science long convert ammonia to nitrate. Once new one that we’ve been wrestling with before we can expect to make a facilities went on line, tracking of the for years is mercury in the Bay. We decision. dissolved oxygen levels demonstrated know mercury moves up the food the problem had been solved. web and concentrates in fi sh, and in • We need to be clear in our mes- people eating the fi sh. We also know sage about what environmental Today it’s not always so simple. mercury impacts bird populations by performance is needed and how Issues that face us now—legacy pollut- affecting their eggs. Relying on RMP we’re going to track that perfor- ants, crashing fi sheries, and emerging data, our Board adopted a long-term mance: we need the public’s trust contaminants—are not as straightfor- and support. RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP THE ROLE OF SCIENCE cleanup strategy for mercury in the “restore,” which implies that we im- to stay away from the policy choices. Bay, but the State Board remanded prove water quality, but to what level? The best way to drive that point that strategy back to us. In this case, 1750? 1850? 1950? home is to recall the development of everyone agreed the science we relied We’ve classically focused more the Bay-Delta Accord in 1994, which on was appropriate and recognized on “preserve” and “protect” than included the creation of CALFED, to be the best available. Our study “enhance and restore,” but it’s clear and was a major reversal of policy at indicated that it could take up to 120 through TMDLs, expanding needs that time. Up until December 1994 it years for the Bay to fully recover, but for mitigation from project impacts, was far from clear that we would be that the actions we were requiring and just about every poster at this able to negotiate an accord because of would reduce new loads of mercury conference, that we need to ramp up how we were handling science—sci- by half in less than 20 years. Politics “enhance and restore.” ence as driven by political positions or no, 120 years was a measure of and negotiating positions. Betsy Rieke, environmental performance the deci- MORE INFO? [email protected] the Assistant Secretary of Interior for sion-makers found too easy to attack. Water and Science, recognized that it We’ll need to change our message as would be impossible to come to agree- we move forward. What Should the ment if we continued to politicize the There are more issues we are science. So she convened a science now learning about that need to be Role of Science Be meeting in Monterey, pulling all the fi t into a structure of clarifying the in the Estuary? scientists and all the policy makers environmental performance needed, and most of the stakeholders into the simplifying the message, and tracking TIM QUINN same room. For the fi rst time there METROPOLITAN WATER DISTRICT that performance. One is ammonia. OF SOUTHERN CALIFORNIA were very short lines of communica- We know that ammonia is no longer tion between the scientists and the causing dissolved oxygen impairment, What are policy makers looking for policy makers. All too often we try to 39 but there is some new research that from scientists? It is pretty straight- separate those groups of people. The indicates that it may be suppressing forward. I’m looking for objective Accord was one of the few times in nitrogen uptake by diatoms. accurate information about the conse- California water we got it right. quences of alternative policy choices. We know that diatoms are Good science done well is a con- That sounds easy enough, but we did extremely important at the base of fl ict reducer: it gets people to agree on it wrong a great deal of the time. the food web—they partly drive the consequences, even if you don’t like biological productivity of the entire There’s a division of labor that some of them. When you politicize system. However, before we require is important to keep in mind. The science, you grow the confl ict. I don’t all sewage treatment dischargers policymaker’s job is to choose amongst think the San Francisco Chronicle, the to provide the additional treatment alternative outcomes that are available Contra Costa Times, or the Sacramen- needed to convert ammonia to ni- to them in diffi cult policy choices. The to Bee are very good places to initially trate, we will need more evaluation of scientist’s job is to make sure there is publish your conclusions and fi ndings. environmental performance—do we accurate information, and to protect But there’s a lot of that going on and know what action to take and how to the integrity of that information. Too it’s not a healthy thing for California track that action? Even if ammonia is often in California water you have water policy or for the environment. shown to be a problem, we want to be people sitting at policy-making tables I’m hopeful that with all of the warn- sure that removing it does not create trying to cross over that line and con- ing signs we’re getting from the Estu- the opposite problem, that of nuisance trol the science for their own negoti- ary we will starting asking the right levels of diatoms. ating advantage. Similarly you have questions—did we get the facts right, scientists who cross the line, making did we do the right thing, set the right We need to be clear as to what judgments about what information policy? our baseline is and/or what our end- should be out there based on what point is. Our Board’s mission takes MORE they think should happen in the proper INFO? [email protected] us in two directions—“preserve” and realm of the policy maker. The policy “protect,” where we’re trying to make maker shouldn’t have control over the sure we don’t allow water quality to information fl ow; the scientist’s job is get any worse; and “enhance” and STATE OF THE ESTUARY 2006 THE ROLE OF SCIENCE Long-term, Large-scale Monitoring: Needs and Prospects

STUART SIEGEL demands that we evaluate past invest- 6. For regional and sub-regional ef- WETLANDS & WATER RESOURCES ments, rebalance the focal point of our forts, include conceptual models political capital when we learn what explaining how what is being Are we giving migratory birds is more effective, and be prepared for monitored is linked to things that more and better habitat? Are fi sh surprises with early warnings of po- could change; monitoring data getting more food from productive tential problems. At present, the San (QA/QC, storage, and public marshes? Do we have more con- Francisco Estuary has no long-term, access); a data analysis sub-pro- nected parcels refl ected in greater large-scale wetland monitoring in gram (looks for trends, patterns, overall species support? The only way place, though several separate efforts covariance, and frames the “why” to know is to monitor natural and contribute key elements. research); and a research sub-pro- restored wetlands beyond status and gram (tests the conceptual models trends to data collection designs based Monitoring is more than collect- and explains why you see what on cause and effect models and scal- ing data on status and trends – it is you do), and identifi es clear, agreed able from specifi c sites to sub-regions analyzing, integrating, applying, and upon goals and management ques- to the Estuary. Monitoring is a way to distributing information. This list tions amongst funders and major observe change in the environment. presents our most pressing monitoring customers. With it, we can evaluate our past needs for the Estuary. investments in resource restoration Funding is the major impediment 1. Distribute monitoring results and management, prioritize and carry to successful monitoring. Monitor- widely and easily via the internet out the most effective future restora- ing typically costs more than is to facilitate their utility. 40 tions, address potential problems, and desired, and decision makers often do support regional planning. Weaving 2. Continue to develop unbiased les- not place high value on monitoring science into estuarine management sons learned from older and more especially with competing demands recent restorations; restoration for implementation dollars, leaving TAKE evolution demands revisiting older us not knowing whether “build it and HOME projects periodically as lessons can they will come” is true and, if so, why. POINTS change after project-specifi c moni- There is a lack of collaborative governance: many divergent views exist • Regional goals for restoration toring ends. about monitoring and restoration; and species recovery need to 3. Conduct fi eld- and laboratory- currently, no forum exists to address be informed by monitoring. based problem evaluation monitor- and resolve those views. We need ing to support problem resolution. • All monitoring needs to be information centralized and available. science-based, driven by 4. Conduct periodic regional as- Aggregating results in a publicly acces- hypotheses, and informed by sessments combining remote sible manner has not occurred, though conceptual models. sensing with focused rapid fi eld a structure now exists (www.wrmp. assessments to inform regulatory org) that awaits a signifi cant informa- • One size does not fi t all. A suite program effectiveness and support tion upload effort. of complementary eff orts is es- planning initiatives. MORE sential. INFO? [email protected] 5. Finish protocols for data collection, • Easy access to information is QA/QC, and analysis and develop vital. decision trees for selecting protocols applicable to the many circum- • Funding is the number one stances we encounter, so we do impediment to monitoring. not keep reinventing the wheel and so that we have confi dence in data. • Avoid power struggles and collaborate to achieve best monitoring results. RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP THE ROLE OF SCIENCE

or the lack of detec- Evaluating tion of target spe- Restoration cies. Understanding ecological processes Holistically and the pace of tidal marsh restoration NADAV NUR AND PETER BAYE PRBO CONSERVATION SCIENCE can help restoration ANNAPOLIS FIELD STATION project engineers evaluate the design In examining the success of tidal and implementation wetland habitat restoration, we need of future restoration to evaluate how well we have restored projects and manage ecological processes as well as com- unexpected outcomes breed in tidal marsh, desirable criteria munity assembly, rather than basing of restoration projects in progress. include breeding density and achieved our evaluations on the mere presence Regulatory agencies need to establish reproductive success at restoration empirical, yet meaningful performance sites. Finally, we recognize the need TAKE criteria for the purpose of permitting HOME for cost-effective, effi cient monitor- and evaluation. Restoration objectives POINTS ing programs that can be sustained in for tidal marshes are often framed the long-term, and the limitations of • In evaluating restored marshes with respect to special-status wildlife, intensive but short-lived monitoring. from the perspective of plants fi sh, and plant species with relatively and animals comparisons should narrow requirements for particular Recent studies of restoring wet- be made with multiple—and the habitat structure, habitat dynamics, or land sites indicate the ecological value most specialized sub-habitats. Aligning tidal of intermediate seral stages (transi- 41 appropriate—reference sites. marsh restoration projects to achieve tional states of restoration sites). It is these requirements is important to therefore valuable to develop success • The same parameters must be justify to the general public major criteria that focus on evaluating young measured. investment of public funds. restoration sites, both to enhance the ecological value of such habitat and These competing objectives pro- • Habitat connectivity is to provide early evaluation of restora- vide a challenge to the development important, and taking a tion practice in a timely fashion, so of restoration success criteria. We regional perspective is vital. that corrective steps may be taken. outline a framework for developing We use recent studies of restored and • Long-term eff ort is needed— restoration performance criteria that restoring tidal marshes to illustrate several years of data collection. considers multiple spatial scales (local conceptual performance criteria that project, project complex, regional, and assess success on short-term and • Restoration success should not Estuary-wide) and multiple temporal long-term scales and support manage- simply be judged as pass/fail. scales. We highlight a basic dilemma: ment decisions regarding all phases Asking what kind of success mandated monitoring of restoration of restoration projects. In 2005, for — or what kind of bottleneck projects is generally short-term (less example, young restoration marshes prevented success — may be than two decades, often around fi ve demonstrated similar reproductive more informative. years), yet the time course for achiev- success for song sparrows as mature ing most important ecological objec- • Tidal marsh restoration tidal marshes. Young restoration tives associated with mature marsh proceeds stage by stage. marshes do not appear to be ecologi- community structure is generally Monitoring and evaluation cal traps. long-term (over two decades). We should be developed appro- emphasize the importance of biologi- MORE priately and include success INFO? [email protected] and cal criteria that refl ect restoration of criteria that focus on important [email protected] ecological processes and community ecological processes for inter- assembly, rather than the mere pres- mediate restoration stages as ence or the lack of detection of target well as mature sites. species. For example, for birds that STATE OF THE ESTUARY 2006 THE ROLE OF SCIENCE BIG PICTURE, WARNING BELLS

ries, and their underlying data, do Fish Advisories impact water management and and You agencies responsible for water quality through the 303(d) list and Total ROBERT BRODBERG Maximum Daily Load process, it OFFICE OF ENVIRONMENTAL HEALTH is important to understand these HAZARD ASSESSMENT, CALIFORNIA ENVIRONMENTAL changes. Evidence indicates that in PROTECTION AGENCY general concentrations of organic chemicals have decreased and that The Offi ce of Environmental mercury concentrations in fi sh have Health Hazard Assessment (OE- remained about the same. Changes HHA) issues fi sh consumption San Francisco Estuary. The very fi rst in the advisory are due to improve- advisories for local water bodies in fi sh advisory in California (1971) was ments in analytical methodology and California. Fish advisories are useful for striped bass in the Bay-Delta and new studies expanding our under- as environmental indicators of water advised fi shermen to eat no more than standing of the toxicology of methyl- quality, but they need to be put in one meal per week of striped bass due mercury and other chemicals. context as a measure of change in the to mercury in these fi sh. That advisory was updated in 1985 (children The primary goal of fi sh consump- and pregnant women were advised tion advisories is to provide informa- TAKE to consume NO striped bass from the tion to the public so that people can HOME Bay-Delta) and again in 1993, resulting reduce their exposure and risk to con- POINTS in a 303(d) listing and TMDLs for mer- taminants already in the environment, cury in the Bay and Delta and PCBs in while still enjoying fi shing as a natural the Bay. It also resulted in signs being resource and health benefi ts from fi sh • There have been no signifi cant 42 posted around the Bay and communi- consumption. Advisory awareness changes in mercury concentra- cation efforts being increased. In 1994 through outreach activities is a critical tions in fi sh in the Estuary. specifi c advice was added for fi sh and ongoing component for public health and safety because processes aimed • Organic chemical concentrations shellfi sh from the Richmond Har- at reducing chemical concentrations in are declining in the Estuary but bor Channel area based on data for fi sh take a long time. not enough to aff ect consump- pesticides and other chemicals. Later tion guidelines yet. in 1994, the current advisory was OEHHA is working to move developed using data from a Regional beyond focusing on water bodies with • New chemicals are being found in Board study. This advisory was based known or suspected contamination fi sh. on mercury and organic contaminants problems to identifying water bodies (e.g., PCBs) in fi sh species from San in which one can catch and eat more • Consumption guidelines are still Francisco Bay, and recommended that fi sh, and developing safe eating guide- protective of human health. adults should eat no more than two lines for them. This requires a coordi- meals per month of Bay fi sh and no • We need to continue to educate nated California program to monitor striped bass over 35 inches. Women a variety of chemical contaminants in and inform the public about con- and children under six were advised to taminants in fi sh. fi sh from the water bodies in which eat no more than one meal per month people are catching them. This type of of Bay fi sh, and no large shark (over • We need to improve the eff ec- monitoring would provide a statewide 24 inches) or striped bass (over 27 tiveness of our advisories. baseline for contaminants, help iden- inches). The advisory was amended tify emerging risks, and track trends in • We need to continue to improve in 1996 to clarify that the same advice water quality as indicated by more fi sh conditions in the Estuary. applied to striped bass and sturgeon in that can be safely eaten from more the whole Bay-Delta area. water bodies. • We need to continue to monitor, Based on the decreasing meal rec- MORE expand our eff orts geographi- ommendations it may at fi rst appear INFO? [email protected] cally, and update our advice that water quality in the Estuary has with an emphasis on safe eating degraded since 1971. Since adviso- guidelines. RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP THE ROLE OF SCIENCE Do Contaminants Harm are being discovered, such as personal care products and fl ame retardants; Estuarine Habitat? techniques are needed to prioritize the contaminants that cause the greatest SUSAN ANDERSON, ET AL. endocrine disruption in mudsucker fi sh harm to aquatic life and to help focus DAVIS BODEGA MARINE LABORATORY at two sites where toxicity was either regulatory action. Through highly relatively low or nonexistent. We have integrated research and improved For decades, managers have used also developed toxicity identifi cation cooperation between research and chemical analyses and laboratory- procedures that can be used to predict management, it will be feasible to cre- based sediment toxicity tests (with what chemicals cause endocrine dis- ate a new paradigm for determining standard test species) to predict the ruption and other reproductive harm when and how contaminants impair effects of contaminants in the Bay. in fi sh. the quality of our estuarine habitat. However, the responses of organ- MORE isms actually living in the Bay are Our Resident Species Portfolio ap- INFO? [email protected] what managers, scientists, and the proach is a fi rst step in making moni- public care most about. Managers and toring of Bay species more practical, scientists alike have been frustrated by and hence minimizing extrapolations the lack of consensus on how pollut- inherent in ecological risk assess- ant effects should be characterized in ment of contaminated sediments. fi sh, invertebrates, and plants of the Numerous emerging contaminants Estuary. It is an opportune time for cooperative investigations that will lead to a solution to this problem.

The Pacifi c Estuarine Ecosystem 43 Indicator Research (PEEIR) consortium advocates the development of an integrated portfolio of contaminant exposure and effects responses using indicator species selected for various Gillichthys mirabilis habitat types. We developed a portfolio of techniques for salt marshes that TAKE • Sediment toxicity tests, chemi- are integrated within fi sh (mudsucker, HOME cal analysis, and invertebrate sur- Gillichthys mirabilis), invertebrate POINTS veys are useful but limited tools. (shore crab, Pachygrapsus crassipes), There are new methods available and plant (cordgrass, Spartina foliosa, • Contaminants cause harmful ef- to discern contaminant eff ects in and pickleweed Salicornia virginica) fects on fi sh and invertebrates— salt marshes. indicator species. We performed sedi- just because certain organisms are present in a marsh does ment and tissue chemical analyses and • In the past, large-scale inter- not mean they have not been analyzed biomarker responses in these agency eff orts have usually impacted. The fact that we don’t species at fi ve marshes in Northern not considered the impact of measure contaminants in fi sh and Southern California. A com- contaminants on species like the and invertebrates doesn’t mean parison to toxicity test responses and Delta smelt. benthic population surveys was per- there aren’t harmful eff ects. formed at a more limited number of • We need a new, integrated • We need better knowledge of stations. While the widely used Sedi- approach linking ecology and the eff ects of contaminants on ment Quality Triad approach is a use- toxicology. Integrated science is resident species. We need to ful screening tool, we found that this powerful and is the wave of the start monitoring their health. approach does not predict the range of future. Such information will aid in effects in resident species. Specifi cally, regional monitoring and wetland we noted reproductive impairment in restoration eff orts. shore crabs and/or ovarian tumors and STATE OF THE ESTUARY 2006 THE ROLE OF SCIENCE TAKE Linking Bay Health to HOME National Ecosystem Indicators POINTS • The San Francisco Bay Index ANITRA PAWLEY measures for the Bay’s aquatic biota synthesizes the results of nearly THE BAY INSTITUTE were decidedly mixed. The condition three dozen science-based of the upper Estuary’s planktonic food In October 2003, The Bay Insti- indicators that measure the web remained very poor and the Fish tute released the fi rst comprehensive ecological health of the Estuary. Index declined. Only the Shellfi sh report card for San Francisco Bay. Key to its success and media Index improved, refl ecting increases The San Francisco Bay Index, part attention is its simple and easily in the abundance of crabs and shrimp of the Ecological Scorecard project, understood Scorecard. Howev- in the Bay. These biological indicators illustrates a unique approach for inter- er, the tiered approach for re- also tell another important story – the preting science in clear and powerful porting results (2003 and 2005 health of the Bay, as measured by the public messages. Nearly 40 indicators reports and technical appendi- conditions and trends for its biota, were chosen based on a conceptual ces) allows the reader to obtain varies dramatically along a geographic framework that ties condition to an- a deeper view of condition for and environmental continuum in thropogenic stressors. The indicators each attribute and component the Estuary. In the lower Estuary, are aggregated into eight multi-metric indicator (see www.bay.org). Central and South Bays, indicators for indexes that track the Bay’s environ- phytoplankton, shrimp populations, ment (Habitat, Freshwater Infl ow, • Multi-metric indexes and their and fi sh all showed fair and generally Water Quality), its fi sh and wildlife component indicators, when improving conditions. But in the upper (Food Web, Shellfi sh, Fish), our man- organized in a consistent frame- Estuary, San Pablo and Suisun Bays, agement of its resources (Steward- work, can be used to evaluate these same indicators were low and ship), and its direct value to the people and summarize ecosystem 44 declining. who use it (Fishable-Swimmable- health across multiple geo- Drinkable). Each index is illustrated Indicator development is an itera- graphic scales. The 2005 Bay by a letter grade, a numeric score that tive process that depends on sound Index covered the entire Estu- refl ects the aggregated results of the science and sustained support. We ary and, using several individual component indicators for the most now have a report card and frame- indicators, also detected and recent data period (e.g., Freshwater work approach that can serve as a compared the variations in eco- Infl ow in 2004), and arrows indicating basis for indicator refi nement, but its logical conditions and trends in short-term (within the past 5 years) success depends on continued use and diff erent regions of the Bay. and long-term trends (over the past 20 refi nement as our scientifi c knowledge or more years). evolves. Today, working as a coalition • Tracking ecosystem health of national (San Francisco Estuary through scientifi cally derived The 2005 update of the Score- Project) and local entities (The Bay indicators is essential for long- card’s Bay Index allows us to refl ect Institute, San Francisco Estuary Insti- term economic and political on recent changes in the Bay’s health tute, Center for Ecosystem Manage- public support for the Bay’s and to compare ecological conditions ment and Restoration), we continue environment. Without such in different regions of the Estuary. In to refi ne, augment, and improve upon communication tools, the San general, long-term downward trends this concept and approach. For exam- Francisco Bay environmental have stabilized or are slowly being ple, the Water Quality Index is being and research communities will reversed for the Indexes that track evaluated, refi ned and expanded upon fi nd it increasingly diffi cult to the health of the Bay’s environment. to become a Contaminant Index that procure funds for restoration The Habitat, Freshwater Infl ow, and incorporates measures of sediment and monitoring in light of a re- Water Quality Indexes all showed quality. The Fish Index is being evalu- duction in available monies for some improvement, refl ecting our ated by a larger team of researchers environmental issues. ongoing investments for restoration and improved by adding additional of shoreline habitats and pollution data sources and sub-regional analy- control, as well as the wetter hy- ses. Wetland quality and bird resourc- drological conditions in the last two es are being evaluated to augment our years. In contrast, the Scorecard’s RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP THE ROLE OF SCIENCE current list of indicators. Additional Program, are planning and develop- to improve the scientifi c underpinnings indicator development efforts are ing suites of ecological indicators or of the indicators and multi-metric occurring at the California Bay Delta “report cards.” While our success is indexes. Finally, increased visibility Authority and at the state level. These serving as one model for these efforts, through widely supported, easily un- efforts will inform and be informed by it also challenges us to link our efforts derstood indicators will enhance public the “Indicators Consortium;” however, to other national indicator frameworks understanding of and support for San progress in this important work can be to enable us represent and compare Francisco Bay conservation and resto- slowed by limited resources, data gaps, San Francisco Bay health to other ration efforts. and political impediments. large-scale ecosystems. Our involve- MORE ment in other national level indicator INFO? [email protected] Meanwhile, other large-scale eco- efforts, ongoing research, and synthe- logical restoration programs across the sis also offers important opportunities nation, such as the National Estuary

THE SCORECARD’S BAY INDEX, 2005 ECO-INDICATORS An ecological indicator is a measurable characteristic related to the structure, composition, or functioning of an ecosystem. Indexes are composed of multiple indicators and can be used just like economic indexes to summarize status 45 and trends for a concise public communication tool. STATE OF THE ESTUARY 2006 THE ROLE OF SCIENCE

How Science Is Guiding Restoration TAKE HOME of the South Bay Salt Ponds POINTS

LYNNE TRULIO how monitoring and applied studies, • The South Bay Salt Pond Res- SAN JOSE STATE UNIVERSITY beginning now in the planning stage, toration Project is ecosystem can be used to address uncertainties. restoration on a landscape The Science Program for the The data produced during planning scale—15,100 acres. South Bay Salt Pond Restoration will be applied directly in the design of Project provides direct scientifi c input Phase 1, to be implemented beginning • It is a long-term restora- into planning for short-term and long- in 2008. The draft AMP also describes tion project and will be term project actions. The project’s how adaptive management will be implemented in phases over Science Team has worked to identify integrated into project implementation approximately 50 years. key scientifi c uncertainties associated to track the project’s ecological and Planning is underway, and with the project and, through techni- social goals and collect data to address implementation of Phase 1 cal workshops and focused literature key questions. Adaptive manage- will begin in 2008. reviews, has collated information on ment—a cyclic process for learning what is known and not known about from management decisions and • Adaptive management will these questions. Using this informa- applying that knowledge as we move tell us how far we can go tion, as well as material developed by forward—will help reduce uncertainty along the way—how much tid- the consultant team and stakeholders, in such areas as mercury, sediment al marsh we should restore, the Science Team drafted an Adap- and mudfl at dynamics, bird use of taking into account the fact tive Management Plan (AMP) for the changing habitat, invasive and problem that salt ponds are habitats Project. This draft AMP illustrates species, and benefi ts to non-avian spe- in their own right. 46 cies. Adaptive management is central • Adaptive management is not PROJECT OBJECTIVES to guiding the design and success of the project. trial and error; it is based Create, restore, and enhance on an understanding of the MORE system. habitats to: INFO? [email protected]

• Assist in recovery of special- status species. DRAFT PROJECT ALTERNATIVES AS • Maintain current migratory bird LANDSCAPE VISIONS species. Tidal Action Managed Pond

• Support increases in native species abundance 50% 50% and diversity.

• Maintain or increase ﬂ ood pro- 75% 25% tection. 90% 10% • Provide for wildlife-compatible public access.

• Maintain or improve water and sediment quality.

• Maintain or improve invasive or nuisance species management. RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP WORKS IN PROGRESS

“Trends going the wrong way can be reversed. In Oakland, we’re taking the Lake Merritt channel and returning it to a tidal slough. We’ve dammed and culverted most of our creeks, yet Measure DD set aside

$198 million that will do lots of good for water quality and restoration.

Measure DD passed by 80 percent of the vote—it was a mandate for restoration.

Many of the 6.4 billion of us on

Earth live in urban areas, which can exacerbate environmental problems but also provide solutions. 47 The biosphere we live in is a thin, fragile layer—only as thick as a coat of paint on a football. We’re starting to see the body of Mother Earth get spastic—droughts, tornadoes, we’re at best light green. We can can help over-consuming people get heat waves like we’ve never seen work toward medium and deep down to a sustainable level. If we before. David Brower talked about green. In Oakland, the mayor’s can reduce waste, we can reduce the ‘great ecological U-turn.’ When offi ce is committed to making envi- energy use as well. I’d like to see each you’re standing on the edge of a cliff ronmental changes, bold changes, generation leave less of an ecological about to fall off , the solution is not paradigm changes. We need to footprint. We can shift from basic very complex. You turn around and reduce greenhouse gas emissions. levels of change to paradigm shifts. take a very diff erent direction. Re- In Oakland, we’ve set a goal of get- We can set the tone for the United cently, ten cities across the country ting to 15 percent below 1990 levels were named as the top ten green States.” by 2010. We want to reduce landfi ll cities—San Francisco, Berkeley, and — Randy Hayes, City of Oakland, waste by 20 percent by 2010. We Oakland were all on the list. But founder RainForest Action Network

Photo courtesy of David Hart and John Sanger STATE OF THE ESTUARY 2006 WORKS IN PROGRESS

San Francisco Bay to monitor the status Stewardship: to involve 5,000 of oyster and eelgrass Volunteers community volun- habitats in the Bay and teers each year in small pilot restoration in Urban wetlands restora- projects that are gener- Restoration tion projects. These ating needed information projects involve for large-scale regional local schools, com- efforts. MARILYN LATTA munity and religious SAVE SAN FRANCISCO BAY 6. Non-Traditional groups, corpora- Partners: We also tions, and Bay Area Restoring habitat in highly urban- partner with groups not residents in Bay ized regions with dense populations traditionally included education and on- and layers of infrastructure poses in the environmental the-ground habitat special challenges. But urban areas movement—businesses, restoration of tidal Source: Save The Bay also present opportunities and re- industry, hunting associa- wetlands. sources that can be applied to advance tions, military reserves, and others. habitat restoration projects. Even 2. Implementing Revegetation Plans In order to truly save the Bay, we highly altered and degraded urban with Community Volunteers: need everyone to participate in landscapes hold habitat creation and Many agencies do not have the the effort and become part of the enhancement possibilities, and densely staff time or funding to do such solution. populated urban areas hold another time-intensive tasks as manual These examples all highlight great resource: thousands of potential removal of invasives, site-specifi c diverse partnerships among state volunteers. Finding and mobilizing seed collection, and site monitor- and federal public resource agen- 48 these “hidden” urban resources can be ing. By implementing sound plans cies, private businesses, community the essential ingredient for a success- that educate people while they foundations, civic groups, non-profi ts, ful habitat restoration project. participate, both people and habitat and local schools. They offer a wide benefi t. Urbanized estuaries can offer nu- variety of ideas and models for anyone merous and varied potential partner- 3. Regional Native Plant Nursery pursuing urban estuarine habitat ships with federal, state, regional and Program: We enhance educational restoration. local landowners, agencies, businesses, values for our volunteers and save MORE and organizations. Even small projects money on plants by growing them INFO? [email protected] can create large interest and present ourselves. We engage volunteers in opportunities to combine talents and site- and watershed-specifi c seed resources, or to match funds among collection, plant propagation and diverse partners. transplanting, and planting more The greatest urban resource of all than 20,000 wetland plants each is people. Find ways to utilize volun- year in native watersheds. teers in a restoration project and they 4. Islands and other unique and sensi- will participate. The key is developing tive sites: Save The Bay partners a sustainable program of volunteer with the U.S. Fish and Wildlife outreach and coordination with the Service at the Marin Islands and restoration project. Here are some Bair Island to engage volunteers in examples of the different types of habitat restoration via canoe and habitat restoration projects we do in kayak. the San Francisco Bay-Delta Estuary: 5. Subtidal Restoration and Moni- 1. Wetlands Enhancement Site toring Projects: Save The Bay is Partnerships: Save The Bay part- partnering with the NOAA Com- ners with local, state, and federal munity-based Restoration Program resource agencies at six sites in and San Francisco State University RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP WORKS IN PROGRESS

planted almost 100,000 native plants VOLUNTEERS = $ Volunteers at Crissy Marsh. The Stevens and Permanente Restore Marshes Creeks Watershed Council has at least 80 full-time volunteers and Uplands “They get a fi rst hand engaged in watershed steward- MICHAEL LEE experience with the ship, including monitoring water GOLDEN GATE resource. For many of quality. In 2005, 1,460 volunteers NATIONAL PARKS CONSERVANCY helped clean up 46 miles of creeks them it’s the fi rst time. in Santa Clara County, removing Since its inception in 1981 as a It’s a way for them to 40,000 pounds of trash. Congressionally designated coop- connect both person- erative association, the Golden Gate “Funding for volunteers National Parks Conservancy has ally and intellectually.” provided the Golden Gate National to stay involved—and to Parks with nearly $78 million in aid to Mike Lee attend stakeholder meet- improve park sites, provide services ings—is a challenge. The and education programs for visitors Taken as a unit, Golden Gate is collaborative process and local communities, engage diverse one of the largest urban national parks tends to be dominated audiences in the parks, and encourage in the world. Established in 1972, as by the agencies. There those who use and value these park- part of a trend to make national park should be a mechanism resources more accessible to urban lands to take a role in their preserva- for the general public to tion. The Golden Gate National Parks populations and bring “parks to the Conservancy is a nonprofi t member- people,” Golden Gate’s 75,398 acres participate.” ship organization created to preserve of land and water extend north of 49 the Golden Gate National Parks, en- the Golden Gate Bridge to Tomales Mondy Lariz hance the experiences of park visitors, Bay in Marin County and south to Stevens and Permanente Creeks Watershed Council and build a community dedicated to San Mateo County, encompassing 59 conserving the parks for the future. miles of bay and ocean shoreline and distinctive coastal habitats. These The Parks Conservancy recruits lands represent one of the nation’s and manages volunteers for conserva- largest coastal preserves and attract tion stewardship projects park-wide. According to the U.S. Fish & Wild- 17 million visitors each year, making In 2004 alone, nearly 16,000 individu- life’s Mendel Stewart, volunteers Golden Gate one of the most visited at the S.F. Bay National Wildlife als provided 382,000 hours of service National Parks in the nation. Refuge complex represent 19 full- in support of park programs — the time staff people, at a dollar value equivalent of 184 full-time It is the dedication and hard work of $470,000. At the South Bay salt employees. of volunteers that create the visible ponds, 15 active docents regularly and lasting impacts benefi ting the take the public on guided walk- Volunteers perform a variety of cultural and natural resources of the ing tours. Volunteers also take tasks, ranging from restoring habitat Golden Gate National Parks, today resource managers by boat to the (site stewardship) and trails, monitor- and into the future. Proper orienta- Farallones. Citizens to Complete ing and banding birds of prey (Golden tion, training, and skillful, personal the Refuge continue the volunteer Gate Raptor Observatory), growing supervision; investing in the continu- and advocacy work they started native plants (Native Plant Nurser- ing education of volunteers; and 40 years ago. ies), leading interpretive walks and genuinely recognizing volunteers for talks, and doing administrative work. their contributions are key ingredients “Citizens like these de- Nearly 3,000 volunteers were in- to successfully recruiting, managing, fi ne what volunteerism is volved with the Parks Conservancy’s and retaining volunteers. all about.” most ambitious and visible project to MORE restore Crissy Field into a premier INFO? [email protected] Mendel Stewart urban National Park site. Under the U.S. Fish & Wildlife Service supervision of Park staff volunteers STATE OF THE ESTUARY 2006 WORKS IN PROGRESS North Bay Restoration: Napa Salt Ponds and Hamilton Airfi eld

AMY HUTZEL AND Department of Fish and Game, and POTENTIAL FOR TOM GANDESBERY U.S. Army Corps of Engineers have LARGE-SCALE RESTORATION CALIFORNIA COASTAL CONSERVANCY completed a Feasibility Study for the ACRES reduction of salinity and restoration or Before the Gold Rush, over 50,000 Napa Salt Ponds 9,850 enhancement of habitats in the former acres of tidal marsh ringed the Bay. salt ponds. Some of the inactive salt Hamilton & SLC 990 Today, less than 20,000 acres exist, ponds currently provide signifi cant Bel Marin Keys 1,585 but we have the potential to almost habitat for fi sh and wildlife, while the double that amount. Two such large- Napa Plant Site 1,400 salinity levels in others exceed that scale restoration opportunities are which is benefi cial to wildlife. The Skaggs Island 3,300 coming to fruition in the North Bay: project objectives for the Napa Salt Sears Point 1,400 the Napa Salt Ponds and Hamilton Ponds are: (1) to restore large patches Airfi eld. The two projects have similar Cullinan Ranch 1,564 of tidal habitats in a band along the objectives but involve very different Napa River, in a phased approach, TOTAL 20,000 sites and different designs. At both to support a wide variety of fi sh, projects, we want to restore tidal and wildlife, and plants, including special non-tidal habitats. and enhancement of 3 additional status species, and (2) to effectively ponds. The work is being conducted In 1994, the Cargill Salt Company manage water depths and salinity by Ducks Unlimited using grant funds ceased the production of salt in the levels of remaining ponds to benefi t from the Wildlife Conservation Board 50 North Bay and sold almost 10,000 migratory and resident shorebirds and acres of ponds and adjoining lands to waterfowl. Restoration began in Fall and the California Bay Delta Author- the State of California for $10 million. 2005 with the commencement of tidal ity. A potential addition to the Project The Coastal Conservancy, California restoration of 3 ponds (3,000 acres) is the use of recycled water to dilute

PREDICTED HABITAT AT YEAR 50, HAMILTON AIRFIELD RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP WORKS IN PROGRESS

TAKE PREDICTED LONG TERM HABITAT AT THE NAPA SALT PONDS HOME POINTS

• The Napa Salt Ponds and Hamilton Airﬁ eld projects both include a mix of tidal and non- tidal wetlands.

• Both sites are worthy of restoration but require diﬀ erent treatments.

• Other North Bay projects (from Pond 2A to Sonoma Baylands) have provided lessons.

• We are using two diﬀ erent designs to achieve vegetated tidal marsh and other tidal habitats in a reasonable time frame.

• The designs are based on site conditions such as elevation, ex- istence of a historical template, 51 proximity to development, and existing non-tidal wetlands.

• Design complexity and costs increase with constraints such as subsidence, proximity to development, lack of historical bittern, a salt production by-prod- material. This wetland restoration template, fl ood control issues, uct, in partnership with the Sonoma project will advance the benefi cial existing non-tidal wetland re- County Water Agency. reuse of dredged material from San sources, etc. Francisco Bay as part of the Long The fi rst phase of the Hamilton Term Management Strategy (LTMS). Wetland Restoration Project will The U.S. Army Corps of Engineers, provide 620 acres of restored tidal San Francisco District, is the lead and seasonal wetlands at a former federal agency for the project and the Army airfi eld and adjacent taxi areas California State Coastal Conservancy on San Francisco Bay in the city of is the local sponsor. Novato, Marin County, California. The Corps of Engineers and State MORE INFO? [email protected]; Coastal Conservancy are planning to [email protected] add the adjoining State Lands Com- mission parcel and the Bel Marin Keys V property to the project to expand the wetlands project size to almost 2,500 acres. The phased approach will be used to complete the design and construction tasks in conjunction with the availability of land and dredged STATE OF THE ESTUARY 2006 WORKS IN PROGRESS PRELIMINARY RESTORATION RECOMMENDATIONS

South Bay 92 Hayward Various Types of Restored Tidal Marsh Various Types of Restored Salt Ponds Protection & Enhancement Restoration Buffer San Mateo Bridge Union City Miles CARL WILCOX 0 1 2 4 CALIFORNIA DEPARTMENT 880 OF FISH AND GAME Foster City 84 Over the last several years, signiﬁ - Fremont cant progress has been made toward South Francisco Bay San

preservation and restoration of tidal k e e r Newark C d o o w wetlands in the South Bay. With the d e R

Dumbarton Cargill Salt Ponds acquisition, 17,700 Bridge acres of diked former Baylands are Fremont in the planning process for restora- Redwood City East tion. These projects include the Eden Palo Alto Menlo k t e C r e e Park C o y o Landing Restoration Project, Bair Palo Milpitas Alto Island, and the South Bay Salt Ponds.

Alviso These projects build on restoration ef- Mountain forts over the past 30 years that have View San Jose Sunnyvale 237 resulted in substantial tidal wetland restoration in the South Bay. to minimize the potential for coloniza- The Baylands Ecosystem Habi- tion once restoration is implemented. TAKE tat Goals Report recommended the The project will use dredge material to 52 HOME restoration of between 16,000 and accelerate tidal marsh development to POINTS 21,000 acres of tidal marsh habitat in minimize potential bird strike concerns the South Bay and the management associated with the nearby San Carlos • Tidal restoration will be advanc- of 10,000 to 15,000 acres of salt pond Airport. Tidal barriers will also be in- ing at a rapid rate in the next habitat. With the current projects, the stalled in two major sloughs to address three years, with approximately objectives for tidal marsh restoration potential sedimentation concerns at 2,500 acres restored at Eden may be achieved within the foresee- the Port of Redwood City. Landing, Bair Island, and the able future. Island Ponds. The South Bay Salt Ponds Res- The Eden Landing Restoration toration Project is developing the • Planning is well underway for Project is currently under construction restoration plan for the 15,100 acres of fi rst phase implementation of and is scheduled to be completed in salt ponds acquired from Cargill Salt the South Bay Salt Pond Resto- the summer of 2006. This project will in 2003. This planning effort will be ration Project in 2008. restore 650 acres of former crystalliz- completed and a fi rst phase restora- ers and salt ponds to tidal marsh while tion project implemented in 2008. In • Managing pond habitat is an art enhancing an additional 200 acres the interim, the Department of Fish that is developing as to how to of managed ponds. One element of and Game and U. S. Fish and Wildlife optimize values for individual the project will be the restoration of Service are managing the ponds under species and species groups approximately four miles of large tidal an Initial Stewardship Plan. Imple- while maintaining pond health channels. mentation of this plan has resulted in and staying within permit conditions for discharges to the Bay. The Bair Island Restoration Project substantial increases in wildlife use but also highlights the complexity of is in the fi nal stages of planning and • We need to perform additional managing large ponds while complying permitting. This project will restore investigation into mercury is- with water quality objectives. approximately 1,700 acres of diked sues associated with South Bay Baylands to tidal infl uence. The timing MORE pond restoration. of restoration is being coordinated INFO? [email protected] with nonnative Spartina control efforts RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP WORKS IN PROGRESS

Evaluating Restoration Success: TAKE HOME The Human Angle POINTS

STEVE RITCHIE human angle is not well-deﬁ ned or • We need to monitor changes in SOUTH BAY SALT POND considered. RESTORATION PROJECT community values and interests, In the South Bay Salt Pond Resto- just like we monitor species’ use Most of the attention on habitat ration Project, successful restoration of habitat. restoration projects is focused on the must fully integrate the human element • We need to make sure restora- success or failure in producing the for a number of reasons. The most tion works for humans as well desired biological and physical results: obvious reason is that the former salt as animals, to be sensitive achieving target populations of birds, ponds are literally surrounded by more to human concerns from the ﬁ sh, plants, etc. CALFED and others than two million people. Restoration of outset, and to work actively to have long recognized that humans the 15,100 acres of ponds now owned understand and address those are a part of the ecosystem that must by the state and federal governments concerns. be considered as part of any restora- must be carried out in a way that en- tion project, but in most projects, the hances the quality of life for residents • We need to use every opportunity to educate folks about POSSIBLE FUTURE BAY the values of restoration and to HABITATS AFTER RESTORATION cultivate community ownership.

of the South Bay area. This is particularly critical at a time when large-scale 53 public funding is hard to come by.

Through its Stakeholder Forum and other processes the Project is working to identify what the broader community desires as a result of the restoration. Those broader public desires need to be considered within the constraints of federal ownership (the Don Edwards San Francisco Bay National Wildlife Refuge) and state ownership (the Eden Landing State Ecological Preserve).

Equally important with the result is the process by which the restoration plan is developed. Transparency of decision-making is key to building public trust and support for the Project. This is true both in restoration planning and in long-term adaptive management. The Restoration Project is working hard to ensure that it earns that trust and support. MORE INFO? [email protected] STATE OF THE ESTUARY 2006 WORKS IN PROGRESS

projects toward the established goals. quality of Bay habitat for wildlife; Successes Analysis of accomplishments since the (c) the impacts of human disturbance in Protecting founding of SFBJV indicate signiﬁ - on waterfowl and other wildlife spe- cant progress toward the established cies; (d) the impacts on wildlife of con- and Restoring acreage goals for acquisition; protec- verting one type of habitat to another the Bay tion of 43,000 acres (40 percent of type of habitat; and (e) the relation- the total goal and 63 percent for tidal ships of migratory wildlife that use wetlands); restoration of 5,023 acres SFBJV habitats to the habitats within BETH HUNING AND (10 percent of total goal); and en- other joint ventures. SANDY SCOGGIN SAN FRANCISCO BAY JOINT VENTURE hancement of 4,982 acres (6 percent MORE of total goal). These accomplishments INFO? [email protected] The San Francisco Bay Joint are being analyzed to cor- Venture (SFBJV) is a partnership respond with each habitat type to help assess future SFBJV ACREAGE GOALS AND of non-governmental organizations, ACCOMPLISHMENTS OCTOBER 2005 utilities, landowners, and agencies focus and priorities of SF- Bay Habitats working to acquire, restore, and en- BJV and locations in focal hance wetlands on San Francisco Bay areas of San Pablo Bay, the 70,000 Goals and the coasts of San Mateo, Marin, South Bay, Central Bay, and 60,000 the coast. Accomplishments and Sonoma Counties. The San 50,000 Francisco Bay Joint Venture is one of Based upon the above 40,000 the 12 wetland habitat Joint Ventures information, the SFBJV operating under the North Ameri- 30,000 Restoration Strategy/Tech- can Waterfowl Management Plan 20,000 nical Committee has (NAWMP), a Congressional agree- 54 recommended a shift in 10,000 ment between the United States, focus toward restora- 0 Canada, and Mexico. The SFBJV Acquire Restore Enhance tion. This emphasis would Implementation Strategy, Restoring include funding, planning for the Estuary, was completed and ap- Seasonal Wetlands restoration, and monitoring proved by NAWMP in 2001. and assessment to guide 40,000 Based on the Habitat Goals Proj- decisions about the habitat 35,000 Goals ect, SFBJV goals include: types needed to accomplish 30,000 Accomplishments the vision and goals estab- 25,000 • Acquisition: 63,000 acres of Bay lished in Restoring the Estu- 20,000 habitats, 37,000 acres of sea- ary. A new project tracking 15,000 sonal wetlands, and 7,000 acres data system has been de- 10,000 of creeks and lakes (107,000 acres veloped by Ducks Unlimited 5,000 total); for SFBJV to provide part- 0 • Restoration: 37,000 acres of Bay ners with the ability to track Acquire Restore Enhance habitats, 7,000 acres of seasonal the progress of each project wetlands, and 22,000 acres of and to analyze each project creeks and lakes (49,000 acres and accomplishment in the Creeks and Lakes total); context of the overall goals. 25,000 The NAWMP assessment Goals • Enhancement: 35,000 acres of Bay 20,000 has also identiﬁ ed additional Accomplishments habitats, 23,000 acres of seasonal monitoring and evaluation 15,000 wetlands, and 22,000 acres of needs to better understand creeks and lakes (80,000 acres (a) whether wintering 10,000 total). conditions in San Francisco The focus of SFBJV for the past Bay contribute to the con- 5,000 four years has been implementation of tinental scaup and scoter 0 declines; (b) the overall Acquire Restore Enhance RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP SCIENCE, LEARNED & NEEDED

“The certainty of our predictions about restoration varies by habitat type. We will learn and adjust as we go forward.”

—Michelle Orr, PWA

Learne 55

“Revegetation is working to restore a diversity and abundance of songbird populations along the Sacramento, Cosumnes, and San

Joaquin Rivers.”

—Geoﬀ Geupel, PRBO Conservation Science

Photo courtesy of David Hart and John Sanger STATE OF THE ESTUARY 2006 SCIENCE, LEARNED & NEEDED A Landscape Ecology Perspective on Bay Wetland Restoration

MAGGI KELLY UNIVERSITY OF CALIFORNIA, BERKELEY

San Francisco Bay is the largest estuary on the Pacifi c Coast; its wetlands provide crucial habitat for a wide range of species, and have a long history of human impacts. The wetland landscape is a complex mosaic of remaining historic wetlands, recently restored wetland sites, and potentially restorable diked bayland sites (farms, former salt ponds, and managed and unmanaged seasonal and peren- the state’s largest urban areas. The nial wetlands), all arranged in one of diverse mosaic separating Bay from upland is crucial in many ways to the future of the San Francisco Bay TAKE Area: for example, these wetlands HOME are an important component of the POINTS 56 Bay’s ecology, and they are part of the • By increasing the spatial scale natural open space valued by a highly we use, landscape ecology urban population. can help us see how individual While it has long been recognized wetlands function together. It that wetlands are ecotonal features can also help us determine how between upland and open water, we existing marsh patches can be also think of this complex of wetlands revisualized for certain species. in the greater San Francisco Bay as wetland patches with ecotonal areas • On a temporal scale, the between them, and displaying within- future of the Bay—a mosaic patch variability that is important of wetlands in an increasingly for species (bird, fi sh, mammal, etc.) urbanized watershed—has to be diversity and survival, and other wet- planned for. land functions. A landscape ecology • We need a vision for planning approach is useful for setting the stage for the ecosytem services for large-scale wetland restoration in provided by wetlands. Context the Bay; the approach incorporates and adjacency aff ect wetland multiple scales and considers inter- functions. actions between patches and fl ows between and across ecotones and patches. Landscape ecological principles such as adjacency, connectivity, heterogeneity, and spatial confi guration can be useful guiding principles for future restoration. MORE INFO? [email protected] RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP SCIENCE, LEARNED & NEEDED Predicting Habitat Changes in Wetland Restoration

MICHELLE ORR, ET AL. tailed models, such as HABITAT EVOLUTION IN THE TIDAL PONDS: LONG TERM SEDIMENTATION PHILIP WILLIAMS & ASSOCIATES a ﬁ ne-grid numerical model, for the assess- 6 Tools that integrate system-wide ment. The physi- Without restoration physical and ecological processes can 4 cal-processes part of be useful for large-scale restoration the assessment is an 2 planning by informing decisions about With restoration examination of the where, how much, and which types of 0 rate at which the re- habitat to restore. In the 15,100-acre stored South Bay salt -2 South Bay Salt Pond (SBSP) Restora- Suspended Sediment Conc.

ponds are expected NGVD) (ft. Elevation -4 600 mg/L tion Project in South San Francisco to evolve from tidal 450 mg/L Bay, successful design requires an -6 mudfl at to marsh, and 350 mg/L understanding of how the ecosystem how the restoration -8 250 mg/L will evolve over time in response to may affect the South possible management actions such as -10 Bay sediment budget 0 1020304050 restoring tidal inundation to salt ponds and ultimately the Time (Years) to create tidal marsh. extent of tidal mudfl at suffi cient sediment is available for tidal and shallow-water habitats within The SBSP Landscape Scale As- marsh restoration and that even the the South Bay. The ecological part sessment is a geomorphic approach to most subsided ponds are expected to of the assessment uses the physical- predicting long-term (50-year) habitat provide tidal marsh habitat within the 57 processes results to predict vegeta- changes within South San Francisco fi fty-year planning horizon. Bay without restoration as well as for tion, habitats, and wildlife use. Even when the large uncertainty inherent MORE different restoration scenarios. Given INFO? [email protected] the inherent complexity of the pro- in this kind of assessment is consid- cesses involved, there are no standard ered, preliminary results suggest that “off the shelf ” tools for this type of prediction. The assessment combines a sediment budget approach SOUTH BAY PRELIMINARY TRENDS with existing analytical models, EROSION historical analysis, and empirical tools. The project planning timeline EAST SHORE precluded development of new de- DEPOSITION

TAKE HOME POINTS

• The certainty of our predic- WEST SHORE tions about restoration varies by habitat type.

• Our restoration plan must be resilient. FAR SOUTH BAY • We will learn and adjust as we go forward. STATE OF THE ESTUARY 2006 SCIENCE, LEARNED & NEEDED Dutch Slough: Restoration and Adaptive Management

JOHN CAIN NATURAL HERITAGE INSTITUTE DUTCH SLOUGH TIDAL MARSH RESTORATION - ALTERNATIVE 2B

The CALFED Bay Delta Author- Low Marsh ity and the State Coastal Conser- High Marsh vancy provided $28 million to acquire Deeply Subsided/ Dutch Slough Open Water a 1,166 acre parcel along Dutch Slough Upland Burroughs in northeastern Contra Costa County Emerson Parcel Parcel Gilbert

Dune Emerson Parcel for tidal marsh restoration. The parcel Slough was previously levied dairy and ranch Tidal Channel Flood Levee

land that was slated for develop- Little Dutch Slough Water Control ment of 4,500 residential units. The Structure Marsh Drainage California Department of Water

Resources has assumed ownership Marsh Creek responsibilities and is working collaboratively with the State Coastal Conservancy, CALFED, the Natural Heritage Institute, and the City of Contra Costa Canal Oakley to plan and implement the 0 0.2 0.4 0.6 0.8 1 mile 58 restoration project within an adaptive management framework. The goals of the project are to: 1) provide shoreline The property is divided into three accretion and slough channel evolu- access, recreational, and educational levied tracts that could be separately tion. Different portions of the project opportunities, 2) restore a mosaic of treated and restored to tidal action site will be restored to different marsh wetland and upland habitats for native in a unique opportunity to design the elevations in an attempt to isolate the species, and 3) increase understand- restoration project as an adaptive role of marsh plain elevation in these ing of ecosystem function through an management experiment. The project various processes. adaptive management approach. partners are working with an interdisciplinary group of scientists to physically design HOW LOW SHOULD WE GO? TAKE the project to test HOME hypotheses regarding POINTS the role of marsh plain elevation and associated • Restoration is contagious—we inundation frequency in MHHW have new partners every day. 1) avian utilization; Yet all of our restoration eﬀ orts 2) growth and survival MLLW will be relatively futile if we of juvenile salmon and are unable to stem the tide of splittail; urbanization in the Delta. 3) colonization of submerged aquatic • Restoration can wait, but the vegetation; 4) produc- MHHW time for acquisition is now. tion and ﬂ ux of methyl MLLW • We need to expand the Delta mercury and dissolved Protection Commission to pro- organic carbon; and 5) tect the Delta’s secondary zone the role of vegetation in from development. freshwater marsh plain RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP SCIENCE, LEARNED & NEEDED

DUTCH SLOUGH TIDAL MARSH RESTORATION - ALTERNATIVE 3 QUESTIONS WE HOPE TO ANSWER:

Open water Build Subsidence Potential borrow areas What is the relationship be- management bridge reversal option tween marsh plain elevation Dutch Slough and

Burroughs Open water • Salmon and splittail growth management Parcel option and survival Emerson Parcel Gilbert Parcel • Fish food production and avail- Emerson Slough ability Little Dutch Slough • Splittail and Delta smelt

Place fill, spawning excavate tidal channels, • Mercury methylation revegetate, Marsh Creek and breach • Dissolved organic formation Community and export park Protect Jersey Island Road, inholdings, and Contra Costa Canal adjacent Restore dunes Lower levees property What is the relationship between marsh scale and channel 0 0.2 0.4 0.6 0.8 1 mile order and • Salmon and splittail growth Low Marsh Tidal Channel and survival High Marsh Flood Levee • Fish food production and Deeply Subsided/ Water Control Structure Open Water availability Slope Protection Upland Marsh Drainage • Splittail and Delta smelt 59 Dune spawning

The planning process has revealed ing, or exotic species, but is more several challenges and potential trad- complicated for capital intensive earth eoffs that can arise when designing moving projects in highly regulated OUR HYPOTHESES: a restoration project as an adaptive environments. If the initial design does management experiment. Designing not perform as desired, is it realis- • Juvenile salmon and splittail will have higher survival rates an experiment into the restoration tic to assume that managers will or on high marsh because there design is an ideal opportunity to learn should physically modify the Dutch will be fewer fi sh predators. but can create confl icts between op- Slough restoration? Or should the • Food resources will be greater timal experimental design and optimal Dutch Slough project be viewed as a in lower marsh due to in- restoration design. For example, divid- one time management intervention creased residence times. ing the restoration site into numer- designed to inform future restorations • Fish survival will be greatest ous cells of different elevations could in the larger Bay-Delta system? with intermediate scale chan- help tease out the role of elevation in MORE nel network because higher numerous ecosystem processes, but INFO? [email protected] order networks will harbor fragmentation of the site into smaller predators, and lower order cells could reduce connectivity of networks lack suffi cient refuge various habitat types and potentially during low tides. preclude important scale dependent processes.

Adaptive management presum- ably implies that managers will change their management if the project does not perform as desired. This paradigm makes obvious sense with efforts to manage ﬁ shery harvest, cattle graz- STATE OF THE ESTUARY 2006 SCIENCE, LEARNED & NEEDED Elevation, Inundation, Vegetation — and Schoenoplectus acutus (formerly Scirpus acutus). There was substan- and Restoration tial overlap and spatial variability in FACTORS AFFECTING both the elevational distributions and JOHN CALLAWAY, ET AL. VEGETATION UNIVERSITY OF SAN FRANCISCO inundation patterns for some of the Elevation dominant species, Tidal wetland restoration ef- including S. acutus, Schoenoplectus cali- forts have focused on establishing Inundation fornicus (formerly Scirpus californicus), the appropriate elevation for plant and T. angustifolia. We found little Oxygen evidence for critical thresholds for colonization, with the assumption that Availability Salinity elevation determines inundation rates plant distributions across all wetlands. and other critical factors for plant Vegetation Other factors that are likely to affect establishment and growth, including Patterns distribution include soil salinity (being soil redox status and salinity. While measured this year), initial vegetation establishment, and competition. With elevation is the key factor driving inun- (IRWM), we evaluated distribu- the IRWM Bird Team, we also are dation rates, within-site variation due tions of plant species across six tidal comparing vegetation patterns to bird to impoundments, pannes, and other wetlands in the north San Francisco use so that we can evaluate how inun- features may affect local ﬂ ooding and Bay Estuary, working closely with the dation affects habitat characteristics draining. Substantial research has IRWM Physical Processes Team to that are linked to wildlife use. In order evaluated elevational distributions of connect these distributions to eleva- to effectively restore tidal wetlands tidal wetland plants in San Francisco tion and inundation patterns across throughout the Estuary it is critical Bay wetlands; however, very little each wetland. Plant distribution and that we better understand the factors work has directly linked elevation to elevations were determined at 200- that affect both large- and small- 60 patterns of inundation across a tidal 500 locations in each wetland and wetland. were related to As part of the Integrated Re- inundation patterns SPATIAL VARIATION ACROSS WETLANDS gional Wetland Monitoring Program from three to four water level sta- Frequently Inundated Rarely Inundated

tions on the marsh Greater Oxygen Stress Less Oxygen Stress TAKE plain. Inundation HOME data were collected Less Salt Stress Greater Salt Stress POINTS for approximately one year at each • Elevation is important, but wetland and were other factors also aﬀ ect plant also compared to distribution. water level data from instruments High Marsh - • More analysis is needed to Low Marsh Mid-marsh Plain Upland Transition in adjacent tidal evaluate the relationship of in- channels. undation and plant distribution. Patterns of vegetation zonation scale patterns of plant distributions. • Plant diversity increases with el- were apparent from our data, with There is evidence that minor shifts evation up to mean high higher species showing peaks in distributions in elevation and inundation (pres- water in Napa River wetlands. across the tidal wetlands. For exam- ence/absence of creeks) can affect ple, at Coon Island, Salicornia virginica plant distributions, and our research • Plant distributions—along with had the most widespread elevational will help to further understand these physical factors—can be good distribution, with a number of species patterns. predictors of wildlife use of occurring at slightly lower eleva- tidal wetlands. These relation- MORE tions, including Spartina foliosa, Typha INFO? [email protected] ships give valuable insight into angustifolia, Bolboschoenus mariti- restoration design. mus (formerly Scirpus maritimus), RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP SCIENCE, LEARNED & NEEDED

Using spatially predicted mod- Monitoring els, we are able to provide resource Bird Response managers with current information on species abundances and distributions to Restored within restored and mature marshes Marshes and to assess the conservation and restoration efforts within the region. In addition, these analytical tools al- MARK HERZOG, ET AL. low us to locate areas of the marsh or PRBO CONSERVATION SCIENCE types of marsh where our predictions Signifi cant restoration is occurring are less certain (i.e., where the model around the Bay. We need to evaluate performance is poor), and therefore restoration success, and birds offer an will benefi t from additional sampling excellent way to do that. The pres- and research. ence and function of particular species The PRBO adaptive monitoring of birds in a given marsh are deter- plants, habitat, and landscape affect protocol, which is currently being mined by physical and biotic factors, the structure and ecological function developed for the tidal marshes in the as well as demographic constraints of the tidal marsh bird community. San Francisco Estuary, will provide a imposed by their life histories. Collab- While not an exhaustive list, specifi c powerful, yet cost-effective approach oration with research teams in other variables we examined included salin- to monitoring avian populations. disciplines, working at the same loca- ity, vegetative species composition, MORE tions, has greatly enhanced our ability distance to specifi c landscape features INFO? [email protected] to study interactions of birds with veg- (such as pond, channel, urban, Bay, etation, which provides food for prey etc.), and a variety of channel metrics 61 species and substrate for nesting. As (channel order, linear density, areal part of our multi-disciplinary studies, density, etc.). we are investigating how bird populations may be limited or infl uenced by PREDICTED COMMON landscape-level factors, and hydrologi- YELLOWTHROAT DENSITY cal and geomorphic processes. We BIRDS/HA AT COON ISLAND are building models that examine how heterogeneity of physical processes,

TAKE HOME POINTS

• Spatial modeling provides an excellent tool to evaluate restoration.

• Spatial modeling also provides a way to address the uncertainty in our model predictions.

• Adaptive monitoring will enable researchers to monitor more eﬃ ciently, where the goal is as much to learn as it is to monitor. STATE OF THE ESTUARY 2006 SCIENCE, LEARNED & NEEDED

Bay. We have sufﬁ cient information Design from these monitoring efforts, and Guidelines for from ‘snapshot’ observations of other restored sites, to provide guidance Tidal Wetland on pragmatic practical design ques- Restoration tions often encountered in restoration practice.

PHYLLIS FABER, ET AL. Funding from the State Coastal PHYLLIS M. FABER AND ASSOCIATES Conservancy to The Bay Institute has allowed the evaluation and documen- Since the early 1970s, over 45 tidal tation of this experience to produce a marsh restoration projects have been Design Guidelines report. The target implemented around San Francisco audience is all those concerned with Bay, restoring tidal action to more practical restoration questions in San than 2,800 acres. More than 20,000 Francisco Bay and includes resource acres are now being planned and management and regulatory agency pate that new insights will be provided designed. As of 2005, we have 33 staff and environmental professionals in future years by continued monitor- years of restoration history and up involved in tidal wetland restoration. ing data from restored sites. to 19 years of systematic monitoring Many of these design questions are MORE data from projects in San Francisco relevant to resource managers in other INFO? [email protected] estuaries.

DESIGN QUESTIONS We structured the Guidelines to identify and assess key design issues 62 Should the site be fi lled? TAKE by HOME Should fi ll be removed? POINTS Should a levee breach and out- 1. Explaining our conceptual model board channel be excavated? of how restored marshes evolve and • Examine physical processes Should wave breaks be con- function based on our own observa- carefully. structed? tions and other researchers’ assess- • Link design decisions with Should the bayfront levee ments of restored marshes. predictions of how the site will be lowered? 2. Describing the planning con- evolve. Should new tidal channels be text used in restoration practice that excavated? creates the framework for design • Have clear objectives at the Should the pre-existing drain- decisions and considering site-specifi c outset. age system be modifi ed? factors as well as geographic variabil- Should the site be graded to ity in the environmental setting and • Better understand the func- encourage panne formation? variation in project objectives. tions and habitat values of the transition zone. How should the wetland-upland 3. Addressing the major design transition be designed? questions that dictate the grading of • Consider the legacy of past hu- Should soil be treated? the site ‘template’ prior to reintroduc- man actions. Should plants be planted? tion of tidal action. How do we provide habitat We recognize that restoration features for target species? practice is still in its infancy, with con- How should public access be siderable uncertainties and unknowns. provided? Early projects were focused on How should we integrate fl ood achieving a vegetated marsh as soon management issues? as possible; we now know that interim habitats and an evolving mosaic of habitats are also important. We antici- RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP SCIENCE, LEARNED & NEEDED Using Birds to INCREASE IN BIRD SPECIES & DIVERSITY ON THE SACRAMENTO RIVER Assess Habitat 20 P<0.0001 Restoration r0=0.58 15 GEOFFREY GEUPEL PRBO CONSERVATION SCIENCE 10

PRBO Conservation Science has been monitoring songbird populations 5 using multi-tiered methods in restored (SW)Riparian Bird Diversity and remnant riparian habitat in major 0 watersheds of the Central Valley for 0 1 3 5 7 9 11 13 the past thirteen years. Objectives include identifying existing areas of Number of years since restoration high bird diversity for protection and enhancement, establishing habitat refl ected in the distribution, abun- weight gain during migration and site relationships, and quantifying popula- dance, and demographic parameters persistence during winter. Results tion response to changes in habitat of a broad spectrum of species. In are used to guide specifi c restoration including pre- and post- restoration, as addition, we study stopover use and practices and develop quantitative performance measures and biological objectives for bird populations at vari- TAKE National Wildlife Refuge is attribut- ous spatial scales across the Central HOME able to planting large dense patches of Valley. At mature sites along the San POINTS shrubs and groundcover—which prevent 63 Joaquin River nest substrate selec- invasive species—interspersed with • Birds are indicators of ecosystem tion for three species was positively trees, as well as meadow species (forbs health. Diff erent species have diff erent correlated with forb cover and shrub and sedges) that increase understory requirements that represent a range cover, underlining the importance of diversity. It is important to provide of critical ecosystem and habitat ele- planting and managing for understory seed source areas for future dispersal. ments. species and structure. The novel focus on restoring understory on a three • Monitoring ecosystems with birds uses • Birds are responding positively to year-old restoration site on the San cost-eff ective, established methods restoration activities. Revegetation Joaquin National Wildlife Refuge has that can be applied across multiple is working to restore a diversity and infl uenced the return of two locally scales. abundance of songbird populations along the Sacramento, Cosumnes, and extirpated species: the yellow warbler (from 0 to 14 nesting pairs) and the • Results from bird monitoring may be San Joaquin Rivers. fi rst documented pair of least Bells’ used to adaptively manage restoration vireos breeding in the Central Valley and enhancement projects. • To ensure diverse and viable population of songbirds, we need to man- in over 60 years. While abundance of • Birds can be used to “audit” the age for a mosaic of riparian habitat birds at restored sites show promising success of restoration and help set that includes a healthy proportion increases in abundance and spe- quantifi able biological objectives. of early-successional stage habitat cies diversity during spring, fall, and (e.g. contains dense herb cover and a winter, nest success of many species, • We plan to maintain long-term monitor- diverse understory). This may require especially in remnant forests, remains ing sites as reference sites for new intensive management (e.g. mechanical problematic and may be too low to sites and to assess the sustainability of disturbance) if the site is not periodi- sustain populations over time in the bird populations. cally disturbed by fl ooding and/or if the absence of restoration of fl oodplain river is disconnected from its fl ood- dynamics or other conservation ac- • We recommend including extensive plain. tions. bird monitoring in all restoration proj- MORE ects, and continue to adapt and test INFO? [email protected] recommendations at multiple sites. STATE OF THE ESTUARY 2006 SCIENCE, LEARNED & NEEDED Will Restored Tidal Wetlands The highly dynamic nature of these food web “loops” is evident from the Benefi t Bay Food Webs? variability in contributions of organic matter sources, and is often tied to that likely integrates with the pelagic CHARLES SIMENSTAD, ET AL. consumer life histories and behaviors, compartment. Recent research us- UNIVERSITY OF WASHINGTON, as well as responses to disturbance SCHOOL OF AQUATIC AND FISHERY ing both traditional methods (food events, such as freshwater fl ooding. SCIENCES habits) and conservative biomarkers (stable isotopes) indicate that tidal The magnitude and signifi cance Understanding food webs in emergent marshes not only support of both wetland “outwelling” and complex estuaries such as the San closely-coupled internal food webs but infl ux of organic detritus and living Francisco Bay-Delta requires com- also provide linkages to the open Bay algal cells is still unresolved. From the prehensive knowledge about how through direct and indirect exchanges “marsh perspective,” there is emerging heterogeneity of the Estuary creates of transient consumers and very likely evidence of both nekton and food web subsystems or compartments of inter- organic detritus. Contrasting marsh interactions between peripheral (and acting food web sources and consum- residents (e.g., benthic invertebrates restoring) wetlands and Bay-Delta ers, especially when we are trying to such as Macoma balthica, Corophium open water ecosystems, but we lack predict or evaluate the potential role spp., and Ischadium demissum; Pa- a system view of their signifi cance. of restoration actions. The dominant cifi c staghorn sculpin, yellowfi n goby, A landscape view that considers base of our knowledge about the food Shimofuri goby, threespine stickle- fl uxes of organic matter and organ- web structure of San Francisco Bay is back, tule perch, rainwater killifi sh), isms across the estuarine mosaic, and founded on a phenomenal accumula- and nursery residents (e.g., splittail, considers tidal and freshwater fl ooding tion of knowledge about open water, Chinook salmon) with more transient forcing, would be a more appropriate pelagic food webs based on phyto- planktivores (e.g., Sacramento splittail, assessment of the role of both open plankton—the “classic” food web of northern anchovy, Pacifi c herring, water and wetland food web contri- 64 Hardy (1924). Even the complexities inland silversides, topsmelt) and preda- butions and interactions. Such a more of the heterotrophic/microbial aspects tors (e.g., striped bass) indicates that integrated “intercompartmental” and are focused in the pelagic realm. The not only does autochthonous produc- dynamic view of San Francisco Bay- paradigm is that the Bay “runs” on tion dominate the emergent wetland Delta food webs would enhance our phytoplankton. food webs but also that it contributes ability to understand both the basis of However, there are shallow to the broader Bay food web. Evidence and variability in support of important water and wetland ecosystems that from stable isotope analyses suggests consumer organisms as well as the once comprised, and now and could that both edaphic microalgae and comprehensive role of wetland resto- in the future comprise a signifi cant emergent marsh macrophytic or- ration in the Bay-Delta. compartment in the Bay’s food web, ganic matter contribute signifi cantly to MORE transient species, while phytoplankton INFO? [email protected] is a comparatively minor contributor. TAKE HOME POINTS

• The Delta is a detritus mill for the Bay, exporting 30-40 percent of its organic matter to the downstream food web.

• We still do not know all of the sources of that organic matter but are using stable isotopes to try to determine them.

• The interactions between tidal wetlands and pelagic areas are still not well understood.

Hardy’s Food Web, 1924 RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP SCIENCE, LEARNED & NEEDED

elsewhere in the Estuary. There is The Importance of Suisun Marsh in little evidence that this productivity Estuarine Productivity is directly transported to the exterior bay and channel habitats, although ROBERT SCHROETER by chlorophyll a, indicates several migratory invertebrates and fi sh may AND PETER MOYLE regions of high productivity within export considerable quantities of UNIVERSITY OF CALIFORNIA, DAVIS the interior of the marsh, likely due to biomass from the marsh through their high residence time of water, nutrient movements. Estuarine tidal marshes are availability, and absence of alien clams. productive habitats that provide the MORE Surrounding bay and river channel INFO? [email protected] conditions and microhabitats neces- habitats had very low levels of primary sary for successful invertebrate and production. Invertebrates, including fi sh rearing and recruitment. They mesozooplankton and benthos are TAKE may also provide, through export, a most abundant within the interior HOME source of productivity to surround- POINTS sloughs and channels, often reaching ing habitats. Tidal marsh habitat in very high densities. Macrozooplank- • Tidal marshes are important the San Francisco Bay-Delta Estuary ton abundance patterns are more rearing areas for fi sh and inver- has decreased by 90 percent over the variable, but are also high within the tebrates. past 150 years. The impact of this loss marsh interior and rivers with declines and the ecological contribution of the observed in some bay and large slough • They are refuges for native remaining tidal marsh habitat in the habitats. These data suggest that species and are highly Estuary are not well understood. We Suisun Marsh plays a signifi cant role in productive—maybe the investigated the productivity of tidal estuarine productivity by providing an most productive—habitats. channels in Suisun Marsh, Solano abundant source of primary produc- County, the largest contiguous brack- 65 tion and pelagic invertebrates, both of • Many key fi sh species—Delta ish tidal marsh on the West Coast of which are signifi cantly depleted in bay smelt, longfi n smelt, splittail, the United States, and compared our and river channel habitats. These lo- and striped bass—are declining fi ndings to data collected by the Cali- calized areas of high productivity may throughout the Estuary. fornia Department of Fish and Game transfer benefi ts up the food chain, in adjacent bay and river habitats • Fish abundance in Suisun Marsh as fi sh abundance for select species (neomysis and zooplankton surveys). does not follow Estuary-wide remains high in the tidal marsh sloughs trends—Suisun Marsh had Primary production, as measured despite considerable declines observed increases in striped bass and splittail.

SEASONAL PREY AVAILABILITY IN SUISUN MARSH • The diﬀ erences are likely due to good prey availability Larval Fish Rearing Period during key seasons and high phytoplankton biomass within Salinity Copepods Suisun Marsh. This abundance is related to the complexity of Salinity the tidal marsh habitat found Copepods there.

• Factors limiting productivity in Mysid Shrimp the bay and river channels surrounding Suisun Marsh include the overbite clam, an effi cient fi lterer of the water column, and discharge from duck ponds Chlorophyll a of organically rich waters, resulting in poor water quality. 123456789101112 Month STATE OF THE ESTUARY 2006 SCIENCE, LEARNED & NEEDED Chinook Salmon and Steelhead independent populations, and over 20 have been extirpated. Like the winter- in the Bay and Central Valley Rivers run chinook population, the extant populations are probably viable in the STEVE LINDLEY, ET AL. of catastrophic risk using tools from short term, but because these popula- NATIONAL OCEANIC graph theory. tions are quite close together, this AND ATMOSPHERIC ADMINISTRATION ESU is at elevated risk of extinction The winter-run chinook salmon due to catastrophic risks that would To help guide recovery planning for ESU consisted of four populations not have threatened the historical threatened and endangered chinook prior to the dam building era; all four ESU with extinction. salmon and steelhead in the Central were extirpated from their natural Valley and San Francisco Bay, we are spawning range, but are represented The situation with steelhead is developing biological viability goals by a single population utilizing the much murkier. There may have been for populations and evolutionarily tailwaters of Shasta Dam. This on order of 80 or more independent signifi cant units (ESUs) of these spe- population of winter chinook satisfi es populations of steelhead, and much cies. We infer the historical population the criteria to be considered a viable of the spawning habitat used by these structure from a combination of his- population, but cannot be considered populations now appears to be behind torical records and GIS-based habitat a viable ESU by itself, because it is impassable dams. It is possible that modeling, develop simple criteria for vulnerable to several catastrophic descendents of the historical steelhead population status based on genetic risks that could easily extirpate the populations persist as resident trout, and demographic models, and assess population, and therefore, the ESU. and new populations may exist in tail- historical and current spatial struc- The spring-run chinook salmon ESU water areas below some dams. ture of ESUs in relation to sources is represented by two or three extant Overall, it appears that habitat 66 conditions in accessible areas have STATUS OF CENTRAL VALLEY SPRING-RUN improved, as indicated by the improv- CHINOOK SALMON POPULATIONS ing status of extant populations. More broadly, however, the large majority of historically used habitat is not accessible to anadromous fi sh, and the presently restricted distribution of the ESUs keeps them at elevated risk of extinction. Further improvements in the status of chinook salmon and steelhead may require access to currently inaccessible habitat. MORE INFO? [email protected]

TAKE HOME POINTS

• Only tiny remnant populations are left. We are going to have to do some creative thinking about Moderate Extinction Risk how to preserve ESUs. Extinct Low Extinction Risk • Eighty percent of our stream Data Deficient reaches are now behind impass- Not Historically An able barriers. Independent Population RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP WORK TO BE DONE

“The future of the Bay and its Baylands depends on watershed restoration to control the quantity and quality of local water and sediment supplies vital to the

Bay and Bayland ecosystems. The challenge is to put the Bay, its Baylands, and watersheds together again.”

—Josh Collins, SFEI

“We need to better explain, in economic

terms, why protecting the natural

environment is important to solving [our]

other problems. Our job is to become the

evangelists who put the environmental

ethic into the economic equation.”

—Will Travis, BCDC

Kite photo of the newly graded Codornices creek channel by Chris Benton STATE OF THE ESTUARY 2006 WORK TO BE DONE California’s Marine Invasive Species Program

MAURYA FALKNER industry representatives are CALIFORNIA STATE LANDS regularly convened to inform COMMISSION MARINE INVASIVE SPECIES PROGRAM management strategies. Two MONITORING COMPLIANCE In October 1999, California TAGs are currently formulat- enacted the fi rst statewide manda- ing recommendations on new REPORTED BALLAST WATER MANAGEMENT - 2004 issues for the program; ballast tory ballast water management law COMPLIANT water treatment technology 9% designed to prevent or reduce the NON-COMPLIANT introduction and spread of nonindig- standards; and management 8% enous aquatic species via ships’ ballast of aquatic nuisance species water into California state waters. through vessel fouling. In areas where priority information NO DISCHARGE While the program’s initial focus was 83% on foreign ballast water management, gaps have been identifi ed, during the 2003 Legislative session the the program provides limited law was reauthorized and is evolv- logistical and fi nancial support. Projects have included ing into a multi-faceted program that SOURCES OF NONCOMPLIANT BALLAST WATER - 2004 more comprehensively pursues the onboard testing of ballast water treatment technolo- CANADIAN WATERS prevention of nonindigenous aquatic 1.4% species via the commercial shipping gies, research on open ocean CARIBBEAN PACIFIC WATERS WATERS exchange verifi cation, and 4.8% CENTRAL AMERICA vector. The program melds educa- 0.7% WATERS research on the vessel fouling OTHER tion and outreach with enforcement 0.6% 19.9% 68 efforts, resulting in compliance rate risk for the Pacifi c Coast. ATLANTIC WATERS 0.1% levels exceeding 90 percent. Stake- Finally, the program maintains a database that has tracked GULF WATERS holder involvement has become inte- 0.2% gral to policy development. Technical ballasting practices of vessels entering California since 2000. MEXICAN WATERS Advisory Groups (TAGs) consisting 72.4% of scientists, regulators, and shipping The system contains a valuable time series of data that can be used to advance the TAKE management of invasives and HOME research in the fi eld. POINTS MORE • The potential for expanding INFO? [email protected] invasions is high.

• We are particularly concerned about voyages within the Paciﬁ c THE MARINE INVASIVE SPECIES ACT OF 2003 Coast region because of the “The purpose of the Act is to move the state expeditiously toward the potential for spread of the Chi- elimination of the discharge of nonindigenous species into the waters of nese mitten crab, the chame- the state or into waters that may impact the waters of the state, based leon goby, the Asian clam, and on the best available technology economically achievable.” the striped barnacle.

• Looking to the future, we hope to improve compliance, improve performance standards, focus on non-ballast water ship-medi- ated vectors, and continue research into treatment technologies. RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP Are We Preventing the Introduction WORK TO BE DONE of Exotic Species?

ANDREW COHEN sites, and pests. Decisions about a. SAN FRANCISCO ESTUARY INSTITUTE how to manage aquaculture should not be left to the industry; we need Exotic species have altered the to involve more effective stakehold- species composition, habitats, food ers. webs, population dynamics, and other aspects of the San Francisco Estuary. On the positive side, because Exotics comprise most of the species, we have made such little progress individuals, and biomass across many in controlling invasives, there is a habitats, making this one of the most lot we can still do. There has been invaded estuaries in the world. A 1995 agreement for a long time that ex- review found that hull fouling, ballast otics were a big problem—but not water discharges, aquaculture activi- agreement in a forum where deci- ties, and ﬁ sheries releases were the sions are made about what to do. most important mechanisms introduc- b. ing exotic species to the Estuary, with MORE INFO? [email protected]; lesser contributions from bait imports, www.exoticsguide.org biocontrol releases, restoration activities, and others.

Studies have also shown that in recent decades, exotic species have 69 been arriving and becoming established in the Estuary at an increasing rate, with ballast water discharges responsible for an increasing share of the introductions. Have our efforts to implement mechanisms for preventing c. the introduction of exotic species into the Estuary worked? Has signifi - cant progress been made? While the reports are reassuring, if you read the fi ne print, many ships are exempted from the new ballast water exchange laws. There is no good method of testing a ship’s ballast water at the end of a voyage. At best, we may be removing 70 to 85 percent of the organisms in the ballast water, but a true fi gure might be closer to 25 to 50 percent. Hull fouling is another big problem. In one study, a large tuna fi shing ship a) Green Crab, Carcinus maenas from Africa that came through the b) Bryozoan, Cryptosula pallasiana, Panama Canal was covered from stem c) Red Beard Sponge, Clathria prolifera to stern with hundreds of species of hydroids. We have not begun to tackle this enormous problem. Aquaculture is also good at moving diseases, para- STATE OF THE ESTUARY 2006 WORK TO BE DONE Non-native Spartina Control in the Estuary

ERIK GRIJALVA The downside: accidental spraying SAN FRANCISCO ESTUARY of non-target plants carries a higher INVASIVE SPARTINA PROJECT likelihood of damage than with glypho- Introduced in the 1970s to control sate. Laboratory tests also indicated a erosion, Atlantic cordgrass (Spartina slight risk to fi sh at highest concentra- alternifl ora) spread rapidly throughout tions. But based on the rates at which the Estuary, hybridized with Pacifi c it will be used in an application, it is cordgrass (Spartina foliosa), and today extremely unlikely that there is a risk threatens thousands of acres of tidal to fi sh. Despite imazapyr’s promise, marshes and restoration projects cordgrass may still be a tough adver- around the Bay. At the outset of the sary, however. Some weed species, 2005 Spartina control season in the including perennial ryegrass and rigid San Francisco Estuary, the Invasive ryegrass, have evolved resistance to Spartina Project (ISP) mapped and the terrestrial version of the chemical, delineated 132 individual areas of marketed as Arsenal and Chopper. varying sizes infested with non-native MORE Spartina. In sum, over 1,200 net acres INFO? [email protected] of Spartina were targeted for control, spread over roughly 11,000 acres of tidal marshland. At least 32 of these 70 infested sites are restored marshlands, and many of the other sites are remnant or historic marshes that are assumed to serve as native propagule Lisa Krieshok sources for planned restoration efforts planning efforts, while providing pre- in the Bay. treatment baseline information as a comparison for post-treatment effects Building upon the knowledge on the systems involved. gained through the successes and setbacks of the 2004 Spartina control In the 2005-2006 treatment TAKE season, the 3rd International Spartina season, the ISP switched to imazapyr HOME Conference held in San Francisco (Habitat), recently registered for use POINTS in November 2004, the ISP’s 2003 in California. A recent report from Le- • In 2004 surveys, we saw a 250 Spartina Monitoring Report, and work son and Associates that summarizes percent increase in non-native to date in other Spartina-infested laboratory and fi eld studies describes spartina from 2001-2003. The areas worldwide, the ISP determined imazapyr as both more effective invasion consisted mostly of that aggressive targeting of all Spar- and less hazardous than glyphosate. hybrids with varied and diverse tina-infested areas within the Estuary Among the report’s fi ndings: ima- genoytopes that can colonize in 2005 was warranted. This control zapyr degrades rapidly in water and anywhere. effort was preceded by a comprehen- inundated soil, leaving no detectable sive survey of the infested habitats for residue after two months; maximum • The greatest threats are to populations of endangered California planned application rates are not toxic mudfl ats and restored tidal clapper rails and an analysis of the po- to mammals, birds, or bottom-dwell- marsh. tential impacts of the various proposed ing organisms; and exposure risks to treatment methods on each individual workers applying the herbicide and to • We have a chance to do some- site. The results of this work informed the general public are minimal. thing right now—to control the timing and strategy of treatment it—before the invasion becomes even worse. RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP WORK TO BE DONE Alien and Native Fish in the Lower San Joaquin River Watershed

LARRY BROWN provide a basis for U.S. GEOLOGICAL SURVEY assessing possible Sacramento Sucker, Illustration: Bill Crary outcomes of rehabilitation efforts. Changes in land and water use in River. In contrast to the lower San the San Joaquin River watershed, as In a comparison of 20 major rivers Joaquin River watershed, the lower well as the deliberate and accidental across the United States, the lower Sacramento River watershed still introductions of alien species begin- San Joaquin River had the highest supports relatively large populations ning in the mid-1800s, profoundly percentage of alien fi sh species (70 of native fi shes, possibly because the changed the aquatic fl ora and fauna percent) and the highest percentage of river channels are used as throughput in this region of California. Studies alien fi sh captured (over 90 per- water delivery systems, thus main- over the last decade in the lower cent) based on data col- taining higher, cooler fl ows than in the mainstem San Joaquin River lected from 1993 to San Joaquin River watershed, where and its tributaries have 1995. Detailed water is diverted from river channels provided much useful analysis of a for off-channel uses. These studies information on the fi sh comprehensive suggest some level of predictability assemblages of the region data set from 20 sites in the response of fi sh assemblages and have identifi ed some of the in the lower San Joaquin to environmental change. However, environmental factors associ- Tule Perch River watershed sampled Illustration: Bill Crary there are likely unknown interac- ated with their distribution during the same time tions between alien and native fi shes, 71 and abundance. Those studies period indicates the presence of four major fi sh assemblages, between fi shes and non-fi sh species, with native fi shes most abundant in and between fi shes and environmen- TAKE the reaches of tributary rivers just tal conditions that make predictions HOME below the large foothill dams. Envi- regarding rehabilitating native fi sh POINTS ronmental conditions below the dams populations uncertain. • The lower San Joaquin River were more similar to conditions in MORE INFO? [email protected] watershed is highly invaded— the streams favored by many of the both compared to other rivers native fi shes, compared throughout the United States to environmental condi- and throughout California. tions in downstream reaches. Analysis of • Native species persist below the annual monitoring data dams. collected from 1987 to 1997 from eight sites • The success of invasive spe- on the lower Tuolumne cies is related to a number of River indicated that the environmental factors, including abundances of native fl ow, temperature, and land use. and alien fi shes captured at a site were associated Carp, Illustration: Bill Crary • The potential for increasing with springtime fl ow conditions and native fi sh populations seems distance from the San Joaquin River. high, but there is also a high Alien fi shes accounted for a greater potential for unexpected out- percentage of the catch when fl ows in comes because of unanticipated the previous year were relatively low interactions between native and and at sites closer to the San Joaquin alien species. STATE OF THE ESTUARY 2006 WORK TO BE DONE What Do The Next Stewards and Scientists: Forty Years Hold the Imperative for Collaboration For The Estuary? JERRY SCHUBEL ENVIRONMENTAL DECISION-MAKING JOE BODOVITZ AQUARIUM OF THE PACIFIC VALUE CHAIN CALIFORNIA ENVIRONMENTAL TRUST For most of my profes- Action Objective Subjective sional career I have attempted Noise Signal Value to Decision-Makers The state of the Estuary is, to identify, develop, and apply Calculation Judgement literally, the state of California. strategies to facilitate the Wisdom San Francisco Bay and its twin, collaboration of scientists the Delta, both lie within one with the decision-makers state jurisdiction. But they are by and stakeholders who are Knowledge no means identical twins, and we so critical to environmental have not treated them as if they sustainability. The invest- were. Information ments of hundreds of millions Data We have made greater progress of dollars in major coastal with the Bay than with the Delta. clean-up and restoration In 2005 we marked the fortieth initiatives too often have failed anniversary of the beginning of • A regional approach to to meet stated goals and stakehold- the San Francisco Bay Conserva- fi nding solutions, that is: tion and Development Commis- ers’ expectations. It is clear that new sion. And we note the work of institutional mechanisms are needed. - Scalable to fi t the issues the CALFED Bay-Delta program There is a better way—one success- - Inclusive and transparent 72 to resolve some of the most dif- ful model that has emerged over my fi cult issues in California—how more than three decades as a student - Futuristic in its orientation to protect and restore the Delta and practitioner is an “environmental while simultaneously providing decision value chain” that has the fol- • Functional institutional mecha- water for agriculture and for the lowing elements: nisms at the regional level, and expanding population of urban California. • Proper valuation of the • An informed, involved, CALFED needs the same resources at risk concerned public. broad public support and MORE understanding that the Save INFO? [email protected] San Francisco Bay Association brought to the campaign to stop the uncoordinated fi lling of San TAKE • We need new approaches and new Francisco Bay in the 1950s and HOME institutional mechanisms for har- early 1960s. Most residents of POINTS vesting what we know. the Bay Area now understand the importance and value of the • Restoration and conservation of • We spend over $100 million a year Bay. Unfortunately, most resi- the Bay-Delta are not limited by a telling the public why agriculture is dents of California do not have lack of scientifi c understanding, but important but less than 10 percent the same understanding of the by a lack of a clear and compelling of that on why oceans and estuaries Delta. vision, and institutional mechanisms are important. Nobody can look forty years to exploit the data and knowledge ahead and tell us what to ex- we have. pect. But we can already see the • Solutions to our current environmental problems depend on our shapes of some things to come: • The evolution of our scientifi c ability to imagine and shape the the possible eff ects of global understanding has outstripped our climate change; the possible future. ability to apply it. eff ects of rising sea levels; the continuing struggles over water • Policies are experiments. We’ve • We need a compelling vision, a supply and water quality; and made a lot of mistakes. We need to proper valuation of resources, a the need for better governance learn from them and move on. of the common resources of the regional approach that is futuris- Delta. tic, and appropriate institutional mechanisms. RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP WORK TO BE DONE to address water quality, species pro- when federal funding is on a down- Where Are We tection, fl ood management, hydrol- ward projection? New bond acts and Headed in the ogy, ocean conservation, and other local/regional funding initiatives will issues if we are to meet restoration be required. The Napa River/Ruth- Next Ten Years? and protection goals for the Estuary. erford benefi t assessment district is a With the creation of the California good example of such a local /regional NADINE HITCHCOCK Ocean Protection Council, the devel- initiative. CALIFORNIA COASTAL CONSERVANCY opment of new incentives to integrate MORE water resources management on a INFO? [email protected] Thanks to the passage of several regional scale, and a greater interest voter-approved state bond acts in in working collaboratively with new recent years, public agencies have partners, we have been able to work in partnership with an unprecedented LIKELY DELTA RESTORATION PROJECTS BY 2015 non-governmental organizations, citi- opportunity to take WITH NO NEW STATE BONDS zen groups, and private foundations to a more seamless acquire over 30,000 acres of historic look at how to Baylands in the San Francisco Estu- manage the Estu- ary. Planning and engineering is now ary, its watersheds, well underway to determine how to and the ocean restore these areas to provide habitat resources to which for endangered species, waterfowl, it is connected. shorebirds, and other native wildlife, to improve water quality, and to How will we provide wildlife-oriented recreational fund future resto- opportunities to the public. During the ration work esti- 73 same period, much attention has been mated to cost over focused on the need to look up into $300 million in the the watersheds and out into the ocean next decade alone

TAKE Coastal Conservancy is funding tion projects in disadvantaged com- HOME several pilot restoration projects. munities such as the restoration of POINTS Yosemite Slough in Hunter’s Point, • A race is taking place around the Bay • In the next 10 years, more signifi cant San Francisco. between people acquiring land for historic tidelands will be restored preservation and those acquiring it • We need to develop a regional vision and enhanced, but there will be for development. for the landscape that identifi es lo- minimal new acquisitions. cal and regional funding sources. • The funding outlook for the next 10 • There will be more desalination years is grim. More needs are going • There is a general trend toward facilities built. to be completing for less funds. ocean ecosystem-based planning • There will be an increased focus on Politically, ecosystem restoration is and management. The California subtidal areas—eff orts include the often thought of as competing with Ocean Protection Council estab- Subtidal Goals Project, new tools traditional engineering projects, and lished in 2004 will have funding for to battle aquatic invasives (ballast there is increased support right now “ocean” projects, including subtidal water exchange and treatment), eel- for funding levee repair and fl ood restoration in the Bay. grass restoration, and native oyster control projects due to earthquake • Another general trend will be toward restoration. predictions as well as the recent natural disasters such as Hurricane watershed ecosystem-based plan- • Much more eelgrass habitat could Katrina. ning and management. The Bay Area be restored in the Bay. We could Watershed Plan—www.bayareawa- restore an estimated 22,000 acres; • Despite the poor funding outlook, tershedplan.net—will guide water- we now have only 2,600 acres. The we need to continue to do restora- shed restoration eff orts. STATE OF THE ESTUARY 2006 WORK TO BE DONE California Water Plan 2005: a Framework for Action

KAMYAR GUIVETCHI vision, mission, and goals for meeting reports regional water conditions and CALIFORNIA DEPARTMENT challenges of sustainable water use activities; it considers multiple future OF WATER RESOURCES through 2030 in the face of uncer- scenarios and their water demands; The Department of Water tainty. It has recommendations for and it describes an approach to im- Resources (DWR) has changed the decision-makers, resource managers, prove data management and analytical process for preparing the California water suppliers, and water-users. tools for future plan updates. And for the fi rst time, the water plan Water Plan and the information it Water Plan 2005 is summarized in includes a proposal for carrying out its contains. The Water Plan has become the Highlights document and present- recommendations. The plan provides a strategic document that describes ed in fi ve volumes: (1) Strategic Plan, a Framework for Action to stimulate the role of state government and the (2) Resource Management Strategies, progress now to ensure a sustainable growing role of California’s regions in (3) Regional Reports, (4) Reference and reliable water supply in 2030. This managing the state’s water resources. Guide, and (5) Technical Guide. The framework will focus and prioritize fi nal California Water Plan Update In preparing Update 2005, DWR state government’s water planning, 2005 was released in January 2006. sought the participation of California’s oversight, and technical and fi nancial water communities, responded to new assistance on several foundational ac- MORE INFO? [email protected], state laws, and, by working with an tions and initiatives. The Framework www.waterplan.water.ca.gov advisory committee, developed a new for Action also identifi es a number of approach to planning California’s wa- essential support activities needed to ter future. DWR signifi cantly expand- accomplish its foundational actions 74 ed the public forum for updating the and initiatives. California Water Plan by establishing a 65-member advisory committee and Water Plan 2005 contains water a 350-person extended review forum, data, information, and studies used to and seeking input from 2,000 other develop the strategic plan. It outlines interested members of the public. today’s water challenges and evolving water management responses; Water Plan 2005 provides Cal- it presents benefi ts and costs of 25 ifornia’s water communities with a resource management strategies; it

PLAN GOALS, STRATEGIES, AND ACTIONS

Vision Vital Economy Healthy Environment High Standard of Living

Initiatives for Reliability Implement Integrated Improve Statewide Regional Water Water Management Management Systems

Foundational Actions for Use Protect Support Sustainability Water Water Environmental Efficiently Quality Stewardship RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP WORK TO BE DONE A BASELINE FOR TIDAL MARSH GOALS Linking Wetlands PERCENT OF HABITAT GOALS 50 to Watersheds PERMITTED ANTICIPATED

JOSH COLLINS 40 SAN FRANCISCO ESTUARY INSTITUTE

Habitat stewards and scientists 30 have been working together to achieve the Baylands habitat goals set in 1999. 20 The size of Bayland restoration projects has increased, the fragmentation of habitats seems to be decreasing, 10 the suite of target habitats has broad- ened, and the amount of collaboration 0 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 2025 2030 on project design and assessment has grown. restoration projects. This is expected to ects comprise level two. Standardized This collaboration has fostered new improve project performance. A three- intensive monitoring to address critical ideas about tracking wetland health tiered approach to comprehensive wet- concerns and test specifi c hypotheses and restoration progress. Multi-disci- land assessment is emerging to support comprises level three. Public informa- plinary teams of technicians and man- project design and tracking. Regional tion management that enables data agers are more likely than before to habitat inventories comprise level one. sharing among regional centers is also give advice on and review the concep- Cost-effective rapid assessments of envisioned. The ongoing State Wet- tual designs and monitoring plans for ambient condition and selected proj- land Inventory, the California Rapid Assessment Method, the growing 75 number of intensive monitoring proto- • We need to set goals for restor- TAKE cols adopted by the Bay Area Wetland HOME ing riparian habitat just like we did Monitoring Group, and the continuing POINTS for wetlands — a “Riparian Habitat development of the Wetland Tracker Goals” project. • We need to embrace the idea that for coastal watersheds indicate signifi - the Baylands really are the edge of cant progress toward implementing the • Setting riparian goals could serve to the Bay (right now they are a kind assessment framework. integrate the science and policy of of “no man’s land”): they have fallen watersheds, wetlands, and estuarine This approach to regional habitat between watershed science and Bay protection. assessment—setting shared goals science. and developing a tiered approach to • Understanding the interactions • The future of the Bay depends on tracking progress toward the goals—is between fl uvial and tidal processes watershed processes. being adopted in other regions, includ- will be increasingly important. ing Elkhorn Slough, Humboldt Bay, • Sediment storage and transport are and the Great Salt Lake Ecosystem. • The interaction of fl uvial and tidal very important. Off -channel wet It is also being used to begin integrat- processes aff ects creek erosion, meadows once played a large role in ing the assessments of Baylands and fl ooding, sediment delivery to the sediment storage and transport, but watersheds in the Bay Area. Through Baylands and the Bay, dredging, fi sh we have lost most of them. the Napa Watershed demonstration passage, and the biodiversity of the project, habitat inventories, probabilis- system as a whole. • The natural functions of alluvial fans tic surveys of ambient condition, and and off -channel wetlands may need • Watershed restoration will need intensive assessments of restoration to be restored. to focus on sources, transport, and performance are being integrated into storage of sediment as well a single report of overall wetland health • Our challenge is to put the Bay, Bay- at the watershed scale. lands, and watersheds back together as water. again. Eff orts to restore each part MORE • We need to reconnect our water- INFO? [email protected] will otherwise fail expensively. sheds with the Bay. STATE OF THE ESTUARY 2006 WORK TO BE DONE San Joaquin River sistance. By the time Friant Dam was to be built, in the early 1940s, salmon Restoration Challenges counts were down to 3,000-5,000 per year. Friant’s fi rst long-term contract, RON JACOBSMA a river, but replacement water from in 1949, was a 40-year commitment FRIANT WATER USERS AUTHORITY the Delta comes in there to meet the to make water available for irrigation. exchange agreement with the histori- There was conscious recognition that The San Joaquin River between cal San Joaquin River water users, the there would be sections of dry river Friant Dam and the confl uence of Exchange Contractors. Parts of Reach and that salmon would be extirpated the Merced River can be broken up 4 are basically an overgrown ditch from the upper San Joaquin. This was into fi ve sections, each with unique with some agricultural drainage water reaffi rmed by a State Water Board challenges for restoration. There is coming in. Reach 5 has fl oodplain decision in 1959 as being in the public a live river for 37 miles below Friant habitat opportunities, but again there interest. The California Department Dam. You hear that water users divert are temperature issues—it’s a fl at-gra- of Fish and Game revisited the issue in 98 percent of the water, but that’s dient system in the hottest part of the the 1970s and recommended focus- not the case. On average 15 to 20 Valley. ing resources on improving existing percent of the water is released below salmon runs elsewhere instead of the the dam, much of it during fl ood fl ow The economy is a big concern to upper San Joaquin. years. Non-fl ood fl ow releases aver- our area, having relied on that water age approximately 116,000 acre feet supply for so long. Twenty-eight There are no easy answers to the per year out of an average run-off of districts in the Central Valley Project tensions on the San Joaquin River. approximately 1,700,000 acre feet per contract for Friant water. We serve NRDC’s lawsuit began in 1988. We year. Flood fl ows average in excess about one million acres, 15,000 small worked with the plaintiffs for four of 200,000 acre feet per year. In late family farms in the top three agricul- years to fi nd a way to restore the river summer and early fall, more water is tural counties of the nation. Forty without adversely impacting Friant 76 released from Friant Dam than would percent of the city of Fresno’s water water supplies. We had some pilot occur in nature. supply comes from the Friant diver- projects but did not reach a settlement. sion, and smaller cities like Orange A back-of-the-envelope analysis pro- Reach 1, the live river, has been Cove and Lindsay are even more de- jected that around $650 million would impacted by gravel mining operations; pendent. We deliver about 1.4 million be needed for river improvements, there are temperature, sedimentation, acre feet per year to our contractors, even before developing alternate water and predator issues. Reach 2, a very leaving 100,000 acre feet to that 37 supplies. One option would be on- porous area, dries up; most of the miles of river. Class 1 districts along stream storage upstream of the dam. water fl ows through a bypass dur- the foothills with little or no ground- Our concerns are a loss of 20 to 50 ing fl ood events. A fi sh ladder would water have a fi rm supply; Class 2 percent of our water supply and water have to be put in at Mendota Dam to districts further down the valley have development costs potentially in excess restore that reach. Reach 3 looks like active conjunctive use programs. of $1 billion.

Friant is not the only dam Without getting into the lawsuit, SAN JOAQUIN RIVER WATERSHED on the system; there are eight Friant is engaged in a lot of activi- ABOVE FRIANT DAM others, most built earlier. The ties, including a possible water quality upper reservoirs are maintained exchange program with Metropolitan. by Southern California Edison, We want to work with river groups the bottom two by PG&E. to improve the water quality on the Friant came into being after lower San Joaquin River. We want groundwater levels dropped to look at upper San Joaquin River drastically and tens of thou- storage basins. And we are very much sands of acres of fertile farm- interested in restoration opportuni- land were taken out of produc- ties that won’t devastate our regional tion. Friant was a cornerstone economy. of the California Water Plan, MORE which ended up being built INFO? [email protected] and structured with federal as- RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP WORK TO BE DONE Low Dissolved Oxygen in the Tidal San Joaquin River ALAN JASSBY, ET AL. exports on San Joaquin fl ow into UNIVERSITY OF CALIFORNIA, DAVIS the ship channel—for example, by preventing discharge down Old River The Stockton Deep Water Ship with a barrier or by using an isolated Channel, a stretch of the tidal San conveyance facility to supply the Joaquin River, is frequently subject to water projects—markedly reduces low dissolved oxygen conditions and hypoxia in the ship channel. annually violates regional water quality objectives. Hypoxia is most com- Upgrades to the Regional Waste- mon during June through September water Control Facility, to be complet- immediately downstream of where ed in 2006, will not eliminate the im- the river enters the ship channel. pact of wastewater loading but should Underlying mechanisms are examined signifi cantly reduce the incidence of here using the long-term water qual- low dissolved oxygen. Although activi- ity data, and the effi cacy of possible ties are also underway to identify and solutions using time-series regression manage nonpoint sources of nutrients models. fueling algal growth in the San Joaquin River, very challenging levels of reduc- At the annual scale, ammonium tion will be required to have an impact loading from the Regional Wastewater on summer-fall hypoxia in the ship Control Facility has the largest iden- channel. tifi able effect on year-to-year vari- 77 ability. The longer-term upward trend MORE INFO? [email protected] in ammonium loads, which have been increasing over 10 percent per year, also corresponds to a longer-term downward trend in dissolved oxygen during summer. At the monthly scale, MAIN MECHANISMS CONTROLLING STOCKTON SHIP CHANNEL DISSOLVED O IN TIME SERIES MODEL river fl ow, loading of wastewater 2 ammonium, river phytoplankton, ship channel temperature, and ship channel Lag Channel DO – phytoplankton are all signifi cant in + determining hypoxia. Over the recent + historical range (1983–2003), waste- Wastewater DO River DO water ammonium and river phyto- Demand Demand – + plankton have played a similar role in ++ the monthly variability of the dissolved Temperature + oxygen defi cit, but river discharge has Wastewater River Load Channel Flow the strongest effect. Load Lag + +– + Model scenarios imply that control of either river phytoplankton or Chlorophyll wastewater ammonium load alone +– would be insuffi cient to eliminate hypoxia. Both must be strongly reduced, Solar River Flow Exports or reduction of one must be combined with increases in net discharge to the ship channel. Model scenarios also imply that decreasing the impact of STATE OF THE ESTUARY 2006 WORK TO BE DONE

Managing Water Quality ton Dissolved Oxygen TMDL and in the San Joaquin River Basin CALFED Directed Action Project. These projects have, for the fi rst time, created an opportunity for basin-wide NIGEL QUINN AND the west-side tributaries to the San water quality modeling and forecast- TRYG LUNDQUIST Joaquin River. Those included sele- BERKELEY NATIONAL LABORATORY ing to minimize real-time excursions nium-affected agricultural land as part of the dissolved oxygen concentra- of the Grassland Bypass Project and Adaptive real-time water quality tion in the Stockton Deep Water Ship seasonal wetland drainage in CAL- management is a strategy for improv- Channel. The long-term goal of this FED-sponsored projects located in ing water quality conditions in an effort is to replace the piecemeal and the Grassland Water District and San impaired water body by providing confl icted TMDL approach to water Luis National Wildlife Refuge. The real-time (immediate) access to fl ow quality management and water data, disseminating river latest implementation of the adaptive real-time water quality management MORE assimilative capacity forecasts using INFO? [email protected] computer-based simulation models strategy is contained in the Stock- and implementing control strategies. The technique is particularly relevant STOCKTON DEEP WATER SHIP CHANNEL 02 DEFICIT to the San Joaquin River Basin where Basin Plan Objectives water quality objectives and regula- 10 9 Measured Dissolved Oxygen - Rough & Ready Island tory constraints on fl ow and contami- 8 Dissolved Oxygen Deficit nant loads are often in confl ict and 7 lead to sub-optimal utilization of river 6 assimilative capacity. In the case of 5 contaminants such as dissolved solids, 4 78 boron, and selenium these ineffi cien- 3 2 cies have led to frequent violation 1 of Regional Water Quality Control Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Board objectives, especially during dry 2001 Model Year TMDL Dissolved Oxygen Deficit is 1,000,000 lbs. and critically dry years. Average daily dissolved oxygen deficit is 10,000 lbs. for 100 days.

We have conducted several experiments over the past decade using adaptive real time water quality TAKE • Agricultural districts implementing HOME real-time water quality manage- management. These experiments POINTS have been interagency collaborations ment should collaborate with regu- that have clearly demonstrated that • When given an incentive, agricul- latory entities to develop interim improved cooperation and coordina- tural districts can decrease their targets and load objectives—creat- tion of agricultural, municipal, and pollutant loads. ing a transition period during which wetland drainage return fl ows with the districts can adapt to the new east-side reservoir releases has un- • One way to do this is to temporarily program. realized potential for improving river store contaminant loads, releasing • We need additional monitoring water quality. As the Water Quality these contaminants during higher stations, more timely and accurate Subcommittee of the San Joaquin fl ow when there is adequate river information from local managers, River Management Program, we assimilative capacity. a decision support coordinator for conducted the fi rst phase of experi- the watershed, and agreements mentation, which concentrated on the • Forecasts of river water quality that recognize the experimental main stem of the San Joaquin River are necessary for real-time water and cooperative spirit of a real time and its major tributaries, and contin- quality management to be prac- water quality management system. ued for a period of fi ve years. During ticed – this can help to guide real- time remedial actions. this period a number of supplemental • Current real-time management projects were initiated that focused on projects may be the model for major contributing watersheds among future basin water quality management. RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP WORK TO BE DONE Climate Change Impacts Sierra Nevada. The reasons behind these contradictory results are higher on the San Joaquin River Basin temperature predictions by the latest GCM runs and almost neutral changes SEBASTIAN VICUNA AND future changes in temperature, pre- in precipitation. JOHN DRACUP cipitation, and other climatic variables UNIVERSITY OF CALIFORNIA BERKELEY based on the interactions between the Using these latest GCMs results land, atmosphere, and oceans. Hydro- to run a hydrologic model (VIC) and Climate change has the poten- logic models then use these changes a water resources model (CalSim) for tial to impact hydrology and water to predict climate change impacts on California, we conclude that these resources throughout the world—and natural runoff. Finally, water resources changes will potentially affect the per- California. Some regions in California, models are used to transfer these formance of the infrastructure in the like the Sierra Nevada mountains, are changes in natural runoff into changes San Joaquin River basin, limiting its especially vulnerable to these impacts in water deliveries and impacts to availability to meet all water resources due to their dependence on snow the water resources systems. There objectives, like water deliveries, accumulation and snowmelt, two have been a vast number of research energy generation, and environmen- processes especially susceptible to activities in the last 20 years that have tal services in the Bay Delta and San changes in temperature. This poten- attempted to assess the impacts of cli- Joaquin River. mate change on California’s hydrology tial risk looks even more relevant if MORE we consider changes in the timing of and water resources systems. These INFO? [email protected]; streamfl ow that are already happening studies have used different GCMs and [email protected] in the Sierra Nevada as suggested by hydrologic or water resources models various studies. at various levels of complexity, but all TAKE of them consistently predict a change HOME The prediction of future climate in timing in streamfl ow runoff due to POINTS 79 change impacts on California hydrol- a consistent increase in temperature. • Climate change is already ogy and water resources is based However, changes in the winter run- happening, as trends in hydro- primarily on the use of General Circu- off are still uncertain, mainly due to logical conditions in the West lation Models (GCMs), which predict uncertainties in precipitation predic- show. tions. The message taken from these studies is simple: there will be more ASSESSING CLIMATE CHANGE • The latest general circulation IMPACTS IN WATER RESOURCES water when we don’t need it and less model output shows greater when we need it. negative impacts on California GHG Emission Scenarios When comparing the relative hydrology and water resources impacts of climate change for different than in previous assessments. General Circulation Model regions in California, most of these studies have shown that the impacts • Impacts will be higher by the Changes in Temperature will be higher in the northern (e.g. end of the century and in the and Precipitation American River) than in the southern southern Central Valley. (e.g. Merced River) Sierra Nevada. Hydrologic Model:VIC • It is important to consider not This is a result consistent with mea- just average results but also sured historical streamfl ow trends and Changes in Runoff impacts during extreme relates to the relative altitude of the conditions. Water Resources Model: basins located in these two regions CalSimII (the high altitude basins in the south- • Models show that we may have ern Sierra Nevada being less affected more water when we don’t want Changes in Reservoir Deliveries by increases in temperature). How- it — early in the Spring —and less ever, recent modeling results suggest later on when we need it more. Economic - Ecological that an opposite effect might happen: Models i.e., impacts could be much higher in • We need to take climate the southern as compared to northern Final change into account in future Impacts management of the Estuary. STATE OF THE ESTUARY 2006 WORK TO BE DONE

Can We Restore Healthy River dams, diversions, and land use on the San Joaquin River have been more Functions to the San Joaquin? severe than on other Sierra Nevada rivers. SCOTT McBAIN to support a species assemblage that McBAIN AND TRUSH includes anadromous salmonids? It is The snowmelt-dominated a challenging task for a river that has hydrograph characteristic of larger Can the mainstem San Joaquin experienced dramatic physical and Sierra Nevada rivers once supported River downstream of Friant Dam, the hydrologic changes since the 1850s, spring- and fall-run Chinook salmon, southern Central Valley’s complement because the cumulative effects of and likely other anadromous ﬁ sh to the Sacramento River, be restored species. While ﬂ oods still occur on

EVOLUTION OF A REACH OF THE SAN JOAQUIN RIVER OVER TIME, CONCEPTUAL

80 RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP WORK TO BE DONE occasion under regulated conditions, channel is indistinguishable from old MORE INFO? most of the other natural hydrograph sloughs, agricultural canals, and drains. [email protected] components have been eliminated, Anadromous salmonids can re- and in some reaches the aquifer has turn, although the challenges will be been severely depleted, water quality TAKE considerable. Furthermore, improving is poor, channel capacity reduced, and HOME healthy river function and the biota POINTS several reaches of the river are peren- supported by that function faces many nially dry. Sediment supply from the • The restoration plan (developed scientifi c and technical uncertain- upper watershed has been eliminated, as part of settlement negotia- ties. How do we reestablish under and the channel has been mined, con- tions in 2001-2003) was devel- highly regulated conditions a cold fi ned, and bypassed. In one reach, the oped to “expeditiously evaluate water anadromous instream and related measures fi shery that must that will restore natural ecologi- migrate through a cal functions and hydrologic and complex system of geomorphic processes of the diversions, pumps, San Joaquin River below Friant and fl ood bypass- Dam to a level that restores and es? How do we maintains fi sh populations in rehabilitate geo- good condition, including but morphic processes not limited to naturally repro- in a system with ducing, self-sustaining popula- lower than average tions of Chinook salmon.” channel slope and sediment supply • Rehabilitation of a riparian compared to other 81 fl oodway has been done on Sierra Nevada other Central Valley streams; rivers? Answers therefore, it can also be done to these questions on the San Joaquin River. will require additional predictive • Slope is a signifi cant constraint modeling, yet will to restoring geomorphic pro- also require more cesses on the San Joaquin River experimental re- in the gravel bedded reach leases and adaptive immediately downstream of management. To Friant Dam. Levees, land use, provide the physi- and changes to the groundwa- cal forces needed ter table are signifi cant con- to restore natural straints to restoring geomorphic processes, and processes in the sand-bedded consequently anad- reaches. romous salmonid habitat, high fl ow • Other scientifi c uncertainties releases will need include temperature modeling to be re-operated. results and salmonid thermal Solutions will also tolerances, how to re-estab- need to incorpo- lish and route extirpated fi sh rate creative water species, ecologically signifi cant operations, channel restoration scale (e.g., what size reconstruction, and shape does the riparian and other mechani- corridor need to be ecologically cal solutions. meaningful to key indicator species), and others. STATE OF THE ESTUARY 2006 WORK TO BE DONE

When, Not If SAN JOAQUIN RIVER FLOWS WERE FLATLINED 20,000 GARY BOBKER 19,000 Average hydrograph for normal years; average yield = 1,680,294 acre-feet THE BAY INSTITUTE 18,000 17,000 WY 1962; Modeled Unimpaired Yield = 1,924,000 acre-feet 16,000 WY 1962; actual regulated yield = 75,000 acre-feet There was a time when the 15,000 San Joaquin River dominated the 14,000 13,000 southern half of the San Joaquin 12,000 Valley and was a major contributor of 11,000 10,000 infl ow to the Delta. It is now a pale 9,000 shadow of its former glory. Histori- 8,000 Discharge (cfs) cally the main stem San Joaquin was 7,000 6,000 a snowmelt driven system support- 5,000 ing some of the biggest salmon runs 4,000 3,000 on the West Coast, up to 500,000 2,000 spring run spawners and 100,000 fall 1,000 0 run spawners. Healthy runs persisted Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep as late as the 1940s when Friant Dam was built. Both runs were extirpated in 1948 with the closure of the dam Peter Moyle at UC Davis and Matt gates. After 1948, fl ow in a represen- Kondolf at UC Berkeley have made tative year dropped from 1.9 million a set of recommendations for restor- acre feet to 75,000 acre feet of regu- ing the San Joaquin that recognize lated yield. Below the confl uence with that pristine conditions will not be 82 the Merced, most of the water in the reestablished and consumptive use of San Joaquin is agricultural drainage. most of the river’s water will continue. The river’s loss of assimilative capacity These include base fl ows of 350 cubic aggravates water quality issues—salt, feet per second for most of the year boron, and dissolved oxygen. with higher spring and fall pulses. The TAKE HOME result, 15-20 percent of unimpaired In 1988, the Natural Resources POINTS runoff, would be comparable to cur- Defense Council, the Bay Institute, rent fl ows on the Merced, Tuolomne, Strategies for replacing some of and other groups fi led suit to restore and Stanislaus. Impact on Friant’s the water now diverted from the the San Joaquin salmon runs, cit- customers could be addressed through river include: ing Fish and Game Code language groundwater banking and other strate- requiring suffi cient water passing over, gies. Moyle and Kondolf also recom- • Implementing groundwater around, or through a dam to main- mend some modifi cations to channels, banking and conjunctive use tain fi sh populations below the dam. levees, and fi sh ladders. The courts have rejected claims that • Re-operating Friant and other the state’s liability to meet the Code We’re not going to get the old river reservoirs requirements has been extinguished. back. But we’re at a tipping point, and After the US Supreme Court declined the thinking has changed. If the river • Using market transfers, includ- to hear the case, the plaintiffs entered is wet, fi sh will want to recolonize it. ing long-term, dry year options settlement talks with Friant. These We are going to have people fi shing, ended without agreement and the hiking, and canoeing on a restored San • Increasing water use effi ciency parties returned to court. Subsequent Joaquin. • Recapturing water downstream rulings held that the operation of Fri- MORE of Friant Dam ant Dam violates the state Fish and INFO? [email protected] Game Code and the Endangered Spe- • Expanding existing surface cies Act. As this report went to press, storage the Judge was deciding whether to adopt a settlement or proceed to trial. • Building new surface storage RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP WORK TO BE DONE

TAKE Re-inventing the Delta: HOME a Call for a New Vision POINTS • The Delta is no longer the MARCI COGLIANESE of industrial, commercial, and retail remote, sparsely populated FORMER MAYOR OF RIO VISTA space. Between 1990 and 2002 an backwater it was 10 years ago additional 12,000 acres of Secondary Only fi ve years after the CALFED when CALFED began. Urban- Zone farmland (including 8,000 acres Record of Decision was signed, key ization is accelerating, fed by designated “prime”) were converted stakeholders in the water and envi- the need to house the state’s to an urban land use designation. ronmental communities are calling burgeoning population. for another new vision for the Delta, When all currently approved one that will endure. Assuming that development is built out, urban land • The Delta is a critical cross- it is possible to design and implement uses in the Secondary Zone will have roads between the Bay Area a long-term plan for an ecosystem as doubled, expanding from one-quarter and the Central Valley. complex and dynamic as the Delta’s, of the zone’s total acreage in 1993 to • Every day a “Tower of Babel” how shall we arrive at a durable new one-half. With the diminishing ability of government agencies infl u- vision for the future? of the Secondary Zone to serve as a ences the Delta without a buffer, the Primary Zone will experi- Water, agriculture, recreation, and shared vision or understanding ence increasing “edge” confl icts along the environment, traditionally identi- of the Delta’s problems. its ag-habitat-urban fringes, further fi ed as key Delta interests, are well- threatening the delicate balances of a represented in the statewide debate • The time is ripe for a broader fragile ecosystem and impacting the about the Delta’s future and would examination of all state poli- continued viability of Delta agricul- all be expected to be a critical part cies aff ecting the Delta. ture. 83 of the new vision. But where do the dozens of Delta-area special districts, • We need a serious discus- cities, and counties, along with local sion of state and local growth landowners, fi t into the process? Not policies such as permitting traditionally engaged as stakeholders, development behind levees Delta-area local governments in six and on fl oodplains. counties are making land use decisions • The fundamental problem with without a common vision and without the Delta is that state gov- recognition of the potential impact to ernment is not supplying the unique resources of statewide impor- leadership needed to deal with tance. hard problems. The six coun- The Secondary Zone of the Delta, ties in the Delta have fallen Science has an important role to as defi ned in the 1992 Delta Protec- through the cracks. play in researching and illuminating the tion Act, is urbanizing in response to impacts of urban development upon the same growth and development • The Delta needs a unifying Delta resources. Without scientifi c pressures being experienced through- force to bring us together. It data, the politically charged issue of out the state. At one time largely is a region without a leader, land use in and around the Delta can- undeveloped, it has served as the without leadership. not be successfully addressed nor can buffer between urban development a durable new vision for the future be • As the governor tries to and the essential resources of the achieved. Delta local governments are refocus CALFED, I urge him to Delta’s Primary Zone. But since 1993, necessary stakeholders in the visioning think broadly and bring local local governments have approved process. governments, state legislators, development on over 44,000 acres and scientists together with in the Secondary Zone, resulting in MORE INFO? water interests. 94,000 new residential units (includ- [email protected] ing thousands of new houses behind • Solutions cannot be imposed levees), and thousands of square feet on the Delta. They must be supported from within to be sustainable. STATE OF THE ESTUARY 2006 WORK TO BE DONE

Economically, housing costs, have to endure terrible Where Do We the Bay is our traffi c congestion, and have to toler- Go from Here? region’s most valu- ate so-so public schools. able resource. It Yet the workers continue to move is the highway for WILL TRAVIS here and stay here because it is a ter- the ferries that can SAN FRANCISCO BAY CONSERVATION rifi c place to live. It has a sensational AND DEVELOPMENT COMMISSION lace our water- quality of life, a lot of which comes front communities from the abundant, beautiful, and Despite our progress in saving and together. The Bay is essential to our healthy natural resources we environ- restoring the Bay, we need to make fl ourishing maritime industry. The Bay mentalists work so hard to protect. a renewed commitment to continue is the equivalent of a national park We are providing the best fringe ben- these efforts in a language most peo- in our front yard where we can sail, efi t Bay Area employers can offer. We ple understand––economics. At a re- swim, fi sh, kayak, and play. And it is may not be able to charge them for it. cent dinner I attended of the Bay Area essential to our tourist industry. Council—a coalition of the biggest But we can remind them how much it employers in the region—there was no is worth. mention of the word “environment” “The decision to save except in the context of the “business TAKE the Bay in 1965 laid HOME environment.” Nor was there any POINTS mention of the word “Bay”—except the foundation for the as in “Bay Area.” economic prosperity our • We need to fully engage in the political process and explain I wondered how the folks at the region has enjoyed over how protecting the Bay-Delta dinner could just ignore the Bay. the past four decades. environment is critical in 84 Then I realized that it isn’t so much making decisions about where that they have forgotten the Bay; it The Bay is probably the new California residents will is that we spend all our time talking best fringe benefi t Bay live, and how they will com- to ourselves. We insist in speaking Area employers can mute. We need to join groups in science––a language few people like the Greenbelt Alliance in understand. As a result, we are mar- offer—the equivalent advocating for infi ll develop- ginalizing ourselves out of the regional of a national park in our ment and drawing the line on political debate. It is inevitable that our front yards where we places where we simply cannot region’s population will grow by about develop. a million people over the next 15 years. can sail, swim, fi sh, Those of us who are concerned about kayak, and play.” • We need to better explain, in the Bay need to fully engage in the po- economic terms, why protecting litical process of deciding where these the natural environment is im- one million new residents will live and The Bay is the heart, soul, and portant to solving problems like work, how to build housing they can visual icon that gives our region its traffi c and housing. Otherwise, afford, and how our new neighbors name, its unique quality, and its those concerned purely with can travel from home to work to identity as a truly special place. The economic issues are more likely school without spending most of their decision to save the Bay in 1965 laid to advance their campaigns lives in traffi c jams. And in this politi- the foundation for the economic pros- than we are. cal debate, we need to better explain, perity our region has enjoyed over the in economic terms, why protecting past four decades. The Bay Area de- the natural environment is important pends on bright, well-educated, inno- to solving these other problems. Our vative workers to make our economy job is to become the evangelists who hum. In competing with other regions put the environmental ethic into the for these workers our employers don’t economic equation. pay appreciably higher salaries even though the workers face outrageous RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP BIG PICTURE, WARNING BELLS

ACRONYM KEY

AMP: Adaptive Management Plan BCDC: (San Francisco) Bay Conservation and Development Commission CALFED: CALFED Bay-Delta Program CANOD: California Aquatic Non-native Organism Database CEMAR: Center for Ecosystem Management and Restoration CEQA: California Environmental Quality Act CVP: Central Valley Project DIP: Delta Improvement Package DFG: California Department of Fish and Game DHS: California Department of Health Services DWR: California Department of Water Resources ESU: Evolutionarily Signifi cant Unit GCM: General Circulation Model GGNRA: Golden Gate National Recreation Area IEP: Interagency Ecological Program IRWM: Integrated Regional Wetland Monitoring Program ISP: Invasive Spartina Project MLML: Moss Landing Marine Lab MWD: Metropolitan Water District of Southern California NEPA: National Environmental Policy Act NMFS: National Marine Fisheries Service NOAA: National Oceanic and Atmospheric Administration NOS: National Ocean Service OEHHA: California Offi ce of Environmental Health Hazard Assessment 85 Bibliography PBDE: Polybrominated Diphenyl Ether PEEIR: Pacifi c Estuarine Ecosystem Indicator Research PRBO: PRBO Conservation Science, formerly Point Reyes Bird Observatory PWA: Philip Williams & Associates RCD: Resource Conservation District SBSP: South Bay Salt Pond Restoration Project SFBBO: San Francisco Bay Bird Observatory SFBCDC: San Francisco Bay Conservation and Development Commission SFBJV: San Francisco Bay Joint Venture SFBRWQCB: San Francisco Bay Regional Water Quality Control Board SFEI: San Francisco Estuary Institute SFEP: San Francisco Estuary Project SFSU: San Francisco State University STRAW: Students and Teachers Restoring a Watershed SWP: State Water Project SWRQB: State Water Resources Control Board TBI: The Bay Institute TMDL: Total Maximum Daily Load UC: University of California USF: University of San Francisco USACOE: United States Army Corps of Engineers USBR: United States Bureau of Reclamation USDA: United States Department of Agriculture USEPA: United States Environmental Protection Agency USFWS: United States Fish and Wildlife Service USGS: United States Geological Survey STATE OF THE ESTUARY 2006 BIG PICTURE, WARNING BELLS

PRESENTATIONS* Hanak, Ellen, Public Policy Institute of Orr, M., C. May, P. Williams, PWA, M. California. California 2025: Putting the Lionberger, D. Schoellhamer, USGS, S. Anderson, S.L., G.N. Cherr, S.G. Morgan, Estuary into the Big Picture. Rottenborn, R. Duke, H.T. Harvey & Asso- R.M Higashi, W.A. Bennett, S.L. Ustin, UC ciates, D. Stralberg, M. Herzog, PRBO, S. Davis, R.M. Nisbet, A. Brooks, UC Santa Hancock, Russell, Joint Venture: Silicon Ritchie, South Bay Salt Pond Restoration Barbara. Do Contaminants Harm Estua- Valley Network. How the Economic En- Project. Tools for Assessing Landscape- rine Habitat Quality? Just Ask the Fish! gine of the Bay Area is Changing: Implica- Scale Habitat Changes in Wetland Resto- tions for Environmental Stewardship. ration Planning. Bobker, Gary, The Bay Institute. When, Not If: The Friant Case and Its Implica- Herzog, M., N. Nur, D. Stralberg, L. Liu, N. Pawley, Anitra, C. Swanson, P. Vor- tions for Restoring the San Joaquin River Warnock, PRBO, K. Tuxen, M. Kelly, UC ster, The Bay Institute, R. Hoenicke, and the Bay-Delta. Berkeley. Response of Birds to Vegeta- B. Thompson, SFEI. Indicators for San tion, Habitat Characteristics, and Land- Francisco Bay: “Scorecard” Update, New Bodovitz, Joe, California Environmental scape Features in Restored Marshes. Developments, and Linkages to Regional Trust. Forty Years Since BCDC’s Cre- and National Eff orts. ation: What Do the Next Forty Hold? Hitchcock, Nadine, California Coastal Conservancy. Looking to the Future: Quinn, Tim, MWD. The Role of Science in Brodberg, Robert, California Environ- Where Are We Headed in the Next Ten the Estuary. mental Protection Agency. Fish Adviso- Yea rs? ries and You. Ritchie, Steve, South Bay Salt Pond Res- Huning, B., S. Scoggin, SFBJV. SFBJV: toration Project. Evaluating Restoration Brown, L.R., USGS. Alien and Native Fish Successes in Protecting and Restoring Success: The Human Angle. Assemblages of the Lower San Joaquin the Bay. River Watershed. Schroeter, R.E., P.B. Moyle, UC Davis. Hutzel, A., T. Gandesbery, California Aquatic Community Structure and Pro- Cain, John R., Natural Heritage Institute. Coastal Conservancy. North Bay Restora- ductivity of a Large Brackish Tidal Marsh Dutch Slough: The Promise of Restora- tion: Napa Salt Ponds and Hamilton in the Upper San Francisco Estuary: The tion and the Challenge of Adaptive Airfi eld. Relative Contribution to the Estuarine Management. Food Web and Insights into Restoration Jacobsma, Ron, Friant Water Users Benefi ts. Callaway, J.C., University of San Fran- Authority. San Joaquin River Restoration cisco, L.M. Schile, M.C. Vasey, V.T. Parker, Challenges. Schubel, J.R., Aquarium of the Pacifi c. San Francisco State University. Elevation, Stewards and Scientists: The Imperative Inundation, and Vegetation: Implications Jassby, A.D., UC Davis, E. Van Nieuwen- for Collaboration. for Restoration. huyse, USBR. Low Dissolved Oxygen in the Tidal San Joaquin River: Mechanisms Siegel, Stuart, Wetlands & Water Re- Cochrane, S., City of Oakland, M. 86 and Models Based on Long-Term Time sources. Long-Term, Large-Scale Wetland Lariz, Stevens and Permanente Creeks Series. Monitoring in the SF Estuary: Needs and Watershed Council, M. Latta, Save SF Prospects. Bay Association, W.M. Lee, Golden Gate Johns, G.E., DWR. Water Planning in National Parks Conservancy, S. Mendel, the Delta: A Case Study in Management Simenstad, C., E. Howe, J. Toft, Universi- Don Edwards San Francisco Bay National Adaptability. ty of Washington, S. Bollens, Washington Wildlife Refuge. State of the Stewards, A State University Vancouver. Food Web Discussion about Volunteer Eff orts. Kelly, Maggi, UC Berkeley. Prospects for Sources and Pathways in Restoring Tidal Wetland Restoration in San Francisco Wetlands: Will They Benefi t the Bay? Coglianese, Marci, City of Rio Vista. Re- Bay: A Landscape Ecology Perspective. Inventing the Delta: The Call for a New Sommer, T., A. Mueller-Solger, M. Vision. Kimmerer, W.J., J. Durand, Romberg Ti- Nobriga, DWR, C. Armor, R. Baxter, P. buron Center for Environmental Studies, Coulston, DFG, M.Chotkowski, USBR, B. Cohen, A.N., SFEI. Progress on Prevent- San Francisco State University. Searching Herbold, USEPA. Where Have All of the ing the Introduction of Exotic Species. for Clues to Declines in the Delta Pelagic Pelagic Fishes Gone? Food Web. Collins, J.N., SFEI. The Next Generation Travis, W., BCDC. Tying All the Loose of Restoration Planning: Linking Wet- Lindley, S.T., R. Schick, R.B. MacFarlane, Ends Together: Where Do We Go from lands to Watersheds. NOAA, B.P. May, UC Davis, J.J. Ander- Here? son, University of Washington, S. Greene, Faber, P.M., Phyllis M. Faber and Associ- DWR, C. Hanson, Hanson Environmen- Trulio, Lynne A., San Jose State Uni- ates. P. Williams, J. Lowe, PWA , G. Davis, tal, Inc., A. Low, D. McEwan, DFG, C. versity. The Role of Science in Guid- The Bay Institute. Lessons Learned: Swanson, The Bay Institute, J.G. William. ing Restoration Design and Adaptive Design Guidelines for Tidal Wetland Status of Chinook Salmon and Steelhead Management. Restoration in the Bay. in the Central Valley and San Francisco Bay. Vicuna, S., J.A. Dracup, UC Berkeley. Cli- Falkner, M.B., California State Lands mate Change Impacts on the San Joaquin Commission. On the Front Line of Lundquist, T.J., N.W.T Quinn, Berkeley River Basin: Evidence from the Historic Prevention – California’s Marine Invasive National Laboratory. Adaptive Real-Time Record and Predictions for the Future. Species Program. Management of Water Quality in the San Joaquin River Basin. Whiteside, Carol, Great Valley Center. Geupel, G.R., N. Nur, R. Cormier, J.N. Challenges of the San Joaquin. Wood, C. Howell, PRBO. Using Birds to McBain, S.M., McBain and Trush, Inc. Can Assess Response to Habitat Restoration We Restore Healthy River Function on Wilcox, Carl, DFG. South Bay Restora- in the San Joaquin Valley. the San Joaquin River? tion: Bair Island, Eden Landing, and South Bay Salt Ponds. Grijalva, Erik, San Francisco Estuary Mount, J.F., UC Davis. The Serial Engi- Invasive Spartina Project. Current Status neering of the Delta: Can It be Stopped? Zuckerman, Tom, Central Delta Water of Non-Native Spartina Control in the Agency. Delta Perspective on the Delta Estuary. Nur, N. PRBO, P.R. Baye, Annapolis Field Improvement Package. Station. Evaluating Restoration Success Guivetchi, Kamyar, DWR. California Wa- from the Perspective of Plants and ter Plan 2005: A Framework for Action. Animals. RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP BIG PICTURE, WARNING BELLS

POSTERS* Avent, S.R., S.W. Siegel, J.R. Kulpa, T. Cassa, M.R., SFBRWQCB. Groundwater- Carson, C. Toms, Wetlands and Water Surface Water Interaction: An Emerging Abbaspour, P., A. Robinson, N. Nur, Resources. Field Methods and Implica- Issue in Regulatory Decision-Making and M. Herzog, L. Liu, N. Warnock, PRBO. tions for the Planning and Management Resource Management. Nest Characteristics and Breeding of the Sears Point Restoration Project. Success Castillo, G, USFWS, K. Fleming, M. Dege, in Tidal Marsh Song Sparrows. Bergendorf, D., A. Marrone, USFWS. R. Mayfi eld, DFG. Population Status of Caulerpa: A Threat to the San Francisco Threatened Delta Smelt in the Sacra- Ackerman, J., USGS ,T. Adelsbach, C. Bay Ecosystem. mento-San Joaquin Estuary. Eagles-Smith, USFWS. Growth Rates of Forster’s Tern Chicks at Three Nesting Bergendorf, D., J. Lewis, USFWS. Imple- Chartrand, S., E. Ballman, B. Hecht, Colonies in the San Francisco Bay. menting a National Management Plan for Balance Hydrologics, Inc., Estimation the Genus Eriocheir (Mitten Crabs). of Passage Flows for Anadromous Fish Ackerman, J., J. Takekawa, C. Marn, through Critical Riffl es in Stevens and USGS. Survival of American Avocet and Bergendorf, D, J. Herod, USFWS, S. Coyote Creeks, Santa Clara County, Black-Necked Stilt Chicks in the South Bynum, Scientifi c Principle, Inc. Boater California. San Francisco Bay: Variable Risks of Gull Assessment in California: Understanding Predation. a Potential Pathway for Zebra Mussels Choi, A., S.E. Kegley, B. Hill, S. Orme, (Dreissena polymorpha) and Other Non- Pesticide Action Network North Amer- Andrew, M.A., S.L. Ustin, UC Davis. Native Species. ica. Water and Pesticides Information Spectral and Physiological Uniqueness Center: Tools for Exploring Relation- of Lepidium latifolium. Best, E.P.H, H.L. Fredrickson, US. Army ships between Pesticide Use and Water Engineer Research and Development Quality Impairments. Andrews, D., Seattle Public Utilities. Center, H. Hintelmann, B. Dimock, Trent Seattle’s Natural Drainage Systems University. Tidal Wetland Restoration at Choi, K.-H., W. Kimmerer, D. Marcal, – Implementing Green Infrastructure the Hamilton Army Airfi eld Site on San Romberg Tiburon Center for Environ- to Manage Stormwater across an Urban Pablo Bay: A Mass Balance Approach to mental Studies, San Francisco State Landscape. Mercury. University. Mate Limitation as a Barrier for Invasions of Zooplankton to the San Andrews, E.S., S. Bozkurt, B. Vallé, PWA. Bluso, J.B, M.A. Colwell, Wildlife Depart- Francisco Estuary. Locating a Remnant Central Valley Land- ment, Humboldt State University, J.Y. scape: Frequently-Flooded Floodplains. Takekawa, J.T. Ackerman, USGS. Space Cocherell, D., A. Kawabata, S.Hamilton, Use of Foraging Forster’s Terns (Sterna L. Kanemoto, J. Webber, D. Kratville, J.J. Andrews J., M. Craig, M. Rajan, B. forsteri) in South San Francisco Bay, Cech, Jr., E.K. Anderson, Z.Q.R. Chen, Mooney, B. Barnett, A. Florance, L. California. H. Bandeh, K. Carr, M. Cayar, I. Haltas, Hoang, M. Khan, Z. Khan, E. Letteney, M.L. Kavvas, UC Davis, C. Wilkinson, M. California State University, East Bay. Briggs, A., Romberg Tiburon Center for McGee Rotondo, R. Padilla, R. Church- 87 Continuous In-Situ Monitoring of East- Environmental Studies, San Francisco well, DWR. A Fish Ladder for Adult ern San Francisco Bay. State University. Mitochondrial COI White Sturgeon? Preliminary Results Analysis of an Invasive Copepod. Arp, A., Romberg Tiburon Center for (A): Passage Effi ciency. Environmental Studies, San Francisco Brosnan, J, Sonoma Land Trust, S.W. Cocherell, D., A. Kawabata, S.Hamilton, State University, A Center for Environ- Siegel, L. Kanemoto, J. Webber, D. Kratville, J.J. mental Research, Education and Com- C. Toms, Wetlands and Water Resources, Cech, Jr., E.K. Anderson, Z.Q.R. Chen, munity Outreach on San Francisco Bay. Inc., R. Leventhal, Far West Restora- H. Bandeh, K. Carr, M. Cayar, I. Haltas, tion Engineering, P. Baye, Coastal Plant Asbury, D., G. Becker, Center for Ecosys- M.L. Kavvas, UC Davis, C. Wilkinson, M. Ecologist, J. Vollmar, Vollmar Consulting. tem Management and Restoration, R.A. McGee Rotondo, R. Padilla, R. Church- Stakeholder-Driven Wetlands Restora- Leidy, EPA, B.N. Harvey, UC Davis. Maps well, DWR.A Fish Ladder for Adult tion Planning: Indicating Historical Distribution and White Sturgeon? Preliminary Results The Sears Point Restoration Project. Current Status of Oncorhynchus mykiss (B): Stress During Passage. in Streams of the San Francisco Estuary, Brusati, E, D. Johnson, California Collins ,W., K. Rhynass, G. Rathwell, California. Invasive Plant Council. Which Weed to Quester Tangent, B. Jaff e, T. Fregoso, V. Whack? Asbury, D., G. Becker, A.J. Gunther, Tomlin, J. Thompson, F. Parchaso, USGS, Invasive Plants of Greatest Ecological Center for Ecosystem Management and S. Sullivan, Sea Surveyor Inc. Map- Concern in California. Restoration. Monitoring of Migrating ping South San Francisco Bay Seabed Diversity. Steelhead (Oncorhynchus mykiss) with an Burau, J.R., K. Taylor, USGS, P. Orton, Internet-Based Video Camera. IBM Center for Advanced Learning. Conaway, C.H., D.J. Steding, A.R. Flegal, Transport in the Delta. Athearn, N.D., K. Goodenough, J.Y. UC Santa Cruz, R.P. Mason, University of Maryland. Estimate of Mercury Emission Takekawa, G.G. Shellenbarger, A.K. Byington, A., K. Coale, Moss Landing Miles, M.K. Saiki, S. Spring, F. Mejia, from Gasoline and Diesel Fuel Consump- Marine Laboratories, G. Gill, K. Choe, tion, San Francisco Bay Area, California. D.H. Schoellhamer, USGS. Napa-So- Texas A&M. Photo-degradation of noma Marshes Pond 3, Hydrologic and Methyl Mercury in the Sacramento-San Davies, S.B., D.M. Talley, J.C. Kooser, Biotic Changes in a Salt Pond Following Joaquin Delta. J.E. Schneider, M. Vasey, T.T. Reed, Breaching. San Francisco Bay National Estuarine Callaway, J.C., USF. Sediment Dynamics Research Reserve. An Introduction to Austin, C., SFBRWQCB, T. Grieb, K. in San Francisco Bay Salt Marshes. Summers, Tetra Tech, Inc. Mercury in the the San Francisco Bay National Estuarine Guadalupe River Watershed: Conceptual Cassa, M.R., SFBRWQCB. Investigation Research Reserve. Model and Regulatory Approach. and Control of Contaminated Ground- Davis, J.A., J.A. Hunt, SFEI, T. Adelsbach, water Discharges to Surface Water in USFWS, D. Crane, DFG, D. Hoover, the San Francisco Bay Region. AXYS Analytical Services Ltd. Monitor- ing Legacy and Emerging Pollutants at the Top of the San Francisco Bay Food Web. STATE OF THE ESTUARY 2006 BIG PICTURE, WARNING BELLS

Demers, S., M. Colwell, Humboldt State Grenier, J.L., J. C. Collins, SFEI. An In- Jaff e, B., A. Foxgrover, J. Takekawa, N. University, J. Takekawa, J. Ackerman, tegrated Wetlands Assessment Program Athearn, USGS, A. Hutzel, California USGS. Space Use of American Avocets in for the San Francisco Bay Area and Coastal Conservancy, J. Hubbard, M. South San Francisco Bay. California. Samant, C. Martin, G. Hovis, NOAA National Oceanic Service, S. Sullivan, Demgen, F., L. Autie, P. Mineart, URS Gross, E.S., Environmental Consultant, Sea Surveyor, C. Vickers, TerraPoint Corporation. Peyton Slough Remediation M.L. MacWilliams, Environmental Con- Canada Inc., S. Newby, TerraPoint USA Removes It from the Bay Area List of sultant, W.J. Kimmerer, Romberg Tiburon Inc. Integrated LIDAR and Bathymetric Toxic Hot Spots. Center for Environmental Studies, San Surveys of the South San Francisco Bay Francisco State University. Simulating Region: New Data for Salt Pond Restora- Doctor, D.H., S.R. Silva, C. Kendall, C.C.Y. Salt Intrusion into Suisun Bay and the tion Planning. Chang, USGS, J. Hench, Stanford Univer- Western Delta. sity, W.E. Fleenor, UC Davis. An Investiga- Jeff res, C.A., UC Davis. Rapid Growth of tion of Low Dissolved Oxygen Conditions Grossinger, R.M, R.A. Askevold, SFEI, C. Juvenile Chinook Salmon (Oncorhynchus in the San Joaquin River Using Stable Richard, Oakland Museum of Califor- tshawytscha) on Central Valley Flood- Isotopic Techniques. nia. Baylands and Creeks of South San plains with Prolonged Inundation. Francisco Bay: A Publicly Accessible Downing, J., City of San Jose. Fate and Map Reveals the Landscape and Cultural Jensen, J.M., P. G. Green, UC Davis. Transport of Mercury in the San Jose/ Context for Restoration. Distribution of Mercury in Salicornia Santa Clara Water Pollution Control and Spartina across a Contaminated Salt Plant. Grosso, C., J.R.M. Ross, S. Lowe, D. Yee, Marsh. A. Franz, P. Stevanovic, SFEI. Facilitating Dunlavey, E., P. Schafer, City of San Jose. the Exchange and Reporting of Monitor- Johnson, C., USFWS. Evaluation of Endo- Seasonal Trends of Copper in the Lower ing Data. crine Disruption on Splittail (Pogonich- South San Francisco Bay. thys macrolepidotus) in Sacramento-San Guignard, J., S. Schubert, DFG. San Joaquin Estuary. Durand, J., W. Kimmerer, Romberg Tibu- Joaquin River Basin-Wide Water Tem- ron Center for Environmental Studies, perature Monitoring/Modeling Project, Jones, G., J. Miranda, S. Chun, J.J. Cech, San Francisco State University. Determi- and Use of the HEC-5Q Water Tem- Jr., UC Davis. Swimming Performance In nants of Seasonal Abundance in Key Zoo- perature Model as a Management Tool Exercise-Conditioned, Cultured Delta plankton of the San Francisco Estuary. on the Lower San Joaquin River and its Smelt. Tributaries. Eagles-Smith, C.A., T.L. Adelsbach, Jones, N.L., S. G. Monismith, Stanford J. D. Henderson, T. Maurer, USFWS, Herod, J.J., H.N. Blalock-Herod, P.D. Cad- University, J.K. Thompson, F. Parchaso, J.T. Ackerman, S.E. Schwarzbach, rett, USFWS. Considerations Regarding USGS. Horizontal, Vertical and Temporal T.H. Suchanek, G.H. Heinz, J.Y. Takekawa, Non-Native Fishes and Adaptive Manage- Variability of Phytoplankton in a Shallow 88 A.K. Miles, S.E. Wainwright-De La Cruz, ment Activities in the Sacramento and System, Franks Tract, San Francisco Bay. S.E. Spring, L. Bowen, J.D. Bluso, S.A. San Joaquin Delta. Demers, M. Ricca, C. Marn, M. Wilson, Jones, N.L., S. G. Monismith, Stanford USGS, C. Strong, SFBBO, N. Warnock, Hieb, K.A., DFG, T. Brown, USFWS. University, J.K. Thompson, F. Parchaso, PRBO. Mercury in Birds of the San Introduction of the Siberian Prawn, Exo- USGS. The Infl uence of Wind-Driven Francisco Bay-Delta: Trophic Pathways, palaemon modestus, to the San Francisco Waves on Vertical Transport, Grizzly Bay, Bioaccumulation and Ecotoxicological Estuary. San Francisco Bay. Risk to Avian Reproduction. Hosea, R.C., B.J. Finlayson, DFG. Con- Kelly, J.P., K. Etienne, M. McCaustland, Foss, S., P. Ode, M. Sowby, M. Ashe,. trolling the Spread of New Zealand Mud Cypress Grove Research Center, Audu- California Aquatic Non-Native Organism Snails on Wading Gear. bon Canyon Ranch, D. Stralberg, PRBO. Database (CANOD). Integrated Regional Wetlands Monitor- Howe, E.R., C.A. Simenstad, University ing (IRWM) Project: Landscape Use by Foxgrover, A., B. Jaff e, S. Higgins, M. In- of Washington. Estuarine Food Web Link- Herons and Egrets in the San Francisco graca, R. Smith, USGS. Long-Term Trends ages of Restored Tidal Wetlands in the Estuary. in Sediment Deposition and Erosion in San Francisco Estuary. South San Francisco Bay. Kirkland, M., R. Beckwith, T. Greene, Z. Hunt, J.A., B.K. Greenfi eld, J.A. Davis, Matica, DWR. Aquatic Restoration Plan- Gaines, S., L. Galal, T. Kendall, J. Lee, SFEI, R. Fairey, M. Sigala, MLML, D. ning in the Yolo Bypass Floodplain. F. Tabatabai, USACOE. The Role of the Crane, K. Regalado, L. Nguyen, DFG. US Army Corps of Engineers in Estua- PCBs, Hg, DDTs and PBDEs in San Fran- Kleckner, A.E., A.E. Parker, K. Lew, V.E. rine Restoration: A San Francisco Bay cisco Bay Sport Fish, 2003. Hogue, F. Wilkerson, Romberg Tiburon Perspective. Center for Environmental Studies, San Hwang, H-M., P.G. Green, T.Y. Young, UC Francisco State University. Temporal Gill, E.C., Alameda County Flood Control Davis. Monitoring of Priority Toxic Pollut- and Spatial Variability of Chlorophyll-a and Water Conservation District. Bank ants in Highway Stormwater Runoff . Versus Particulate Carbon and Nitro- Restoration of a Flood Control Channel gen Relationships in San Francisco Bay: in a Muted Tidal Marsh. Hwang, H-M., P.G. Green, T.Y. Young, UC Importance for Estimating Biomass and Davis. Historical Trends of Organic Con- Ecosystem Modeling. Green, G., Ducks Unlimited, B. Turner, taminants and Trace Metals in Salt Marsh, Wildlife Conservation Board, A. Hutzel, San Francisco Bay, California. Knittweis, G., K. Nelson, D. Ray, North California State Coastal Conservancy, Delta Programs, Division of Flood Man- L. Wyckoff , DFG. Napa-Sonoma Marshes agement. Enhancing Ecosystem Function Wildlife Area: Napa River Unit Restora- by Improving Levee Stability: Suisun tion Phase 1 — Lower Ponds 1,1a, 2, 3, 4, Marsh-Delta Project Summary. and 5. Kramer, S., L. Dusek, S. Kramer, S. Greig, D.J., F.M.D. Gullad, The Ma- Wilcox, Stillwater Sciences, M. Dietl, rine Mammal Center. Leptospirosis in USACOE. Annual and Seasonal Variation Stranded California Sea Lions: What is in Species Assemblages in Created and the Source of Infection? Restored Habitat, Napa River, California. RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP BIG PICTURE, WARNING BELLS

Kulpa, J.R., S.R. Avent, Environmental Malamud-Roam, F., L. Ingram, UC Moore, S.M., A. Senter, M. Cover, Data Solutions. Field Methodology and Berkeley. Sediment Source Study for SFBRWQCB. A Rapid Trash Assess- Summary of South San Francisco Bay Novato Creek Marsh in the San Francisco ment Method Applied to Waters of the Winter-Spring 2004 Monitoring Data. Estuary. San Francisco Bay Region: Region-Wide Results of Systematic Measurement of Langridge, S.M., UC Santa Cruz. Pests Marrone, A., L. Mclaughlin, USFWS. Trash in Streams. and Pest-Control at the Interface CALFED Non-Native Invasive Species between Restored Riparian Habitat and Program and Reference Collection. Moran, K.D., TDC Environmental, LLC. Orchard Crops in the Sacramento River Sources of Pyrethroids in Urban Runoff . Conservation Area. Martin, M., J. Fram, M. Stacey, UC Berke- ley. Seasonal Phytoplankton Exchange Nilsen, E.B., R. Rosenbauer, K. Kuivila, K. Langridge, S.M., A. Shattuck, M. Richards, between the Coastal Pacifi c and Central Smalling, F. Hostettler, USGS. Assessing UC Santa Cruz. Spatial Distribution of San Francisco Bay. Impacts of Anthropogenic Contaminants Weeds on Cropland Associated with on Sedimentary Microbial Communi- Large-Scale Restoration on the Upper May, C., P. Williams, G. Misra, M. Orr, ties and Organic Matter Composition in Sacramento River. PWA, M. Lionberger, D. Schoellhamer, South San Francisco Bay Using Organic USGS, S. Ritchie, SBSP Restoration Proj- Geochemical Techniques. Lawton, R., Sonoma Ecology Center. ect. Landscape-Scale Geomorphic Ef- Measuring Sediment in Jack London’s fects of Wetland Restoration Associated Opperman, J.J., P.B. Moyle, UC Davis. Streams: Historical Land Uses, Today’s with the South Bay Salt Pond Restoration Can Ecological Function Be Restored to Roads, and the Sonoma Creek TMDL. Project. Central Valley Floodplains? A Conceptual Model. Lebednik, P.A., P. Martos, LFR Levine- May, M., M. Delaney, T. Featherston, Fricke, K. Kobrin, The Nature Conser- E. Zhang, J. Collins, SFEI, A. Breaux, Orlando, J., J. Drexler, USGS. Elevation vancy, R. Lafrenz, EDAW, Inc., C. Law- SFBRWQCB, M. Martindale, USACOE, K. Ranges for Salt Marsh Plants In South San rence, CH2M Hill. Long-term Changes Tuxen, UC Berkeley. www.WetlandTrack- Francisco Bay. in Vegetation Related to Natural and er.org — The Wetland Project Tracker. Anthropogenic Environmental Factors in Owens, J., B. Hecht, S. Brown, S. Char- an Intermittently Tidal Brackish Marsh of May, M., T. Featherston, K. Larned, S. trand, Balance Hydrologics, Inc. Sedi- the Suisun Bay Watershed. Pearse, E. Zhang, SFEI. South Bay Salt ment Transport Trends in Watersheds of Pond Restoration Project Interactive the San Mateo Peninsula. Lehman, P.W., S. Waller, K. Gehrts, S. Map. Philippart, DWR, G. Boyer, State Uni- Parenti, M., L. Marshall, J. Gain, C. versity of New York, C. Hall, UC Davis. McCord, S., T. Dunham, Larry Walker Paulson, Brown & Caldwell, M. Marvin- Beauty and the Beast: The New Cyano- Associates, C. Engel, City of Woodland. DiPasquale, USGS, M. Stephenson, W. bacterial Bloom of Microcystis aeruginosa Yolo Bypass Water Quality Management Heim, MLML, K. Abu-Saba, Larry Walker in the San Francisco Estuary. Plan. Associates. South Bay Salt Pond Restora- 89 tion — Water Quality. Liu, L., N. Nur, M. Herzog, D. Stralberg, McCrea, B., C. Sweeney, SFBCDC. PRBO, J. Evens, Avocet Research Associ- Shoreline Spaces: Public Access Design Parker, V.T., L. Schile, M. Vasey, SFSU, J. ates. California Clapper Rail Population Guidelines for the San Francisco Bay. Callaway, USF. Comparative Vegetation Trends in the San Francisco Bay Estuary. Development in Diff erent Aged Brackish McGowan, M. F., H. E. Harris, Maristics. Tidal Wetlands along the Lower Napa Looker, R.E., SFBRWQCB, P.A. Lebednik, Native Oyster Restoration in San Fran- River, San Francisco Estuary, California. LFR Levine-Fricke, M. Brockbank, SFEP cisco Bay: Ecosystem Enhancement and and Association of Bay Area Govern- Conservation of Native Species. Paz, L., W. Carson, LFR Levine-Fricke. ments. Wetland Design and Management Seasonal Wetland Design Using a Simpli- Options for Control of Mercury in San McKee, L.J., SFEI. Characterization of fi ed Soil Moisture Accounting Model, Francisco Bay. Mercury Concentrations in Suspended Berkeley Meadow, Berkeley, California. Sediment Loads in Guadalupe River and Lowe, S., J.R.M Ross, C. Grosso, A. Franz, Coyote Creek, San Jose, California: Can Pearce, S., L. McKee, SFEI, C. Arnold, SFEI, D.L. Stevens Jr., Oregon State Uni- TMDL Targets Be Met? Contra Costa County Resource Conser- versity. Using a Spatially Balanced, Ran- vation District, L. Hokholt, USDA. Pinole dom Sampling Design to Assist Informed McLaughlin, L., J. Herod, USFWS, R. Creek Watershed Sediment Source As- Management Decisions. Fairey, MLML T. Light, Shippensburg sessment: A Sediment Budget Approach University, E. Grosholz, P. Moyle, UC Highlighting Watershed-Scale Sediment- Luengen, A., A.R. Flegal, UC Santa Cruz. Davis. Ecological Surveys of Non-Native Related Processes and Supply to the Bay. Contrasting Biogeochemistry of Six Trace Aquatic Species in the Sacramento-San Metals During a Spring Phytoplankton Joaquin Delta. Petrik, K., Ducks Unlimited, X. Wei, S. Bloom in San Francisco Bay. Scoggin, SFBJV. San Francisco Bay Joint McLaughlin, K., A. Paytan, Stanford Venture Habitat Project Tracking System. Lux, R., A. Warwas, H.N. Blalock-Herod, University, C. Kendall, S.R. Silva, USGS. USFWS. Characterization of Fish As- Phosphate Oxygen Isotope Ratios as a Phillips, J., I. Werner, UC Davis. Acute semblages within San Francisco Bay: Tracer For Sources and Cycling of Phos- and Sublethal Eff ects of Lambda Cyha- Implications for Biological Monitoring phate in North San Francisco Bay. lothrin on Early Life Stages of Chinook Strategies and Design of Habitat Restora- Salmon. tion Projects. Mejia, F., M. Saiki, USGS. Fish Species Assemblages in Selected Salt Ponds and Porter, S.A., S. Brown, B. Hecht, Bal- Mackay, K., K.M. Schwarz, Jones & Stokes Sloughs in South San Francisco Bay. ance Hydrologics, Inc. Geomorphic Associates. Survey of Current Restora- Field-Based Methods for Assessing the tion and Water Management Projects in Mierzwa, M., J. Wilde, B. Suits, DWR. Impacts of Hydromodifi cation on Stream the Napa River Watershed. Benefi ts of Multiple Conservative Water Channels. Quality Constituents in Historical and Madrone, A., A. Fatemen, Contra Costa Forecast Simulations. Redfi eld, T., N. Stein, J. 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Rippey, K., USACOE, T. Gandesberry, Showalter, P., S. Akin, D. Arnold, J. Ujihara, A., D. Lee, DHS, E. Silver, J. State Coastal Conservancy, J. Wondol- Abel, Santa Clara Valley Water District. Kaslow, M.L. Tan, S. Lee, Impact Assess- leck, CDM.. San Pablo Bay Watershed Fisheries and Aquatic Habitat Collabora- ment, Inc. Understanding and Reducing Restoration Program — Promoting Revi- tive Eﬀ ort: An Innovative Approach to Human Exposure to Mercury in the talization of the Watershed’s Wetlands, Resolving a Water Rights Complaint that California Delta Watershed. Rivers, Lakes, and Streams, and Improv- Balances Water Supply Operations and ing the Health of San Pablo Bay. Protects Fisheries for the Stevens Creek, Vasey, M., L. Schile, V.T. Parker, SFSU, K. Coyote Creek, and Guadalupe River Tuxen, UC Berkeley, J. Callaway, USF. Im- Roberts, T., D. Sicular, M. Lowe, Environ- Watersheds. pacts of Fire on Plant Species Diversity mental Science Associates. Salt Marsh in Two Brackish Tidal Wetlands along the Hydrological and Ecological Performance Showers, D., DWR and M. Philipp, DFG. Upper San Francisco Bay Estuary. Indicators 10 Years After Restoring Tidal Decker Island Habitat Development/Le- Action. vee Improvement Project. Wankel, S.D., C. Kendall, USGS, C.A. Francis, A. Paytan, Stanford University. Rogers, L., J Parodi, R. Hicks, B. Siegel, S.W., Wetlands and Water Re- Nitrogen Sources and Cycling in the San Dempsey, D. Hitz, E. Allen, The Bay sources, Inc, N. M. Kelly, UC Berkeley, V.T. Francisco Bay Estuary: A Nitrate Dual Institute. STRAW: Students and Teachers Parker, M. Vasey, E. Carpenter, R. Dug- Isotopic Composition Approach. Restoring a Watershed: A Project of the dale, F. Wilkerson, SFSU, C. Simenstad, Bay Institute. University of Washington, D. Stralberg, N. Warner, C., SFBJV. San Francisco Bay Nur, G. Page, PRBO, S. Bollens, Washing- Joint Venture Habitat Goals and Accom- Rogers, M., UC Berkeley, W. Stringfellow, ton State University, Vancouver, J. Lowe, plishments. Lawrence Berkeley National Laboratory. PWA, J. Callaway, USF, P. Bachand, Bach Meta-Analysis of West Stanislaus County and Associates, Inc., J.N. Collins, M. May, White, C., J. Owens, B. Mallory, D. Shaw, Pesticide Monitoring Studies: GIS Site SFEI. Integrated Regional Wetland Moni- B. Hecht, Balance Hydrologics, Inc. Bear Suitability Analysis for Agricultural Best toring Pilot Project — Overall Project Creek Water Quality Study, 1999–2002, Management Practices. Purpose. Woodside, San Mateo County, California.

Ruch, S.A., ReMetrix LLC, and California Siegel, S.W., T. Carson, C. Toms, S. Avent, Wilkerson, F.P., K. Lew, R. Dugdale, A. Department of Boating and Waterways Wetlands and Water Resources, Inc., Marchi, V. Hogue, F. Koch, Romberg Aquatic Weed Unit. Utilizing Diff erential P. Bachand, Bachand Associates, Inc, Tiburon Center for Environmental Stud- Quantitative Mapping Technologies and J. Lowe, PWA, J. Kulpa, Environmental ies, San Francisco State University. Daily Traditional Botanical Knowledge to Assist Data Solutions. IRWM Physical Processes Monitoring of Estuarine Water Quality Brazilian Waterweed Management in the Monitoring in Restored and Reference (Eutrophication and Phytoplankton Sacramento-San Joaquin Delta. Tidal Marshlands. Blooms) in San Francisco Bay. Sassone, E.R., W.A. Heim, A. Byington, Wood, M., C. Foe, G. Marquis, J. Cooke, 90 Spautz, H., Olofson Environmental, Inc. K.H. Coale, MLML, M. Stephenson, DFG. and SFEI, E.K. Grijalva, K. Zaremba, Central Valley Regional Water Qual- Habitat Makes a Diff erence: Methyl San Francisco Estuary Invasive Spartina ity Control Board. The Delta Mercury Mercury Export from Two Wetlands on Project, J. Albertson, Don Edwards San TMDL: Reducing Methylmercury in Fish Twitchell Island. Francisco Bay NWR, J.G. Evens, Avocet and Water. Research Associates. Invasive Spartina Woyshner, M., B. Hecht, Balance Hydro- Satkowski, R., California Water and Control Strategy: An Adaptive Manage- Environmental Modeling Forum. The logics, Inc., T. Yurovsky, SRT Consultants, ment to Minimize Impacts to the Endan- G. Irving, Montara Water and Sanitary California Water and Environmental gered California Clapper Rail. Modeling Forum: Promoting Excellence District. Spring-Supported Wetland and and Consensus in Water and Environmen- Stewart-Deaker, A., D. Katzev, J. Haltiner, Riparian Habitat, a Core for Managing tal Modeling. R. Battalio, PWA. Integration of Fluvial Bedrock Ground Water. and Coastal Flood Management with Schile, L., V.T. Parker, M. Vasey, SFSU, J. Yee, D., S. Lowe, J. Ross, SFEI, G. Scelfo, Wetland Restoration for the South Bay C. Conaway, UC Santa Cruz. Methyl- Callaway, USF. Non-destructive Methods Salt Ponds Restoration Project. for Estimating Productivity of Dominant mercury in San Francisco Bay Surface Vegetation in Tidal Marshes of San Fran- Strong, C.M., A. Jaramillo, SFBBO. Avian Sediments. cisco Bay, California. Use of a Managed Pond: A Case Study in Zaremba, K., San Francisco Estuary South San Francisco Bay. Sellgren, C., Contra Costa County Flood Invasive Spartina Project. 2004 Invasive Control and Water Conservation District. Talianchich, R., W. Kimmerer, Romberg Spartina Project Monitoring Program Rethinking Flood Control in the Lower Tiburon Center for Environmental Stud- Results. Walnut Creek Watershed in Contra ies, San Francisco State University, E.S. Costa County. *Titles within the Presentations and Post- Gross, Independent Consultant. Fish-X2 ers sections based on abstracts submitted Relationships Examined: A Behavioral Sellgren, C., Contra Costa County Flood prior to the conference. Some details may Particle Tracking Model for San Francisco have changed since then. For Cochrane Control and Water Conservation District. Estuary. Cultural Sensitivity In the Expansion of a presentation, see Lotta and Lee abstracts. Needed Stormwater Detention Basin. Tashjian, D.H., A. Sogomonyan, S.S.O. Hung, S.J. Teh, UC Davis. Bioaccumula- Sellgren, C., Contra Costa County Flood tion and Chronic Toxicity of Dietary Control and Water Conservation District. L-Selenomethionine in Juvenile White Preserving and Restoring Creeks and Sturgeon (Acipenser transmontanus). Providing Flood Protection in Pleasant Hill, California. Teh, S.J., D.F. Deng, G.H. Zhang, F.C. Teh, UC Davis. Eff ect of Dietary Methylmer- Shellenbarger, G.G., US Geological cury and Selenium on Splittail Larvae. Survey, A.B. Boehm, Stanford University. Potential Degradation of Water Quality Trivedi, D., H. Frank Du, Moff att & Nichol, by Bird Feces in and around Managed Robert Coats, Hydroikos Associates. Wetlands. Analyses of Cullinan Ranch Wetland Restoration Alternatives. RESTORING THE ESTUARY: SCIENCE AND STEWARDSHIP CREDITS

PUBLISHED BY The San Francisco Estuary Project and CALFED July 2006

To order additional copies, contact Paula Trigueros at the S.F. Estuary Project 1515 Clay Street #1400 Oakland, CA 94612 (510) 622-2499 [email protected]

REPORT CREDITS

SFEP PROGRAM MANAGER Marcia Brockbank

CONFERENCE DIRECTOR Karen McDowell

REPORT EDITOR Lisa Owens Viani 91

RESEARCH AND EDITING ASSISTANCE Joe Eaton Ron Sullivan

ILLUSTRATIONS Vital Statistics Section: Lisa Krieshok; graphics elsewhere as noted.

DESIGN Darren Campeau, www.dcampeau.com

THANK YOU to the CALFED Science Program for reviewing a draft of this report and providing financial assistance for publication.

Cover photograph and photo on page 26 courtesy of James A. Martin from Islands of San Francisco Bay, www. IslandsofSFBay.com

Section cover photographs courtesy of David Hart and John Sanger from San Francisco Bay: Portrait of an Estuary, University of California Press, 2003; www.sanfranciscobaybook.org STATE OF THE ESTUARY 2006 NOTEWORTHY

A Note to State of the Estuary Conference Participants

This report includes a mixture of original unpublished and published research presented at the October 2005 State of the Estuary (SOE) conference.

Thank you to all those who responded to our call for updated abstracts after the conference. The Estuary Project appreciates your ex- tra work in helping us put together this report. Due to budget and space constraints, information from some posters and presentations could not be included in this report, especially if not submitted in digital form as requested soon after the conference. Apologies to any of those we were not able to include. Informa- tion from all posters and presentations can still be found in the original conference abstract book.