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Home , Estuary, Joseph Alioto, Reber Plan

STATE OF THE ESTUARY 2002

SCIENCE & STRATEGIES FOR RESTORATION

San Francisco Sacramento- San Joaquin Delta Estuary

San Francisco Estuary Project & CALFED OPENING REMARKS

his Report describes the migrating along the Pacific Flyway tive state-federal effort, of which currentT state of the San Francisco pass through the Bay and Delta. Many U.S. EPA is a part, to balance Bay-Sacramento-San Joaquin Delta government, business, environmental efforts to provide supplies Estuary's environment -- , and community interests now agree and restore the in the , wildlife, watersheds and that beneficial use of the Estuary's Bay-Delta watershed. the . It also high- resources cannot be sustained without lights new restoration research, large-scale environmental restora- explores outstanding science ques- tion. tions, and offers management cues for those working to protect This 2002 State of the Estuary Report, 's water supplies and and its Posterbook appendix, summa- endangered species. rize restoration and rehabilita- tion recommendations drawn and the Delta from the 48 presentations and CONTENTS combine to form the West 's 132 posters of the October largest estuary, where 2001 State of the Estuary from the Sacramento and San Conference and on related Joaquin and watersheds flows research. The report also pro- Executive Summary ...... 2 out through the Bay and into the vides some vital statistics about STATE OF THE ESTUARY Pacific . In early the 1800s, the changes in the Estuary's Bay covered almost 700 square miles and wildlife populations, pol- Vital Statistics ...... 5 and the Delta's rivers swirled through lution levels and flows over the a vast Byzantine network of 80 - past three years, since the 1999 RESTORATION like and hundreds of miles of State of the Estuary report was pub- braided channels and . Back lished. Watershed ...... 17 then, almost a million fish passed through the Estuary each year and 69 The report and conference River-Delta ...... 25 million acre-feet of water crashed are all part of the San Francisco down from headwaters Estuary Project's ongoing ...... 35 toward the . But in 1848 the Gold efforts to implement its Rush began and hydraulic mining Comprehensive Conservation and Bay ...... 53 plugged the rivers and bays with more Management Plan (CCMP) for the than one billion cubic yards of sedi- Bay and Delta and to educate BIG PICTURE ...... 73 ments. Over time, farmers and city and involve the public in pro- builders filled up more than 750 tecting and restoring the BIBLIOGRAPHY ...... 77 square miles of tidal and engi- Estuary. The S.F. Estuary Project's CCMP is a consensus neers built dams to block and store To find the page number of a specific paper or author, the rush of water from the plan developed cooperatively by see the conference bibliography. into the Estuary, and massive pumps over 100 government, private and to convey this water to and community interests over a thirsty cities and farms throughout five-year period and completed the state. in 1993. The project is one of 28 such projects working to protect the Today's Estuary encompasses water quality, natural resources and roughly 1,600 square miles, drains economic vitality of estuaries across more than 40% of the state (60,000 the nation under the U.S. square miles and 47% of the state's Environmental Protection Agency's total runoff), provides drinking water , which to 20 million Californians (two- was established in 1987 through thirds of the state's population) and Section 320 of the amended Clean irrigates 4.5 million acres of farm- Water Act. Since its creation in land. The Estuary also enables the 1987, the Project has held five State nation's fourth largest metropolitan of the Estuary Conferences and region to pursue diverse activities, provided numerous publications including shipping, fishing, recre- and forums on topics concerning ation and commerce. Finally, the the Bay-Delta environment. In Estuary hosts a rich diversity of flora 2001, CALFED joined the Estuary and fauna. Two-thirds of the state's Project as a major sponsor of the and nearly half the birds conference. CALFED is a coopera-

1 STATE OF THE ESTUARY

EXECUTIVE accompanied by a recognition that Californians practicing a minimal SUMMARY "the objectives of any group or level of conservation managed to interest will not be achieved simply shave 10-14% off peak demand lev- (Reprint of an October 2001 by voicing unyielding denials of the els. "The regulators need to watch article in ESTUARY newsletter) objectives of others." Nichols closed the generators," he cautioned. by mentioning a number of chal- Eight hundred people lounged in lenges for the future, among them Shaving demand might also help the red seats of the Palace of Fine predicting what would be the with the global warming problem, Arts auditorium in San Francisco regional effects of local construction which the U.S. Geological Survey's this October to hear 48 experts or restoration projects; judging how Mike Dettinger described as just one present the newest research, the best non-lethal contamination levels in part of the region's long history of maps, the latest technologies, and the Estuary's invertebrates and fish climatic variability. As a result of the hottest debates over the affect the fish, wildlife, and humans warming, Dettinger predicted resources, health and restoration of who eat them; and overcoming the "fresher winters and saltier sum- the S.F. Bay-Delta Estuary. "reticence of our institutions to take mers," for the Bay, and less than a whole system approach." 25% of snowpack levels in some areas by mid-century. "In the past 1,000 years, there have been much drier centuries with 100 year "When I first started thirty years ago, we’d pull in 80 tons droughts and extreme periods. These old trends, superimposed by a day of garbage. People used the Bay as a dump. global warming impacts, promise Over the last 10 years, it’s gotten much cleaner." that major hydroclimatic changes threaten the Estuary in the near future," he said.

ERIC CARLSON Another threat will be earth- Retired Army Corps Debris Boat Captain quakes, said Mary Lou Zoback, also of the Geological Survey. Zoback spoke of a 60-70% chance of a First up at the podium was Further talks on urban challenges major earthquake shaking the Richard Katz, a member of the State followed, with Tom Schueler of region's bridges and before Water Resources Control Board, 's Center for 2030, but more ominously of the who hammered at the theme of good Watershed Protection reminding lis- likely return to the days before 1906 science leading to good policy. His teners that "the greatest threat to when the region experienced a mag- homework for the audience was to estuaries continues to be the con- nitude six quake every four years. stop just talking to each other in sci- version of natural spaces to car "The stress shadow of the 1906 ence speak and to get out and edu- ." He said research shows a quake created a docile environment cate "newbies" in the state assembly decline in sensitive species at about in the Bay Area," she said. "Future about how this ecosystem we are try- 30% impervious cover, a decline of quakes will be larger, closer together ing to save provides drinking water food variety and abundance at about and more costly." In terms of the to 20 million Californians and 15% and a rise in chronic coliform Estuary, they might not only wipe affects jobs and the economy. After (fecal) contamination at less than out some levees, but also release a the dose of political realism came a 10%. lot of old contaminants buried in little history from author Malcolm the soft Bay , she added. Margolin, who commented on how The water-energy connection was After lunch, the Point Reyes Bird impressive the knowledge level of then made by Peter Gleick of the Observatory's Nils Warnock spoke environmentalists attending such Pacific Institute - every acre foot of about factors affecting bird life in conferences had become. "Thirty- water we use costs about 2-3,000 the Bay today, among them habitat five years ago carrying a picket sign kilowatts of power, he said. "The changes (conversion of salt to and having a flimsy poetic idea was more water we save, the more energy ), proposed airport run- enough, but today's activists have we save," he said. Gleick debunked a ways, the spread of invasive cordgrass extraordinary scientific, political, number of popular "myths," among and contaminants. Some of the economic, and technological them that there are water and energy contaminants come from the birds' expertise," he said. shortages. He attributed both these problems not to a lack of the food - invertebrates, A coming of age also figured in resource, but to a shortage of and fish - whose status was surveyed the subsequent speech by the U.S. "intelligent management." He by Cal Fish & Game's Kathy Heib. Geological Survey's Fred Nichols, added that there were no rolling Heib said a long-term shift from a who noted that progress made in black outs in the summer of 2001 warm to a cool ocean climate has such things as reducing the impacts not because, as the TV ads would benefited some species, like chinook of raw sewage and learning about the have us believe, we've quickly built salmon and English sole, but not Estuary's natural processes has been new power plants but because others. A plant that is not benefiting

2 Executive Summary

anyone, however, is exotic Atlantic a snake adrift on a clump of peat Some of the substrate is so low cordgrass and it's hybrids, which moss. that restoration via such processes as Peter Baye of U.S. Fish & Wildlife microbial decomposition is fast said continues to colonize - Day two of the conference opened becoming the only option, accord- flats and reshape the shoreline. "If with the theme of ecosystem restora- ing to the Department of Water we forge ahead and do restoration tion, which CALFED's lead scientist Resources' Curt Schmutte, referring without getting rid of invasive Sam Luoma said required three to his work on subsided Delta plants, we won't achieve a lot of our things to be successful: a sophisti- Islands. "The only other option is to objectives for ecosystem recovery," cated investment strategy; careful let these holes get deeper and deep- he warned. As of 2001, a total of documentation of what works and er," he said. 237 invasive species (both flora and what does not; and an institutional fauna) were well documented within system that responds to the evalua- Further downstream, Bay restora- the Estuary, added the S.F. Estuary tion of effectiveness. tion is now revolving around the Institute's Andy Cohen. Ecosystem Habitat Goals completed Three groups of speakers then by scientists in 1999. Much work has Getting down to ground level, addressed restoring Central been done in the North Bay, hydrologist Phil Williams then dis- rivers, the Delta and the Bay. The according to consultant Stuart cussed how our view of as a Resource Agency's Tim Ramirez Siegel, whose new inventory of nuisance - choking shipping chan- kicked off by examining how salmon North Bay restoration projects esti- nels and muddying swimming have responded to river restoration mates 13,569 acres of tidal marsh - has changed over the last strategies. Then U.C. Davis' Jeff has been or will be constructed in few decades. But declining sediment Mount said "flood management is the near future - a big leg up on the delivery to the Bay (only 5 million the single most useful tool of Goals Project's recommendation of cubic yards per year now), along ecosystem restoration," but four 28,000 acres of this sub-region for with and the creation hurdles had to be overcome to use optimum ecosystem health. A of large new sediment sinks it: a 150-year history of hard engi- healthy ecosystem comes not only (restoration of subsided Delta neering approaches to river man- from bay wetlands, but also from islands, for example) will all reduce agement; working within a system healthy creeks and watersheds, the mud supply. "Managing mud specifically designed to limit inter- according to the next speaker, the will be as important as managing change between the and the S.F. Estuary Institute's Laurel toxics and exotics in the future," he ; the often small and dis- Collins. Collins showed intriguing said. "Large-scale restoration will be connected scale of restoration proj- charts comparing levels of , constrained by the small sediment ects; and the need to embrace debris, sediment, vegetation and supply." restoration as a social, not just bio- other factors along nine creeks logical and physical, science. draining into the Bay. Other speak- After Williams, Stanford's Steve ers expanded on shoreline and We also need to recognize, said Monismith gave an overview of how watershed restoration efforts. numerical models have helped us Stanford's David Freyberg, that understand hydrodynamic processes ecosystem restoration is "fundamen- After lunch, the subject matter and the S.F. Estuary Institute's tally a design process, and that honed in on Suisun Bay - that piv- Rainer Hoenicke described strides design is a different activity than otal zone of the Estuary that has one in reducing toxicity in the Bay. One discovery," which is what most sci- foot in the Delta and one foot in pollutant reduction effort has been entists perceive their work as being. San Francisco Bay. A parade of the negotiation of TMDLs, a regu- The challenge then, he said, is to speakers explored layer upon layer latory tool that sets a regional goal design for complexity, variability of Suisun science, from the impacts for a total allowable maximum daily and long term change using tools - of long-term rises in load of a contaminant. The Bay's dams, channels, levees - designed to levels since the 1930s (a 5 ppt new TMDL "beats on all simplify the ecosystem. You can't increase, according to speaker Noah the sources," said the S.F. Bay rely on nature to do all the rest of Knowles) to changes in sedimenta- Regional Board's Khalil Abu-Saba. the work either, said Denise Reed of tion rates from a historical deposi- But because five old mines account the University of New Orleans, who tional situation in which 3 million for about 90% of the mercury went on to debunk other restoration cubic meters (mcm) were being problem, he said, "We need more "myths," including "build it and deposited in the Bay every year to bulldozers and fewer Ph.D.s to work they will come." Reed said "We more recent times when 1-2 mcm on this." Three more speakers shouldn't expect the system to have are eroding away annually, accord- wrapped up the day, with talk of enough sediment in it to build new ing to the Geological Survey's Bruce , biomarker research, and land, because it's not what our rivers Jaffe. attributes of a healthy ecosystem. ever did before. We don't need to And retired Army Corps debris boat build new marshes as high as natural Other changes include revisions captain Eric Carlson sent everyone ones, but we do need to rebuild the to the circulation model for the Bay home with first hand tales of rail- substrate to the level where vegeta- and Carquinez , said the road cars full of whiskey stuck in the tion can take over." Survey's Jon Burau, who showed Bay mud, sea lions on his deck, and slides of where scientists now think

3 STATE OF THE ESTUARY

the water goes, and how , cur- Marsh showed natives favored the rents and topography influence tur- small sloughs. "This helps us choose bidity, food production and sedi- from the universe of shallow water ment movement. Indeed scientists habitat restoration options - we now know the area of maximum tur- want the ones that look like small bidity is not necessarily where the sloughs," he said. salinity hits 2 practical salinity units (or "x2"), as until recently thought, Other speakers talked about but on the seaward side of sills such and the benthic as as Garnet Sill adjacent to Grizzly community, and Water Resources' Bay, according to presentation by Brad Cavallo closed with the prover- the Survey's Dave Schoellhamer. bial big fish in the : salmon. He said we had to stop trying to Two other scientists went on to manage them as "freeway fliers" explore the impact of the invasive speeding straight up and down the Asian clam Potamocorbula on the rivers, and start noticing that they're Suisun Bay , and how con- more like "Sunday drivers" stopping taminants affect the clams and the off here and there in side channels birds and fish that eat them. The and often moving back and forth. Survey's Robin Stewart, for exam- "Fish don't follow the robotic life ple, showed a chart indicating a big history we invent for them," he said. increase in selenium concentrations "So we can't just continue to focus in top predators like Suisun Bay on minimizing mortality at bottle- , which feed on the clams, necks." between 1986 and 1999 but no increase for striped bass which feed on other organisms. On the heels of all this science was a multi-agency "If we forge ahead and do restoration management presentation describ- ing the current acrimonious debate without getting rid of invasive plants, over how much of should be kept as heritage waterfowl we won't achieve a lot of our objectives habitat and hunting grounds and for ecosystem recovery." how much converted to much- needed tidal marsh.

Day three of the conference PETER BAYE dawned with snapshots of key bio- U.S. Fish & Wildlife Service logical components of the ecosystem - fish, habitat and flows. U.C. Davis' Peter Moyle looked at the ever Near the end of the conference, changing balance between native and two old hands in Estuary manage- alien , but said both kinds of ment provided some interesting populations are in decline: "the perspectives. Steve Ritchie, formerly peaks and valleys in their numbers of the water quality board and are both getting lower" (see graph CALFED, looked at our manage- p.5). Habitat for the fish came next, ment track record and said that the with S.F. State's Wim Kimmerer S.F. Estuary Project's 1993 consen- discussing characteristics of the fish- sus-based plan for the Bay-Delta friendly low salinity zone in the "changed the way we do our busi- Estuary, and how it moves with ness, moving from legislative to changing flows (x2), and the U.S. more collaborative efforts like Geological Survey's Larry Brown CALFED." But the eloquent words exploring the benefits of "shallow that rang in the ears of many leaving water habitat" (, marshes, the conference were those of U.S. river flood plains) for fish. The EPA retiree John Wise: "It's time to recent push to create new shallow move science into the public water habitat, and the use of this domain, to communicate the beau- new habitat by alien species, has tiful chaos of the Bay-Delta system raised many questions about what to those around us, and to re- kind of habitat is best to restore for engage the public in long-term pro- natives. Brown says research on alien grams to protect the Estuary." and native fish abundance in Suisun

4 Vital Statistics

STATE OF THE ESTUARY Vital Statistics 1999-2002

"I have an image of an early captain going along the coast, the sea flashing with silver smelt, rising off rocky islands, surrounded by pods of whales whose spoutings were so thick the crew could scarcely breath for the stench. It was a time when it seemed we could walk across the river on the backs of salmon, hear a hurricane in the of a flock of birds taking flight. The world wants to be beautiful, even as ugliness spreads all around."

MALCOLM MARGOLIN Author

5 PERSPECTIVE

DETERMINING HEALTH of Sciences and the Science In conclusion, consider this Advisory Board of the EPA have thought: when you need a car, you ANDREW GUNTHER provided or will soon be providing don't go to the parts department. Center for Ecosystem guidance on approaching this Similarly, if we want to create a Management and Restoration problem. cogent assessment of the ecologi- cal condition of the Estuary, we The health of the Estuary is not Second, we must recognize should not examine and approve an objective characteristic that we that developing a meaningful each part separately. Instead, we can measure, but rather a subjec- assessment of the ecological con- must build a complete assess- tive assessment that we make by dition is a long-term proposition ment and take it out on a test considering measurements of the that may require specialized insti- drive, and then recommend alter- ecosystem’s important attributes. tutions. We need to consider all nate parts based upon the per- We can simplify the problem a lit- alternative institutional structures formance of the complete product. tle if we inquire about the relative to identify those particularly well- condition of the ecosystem over suited to this task. If we are going It has taken us a long time to time. And so we arrive at the ques- to track cycles in our modify the Estuary to its present tion, “Are things getting better or for decades, this task should be state, and it will take a long time worse?” assigned to institutions with a for us to authoritatively document long-term mission and long-term trends in its condition. Those of Answering this question funding mechanisms. us who study the Bay on a regular requires that we identify essential ecosystem attributes that are pub- licly meaningful and scientifically justified. We then must track the “Although a complete and compelling status of these attributes, or indi- presentation of the health of the Estuary cators of them, over time to build a record of ecological condition is presently outside of our experience, for the Estuary. there is no reason to think that it is What I am suggesting here is beyond our capabilities.” not really news. In fact, work reported in the last State of the Estuary proceedings identified nine ecosystem attributes and a Third, we must recognize that basis owe our fellow citizens a set of 13 ecological indicators for developing a meaningful assess- straightforward answer to the the Bay-Delta and its watershed. ment of ecological conditions question, “are things getting bet- Moreover, we have much raw requires more than the collection, ter or worse.” If we commit to the material to work with, from both a documentation, and publication of attempt, there can be no doubt policy and a scientific perspective, data sets. that the product will inform our through our adopted public goal debate, and that we will learn over statements and the results of sci- Finally, we must recognize that time how to improve our assess- entific research and monitoring. we will have to learn as we go. ment and make it more useful. Whatever indicators are used to Our imperfect attempts to answer Yet we still need to integrate assess ecological condition will be this question will not reflect as this raw material into an assess- imperfect, and reaching agree- poorly on us as our unwillingness ment of ecological condition. Let ment on benchmarks of evalua- to try in the first place. Although a me suggest some strategic consid- tion will take time. There will obvi- complete and compelling presen- erations if we are to accomplish ously be alternative assessments tation of the health of the Estuary this task. First, there are many that could be created from the is presently outside of our experi- opportunities to learn from what same data, and our first attempts ence, there is no reason to think others are doing, as we are not at an overall assessment of condi- that it is beyond our capabilities. alone in this effort. Across the tions are likely to be soundly criti- (Gunther, SOE, 2001) nation those responsible for the cized. In the long view, our assess- health or integrity of aquatic ment of condition will need to be MORE INFO? ecosystems are trying to establish repeated on a biannual or triennial [email protected] meaningful ecosystem goals, and basis, and there will certainly be find consensus metrics to evaluate an opportunity for multiple progress. The National Academy authors to take their turn.

6 Vital Statistics PERSPECTIVE

CAN YOU HEAR California Department of Fish & THE CANARY SING? Game calling a halt to the planting of this fish-eating, introduced predator. RANDALL BROWN CALFED Science Program Subsequently, state and federal agencies formally consulted on a The San Francisco Estuary is a plan to stock limited numbers of complex and ever-changing juvenile striped bass, with a goal ecosystem which has been altered of stabilizing the adult population dramatically over the past 150 at about 1.2 million. The latest years, largely by water storage and estimates on adult bass indicate withdrawal systems that change that the population goal has at the amount and timing of freshwa- least been temporarily achieved ter inflow. Management agencies and, consistent with the federal have struggled to find an index or biological opinion, Fish & Game measure that can demonstrate curtailed planting juvenile striped that efforts to balance beneficial bass. uses of freshwater inflow are work- ing. From the late 1950s into the 1980s, such an index, likened to a miner’s canary, was an index of the summer abundance of young- “Management agencies have struggled to find of-the-year striped bass when their an index or measure that can demonstrate average size was about one inch. The index, which was positively that efforts to balance beneficial uses of freshwater correlated with spring outflow and inflow are working.” negatively correlated with spring diversions, was to indicate the health of the northern estuary.

In 1978 the State Water Board The strength of the canary’s issued Decision 1485, stipulating song (the striped bass index) did spring flow and pumping condi- follow other indicators (native fish tions intended to result in an aver- abundance) demonstrating that age striped bass index of about 78. conditions in the northern estuary It quickly became apparent, how- deteriorated in the 1987-1992 ever, that the relationship between drought. The apparent lack of sen- flows, pumping and the index was sitivity of the index to generally changing. In the 1980s, the index improving conditions from 1993 fell to new lows and for the last shows that it may have biases that decade it has generally been less make it inappropriate for use as than 10 – even in those years with an indicator of estuarine health. In apparently favorable flow and keeping with restoring native pumping. The adult striped bass species, perhaps we should be lis- population plummeted as well, tening to the Suisun song sparrow with fewer than 500,000 adults in instead of the canary (Brown, the early 1990s as compared to 1.5 SOE, 2001). -1.9 million in the early 1970s. MORE INFO? In the late 1980s, for the first Brown.randall time, resource managers planted @attbi.com juvenile hatchery striped bass in the Estuary to help restore this economically important sports fish. Within a few years concern about declining abundance of sev- eral native fish resulted in the

7 STATE OF THE ESTUARY

FLOWS FRESHWATER FLOWS TO THE SAN FRANCISCO ESTUARY, 1980-96 IN MILLIONS OF ACRE FEET RECENT INFLOWS 70 Total Delta Inflow Normal or above normal rainfall 60 Net Delta Outflow has meant improved Delta inflows in (after export and in-delta use) recent years. Inflows to the Delta and 50 Estuary were 25.2 million acre-feet 40 (MAF) in water-year 2000 (October 1, 1999 - September 30, 2000) and 30 13 MAF in 2001. Delta outflows were 20 18.2 MAF in 2000 and 7 MAF in 10 2001 (IEP, 2002). 0 '80'81 '82 '83 '84 '85 '86 '87 '88 '89 '90 '91 '92 '93 '94 '95 '96 '97 '98 '99 '00 '01

DIVERSIONS FOR Source: DWR, , Dayflow QTOT BENEFICIAL USE WATER USE EFFICIENCY

Water is diverted both within the Water use efficiency, conservation Services District recycling facility's cur- Delta and upstream in the Estuary’s and recycling projects within the Bay- rent treatment capacity is 3 mgd, with watersheds to irrigate farmland and Delta region aim to provide a 10 miles of distribution installed. supply cities. In-Delta exports have “drought-proof” source of water to Planned capacity for this facility is 9.6 largely remained within the range of 4 help meet the needs of cities, indus- mgd. The East Bay Municipal Utility to 6 MAF per year since 1974, but the tries and agriculture. CALFED is District's East Bayshore Recycled Water percent of Delta inflow diverted can sponsoring a new water-use efficiency Project, currently in the design phase, vary widely from year to year. In program that could save 1 to 1.3 MAF will ultimately run up to 24 miles of water-year 2000, 6.3 MAF were per year within seven years. The pro- pipeline through Oakland, Berkeley, diverted, and in 2001, 5.1 MAF. The gram involves setting ecological, water Emeryville, and Albany. average percentages of total Delta quality and water supply objectives; EBMUD expects to start deliveries in inflows diverted were 37.6 in 2000 assessing local and regional flow pat- 2003, and aims to save 2.3 mgd (more and 41.7 in 2001 (IEP, 2002). terns; evaluating how cities and farms than 2,500 acre-feet/year) once enough might change their water use to users are hooked up to the system. achieve the objectives; and then pro- PERCENT OF INFLOW DIVERTED viding appropriate financial incen- MORE INFO? 50 tives. Meanwhile, 65 water conserva- [email protected] tion projects (37 urban, 28 agricul- [email protected] tural) received a total of $13.3 million statewide in CALFED funding in 40 2001; local matching funds added another $9.1 million. CALFED expects that these projects will collectively save % 30 30,000 acre-feet of water per year. At the local level, the Bay Area Water Recycling Program's (BARWRP) 20 Master Plan, now complete, calls for recycling 125,000 acre-feet per year in the Bay Area by 2010, and about 10 240,000 af/year by 2025. Many Bay ‘97 ‘98 ‘99 ‘00 ‘01 Area agencies are forging ahead with Source: DWR, ExportsTOT the design, construction and operation of water recycling projects. For exam- ple, the City of San Jose's South Bay Water Recycling Program delivers an average of 10 million gallons per day (mgd) during the summer season to over 350 customers in San Jose, Santa Clara and Milpitas. The next phase of this project, currently in design, will double the delivery amount by the year 2008. The Dublin-San Ramon

8 Vital Statistics

FISH & AQUATIC number since 1975. Abundance of the sloughs of Suisun Marsh, in the juvenile splittail was low in 1999 and center of the Estuary, has revealed ORGANISMS 2000, although adult numbers have trends in 29 fishes, 14 of them alien ZOOPLANKTON, increased recently due to very strong species. The study shows that most CRABS & FISH year classes in 1995 and 1998. native and alien species are generally in decline in the upper Estuary, Abundance of , although the invasion of the shimo- The status and populations of which reproduce in the rivers but furi goby in the 1980s boosted alien aquatic species in the San Francisco rear in the ocean, is affected not numbers. The major driving force Estuary is influenced by physical and only by riverine, estuarine, for relative abundances of species is biological factors including the and oceanic conditions, reproductive success both inside and magnitude and timing of but also commercial outside the Estuary. Success of freshwater flows, both in and sport harvest. The reproduction as reflected in recruit- the rivers and through the Central Valley chi- ment success is the key factor limit- Delta; ocean tempera- nook salmon index ing native fishes of concern (e.g., ture; and ocean cur- was the fourth high- , longfin smelt, splittail, rents, such as coastal est in 2000 for the chinook salmon). Estuarine fish . Since 1999, period of record assemblages appear to be fairly freshwater flows have been (1970-2000). unpredictable, due to (1) the natural lower than during the pre- Escapement of fall-run fluctuating conditions of estuaries ceding four years, while chinook salmon to the in general, especially in the brackish ocean temperatures have been system in regions, where species come and go cooler and coastal upwelling 2000 was approximately according to changes in temperature stronger. There is strong evidence 400,000 fish, the highest for the and salinity, (2) the general decline that the ocean climate along the period of record, while escapement in fish abundance in the brackish Central coast underwent a regime of fall-run chinook salmon to the and freshwater portions of the shift in 1999 from a warm to cool system was the Estuary, suggesting a high level of phase. highest since the mid-1980s (Hieb, anthropogenic disturbance, and (3) SOE, 2o01) Cooler ocean temperatures in the frequent invasion of alien species of both fish and inverte- recent years have benefited some MORE INFO? brates. These results suggest that species, but have been detrimental [email protected] to others. Over the past three years there will be continue to be a high abundance of juvenile Dungeness degree of unpredictability in fish crab and English sole, both cold- FISH ASSEMBLAGES abundances (as reflected in assem- temperate species, has been near or blage structure) until estuarine at record high levels in the Estuary The fishes of the San Francisco processes return to some semblance for the period of record (1980- Estuary are a mixture of native and of their natural range of variability 2001). Concurrently, abundance of alien species. The Estuary's marine and until invasions of alien species subtropical species, such as portions are dominated by native are halted (Moyle, SOE, 2001). California halibut and Pacific sar- fishes but the freshwater and brack- MORE INFO? dine, has slowly declined. ish portions are dominated by alien [email protected] species. A 22-year study (monthly With the exception of copepods, sampling) of the fishes inhabiting abundance of all types of zooplank- ton in Suisun Bay and the Delta has declined in recent years. Total cope- SUISUN MARSH ANNUAL AVG. CATCH, 1980-2001 pod abundance has increased since 6 the early 1990s, but this was due to Water Gobies non-native species introductions. Management Aliens except gobies Changes 5 Natives except sticklebacks Species that in the lower Major Flood Event Sticklebacks rivers or upper Estuary and rear in 4 Shimofuri Goby the Estuary, such as Delta smelt, First Collected longfin smelt, striped bass, and split- 3 Overbite Clam Reaches tail, have varied abundance trends High Densities Wet over recent years. Delta smelt abun- 2 dance was relatively high in 1999 and Dry 2000, while longfin smelt abun- 1 dance oscillated. Abundance of juve- Drought nile striped bass has been very low 0 since the late 1980s, but the most ‘80 ‘82 ‘84 ‘86 ‘88 ‘90 ‘92 ‘94 ‘96 ‘98 ‘00 recent population estimate for adult Source: Peter Moyle bass was 1.8 million, the highest

9 STATE OF THE ESTUARY

delta smelt's decline include reduc- SALMON RUNS OF CONCERN tions in Delta outflow, high outflows IN THOUSANDS OF ADULT FISH RETURNING TO SPAWN (which push them too far down the Estuary), entrainment losses at water 70 Winter-Run to Upper Sacramento River diversions and pumps, food changes, toxic substances, disease, Fall-Run to San Joaquin River 60 competition and . The 50 Spring-Run to Upper Sacramento River abundance of delta smelt, after a 40 dramatic decline in the 1980s, gen- erally increased throughout most of 30 the 1990s. Although recent moni- 20 toring results indicate this upward trend may have downshifted again, 10 the species appears to be faring bet- 0 ter than in did in the 1980s. '80 '81 '82 '83 '84 '85 '86 '87 '88 '89 '90 '91 '92 '93 '94 '95 '96 '97 '98 '99 '00 '01 Scientists believe the 1990s popula- Source: CDFG tion increase can be attributed to multiple synergetic factors, includ- CENTRAL VALLEY SALMON (EWA) was used for the first time in ing the above-normal outflow con- 2000 to reduce impacts of Delta ditions, which aided in the trans- Most populations of Central pumping operations on the winter- port of larval/ from the Valley chinook salmon seem to be run, spring-run and San Joaquin Delta to their rearing grounds in holding steady. These salmon occur fall-run chinook salmon, but it is Suisun Bay. Cal Fish & Game moni- in four discrete runs — winter-run, too soon to determine whether this tors the relative abundance of delta spring-run, fall-run and late fall- effort will provide population-level smelt through two long-term moni- run (run refers to the season in benefits (Kano, Pers.Comm., toring programs: the Townet Survey which adults return to their native 2002). (TNS) and the Fall Midwater Trawl to spawn). The winter-run Survey (MWT). The 2001 TNS chinook, with the lowest population, MORE INFO? index for delta smelt was 3.5, a has been listed as a both a state and [email protected] decrease from 2000 (8.0) and 1999 federal endangered species since (11.9). Meanwhile, the 2001 MWT 1994. In 1999, returning salmon DELTA SMELT index was 603, a decrease from numbered 3,288, the highest return 2000 (756) and 1999 (864). since 1985. The population The silvery-blue delta smelt, a 55- CALFED's new Environmental dropped to 1,352 in 2000, then 70 mm-long translucent fish once Water Account was used for the first jumped to 7,572 in 2001. This common in the Estuary, was listed as time in 2000 to reduce impacts of fluctuation is likely due to a differ- a state and federal threatened Delta pumping operations on this ence in techniques used to estimate species in 1993. Delta smelt are species, but it is too soon to deter- the population; a comparison of considered environmentally sensi- mine whether this effort will provide survey results based on current and tive because of their one-year life population-level benefits (Dege, past estimation techniques is now cycle, limited diet, low egg produc- Pers. Comm, 2002). under analysis. The next most sensi- tion and larval survival rate, and tive stock, the spring-run, was state MORE INFO? restricted distribution within the listed as a threatened species in 1998 [email protected] Estuary. Possible reasons for the and federally listed in 1999. The spring-run population was 10,134 in 1999, 9,404 in 2000, and DELTA SMELT ABUNDANCE INDEX, 1967-2001 15,794 in 2001. Sacramento fall- FALL MIDWATER TRAWL run are the most abundant chinook stock, with 434,018 returning in 2000 and 569,976 in 2001 1,500 (includes both hatchery and in-river spawning fish; the exact proportion of each within the river is 1,000 unknown). Returns of the San Joaquin fall-run in 2000, at

44,514, and in 2001, at 29,182, 500 were both above the 1967-1991 aver- age annual return of 22,319. The late fall-run (distinct from fall-run) 0 No Sampling No Sampling No Sampling population was 12,746 in 2000 and '67 '69 '71 '73 '75 '77 '79 '81 '83 '85 '87 '89 '91 '93 '95 '97 '99 '01 13,148 in 2001. CALFED's new Environmental Water Account Source: CDFG

10 Vital Statistics

LONGFIN SMELT given water conditions, but the index and adult abundance makes it diffi- for 2001 was unexpectedly high. cult to predict the future course of Longfin smelt in the Estuary rep- Presumably, the combination of high the population (Gartz, Pers. resent the southernmost spawning spawner numbers (first spawning of Comm., 2002) population in North America. females from the extremely large Their local abundance continues to 1998 year-class) and two narrowly MORE INFO? be positively correlated with Delta separated week-long periods of [email protected] outflow during their larval period, floodplain inundation in late December through May (Baxter February and early March, with COMMERCIAL FISHERIES 1999). Between the extremely wet probable ponding in between, was winters of 1998 and 2001, Delta sufficient to produce the better- Since the 1997 El Niño, the outflow during the December than-expected age-0 abundance spawning of Pacific herring, through May period declined annu- index (Baxter, Pers. Comm., 2002). which supports the Bay’s largest ally and so has the abundance of commercial fishery, has remained longfin smelt, as measured by Cal MORE INFO? below the long-term (since 1978) Fish & Game's Fall Midwater Trawl [email protected] average of 52,966 short tons. In Survey. In 2001, the abundance response to this decline, Cal Fish & index dropped severely to 247, a STRIPED BASS Game, which manages the fishery, level not seen since the drought has lowered catch quotas. Although broke in 1993. On a positive note, a Cal Fish & Game mark and recap- ocean has been favor- recent increase in the incidence of ture estimates for legal size (18 able for herring over the past two 120-140 mm FL (fork-length or inches or longer) striped bass, the years, a large recruitment of young length measurement from the tip of most important sport fish in the fish to the spawning population has the snout to the fork in the tail) Estuary, increased 70% from 1998 yet to occur. Following record high spawners (about 3 years old) cap- (1,340,693 fish) to 2000 biomass levels of 99,050 tons in tured in trawl sampling suggests that (2,276,227 fish), but the reasons 1995-1996 and 89,570 tons in survival has increased from juvenile for this increase are unknown. 1996-1997, spawning biomass to adult (age 2) and beyond. This Unexpectedly, abundance indices of plunged to 20,000 tons following bodes well because age-3 females striped bass in their first year of life the 1997 El Niño. Since then, can produce over twice as many eggs (young-of-the-year fish) from the spawning biomass estimates have as age-2 females, and such spawners Midsummer Townet Survey and Fall been 39,500 tons for 1998-1999, can help buffer against poor year- Midwater Trawl Survey did not 27,400 tons for 1999-2000 and classes (Baxter, Pers. Comm., increase during the 1990s. Also, 37,300 tons for 2000-2001 2002). supplemental fish from Cal Fish & (Watters, Pers. Comm., 2002). MORE INFO? Game's Striped Bass Hatchery MORE INFO? [email protected] Program made up only 1.95% of legal-sized striped bass in 1998 and [email protected] 6.21% in 2000; not enough to account for the observed increase. SPLITTAIL This disjunction between juvenile Splittail exhibited moderate overall abundance and fair recruitment LEGAL-SIZED STRIPED BASS POPULATION ESTIMATE (number of age-0 surviving to the Population Estimate (No. of Fish in millions) NO. OF FISH IN MILLIONS fall) in the past three years. This sil- very-gold minnow, found only in 2.5 Central Valley rivers and the Delta, is listed as threatened under the federal Endangered Species Act. Splittail are 2.0 known to spawn on inundated terres- trial vegetation, and its recruitment appears most strongly associated with 1.5 the magnitude and duration of floodplain inundation during its late February-May spawning period 1.0 (Sommer et al. 1997, Moyle et al. 2001). Floodplain inundation occurred only during the first third 0.5 of the spawning period in 1999 and 2000, and only for a couple of weeks in 2001. Age-0 indices for 1999 and 0 2000 were about what was expected '70 '72 '74 '76 '78 '80 '82 '84 '86 '88 '90 '92 '94 '96 '98 '00

Source: DWR

11 STATE OF THE ESTUARY

INVASIVE SPECIES CHINESE MITTEN CRABS 2002 than in winter 1998-1999. The number collected at the BurRec fish BAY-DELTA INVASIONS The Chinese mitten crab (Eriocheir salvage facility in the south Delta, sinensis) is one of the most successful however, was much lower in fall 2001 The San Francisco Estuary con- of the species recently introduced to than in fall 1998. The apparent dis- tinues to be one of the most highly the Estuary. In summer 2001, the crepancy between the 2001 state and invaded aquatic ecosystems in the mitten crab ranged from north of federal numbers may be because a world. Between 1995 and 2001, the Colusa on the Sacramento River to larger proportion of crabs reared in number of well-documented inva- the of the San Joaquin the Sacramento River watershed (and sive species in the S.F. Bay-Delta and Merced rivers (most reports of away from potential migration routes Estuary grew from 212 to 237. In age-1 crabs came from the Delta and past south Delta fish facilities) that the S.F. Estuary, there are 165 inva- the Sacramento River basin). year than in previous years. The mit- sive species in salt/brackish waters Although the 2001 distribution ten crab's major impacts continue to and 87 in freshwater systems. appeared to be very similar to that of be interfering with South Delta fish Exotics are expanding their domi- 1998, crabs were not reported from salvage activities, stealing bait from nance among zooplankton and in as far north or as far south in 2001. sport anglers and clogging West Delta salt marshes (Cohen, SOE, 2001). In 1999 and 2000, the crab's popu- power plant cooling water systems. lation declined from the record high MORE INFO? level of 1998, but it increased again MORE INFO? [email protected] in 2001. The number of adult crabs [email protected] collected between and the western Delta by Cal Fish & Game GREEN CRABS trawls was higher in winter 2001- The European green crab () is now established in every BAY-DELTA MITTEN CRAB SPREAD significant bay and estuary between Monterey, California, and Gray's , . It appeared in South San Francisco Bay in the early 1990s and has spread north at least as far as the . Salinity limits the crab's distribu- tion: crabs have been collected from water ranging from 5-31 parts per thousand (ppt) salt to water, but few from water with less than 10 ppt. A nine-year study in Bodega Bay found that in contrast to their slow growth rates in Europe, green crabs here grew rapidly and reached sexual maturity in their first year. Over the course of the study, the green crab severely reduced the abundance of three common invertebrate species but did not impact the shorebird food web (Grosholz et al., 2000). While eradication is not possible at this point, a National Green Crab Management Plan now being com- pleted recommends strategies for local population control. These include early warning methods for new range expansions, prevention measures against new introductions and coordinated monitoring of population trends, new outbreaks and losses to commercial fisheries. MORE INFO? [email protected] Distribution of the Chinese mitten crab in the San Francisco Estuary and its watershed, 1992, 1994, 1996, and 1998. Solid blue area or lines indicate presence of the crab. Source: CDFG

12 Vital Statistics

PIKE CORDGRASS GOBIES

The voracious Northern pike, Species of Spartina (cordgrasses) Four types of non-native gobies native to Canada and the Midwest, introduced into the Estuary in the (all of which probably arrived in was illegally planted in the 85,000- 1970s, have spread rapidly and pose ballast water) continue to inhabit acre-foot Lake Davis reservoir in the a serious threat to the success of Estuary waters. The yellowfin goby early 1990s. In 1997, Cal Fish & future tidal marsh restoration () is the most Game treated the lake with Rotenone throughout the Estuary (see also abundant and widespread of the to prevent pike from eating lake trout p.62). The impacts associated with introduced gobies. Cal Fish & and escaping into and corrupting the the spread of Atlantic cordgrass Game S.F. Bay Study catches of Delta ecosystem. The treatment tem- (Spartina alterniflora) include the chameleon goby (Tridentiger porarily shut the lake to all recre- hybridization with and likely local trigonocephalus) and the shimofuri ational uses and compromised local extinction of native Spartina foliosa, goby (T. bifasciatus) have remained water supplies. In May 1999, about a regional loss of unvegetated tidal relatively stable over the past five year after more than a million trout habitat, elimination of small tidal years. In contrast, the catch of the were planted and the lake had channels and loss of pickleweed shokihaze goby (T. barbatus) has reopened, the pike reappeared. habitat essential to the endangered increased dramatically, jumping Biologists have pulled almost 8,000 harvest mouse. The from 11 in 1999 to 559 in 2001. pike from the lake since 1999, mainly majority of creeks and from shallow areas such as Mosquito channels in the Central and South , a weedy channel into the bays are infested with invasive S. lake. In February 2000, a Lake Davis alterniflora. Local flooding and navi- steering committee, comprised of gation issues are expected to Plumas County and Cal Fish & Game increase if the population continues officials and local citizens, released a to expand. In early 2000, the management plan recommending 13 California Coastal Conservancy “control and contain” measures, began coordinating an eradication including several types of barrier project to prevent the spread of S. The impacts of this increase have nets, increased electro-fishing, alterniflora into the North Bay and not yet been determined. Within the underwater explosions and fishing reverse the spread of the species Estuary, adult shokihaze gobies are derbies. In spring 2002, biologists throughout the Estuary. The pro- found primarily in Suisun Bay, conducted a detonation cord “test” of ject's mapping effort, completed in where they have the potential to one acre, to assess the range of the 2001, showed that S. alterniflora and harm native gobies, sculpin, Delta kill zone, and water quality and noise hybrids cover 469 net acres within smelt, longfin smelt and and impacts. Based on the test results, a the Bay (acres counted as if there other invertebrates by competing for dozen detonations of up to 10 acres were no gaps in coverage). resources and through predation. each are planned for 2003 and Adult shokihaze gobies have been 2004. Despite the increased num- Meanwhile, S. densiflora (trans- found in water with salinity ranging bers of pike in the lake, they have not planted from ) covers from 0.44-28.81 parts per thou- been found outside of Lake Davis. approximately 13 net acres; S. patens . Yet until recently, the shoki- (from the East Coast) covers half an haze goby had not extended its MORE INFO? acre; and S. anglica (originally from known range seaward in the Estuary, [email protected] England but introduced to the Bay since it was found in San Pablo Bay Area from Washington State) covers in December 1997. But in February .09 acres. In the East Bay, non- 2002, the Bay Study caught two native spartina species have spread as shokihaze gobies south of the far north as Point Pinole, and in the Dumbarton Bridge (Greiner, Pers. West Bay, to northern San Rafael. Comm., 2002). S. densiflora has been found in the . Work is pro- MORE INFO? gressing on the eradication project's [email protected] EIS/EIR, permits and planning documents. Maps, species identification guides and For information on the Asian project documents are available. Clam, see p.66. MORE INFO? [email protected] www.spartina.org

13 STATE OF THE ESTUARY

WETLANDS & CALIFORNIA no major projects planned or in WILDLIFE CLAPPER RAIL progress that would affect the mice (Shellhammer, Pers. Comm., 2002) WETLANDS Current Bay-wide population esti- MORE INFO? mates for the endangered California Acquisitions of fields, creekbanks, clapper rail (Rallus longirostris obsoletus) [email protected] islands, and other for- are not available, but surveys in the mer, current and future wetlands mid 1990s placed their numbers at SALT MARSH have tripled since the last three-year about 1,200 (up from a low of 300- SONG SPARROWS reporting period, with at least 500 birds in 1991). While Central 33,042 acres secured and protected and South Bay populations continue Reproductive success of salt marsh in the 12 Bay-Delta counties between to hold steady, there is some indica- song sparrows increased slightly in April 1999 and September 2001. tion that North Bay populations are 1999 compared to 1998, which was Restoration and enhancement work in precipitous decline. Recent field the poorest year recorded to date; in continued at a steady pace, mean- studies reveal that the rails in the 2000 and 2001 reproductive suc- while, with 11,453 acres and 1,320 more pristine North Bay marshes are cess continued to rise. Despite the linear feet of completed projects in faring less well than those in urban- relative increase in reproductive the same time period. Plans for 24 ized areas. The estimated 13 pairs success, the overall success observed and riparian habitat projects present in in 1993 at most marshes (only about 19% of will improve approximately 27,500 dropped to 1-3 pairs in 1998, and in nesting attempts result in any acres and 36,020 linear feet. The 2001, no rails were found. Along the fledged young) is below the level amount of wetlands lost during the , an estimated 16 pairs necessary to ensure a stable popula- same period remained small, though surveyed in the 1990s dropped to 4-7 tion. The greatest cause of mortality the extent of Delta losses is not pairs in 2001. Heavy rains in the win- is predation. Current efforts are known. In the Bay region, 122 acres ter of 1997-1998 may have caused being directed toward identifying of wetlands were filled and 204 acres some declines in the North Bay, as predators (potentially mammals, gained as a result of 401 certification residual high water, particularly along snakes, and crows and jays). In waivers and development mitigation the North San Pablo Bayshore, addition, about 10% of nests fail projects. Regional interests have also impacted nesting success (Albertson each year due to flooding during the continued with plans, partnerships and Evens, 1998), and there is con- highest tides. Estimated numbers of and fundraising to implement the cern that predation by non-native breeding Alameda song sparrows Baylands Ecosystem Habitat Goals. Though mammalian predators (primarily red (Melospiza melodia pusillula), restricted no resulting regulatory-based region- fox) may be further impacting North to Central and South San Francisco al wetlands management plan has Bay populations. Predators in more Bay, range from 12,000-18,000 been developed, in 2001, 26 agen- urbanized South and Central Bay individuals; of Suisun song sparrows cies, organizations and private com- marshes may be finding less refuge (Melospiza melodia maxillaris), found in panies signed on to the S.F. Bay Joint than in the wilder wetlands to the Suisun Bay, from 36,000-53,000; Venture's implementation strategy north (Evens, Pers. Comm., 2002). and of San Pablo or Samuel’s song (Restoring the Estuary), which is based on sparrows (Melospiza melodia samuelis), the Goals. CALFED poured hun- MORE INFO? found in San Pablo Bay, from dreds of millions of dollars into [email protected] 65,000-85,000. The presence of restoration projects and ecosystem salt marsh song sparrows is not planning and processes. Other points SALT MARSH strongly linked to any one species of of progress in regional wetlands plant, but the population density of HARVEST MOUSE planning included the updating of song sparrows is nonetheless corre- the wetlands and wildlife section of lated with landscape features. the S.F. Bay Commission's Bay Plan, It is not known whether the popu- Density is greatest where the land the launching of a regional wetlands lation of the Bay's endangered salt adjacent to the marsh contains less monitoring program and the cre- marsh harvest mouse (Reithrodontomys urbanized areas, while density is ation of a Joint Aquatic Resource raviventris) has changed significantly lowest in small, isolated marshes. Permit Application Center by the over the past three years. Population All three song sparrow subspecies S.F. Estuary Project, ABAG and local studies are conducted only when are state Species of Special Concern. agencies. Funding and technical development projects or changes in (Nur, et al., SOE poster, 2001) assistance to individual landowners land use threaten the mice, and few has also increased since 1999 (SFEP, such studies have been required dur- MORE INFO? 2001). ing this time. When such studies are [email protected] conducted, their piecemeal nature www.prbo.org MORE INFO? makes it difficult for scientists to get a See Appendix A at take on overall population trends. www.abag.ca.gov/bayarea/sfep/ Several marsh restoration projects reports/sfep_sep01.pdf that could impact mice populations are planned in the North Bay, but until those are underway, there are

14 Vital Statistics

SALT MARSH YELLOWTHROAT threatened. While the South Bay did fall 2002 into the first recipient site, not historically support 500 birds, located at the San Joaquin River Surveys of tidal marshes in 2000 coastal areas are heavily impacted by National Wildlife Refuge. Two more detected few salt marsh yellowthroats human activities, making it difficult breeding enclosures were being built (Geothlypis trichas sinuosa), a state Species to protect plover populations there. in 2002, and scientists expect the full of Special Concern, in San Francisco Managing salt evaporation ponds, state-federal, multi-agency program Bay itself; likely only a few hundred which are typically less disturbed by to be underway by summer 2003. are present. In San Pablo Bay, the humans, for snowy plovers is an (Chaltry, Pers. Comm., 2002) estimated density was also low, with an opportunity for S.F. Bay to play a estimated total population of 3,000 significant role in the recovery of this MORE INFO? or fewer breeding individuals. In species, especially since the birds (916)414-6655 many marshes in San Pablo Bay, yel- migrate not only up and down the (559)487-5202 lowthroats were completely absent. In coast, but from the coast to the Bay and vice versa. (Albertson, Pers. Suisun Bay, however, densities HARBOR SEALS observed were quite high (10-fold Comm., 2002) higher than in San Pablo Bay); Point Reyes Bird Observatory scientists esti- MORE INFO? Bay (Phoca vitulina) num- mate 10,000 to 15,000 breeding (510)792-0222 bers have remained fairly stable over individuals in Suisun Bay. An addi- the past decade. Depending on the season — pupping, molting, fall or tional unknown number are present RIPARIAN BRUSH RABBIT in brackish and freshwater marshes. winter — they can be found in large Salt marsh yellowthroats appear to numbers at one of three main haul- Populations of the federally listed respond to specific vegetation compo- out sites. During pupping season riparian brush rabbit (Sylvilagus bach- sition and are more abundant where (mid-March-May), harbor seals are mani riparius) are largely restricted to there is a greater amount of Scirpus most plentiful at , riparian habitat along the Stanislaus (the genus that includes tule and bul- where approximately 270 seals (not River in Caswell Memorial State Park rush), rush and peppergrass (a non- including pups) were counted during and to some private land along the native herb). In addition, they are 2000 and 2001, representing an San Joaquin River near Stockton. more abundant where the vegetation increase from 1999's count of 201. While the 2002 trap census for the structure is more complex, for exam- Between 80 and 100 pups were Caswell population was higher ple, where there is more diversity in counted here each year during than that for 2001, it was the height of herbs. See Posterbook. the 1999-2001 pupping sea- still such a low number (Nur, et al., SOE poster, 2001) sons. In the winter that population esti- months, when Pacific MORE INFO? mate tools will not herring are spawning in [email protected] work. It is likely the Bay, seals are most www.prbo.org there are fewer than plentiful at Yerba two dozen rabbits Buena . In the left in the park. WESTERN SNOWY PLOVER winters of 1999-2001, Rabbits at the San researchers counted Joaquin River site fared between 200-240 seals each In the Bay Area, the Western snowy better last year. Broad esti- year at this site. , a plover (Charadrius alexandrinus nivosus) is mates based on visual observation chain of rock clusters just south of primarily associated with commercial and limited trapping suggest the rab- the Richmond Bridge, is used year salt evaporation ponds and levees, bits were at a high point —200 or round, although more seals use the which means scientists have not to fewer — in their population curve rocks during pupping and molting date been able to actively manage (the rabbit population fluctuates nat- season (June-mid-August). Since resources for the species. However, urally, like those of many other small 1996’s low of 96 seals, numbers have the Eden Landing Ecological mammals). Plans for residential increased slightly each year during Reserve, a former salt evaporation development at the San Joaquin site the molting season — 141 in 1999, pond now owned by Cal Fish & could help the rabbit; a comprehen- 155 in 2000 and 172 in 2001. Game, will be managed for plovers by sive management plan from develop- Seismic retrofit work began on the 2003, primarily through habitat ers calls for more and better rabbit Richmond Bridge in early 2001, and enhancement, along with nest pro- habitat. Meanwhile, biologists have researchers from San Francisco State tection and predator control. The begun a captive-breeding program. University are monitoring what purchase and management of addi- Six rabbits (three males and three effect, if any, the construction is hav- tional ponds could also aid the females) were released into the first ing on seal numbers and behavior. plover. A U.S. Fish & Wildlife draft of three breeding enclosures during See also p.16. (Green, Pers. Comm., recovery plan calls for increasing the winter 2002; by the end of March, 2002). South Bay breeding population from seven young rabbits had been caught its current level of 150-200 individ- in the pen, and scientists believe MORE INFO? uals to 500 to help spur recovery of there are probably more. The cap- [email protected] the plover, which is federally listed as tive-bred young will be released in

15 STATE OF THE ESTUARY

WATER & exempting discharges from irri- DELTA & UPSTREAM gated lands from waste BAY CONTAMINANTS CONTAMINANTS requirements, but may add some new conditions to the waiver aimed In the Bay, most contaminant The freshwater side of the Estuary at curbing agricultural . does not have a systematic monitor- guidelines are being met, but the level MORE INFO? ing program to evaluate contami- of contamination today is probably [email protected] high enough to impair the health of nant levels in water, sediment, or the ecosystem (indications of impair- biota. However, contaminants doc- ment include the toxicity of water and umented to exceed either water HARMFUL CHEMICALS sediment samples to lab organisms and quality objectives or concentrations IN HARBOR SEALS the frequent presence of contaminant toxic to aquatic organisms in the concentrations exceeding water, sedi- Delta have been given the highest Bay harbor seal tissues contain ment and fish guidelines). A relatively priority by the Central Valley PBDEs (polybrominated diphenyl small number of problem contami- Regional Water Quality Control ethers) at levels as high as 8,325 nants makes it rare to find clean water Board for development of regional nanograms per gram of fat (equiva- or sediment in the Bay. Of all the load reduction and control pro- lent to parts per billion), with a mean contaminants measured by the grams (TMDLs) under the Clean of 1,730 nanograms per gram of fat, Estuary's Regional Monitoring Water Act. In 2003-2004, the according to a recent study (She et al., Program (RMP), results suggest that Board is expected to consider 2002). The PBDE levels found in those of greatest concern are mercury amendments to its Basin Plan to seals here are the highest reported to and polychlorinated biphenyls address water quality problems asso- date anywhere in the world. The study (PCBs). Also of concern are diazinon, ciated with elevated levels of diazi- also found that concentrations of chlorpyrifos, copper, nickel, zinc, non and chlorpyrifos, mercury and PBDEs in seal tissues doubled every DDT, chlordanes, dieldrin, dioxins low dissolved oxygen in the Stockton 1.3 years (on average) in the decade and polycyclic aromatic hydrocarbons Deepwater Ship Channel. The Basin between 1989 and 1998, which repre- (PAHs). Work outside the RMP sug- Plan amendments for each will sents a nearly 15-fold increase over gests that selenium is also a concern. include an implementation plan the sampling period, the greatest rate Looking back over seven years of RMP with a schedule and monitoring for of increase reported worldwide to data, scientists do not see any clear compliance. Each plan will likely date. PBDEs — unregulated chemicals trend toward either improvement or contain a reopener clause, probably used in relatively high concentrations deterioration. And a rough compari- after 5-10 years, to ensure that as flame retardants in electronic sion with Washington's monitoring results and new scientif- equipment, computers, TVs, textiles and 's Chesapeake Bay indi- ic findings are incorporated into and many home furnishings, particu- cated no significant difference from revised implementation plans. larly those containing polyurethane the Bay, and a similar scale of mercury Money is available through foam — have become ubiquitous over and PCB contamination. In the Bay Proposition 13 to fund some imple- the last decade. California, in partic- itself, sites in the lower South Bay, the mentation work (Foe, Pers.Comm, ular, mandates the use of flame retar- Petaluma and Napa river mouths, San 2002). Upstream of the legal Delta dants in all furnishings. While there Pablo Bay and are more in the San Joaquin River watershed, are some point sources (foam manu- contaminated than other sites (SFEI, selenium remains an issue but load facturers and electronic equipment 2002). reduction targets are being met. In dismantlers, for example) of PBDEs, the Central Valley, as of December MORE INFO? scientists do not yet understand all 2002, the state was considering their pathways into the Bay. PBDEs www.sfei.org renewal of a long-standing waiver are suspected of altering the regula- tion of both thyroid and steroid hor- % BAY SAMPLES MEETING WATER QUALITY OBJECTIVES* mones, but their effect on harbor seals is unknown at this point, and 1994 1995 1996 1997 1998 1999 2000 long-term effects may not become Chromium 100% 100% 100% 100% 100% n/a n/a apparent until a population is Copper 83 85 88 90 97 95 n/a exposed to additional stress. The Mercury 56 68 80 50 61 62 n/a effect of adding a new contaminant to Nickel 99 97 97 99 100 99 n/a the existing mix of harmful chemicals Lead 100 100 100 100 100 100 n/a and metals in the Bay is also Selenium 100 100 100 97 99 99 98 unknown. Zinc 100 100 100 100 100 100 n/a MORE INFO? PAHs 61 68 50 60 43 44 50 [email protected] Diazinon 93 100 93 100 100 100 100 Dieldrin 80 95 93 54 87 85 88 See also pp. 30, 32, 43, 68 Chlordanes 100 93 84 89 75 87 89 DDT 67 66 44 52 20 57 72 PCBs 2 9 6 19 20 19 6

*Bay data from Regional Monitoring Program, SFEI 2000. Data from 1998 are preliminary. 16 Watershed

RESTORATION Watershed

“The Estuary continues to change as we try to understand and manage it: exotic species continue to arrive; climate change is altering the timing and amounts of river flow, with consequences for the Estuary’s salinity; and sea level rise and earthquakes threaten the Bay’s shoreline.”

FRED H. NICHOLS, U.S. Geological Survey, (Retired)

17 PERSPECTIVE

TODAY’S CHALLENGES Third, institutions that are con- ducting research and monitoring FREDERIC H. NICHOLS with different objectives still have a U. S. Geological Survey, (Retired) tendency to carry out their work independently, with the result that Over the past three decades we monitoring and research data in have greatly expanded our knowl- many cases are not integrated and edge of the San Francisco Bay-Delta synthesized; individual investigators ecosystem and our understanding of are often reticent to place their human impacts. We better under- studies into a whole-system context. stand key food web interactions and Fourth, we will continue to be the sources of organic matter that challenged about how to allocate our support the food web. We more restoration resources most effective- clearly recognize the stressors that ly to achieve the highest level of affect threatened and endangered overall success. We must ensure, for species, including the impacts of example, that our actions have a lost habitat, flow alterations, con- basis in solid scientific understand- taminants and exotic species. ing, and that we are prepared to Managers, policy makers and the make political and resource man- public better appreciate the trade- agement decisions to change long- offs that are involved in managing held perceptions, practices and the watershed and Estuary for both policies. human use and for protection of species and . We are making particularly great progress on two important fronts: we are achieving “There is a natural tendency to worry about the small parts an unprecedented level of coopera- tion and collaboration among sci- of the ecosystem without considering the larger parts.... entists from agencies and academic We must avoid the temptation to undertake restoration institutions, and the increased emphasis on and funding for action simply because it seems an appropriate response restoration (largely through CALFED) is energizing scientists to a perceived need.” and local groups to undertake a broad array of new restoration proj- ects and research studies. In addi- tion, the Habitat Goals Project has given us the first comprehensive Finally, we need to assure the blueprint for restoration around the public that their investment is being Bay. well spent, by demonstrating that all Yet we still face important chal- of our research and restoration lenges. First, we lack understanding activities are fully transparent and of critical problem areas, such the openly and objectively reviewed, and most sensitive times in the life cycles that the results of these activities are of threatened and endangered readily accessible in understandable, species, the regional effects of local useful formats (Nichols, SOE, projects, such as the proposed 2001). expansion of San Francisco MORE INFO? International Airport, and the effect [email protected] of nonlethal contamination of indi- vidual fish or invertebrates on the well-being of their populations. Second, the Estuary continues to change as we try to understand and manage it: exotic species continue to arrive; climate change is altering the timing and amounts of river flow, with consequences for the Estuary’s salinity; and sea level rise threatens the Bay’s shoreline.

18 Watershed

FLOODS & DROUGHTS: which time there Observed Half-Way Dates for Streamflow A SIERRA NEVADA PERSPECTIVE have been much OBSERVED EARLIER STREAMFLOWS drier centuries, with MIKE DETTINGER 100-year droughts Eight Rivers U.S. Geological Survey and extreme flood June 1 periods. The San Francisco Bay Estuary is Climate change May 1 at the receiving end of a cascade of due to increasing climatic influences. Winter storms, greenhouse-gas con- droughts, El Niños and La Niñas, April 1 centration may soon Pacific decadal regimes — all affect augment such his- the Bay through changes in runoff torical and prehis- March 1 from the Sierra Nevada. Therefore, of Mass WY Flow Center torical climate varia- climate variability is an important tions. With global science topic with broad policy warming would come 1900‘10‘20 ‘30 ‘40 ‘50 ‘60 ‘70 ‘80 ‘90 2000 implications for long-term less snowfall (less planning and adaptive management than 25% of current snowpack levels for the Bay. Halfway dates for streamflow. During the past in certain areas by mid-century), 50 years, streamflow from the Sierra Nevada and droughts play particu- more rainfall, earlier snowmelt and has come progressively earlier in the year, as a larly important roles in the Estuary less spring and summer runoff. The result of warmer winter and spring temperatures dry summer regimes that typically over California which have fueled earlier and its watershed, not only because snowmelts. they inflict social and environmental result in the highest estuarine salin- damage, but because they can over- ities would become more intense if ride water quality management Sierra Nevada streamflow declines strategies. Large-scale Pacific atmos- earlier each year; winter floods pheric systems always play a role, but could also become more severe. there is no unique pattern that Indeed, Sierra Nevada streamflow causes either flood or drought. For has already begun to come earlier in example, despite the varied large- the year, by about two weeks, leaving scale climate conditions that pre- less runoff during the warm seasons vailed during the 1987-1992 (see graph). drought, which included both El Planning for the Estuary would Niños and La Niñas, that period benefit from improved understand- yielded persistently low streamflow ing of the climatic and hydrody- rates from the Sierra Nevada, and as namic variability of the Sierra a result, Bay were persist- Nevada (Dettinger, SOE ently elevated. 2001). Paleoclimatic records (from tree MORE INFO? SCIENCE rings, lakes and coastal sediments) [email protected] indicate that floods and droughts in Questions California during the historical period (the last 100 years or so) are • To what extent did major, long- small and brief compared to climatic term droughts of the past 1,000 extremes experienced at other times years in various parts of the Sierra during the last 1,000 years, during Nevada affect the Bay and Delta? • How likely are such droughts (and Merced River Responses to PCM-Simulated Climates SIMULA(a) RainfallTED as a Fraction RAINFALL of Total Precipitation AS A FRACTION OF their wetter than normal comple- PRECIPITATION, MERCED RIVER BASIN ments) to recur within various planning horizons? B06.22B06.22 (Historical) (Historical) 60 B06.44B06.44 (Business (Business as usual) as usual) • What is the likely, plausible range of climate variations over the Bay, Delta, and their watersheds dur- 40 ing the 21st century, given both past climate variations and projec- tions of greenhouse warming? 20 • What are the most likely respons- Percentage of Precipitation es to such climate changes in 1900 ‘20 ‘40 ‘60 ‘80 2000 2020 2040 2060 2080 2100 terms of Delta inflows, Bay and Delta sediment budgets, and Bay and Delta ecosystems? 19 RESTORATION QUAKE HISTORY & ODDS

HOW EARTHQUAKES MAY SHAPE THE BAY AREA ENVIRONMENT

MARY LOU ZOBACK U.S. Geological Survey

The topography and physical environment of the have been shaped by many millennia of earthquakes, but recent growth and development in the region will make future quakes have a far greater fiscal impact on society than those of the past. The Bay Area is transected by a network of active faults that accom- Large magnitude earthquakes (magnitude 5.5 or greater) in the greater San Francisco Bay-Delta modate the northwest motion of the region since 1850. The decrease in rate of large earthquakes in the 20th century has been widely attributed to a regionwide drop in stress due to the 1906 magnitude 7.8 earthquake. Pacific Plate relative to North America. In addition to sliding past region before 2030. Furthermore, efforts beforehand, relative to the North America, the Pacific Plate is it is likely that eventually the region large reconstruction costs after dis- also slightly colliding with it, creat- will see a return to the days before asters (Zoback, SOE 2001). ing the geologically young mountain 1906 when a magnitude 6 or greater belts parallel to the main strike-slip quake occurred every four years. MORE INFO? faults. Since Bay Area faults are part [email protected] of global plate motions, we are The impact of a given earthquake http://quake.wr.usgs.gov assured that these earthquakes will depends on the characteristics of the continue into the future. earthquake source (size, location, depth, rupture direction), charac- Scientists are currently unable to teristics of the path the seismic predict earthquakes in the short energy travels, and finally local site SCIENCE term; however, many advances have conditions, such as the strength of been made in quantitative forecast- the soil. Scientists' ability to define Questions ing of the likelihood of future both the likelihood of future earth- • How vulnerable is the Delta earthquakes and their impacts. It is quakes and the regions where earth- now clear that the occurrence of one quake effects will be most severe can system to effects of ground shak- large earthquake (like 1906) can be used to develop effective mitiga- ing and ground failure? What have profound effects on the rate of tion strategies. However, because of would be the impact of massive occurrence of earthquakes on adja- recent rapid growth and expansion levee failure and inundation of cent faults. The relative aseismicity it is clear that future earthquakes in Delta islands on the hydrodynam- of the Bay Area since 1906 contrasts the Bay Area will be far more costly ics of the Bay system? Can levees markedly with a high rate of occur- than in the past and may have be strengthened to prevent failure rence of large earthquakes in the national/global economic repercus- from future quakes? 50-70 years prior to 1906 (see sions. chart). The rapid growth and • What amount of mercury, PCBs, urbanization of the Bay Area in the Future quakes could have dramatic DDT and other legacy contami- 20th century has been facilitated by effects on the San Francisco Bay and nants could potentially be the low level of seismicity due to a Delta. Strong shaking and ground released into the aquatic ecosys- “stress shadow” produced by the failure accompanying such quakes tem by massive quake-generated 1906 earthquake. The extent to could result in massive levee failures liquefaction and sand venting? which we are emerging or have and disrupt aqueducts. In addition, What would be the impacts on the extensive ground failure in soft Bay emerged from this stress shadow is ecosystem and the food web? still a subject of intense scientific sediment, particularly liquefaction debate. A consensus report by the and venting of sand lenses within • How will the slip in future U.S. Geological Survey on the like- the , potentially could mobilize quakes impact sediment move- lihood of future damaging earth- older contaminants now suspended ments in the Bay and Delta? quakes in the San Francisco Bay in the mud. Should resistance to strong shak- region has concluded that there is ing be considered in design and about a 60-70% chance of at least As with many environmental questions, society needs to make planning for the restoration of one magnitude 6.7 or greater earth- large areas of soft bay mud to quake striking the San Francisco Bay hard choices about how much to invest in earthquake mitigation tidal wetlands?

20 Watershed

WATER & ENERGY There are similar myths sur- CONNECTIONS rounding both water and energy: SCIENCE MYTH 1: There is an energy shortage. Questions DR. PETER H. GLEICK There is no energy shortage, but Pacific Institute for Studies rather a shortage of companies will- • What demand management tools in Development, Environment, ing to sell it because of the structure can help us avoid future energy and Security of deregulation. and water crises? In the wake of the “California MYTH 2: There is a shortage of water. Energy Crisis” of 2000-2001, Again, there is no shortage. There many are asking if water is to be the is a shortage of intelligent manage- The parallels between water and next crisis. Indeed, there are ment of the discrepancy between energy offer some important lessons important connections between where demand is and where supply to improve water management in water and energy, and worrisome is. There is an inadequate effort to the future: parallels between the mismanage- redirect water from one user to ment of the state’s energy situation another. • There should be formal and and mismanagement of our water effective programs to manage MYTH 3: There were no rolling blackouts problems. We use water to produce demand. energy, and energy to produce in the summer of 2001 because of quick efforts water. Twenty percent of to build new power plants. • We should not build supply sys- California's electricity comes from There were no rolling blackouts tems that are more expensive the hydroelectric dams that line the that summer because of the success than demand management. of rapid conservation, which led to a Sierra Nevada from north to south. • Private companies should not More water goes to cool the fossil demand reduction of 3,100 megawatts. have monopoly power over pub- fuel and nuclear power plants that And because regulators were moni- meet the lion's share of our current toring generators more closely to lic goods, without strong gov- demands. prevent market manipulation. ernment oversight. MYTH 4: Water shortages are • We must protect water as a public inevitable because water deregula- good (Gleick, SOE, 2001). WATER SYSTEM ELECTRICITY USE SOUTHERN CALIFORNIA tion is on the way and new supplies MORE INFO? KW HR / ACRE-FOOT have not been built. [email protected] 3000 The problem is a demand www.worldwater.org one, not a supply one. And www.pacinst.org 2500 there is no deregulation on the horizon. 2000 Water and energy are both 1500 vital resources. The supply 1000 and distribution of both are also natural monopolies, 500 subject to the abuses of monopoly power. Private 0 Supply Distribution Waste Total corporations are Treatment playing increasing- ly powerful roles in ENERGY FOR WATER the provision of KW HR / ACRE-FOOT We also use energy to produce both resources. Meanwhile, 4500 water — to treat, pump and use we have ignored or under- water resources. Energy is required estimated the vast potential 4000 to run pumps for for efficiency improve- 3500 ments that can delay or farmers, to move water over the 3000 Tehachapi Mountains to the Los prevent Angeles basin, and to operate the a crisis. 2500 wastewater treatment plants that 2000 clean our wastes and protect our 1500 rivers, lakes, and beaches. Every acre-foot of water we use requires 1000 2,000 to 3,000 kilowatt hours of 500 electricity to collect, clean and 0 deliver. The more water we save, the Desalination State Water Colorado Recyding Groundwater more energy we save. Project

21 RESTORATION

IS THERE grew bigger; and fetches as European colonization resulted in ENOUGH SEDIMENT? grew longer. Wave action eroded the drastic changes in the processes that bayfront edge of the marsh creating sustained the landscape. A combina- PHILIP B. WILLIAMS extensive intertidal . tion of , , Philip Williams & Associates, Ltd. floodplain reclamation, and most The Estuary's marshes, mudflats importantly, hydraulic mining caused and tidal channel habitats have Those concerned with the long- huge increases in the amounts of sed- evolved and persisted for thousands term management of the Estuary are iment delivered to the Estuary. This of years, sustained by the inflow of changing their attitudes about the “Sierra mud wave” caused mudflats in sediment. Most of the sediment sediment that moves around the San Pablo Bay to rise 3-4 feet in ele- entering the Estuary eroded from Bay. Only a few years ago, many of vation, allowing fringing marshes to Central Valley watersheds and was us assumed that the Bay had too advance. conveyed downstream during large much sediment. We viewed sediment winter floods on the Sacramento In the 2oth century, sediment as an expensive nuisance that choked and San Joaquin rivers. Floods and delivery declined with the closure of shipping channels and muddied rivers deposited coarser sediments gold mines and the construction of swimming beaches, and the region upstream on the vast floodplains, dams that captured sediment and struggled with the problem of where leaving the clays and to settle reduced flood flows. Researchers to put all the mud that we dredged. out in the shallows of Suisun and (Jaffe et al., see also p.42) recently Today, scientists, engineers and San Pablo bays and occasionally, documented the lowering of inter- planners are starting to recognize during large flood pulses, in the tidal mudflats of San Pablo Bay, and that sediment is a valuable resource South Bay. Typically later in the resulting losses of about 90 acres that recreates and sustains habitats year, wind waves would resuspend per year of mudflats between 1951 we value, such as salt marshes and these muds, and tidal currents and 1983. If this trend has contin- mudflats. We are also recognizing would redistribute them to all parts ued in the last two decades, probably that we may have been somewhat of the Estuary. no more than 5,000 acres of mud- overconfident about relying on nat- flats remain — about the same Sediments are thus in motion ural to restore wet- acreage present in the Bay in 1850. through the Bay in all seasons and land processes in subsided areas. In If it continues into the future, our the mudflats and shallows act as other words, instead of too much mudflats will be practically gone in huge sediment reservoirs. The sediment, there may not be enough. the next 50 years. amount of this sediment recircula- To better manage estuarine sedi- tion is very large — probably more As we continue to alter the physi- ments in the future, we need to than 100 times as much sediment cal processes that sustain the mor- understand how sedimentary moves around within the Estuary, as phology of the Estuary, the rate of processes created the historic habi- comes into it via rivers and floods, change in estuarine habitats over the tats of the Bay, and how we have and within any given year. This is why next century could be as dramatic as will be changing those processes. San Francisco Bay's waters are so those of the past. Three trends are muddy. likely: San Francisco Bay, like all estuar- ies, is a dynamic evolving system, The form and whose shape is an expression of a extent of estuar- ESTUARY ANNUAL SEDIMENT BUDGET changing equilibrium between com- ine habitats is MILLIONS OF CUBIC YARDS peting physical processes: sedimen- ultimately tation, sea level rise, river flows, shaped by the tidal flows and wind wave action. sediment budget of the Estuary, 0.4Mcy 6.1Mcy The Bay is a geomorphically the balance Dredging Into Delta to upland 3.9Mcy young estuary formed only about between sedi- or ocean Into SF Bay 10,000 years ago when rapidly ris- ment delivered disposal ing sea level from melting ice caps by the rivers, inundated the mouth of the sediment stored Sacramento River through the on marsh plains 2.0Mcy . About 7,000 years or in deep water, Inflow and sediment from local 0.5Mcy ago the rate of rise of sea level Dredging slowed. Marsh plants kept pace with discharged to the to upland the 1-2 millimeters per year sea level ocean. 1.4Mcy 1.6Mcy disposal Golden Diverted rise by capturing sediment and Gate in water Sediment outflow withdrawals building peat, creating extensive 4.1Mcy marsh plains that gradually rose and delivery has Bay engulfed the surrounding topogra- changed dramat- phy. As the Estuary grew larger, the ically in the last tidal channels feeding the marshes two centuries (see graph p.23),

22 Watershed CENTRAL VALLEY SEDIMENT DELIVERY TO ESTUARY MILLIONS OF CUBIC YARDS will occur, particularly ment (either via natural deliveries or in the Delta where some dredged material placement) to 20 areas have subsided eventually recreate a mature vegetat- more than 20 feet ed marshplain on this acreage. below sea level. In the last 20 years, about With the creation of new sediment 10 3,500 acres of diked sinks both in the Delta and the Bay, subsided land have been and with the reduction of sediment returned to tidal action inflows, we will create a sediment Grazing Hydraulic Mining Dams &Diversions through levee failure in budget deficit, resulting in the 0 depletion of the sediment reservoir 1800 1850 1900 1950 2000 the Delta. in the shallows of the Estuary (see When we abandon a caption p.24). As a result, San 1. There will be further declines breached subsided site, such as Francisco Bay waters will likely in sediment delivery to the Delta. , we create a large sed- become less muddy. Stated more Average suspended sediment con- iment trap. In 1983, when the 1,000 scientifically, average suspended centrations are declining as the full acre Mildred's levee failed, the island sediment concentrations (ssc) in the effect of dams and diversions come was about 15 feet below sea level, cre- will decrease, and this to bear. Average annual Delta sedi- ating a sediment sink of about 24 decrease will directly affect how ment inflow is now probably only mcy. For the island to in, and quickly restoration projects that rely about 4.5 million cubic yards (mcy), return to the freshwater tidal marsh it on natural sedimentation, will about half its 1960s level, and barely once was, would require the equiva- evolve. Most restoration projects double that of the undisturbed lent of about five years of average completed so far have been in favor- landscape of 200 years ago. sediment delivery for the entire able locations where ssc is high and Estuary. Since much less than this wind wave action low. This allows 2. Sea level rise will accelerate due finds its way into Mildred, rapid natural sedimentation, as can to the greenhouse effect. According researchers estimate it could be more be seen at Carl's Marsh near to the latest predictions, rates will like a century or more before it is Petaluma after only six years since double over the next 50 years and shallow enough for a marsh to form. breach. Larger projects with lower double again in the succeeding 50 local suspended sediment concen- years. Thus while the Bay's water vol- The Mildred experience illustrates trations, however, may take much ume increases by about 2.5 mcy every a major restoration dilemma. longer to become vegetated or may year today, these annual increases will Freshwater tidal marsh habitat is stabilize as intertidal mudflats. swell to 10 mcy/yr in the next centu- now nearly extinct in the Delta. Alternatively, to compensate for ry. As the Bay increases in volume, Current proposals to restore up to slower natural sedimentation rates, deeper waters will capture more of 20,000 acres of islands as tidal projects like the Muzzi Marsh have the recirculating sediment. marsh would require very roughly used dredged materials to fill sub- 320 mcy of sedimentation (the sided sites and allow for rapid reveg- 3. Increasing amounts of estuar- equivalent of 70 years of sediment ine sediment will be captured in new etation (for project locations, see inflow), assuming an average of 10 map p.60). sediment “sinks” within the Estuary. feet of subsidence. The dilemma is, The direct effect of sea level rise in if such a large portion of the capturing sediment is relatively Estuary's sediment dis- small in comparison to its potential charge is captured in the indirect effect of causing failure of Delta to recreate valuable FUTURE AREA OF SAN FRANCISCO BAY levees surrounding diked subsided wetland habitat, will there land. Over the last 150 years, we be enough sediment left to 10 have diked, drained and pumped restore and sustain exten- 90% of the Estuary's former tidal sive tidal wetlands around Sea level with 1meter rise marshes. As a result, these lands the Bay? 0 have subsided below level, cre- Existing sea level ating a huge artificial hole around The largest regional onditions the Estuary. If all the Bay's levees wetland restoration initia- Complete levee failure failed, the Estuary would more than tive, coordinated by the -10 double in size and triple in volume San Francisco Bay Joint Existing C (see graph). At present sediment Venture, proposes to Elevation(feet NGVD) delivery rates, the resulting sediment restore about 37,000 -20 sink would take more than 1,500 acres of tidal marsh years to fill. around the Bay over the next 20 years. Assuming While no-one is contemplating -30 typical subsidence of about 0 200 400 600 800 1000 1200 any management scenario that con- four feet, we would need Area(x 1000 Acres) siders complete levee failure or about 250 mcy of sedi- removal, accidental levee failures

23 RESTORATION

SEDIMENT RESUSPENSION SCIENCE Levee Questions • How does sediment move around within the Estuary in response to tides, wind waves and flood MHHW events over long time periods? Mudflats Resuspension • Can we better predict how reduc- tions in sediment inflow to the Estuary, large-scale restoration projects, and sea level rise, will Sediment MLLW Reservoir change the shape and habitats of the Estuary, 10, 50 and 100 years into the future?

How big is the Estuary's sediment reservoir? To get this number, it's important to understand that mudflats and shallows are formed by the balance between deposi- tion and wind wave erosion. With reduction of sediment deposition the mudflats will erode to compensate. The amount of this erosion is limited by the size of the largest will actually sustain in the Estuary of waves scouring the shallows at low tide. Assuming that the Estuary's active sediment the future. This may mean we refo- reservoir is roughly the erodible wedge between mean sea level and 6 ft. below sea cus on restoring our diminishing level, it is not infinite. The reservoir greatly depends on whether we let the natural intertidal mudflats, or give higher shoreline retreat landward, releasing more sediment to the Estuary through erosion of priority to allowing marshes to the marsh edge. If we assume we do not do this, and instead reinforce our levees, expand inland. there are now (as of 1986 mapping) approximately 80,000 acres of shallows between msl and -6ft ngvd. If this entire area were to erode down to -6ft, it could Last but not least we need to rec- provide about 400 mcy of sediment to the Estuary. ognize that managing mud may be as important to S.F. Bay as the long- In conclusion, Estuary-wide how quickly or whether sites will standing effort to manage its supply changes in sediment dynamics have evolve to vegetated marsh for large of freshwater (Williams, SOE, many implications for habitat deeply subsided sites with limited 2001). restoration planning: sediment supply. MORE INFO? First, we need to understand the Fifth, we need to revisit our [email protected] Estuary as a dynamic evolving physi- restoration goals and priorities to cal system whose habitats will be match the habitats we want to restore changing with or without human with those that physical processes intervention. This also means we need to focus research on sediment CORDGRASS COLONIZATION LEVELS dynamics. 5 Second, we need to be planning for the future physical evolution of 4 the Estuary on an Estuary wide scale. This means recognizing that actions 3 that impact sediment dynamics like dredging, hardening levees, tidal restoration, or airport fills can have 2 significant long-term impacts on Approximate Spartina pioneer colonization elevation estuarine habitats. 1

Third, we need to value our sedi- 0 100 mg/l ment. Specifically this means maxi- 200 mg/l

mizing the reuse of dredged materi- Ground Surface Elevation(feet NGVD) 300 mg/l -1 als within the tidal zone of the 400 mg/l Estuary system, particularly for wet- land restoration. -2 0 10 20 30 40 50 60 70 80 90 100 Fourth, we need to be realistic in Years Since Breach addressing the long-term physical constraints on tidal wetland restora- How mudflats build up in a typical subsided site at different average suspended sediment concentra- tion — specifically understanding tions. If ssc is reduced from 200 to 100mg/L, it can make the difference for a in a breached subsided site reaching the colonization elevation for spartina in 40 yrs instead of 10 yrs.

24 Rivers & Delta

RESTORATION Rivers & Delta

“The variability of streamflow and sediment flux is one of the stunning complexities of the natural environment. Water resources development and land use changes alter and suppress this variability. Restoring the Delta and Central Valley ecosystem is about restoring variability and complexity.”

DAVID FREYBERG Stanford University

25 RESTORATION

THE DELTA-CENTRAL VALLEY specific systems or behaviors are gen- graphs to make decisions about what SETTING: HYDROLOGIC eralized into conceptual understand- size to make reservoirs, channels, COMPLEXITY AND ing. The tools of design are similarly screens or other water control facili- RESTORATION different from the tools of analysis. ties. And that is exactly what's appro- Of particular interest is the role of priate if the facility or system being DAVID L. FREYBERG complexity in the design process. designed is supposed to reduce com- Stanford University plexity. However, these same tools The variability of streamflow and may not be appropriate if our goal is Ecosystem restoration is funda- sediment flux is one of the stunning designing for variability and com- mentally a problem of design. The complexities of the natural environ- plexity. Much riverine restoration design process translates conceptual ment, and the role of this complexity design is struggling to adapt design understanding of ecosystem structure in the ecosystem restoration design concepts and tools based on reducing and function into concrete changes at process is fascinating. Water complexity to problems of restoring a particular site. This process is quite resources development and land use complexity. different from the discovery process changes alter hydrologic variability of science, in which observations of and, in general, suppress variability No matter how well we understand and complexity. This is always true the underlying scientific principles, for in-channel or flood plain struc- or how carefully we analyze a prob- IMPACTS ON FLOW tures and diversions, and often true lem, all design proceeds through fail- for land use changes. Reducing ure. It does not matter whether we Monthly Mean Daily Flows (cts) complexity is their purpose. are talking about software, bridges, 30,000 Post-Shasta Dam dams, water supply systems, or The Delta and its rivers 25,000 Pre-Shasta Dam ecosystem restoration. Because total are a complex hydrologic system failure can be catastrophic when we 20,000 characterized by tremendous vari- are designing for species and ecosys- ability. Streamflow varies over a tem health, an adaptive process, 15,000 broad spectrum of time scales from grounded in observation and analysis 10,000 seconds to tens of thousands of of performance, is essential for suc- years. Hydrologic science provides cessful restoration design (Freyberg, 5,000 partial predictability over some time SOE, 2001). scales, but streamflow, and with it 0 Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep heat, sediment, and chemical trans- port, remain largely unpredictable MORE INFO? Relative Variability of Daily Flows Daily Flow Coefficient of Variation and apparently random over many [email protected] 1.6 other time scales. Central Valley 1.4 and Delta ecosystems have evolved 1.2 in the presence of this hydrologic variability, and riparian and wetland 1.0 SCIENCE 0.8 ecosystem structure and function are clearly coupled to this variabili- 0.6 ty. Our use of water as a resource Questions 0.4 necessarily entails altering the natu- 0.2 ral variability of streamflow, both to • To what extent does ecosystem 0.0 synchronize availability with use and restoration depend on restoring Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep to buffer unpredictability. Different the entire streamflow variability Skew of Daily Flows uses have different effects on differ- 9.0 ent time scales, but essentially all spectrum? 8.0 uses involve hydrologic time-shift- • To what extent are ecosystem struc- 7.0 ing (see graphs). ture and health robust with respect 6.0 to hydrologic variability? 5.0 Restoring the ecosystem of the 4.0 Delta and Central Valley is at some • How should we characterize the 3.0 point, therefore, about restoring complexity of hydrologic variability? 2.0 variability and complexity. This • Are there portions of the streamflow 1. 0 provides a peculiar challenge to the spectrum that are less important? 0.0 design process. Most of our familiar -1.0 Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep hydrologic design tools and design • What characteristics of streamflow criteria are focused on problems of should we be measuring over what coping with or reducing variability. temporal and spatial scales? Changes in flow variability due to the con- We try to find ways to simplify com- struction of Shasta Dam, as measured at the plexity to make design decisions. For • How important is predictability USGS gaging station on the Sacramento example, we use statistical tools such in restoration design? River above Bend Bridge near Red Bluff, CA (Station No. 11377100). as design floods and design hydro-

26 Rivers & Delta

RECIPROCAL RELATIONS fit that lowland river restoration BETWEEN CENTRAL VALLEY provides for the Bay-Delta. SCIENCE RIVERS AND FLOODPLAINS Restoration of Central Valley low- Questions JEFFREY F. MOUNT land rivers involves reestablishing U.C. Davis the drivers that support food webs • What is the role of interchange between and energy flow, heterogeneity of river channel and floodplain in maintain- The historic lowland rivers and landscapes and processes, and com- ing or restoring ecosystem integrity in floodplains of the Central Valley munity structure of top-level con- the Sacramento / San Joaquin system? were one of the key biogeochemical sumers (fish, birds). The driver of engines that fed ecosystems in the ecosystem integrity in this system was • How can we create “learning laborato- Bay-Delta. Changes associated with the reciprocal hydrologic, sedimen- ries” within the CALFED region of inter- river regulation and channelization tologic and biogeochemical relations est in order to test and evaluate flood- have significantly degraded this vital between the river channels and plain and channel restoration efforts? ecosystem function. The learning floodplains. Where reconciliation of • Are we getting our money’s worth for this regionally dysfunctional rela- laboratories of the Central Valley, restoration? Can we quantify the hydro- such as the Yolo Bypass and the tionship has occurred, there has logic and ecological benefits associated Cosumnes/Mokelumne River flood- been a significant beneficial plains, demonstrate the direct bene- response. with restoration projects, and the impor- tance of scale in these systems?

RIVER-FLOODPLAIN CHL = chlorophyll INTERACTIONS DOC = Dissolved organic carbon CPOM = coarse particulate organic matter Stage I FPM= fine particulate organic matter Low Flow In order to restore lowland rivers in the Central Valley, the winter flood pulses and the smaller, but equally important, spring snowmelt pulselets must be able to reach a sig- Disconnected, Closed-system • High Residence Time nificant portion of the historic Autogenic Sink • Moderate Primary Productivity floodplain. The magnitude and duration of these flood events, cou- pled with their hydraulic interaction with the floodplain, dictate land- Stage II Near-Bankfull Flows CHLa scape heterogeneity, as well as pro- DOC ductivity and succession in linked aquatic and terrestrial ecosystems. The length and duration of trans- • Wetland Connection port pathways on floodplains and in Connected, Open-system • Channel Migration flood basins plays a critical role in • High Residence Time regulating interchange with the river Autogenic Source • Moderate Primary Productivity (see opposite). Several hurdles stand in the way of Stage III Sediment attempts to restore ecosystem func- Flood Flows CPOM FPOM tions and attributes in lowland rivers and floodplains in the Central Valley, among them institutional preferences for a hard-engineering • Channel Migration approach, a water supply and con- Connected, Open-system • Floodplain Accretion Autogenic Source • Moderate Residence Time trol system designed to limit floods, • Moderate Primary Productivity inappropriate restoration project scales, and a reluctance to embrace restoration as a social science and not simply a physical/biological sci- Stage IV Sediment Flood Flows CPOM ence (Mount, SOE, 2001). FPOM

MORE INFO? • Floodplain Accretion and Scour [email protected] • Channel Switching Connected, Open-system • CPOM & FPOM Exchange http://watershed.ucdavis.edu/crg/ Autogenic Sink/Source • Low Residence Time • Low Primary Productivity

27 RESTORATION

SCIENCE CENTRAL VALLEY RIVER pying every niche of Central Valley RESTORATION AND river ecosystems, all four runs of Questions SALMONIDS chinook salmon (winter, spring, • What are the impacts of improved late-fall, and fall) and steelhead are fish passage and large-scale channel TIM RAMIREZ now listed (or candidates for listing) restoration on populations of California Resources Agency under state and federal endangered endangered and threatened species acts. The success of efforts to restore salmon and steelhead? Central Valley rivers and their Two strategies are proposed for • Can rivers below large dams (e.g., ecosystems is often measured — for both looking back to measure the Tuolumne River) be managed to better or for worse — by chinook impact of previously funded projects restore physical processes that mimic salmon and steelhead populations. and charting a course for future historic hydrology (magnitude, timing, investments. frequency, and duration) at a level that CREEK SPRING-RUN CHINOOK First, we need to will support native salmon and steel- RESTORATION EFFORTS (NO. OF FISH) restore access to areas head populations? 25,000 where historically these Western siphon installed; two dams removed Durham Mutual fish screen and ladder completed species thrived. Winter- Adams Dam fish screen and ladder completed run and spring-run chi- Gurrill Dam fish screen and ladder completed nook salmon and steel- 20,000 sheds for the recovery of winter-run head all developed life and spring-run chinook salmon and cycles that depend on steelhead. The dramatic increase of high elevation habitats 15,000 spring-run chinook salmon on M&T water exchange (e.g., cold water and Butte Creek, where dams have been provides 40 cfs base flow cool above the removed and ladders and screens valley floor). Dams on 10,000 have been constructed, is particular- almost all Central Valley Parrott Phelan ly encouraging. installed rivers now prohibit this movement upstream. 5,000 Second, we need to restore flood- Point Four However, in some way corridors to allow for the his- Dam removed watersheds with small toric connectivity between rivers and dams, efforts are under- 0 their floodplains. Physical processes ‘80 ‘82 ‘84 ‘86 ‘88 ‘90 ‘92 ‘94 ‘96 ‘98 ‘00 ‘02 way to remove migration are the underpinnings of a healthy barriers and/or improve , and floods are the upstream passage for heartbeat of a river. Large dam con- The recovery of these charismatic adults and downstream migration struction has eliminated winter and species is called for in both state and for juveniles. Investments have been spring floods in reaches down- federal law, and salmonids have a made to restore access on Butte , and channel manipulation rich cultural and economic heritage Creek, Battle Creek, and Clear and levee construction have isolated in California’s history. Once occu- Creek, and these are critical water- floodplains from their rivers. Efforts on Clear Creek and the Tuolumne River are underway to TUOLUMNE RIVER FLOODWAY EXPANSION(IN FEET) address both the physical structure of floodway corridors and to mimic 125 Existing 5,000 CFS Water Surface Valley Oak Tuolumne 9,000 CFS Water Surface Fremont Cottonwood River seasonal hydrology (e.g., winter 115 15,000 CFS Water Surface White Alder Floodway rain and spring snowmelt floods) 105 Narrow Leaf Willow that sustains salmon and steelhead. Warner Pond 95 (Under Excavation) Tulare Pond Large-scale channel restoration on 85 the Tuolumne River is being 75 designed in the context of current flood management strategies, and 65 is perhaps the best opportunity in 0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 the San Joaquin Valley to mimic seasonal hydrology to support fall- 125 Proposed run chinook salmon. 115 Tuolumne River Floodway The restoration of Central Valley 105 Warner Pond Modified rivers and their salmonids is an 95 (Under Excavation) Tulare Pond unprecedented challenge in river 85 and species management, but will 75 not require an unprecedented 65 investment. Gold mining and water 0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 development have transformed the 5x vertical exaggeration

28 Rivers & Delta

SCIENCE Central Valley landscape over the SALMONID LIFE HISTORIES: last 150 years. If we are to meet this FREEWAY FLIERS Questions new challenge, then our restoration OR SUNDAY DRIVERS? • What is the population impact of efforts must be at the same (or salmonid mortality sources? Are these greater) scale as our actions that BRADLEY CAVALLO sources of mortality sufficient to drive degraded (and in some cases, con- Department of Water Resources tinue to degrade) these river ecosys- overall patterns of salmonid abun- tems and threaten the extinction of Strategies for conservation and dance? If not, why are we devoting such our Central Valley salmon and steel- management of species are strongly a large portion of our efforts to mini- head. influenced by our underlying mizing these sources of mortality? assumptions about life histories, Relative to predation, diversion and Since 1995, the CALFED behaviors and critical habitats. stranding losses, what are the popula- Ecosystem Restoration Program for Often these conceptual models are tion benefits (or losses) provided by the Bay-Delta watershed has funded not identified explicitly, yet they complex and functional riverine and over 320 projects at a cost of more shape restoration actions and per- estuarine habitats? than $330 million. The CALFED ceptions of factors thought to limit Record of Decision, signed in species abundance. August 2000, calls for at least $150 channels) and small, low-elevation million to be available annually for Until recently, management of tributaries increasingly appear to serve the Ecosystem Restoration Program salmon and steelhead in the as critical habitats for many salmonid for each of the following four years. Sacramento-San Joaquin system has life stages. Dive surveys of the Feather In order to account for the per- been based upon a simplified life River, for example, indicated that a formance of the projects funded to history, consisting of freshwater and majority of juvenile steelhead were to date and to guide our future efforts, ocean phases linked by a simple be found in small, side channels, the Ecosystem Restoration Program riverine corridor. This view has been despite the fact that side channels needs to develop a sound strategy termed the monitoring or “produc- represent a very small proportion of for measuring the impact of these tion” approach to salmonid study the total habitat available in the river investments at the landscape level and management. Guided by this (see chart). Similarly, salmon have scale. This evaluation must also paradigm, managers often sought to been found to heavily utilize and ben- include a feedback mechanism to identify bottlenecks for salmonid efit (in terms of growth and survival) ensure that project monitoring production within a particular com- from seasonal habitats such as flood- results are analyzed and used to ponent of the environment (e.g., plains and intermittent tributaries. direct future activity (Ramirez, estuarine predation). However, The value of life history plasticity SOE, 2001). recent studies suggest the need for an alternative framework driven by (opportunism) and diversity are also MORE INFO? ecological understanding. evident in the rapid adaptations [email protected] salmonids show to altered environ- http://calfed.ca.gov This new framework acknowledges mental conditions in regulated rivers. the opportunistic tendencies increas- With regard to factors regulating ingly evident among salmonid popu- salmonid abundance, studies increas- lations. With complex and ingly show that oceanic conditions dynamic life cycles, salmonids play an important role. In the north- JUVENILE STEELHEAD FEATHER RIVER capitalize on a variety of avail- ern Pacific Ocean, measures of 1999-2001 able habitats that extend oceanic currents are now known to 100 beyond those acknowledged by strongly regulate productivity of zoo- No. of Fish the traditional “production” and, in turn, productivity of Observations 90 driven approach. In this con- salmonids. Habitat Available text, distribution and abun- Application of ecological minded 80 dance of healthy salmonid pop- ulations will depend upon the studies rather than relying on “pro- 70 complex array of habitats which duction” driven monitoring studies permit life cycle diversity, and has already yielded many new and sig- 60 on ecological processes such as nificant insights to salmonid life his- 11,883 tory and behavior. Integrating these % changes in food webs and envi- 50 ronmental conditions. findings into our conceptual under- 9,407 standing will enhance our ability to 40 Evidence supporting this manage salmonid populations and approach comes from studies implement effective restoration and 30 of habitats often ignored by conservation actions (Cavallo, SOE, traditional approaches as 2002). 20 insignificant or even detrimen- MORE INFO? tal. Off-channel habitats 10 (floodplains, ponds, river side- [email protected]

0 Side Channel Main Channel 29 RESTORATION SCIENCE TRACKING Researchers recently conducted Questions EFFECTS ON NATIVE FISH genetic biomarker research on a WITH BIOMARKERS Central Valley native fish, the • What chemical is causing the geno- Sacramento sucker (Catostomus occiden- toxic responses observed in the San SUSAN ANDERSON talis), to explore pesticide effects. Joaquin River? Are effects related to Davis Bodega Marine Laboratory Agricultural pesticides contaminate pyrethroids? Will these effects harm waters of the Sacramento and San fish populations? Researchers using genetic bio- Joaquin watersheds at concentra- • What techniques provide the best marker techniques have some new tions toxic to test invertebrates (see clues as to contaminant effects on a de Vlaming, p.32). However, effects indicators of agricultural chemical native fish species in the Central on resident native fish are only now contamination? Valley of California. These biomark- being examined. er techniques track genetic damage to organisms, such as breaks in DNA Researchers performed experi- Ongoing studies seek to further strands, that may lead to mutations ments using both field caging and investigate the cause of the genetic and reproductive changes. The prin- laboratory exposure (to field-collect- toxicity observed and to further ciple utility of biomarker techniques ed water) to test whether pesticide evaluate the effects of low-level con- is to evaluate sublethal effects of toxi- exposures are correlated with bio- tamination on individuals and pop- cant exposure in resident aquatic marker responses in the Sacramento ulations. In this case, the biomark- species. Although chemical analyses sucker. Experiments were timed to ers and mutagenicity studies may and toxicity tests characterize toxicant coincide with the first rainstorm have uncovered the presence of toxi- exposure and effects, they cannot event after dormant-season applica- cants that are detrimental to the define latent and sublethal responses. tion of organophosphate (OP) health of fish, but that are not yet pesticides to orchards. Researchers well characterized. Biomarker measured various biomarker research is also underway to evaluate responses, including the health of juvenile chinook DNA strand breaks salmon and endangered delta smelt. DNA STRAND BREAKS IN SAN JOAQUIN RIVER SUCKERS (Comet Assay), and Any application of such biomarker also evaluated pesti- 80 300 techniques should occur with some cide concentrations. SJ Strand Breaks basic principles in mind. For exam- 70 OU Strand Breaks ple: 1) multiple biomarkers should be ChE Inhibitors Conc. 250 In terms of the 60 DNA damage, strand used to characterize both exposure and effect, 2) time- and tissue- ail 200 break data indicate 50 significantly elevated dependent responses should be con- oncentration (ng/L) omet T sidered, 3) laboratory and field stud- 40 150 damage from the San Joaquin River ies should be integrated to maximize 30 (38.8%, 28.4%, and the scope of inference in any study 100 and, 4) exposures should be well % DNA in C 53.6% DNA strand 20 characterized with chemical analysis. Cages In Cages In breakage in 2000 50

otal OP Pesticide C The relationship between a biomarker 10 T field, 2000 lab, and 2001 field exposures, response and a change in the fitness 0 0 respectively) com- of an organism may vary depending 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 1 2 3 4 5 6 pared to a nearby ref- on the type of technique selected. January February erence site (15.4%, Although techniques are sometimes 8.7%, and 12.6% in DNA strand breaks (comet assay) in red blood complicated, they can be applied to 2000 field, 2000 lab, and 2001 cells of fish caged at SJ during dormant sea- relatively simple problems. For son pesticide runoff events in 2001. One pair field exposures, respectively). example, they may be utilized in of cages was deployed on Jan. 17 and Though the data confirmed genetic studies to simply determine whether retrieved pre-runoff, and two pairs of cages damage correlated with rainstorm contaminants are involved in poor deployed at the onset of rain (Jan. 25) and events, researchers found no corre- retrieved at different times during the runoff health of a species. More complex lation between the damage and OP event. Light blue bars represent mean DNA programs can later be devised to pesticide concentrations, leaving the strand breaks (% DNA in comet tail) (± stan- determine the severity of effects, the dard deviation) in fish caged at San Joaquin cause of the toxicity unknown. nature of the contaminants, and the River near Vernalis (SJ), and medium blue bars represent DNA strand breaks in fish caged at In 2001, the Ames mutagenicity possibility of population-level effects the field reference site (Orestimba Creek at assay, a rapid bacterial test that exam- (Anderson, SOE, 2001). Orestimba Road; OU). Line graph indicates ines genetic mutations caused by MORE INFO? total concentration (ng/L) of cholinesterase- contaminants, was applied to field- inhibiting pesticides detected in water samples [email protected] collected water. The assay indicated from SJ. Same letter indicates no significant (p www.bml.ucdavis.edu/peeir < 0.05) differences among mean DNA strand that San Joaquin River water was sig- breaks. Source: Whitehead & Anderson, SOE, nificantly more mutagenic than the 2001 reference site.

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SHALLOW-WATER HABITAT: In the Yolo Bypass, recent studies GOOD FOR FISH? (Sommer et al. 2001, 2002a,b) SCIENCE demonstrate the value of floodplain LARRY BROWN to native splittail (Pogonichthys Questions U.S. Geological Survey macrolepidotus) and chinook salmon (Oncorhynchus tshawytscha). When the • Do we need a more precise definition of In the last decade, many people Yolo Bypass remains flooded for shallow-water habitat? assumed that recovery of native fish more than three weeks during the • Is there strong evidence that native species in the San Francisco Estuary, spawning period of splittail, spawn- species are being limited by the absence particularly threatened fish species, ing is very successful. Similarly, a of such habitat? depended at least partially on the flooded Yolo Bypass appears to pro- restoration of shallow-water habitat vide better rearing habitat for juve- • How well do fish communities respond — a logical assumption given the nile chinook salmon than the to habitat restoration projects? tremendous losses of habitats such as Sacramento River. These data indi- tidal wetlands over the last 150 cate that a flooded Yolo Bypass is a years. The general acceptance of this good thing for native species of restoration projects to mimic habi- assumption, however, occurred in concern. the absence of a precise definition tat conditions in the small sloughs, of shallow-water habitat and strong In the central Delta, recent stud- the likelihood of promoting native evidence that native species are ies (Simenstad et al. 2000) of tidal fish species is increased. being limited by the lack of such wetland and marsh habitats show Studies of existing shallow-water habitat. that the fish communities are com- habitats should continue so that the posed of mixtures of native and responses of the fish communities to The phrase “shallow-water habi- introduced species. The introduced habitat restoration projects can be tat” is really not very useful unless a fishes strongly dominate the com- better predicted. Similarly, habitat more detailed description of the munity. The presence of the intro- restoration actions should continue habitat in question is available. duced water plant, Egeria densa, but within the framework of adap- Types of shallow-water habitat often appears to be an important factor in tive management and with a willing- discussed in the Estuary include determining the fish community. In ness to change or discontinue prac- shoals around deeper bays, tidal areas where this plant is abundant, tices that do not fulfill objectives marshes and wetlands, permanent native fishes are extremely rare, and (Brown, SOE, 2001). and seasonal marshes and wetlands, the fish community is dominated by and river floodplains. introduced fishes such as large- mouth bass, redear sunfish, and MORE INFO To humans, perceptions of shal- bluegill. The presence of the plant [email protected] low and deep are dependent on a and associated predatory fish may person’s height. For fish, shallow www.estuarynewsletter.com/ disrupt natural patterns of habitat and deep are best interpreted in 2001_12/feature_2001_12_01.pdf use by native fishes and may also terms of a species’ life history. For result in increased mortality due to example, scientists hypothesize that predation. delta smelt (Hypomesus transpacificus) spawn on hard structures along In Suisun NATIVE/ALIEN FISH MIX IN SLOUGHS channel margins that are consider- Marsh, studies ably shallower than the open chan- (Matern et al. 8.28 6.27 5.23 3.12 5.39 6.17 2.61 4.84 3.34 1.72 nels and bays where they spend most 2002) show 100 of their adult life. They also that smaller hypothesize that the newly hatched sloughs appear 80 smelt survive better and grow faster to provide when their rearing habitat is near better habitat 60 extensive areas of shoals in Suisun for native Bay, rather than confined to deeper fishes than do 40 channels upstream of Suisun Bay. larger sloughs. Thus smaller % Catch (Fish/Min) More recently, restoration of 20 sloughs may shallow-water habitat has evolved to Peytonia Spring Branch Cutoff Nurse Suisun-Lower Denverton Good Year Boynton Montezuma provide a tem- Suisun-Upper mean restoration of floodplain in 0 plate for Resident Alien Seasonal the upstream part of the watershed Resident Native designing and restoration of tidal wetlands and Excludes Stickleback Catch habitat the marshes in the Estuary. Recent restoration studies in Yolo Bypass, the Central Percentages of resident native, resident alien, and seasonal fishes captured projects in Delta, and Suisun Marsh illustrate in Suisun Marsh sloughs. The number on the top of the indicates the Suisun Marsh. the benefits and challenges associat- average number of fish caught per minute of trawling. Suisun Slough, Presumably, ed with habitat restoration. Montezuma Slough and Nurse Slough are considered large Sloughs. by designing Number at top of each is average fish/minute. Source: Scroeter & Moyle, U.C. Davis.

31 PERSPECTIVE THE CENTRAL VALLEY INSECTICIDE SAGA DELTA RESTORATION order to effectively restore them. PRINCIPLES These marshes did not form as the Sacramento and San Joaquin rivers VICTOR DE VLAMING DENISE REED U.C. Davis brought down sediment and built University of New Orleans new land out into open water (as the Mississippi delta formed); they Water quality regulators discovered The call for wetland restoration in formed as the sea level rose and organophosphorus (OP) insecticide contam- the Sacramento-San Joaquin Delta flooded the land, spreading tidal ination of Central Valley aquatic ecosystems arises from the recognition that not influence landward. Restoration in the mid 1980s, when water samples col- only has a vast acreage of wetlands planners should not, therefore, lected from the Sacramento River and San been lost but also that tule marshes expect riverine or tidal processes to have value both for at-risk species Joaquin River watersheds for toxicity tests build marsh substrate into open and society as a whole. Experience water areas (e.g., flooded islands). were lethal to the zooplankton test species. from other Follow-up investigations by the Central Valley large-scale Regional Water Quality Control Board identi- ecosystem SHALLOW BREACH fied diazinon and chlorpyrifos as the primary restoration Agricultural Phase causes of the toxicity, and land use practices programs and MHHW as the source, and provided estimates of the from contin- magnitude, duration, and geographic extent ued studies of MLLW of toxicity. Results demonstrated that in agri- the Delta tells culture-dominated areas, almond and stone- us that to be fruit orchards were the primary source of the successful in the long-term ~1 Year Post Flooding OPs. These insecticides are applied to MHHW we must have orchards in late December and January. OPs clear objec- are relatively water soluble, and the insecti- tives, use what MLLW cide-caused toxicity was recorded in water- we know, and ways during January through mid-March continue to during and following rainstorms. develop new 2-3 Yrs Post Flooding information as MHHW In urban-dominated waterways OP- we proceed.

caused toxicity was seen following storm MLLW water runoff, but also at other times of the The princi- year. Extensive home, landscape, green- ples offered here for tidal house, and industrial use of OPs was con- marsh restora- sidered to be responsible for contamination ~20 Yrs Post Flooding tion in the MHHW of urban streams. Delta are intended to OP insecticide use in the Central Valley MLLW guide our peaked in 1995, and is now diminishing (as efforts from a substitutes come into play). In 1995, about system-level 8,336,100 pounds of OP active ingredients perspective, Artificial & Natural Levee Agricultural Surface Tules Marsh Soil were applied, or about 184 pounds per and provide Post-breach Alluvial Fill Submerged Aquatic square mile of agricultural lands in California. context for the Vegetation conceptual In 1998, more than ten years since the models behind individual restoration projects. Four initial observation of the OP insecticide In addition, the rivers themselves common restoration myths inspired problem, the Regional Board placed various have been fundamentally altered and my suggestion of these principles: waterways on the (CWA) restoration must proceed, at least in §303(d) list of impaired water bodies, and the near term, under the current initiated the allocation of allowable loads 1) Let nature do the work. discharge and sediment regime. For among sources of the contaminants 2) Build it and they will come. the time being, restoration planners can't, for example, propose taking (TMDLs) in the Sacramento and San 3) The secret is finding enough sediment. Joaquin watersheds. Two groups, one of down Shasta Dam or taking out the stakeholders and one a grower-pesticide 4) Enough of the studies, we need a plan of Sacramento River navigation chan- industry group, are now assisting the board action for Delta restoration. nel. Delta wetland restoration thus largely involves rebuilding substrate and the region with insecticide reduction that has been lost to subsidence, and efforts (de Vlaming, SOE, 2001). Let nature do the work: It is imperative where necessary adding new materi- to understand the natural processes al. Contemporary processes can MORE INFO? that formed the Delta's marshes in then maintain wetland elevations in [email protected]

32 Rivers & Delta INTERVENTION WITH DREDGED MATERIAL 2-3 yrs Post-Flooding MHHW tion between hydrol- SCIENCE MLLW ogy (river and tides) with landscape struc- Questions ture (marsh plain, channels, ponds). • What value do the various bio-- Intervention Superimposed on MHHW physical attributes (e.g., marsh edge, this is the complexity marsh channels, ponds) of Delta of food web dynamics MLLW marshes provide to at-risk species? and small-scale habi- tat structures provid- • What values do these various attrib- ed by submerged utes provide to society (e.g., bird Artificial & Natural Levee Marsh Soil aquatic vegetation, Tules watching, fishing/hunting)? Agricultural Surface Unconsolidated edge and periodically Organics • Do the present-day lower elevation, Post-breach Alluvial Fill Submerged inundated surfaces. Dredged Material Aquatic tule-dominated restored marshes pro- Vegetation Creating multiple characteristics in a vide the same ecological and societal values as the historic Delta plain did? the face of sea-level rise and even marsh - shallows, build within the . edges, channels — will lead to multi- • Does restoration of Delta marshes for Delta restoration principle #1 ple uses by different plants and at- ecological reasons alleviate other risk species, and multiple benefits in should be: Understand the natural problem areas, such as water quali- terms of levee protection and water processes that formed marshes but ty/quantity and levee protection? Are acknowledge that restoration must quality and supply. Restoration planners should ensure a mix of there regions of the Delta where work within the constraints of cur- restoration should be a higher priority rent processes. both structural and dynamic habitat attributes and not simply seek to because of synergistic benefits in Build it and they will come: The value increase the acreage of tules. multiple problem areas? we associate with natural marshes Therefore, Delta restoration princi- comes not from the vast acreage of ple #2 should be: Restore marshes as tules but from the dynamic interac- one component of a flowing and flooding landscape. marsh elevations in the face of sea- level rise. Therefore, Delta restora- The secret is finding tion principle #3 should be: Marsh DEEP BREACH enough sediment: One of restoration is an exercise in biogeo- the major challenges Agricultural Phase morphology and must appreciate in restoration of tidal MHHW physical, biotic and sediment-relat- wetlands in the San ed processes. Francisco Estuary is MLL the availability of We’ve done enough studies, let's get on with sediments to build the real work and make a plan of action for back substrate in Delta restoration: Having established ~1 Year Post Flooding highly subsided areas our goals we need a plan of how to MHHW (see also Williams get there but this must encompass p.22), but the role of our uncertainties both about how MLL vegetation must also the system works and about future be considered. conditions. We must also ensure our Several freshwater plans and approaches are sufficiently marsh species pro- flexible to take advantage of oppor- 2-3 Yrs Post Flooding MHHW duce substantial tunities that may arise— from bene- below-ground bio- ficial use of dredged material to MLLW mass and tules grow mitigation or even floods. below the level of Therefore, Delta restoration princi- Delta marsh plains. ple #4 should be: Be prepared for Restoration efforts surprises and make the most of must ensure a mini- opportunities (Reed, SOE, 2001). ~20 Yrs Post Flooding MHHW mum substrate eleva- tion but it is not MORE INFO? MLL always necessary to [email protected] rebuild substrate all www.estuaries.org the way up to the nat- Artificial & Natural Levee Marsh Soil Tule ural marsh levels Agricultural Surface Unconsolidated because vegetative Organics Submerged Post-breach Alluvial Fill Aquatic contributions can Vegetation develop and maintain

33 RESTORATION SCIENCE INTEGRATING needs simultaneously – single issue Questions RESTORATION SOLUTIONS solutions are unlikely to be success- ful. Integrating ecosystem restora- • How are large scale restoration efforts CURT SCHMUTTE tion and enhancement with water in the Delta and Suisun Marsh affected Department of Water Resources quality and flood control benefits is by , non-native possible, even as we control and species growth, mercury methylization, Tidal brackish and freshwater wet- reverse the effects of subsidence in subsidence reversal, and salinity land ecological resources in the Bay- the Delta and Suisun Marsh. Phased responses to plan form changes? Delta Estuary have experienced sig- construction of habitat nificant quantitative and qualitative projects within existing ecological declines over the last century, pri- gradients, for example, can reverse marily as the result of land reclama- the effects of subsidence through ficial to the ecological functioning tion and subsequent development. bioaccretion and eventually return of the complex Bay-Delta Estuary Restoration of tidal wetland habitats large floodplains to tidal action, as system. Implementation will also and enhancement of associated well as improve Delta flood con- require optimism beyond reason. upland transition areas within the veyance. Large sediment loads could Estuary require large-scale, inte- once again be deposited onto Delta Toward this end, small demon- grated and innovative solutions. islands, reducing the effects of 140 stration projects can help improve Good examples of recent innovation years of subsidence. Large, wide regionally appropriate restoration include: 1) application of hydrody- habitat levees will create new science and try our hand at locally namic modeling approaches to riparian and upland transition meaningful adaptive management. identify critical site-specific Bay- areas, mimic the natural topogra- However, large-scale solutions are Delta -related plan-form phy, and provide much-needed critical if we are to restore native geometries that may enhance water habitat diversity while protecting habitats and endangered species. quality system-wide; and 2) applied tidal marsh corridors and reducing Research alone will not restore these research focused on identifying ways salinity intrusion. ecological resources; nor will poli- to increase elevations on subsided cymaking or agency action without islands using bioaccretion and sedi- Implementing a large-scale estu- science. ment trapping. arine restoration program will MORE INFO? require problem-solving interdisci- Restoration solutions need to be plinary teams empowered with the [email protected] integrated by identifying multiple authority and funding to identify project goals and solving multiple and clarify restoration actions bene-

LANDSCAPE RESTORATION CONCEPTUAL MODEL Long Term Intermediate Short Term Existing

Suisun Marsh

Sacramento River

San Joaquin River

Migration corridors comprised of emergent aquatic vegetation and shallow tidal sloughs provide transient habitat value to migrating aquatic and near-aquatic species not currently provided by riprap and steep-sided levee banks. Regional linkages reduce isolation effects of piecemeal project implementation. Regional biogeochemical cycling is linked to sediment movement and establishment and maintenance of first-order tidal channel networks.

34 Suisun Bay

RESTORATION Suisun Bay

“The last decade’s research has produced a revolution in our core ideas about the movements of water, salt and sediments in Suisun Bay, the sources and biological effects of contaminants, and the productivity of the estuarine foodweb.”

JIM CLOERN U.S. Geological Survey

35 PERSPECTIVE

APPLYING INTEGRATED Of direct relevance to these man- reserve fleet channel), and that the SCIENCE TO SUISUN BAY agement questions are the results of presence/absence of gravitational cir- an integrated research effort by the culation and null zones are strongly U.S. Geological Survey in Suisun influenced by the shape of the JIM CLOERN Bay. These results, with examples seafloor (see Burau p.39). U.S. Geological Survey presented in the following pages (pp. 36-45), have led to a revolu- Second, we used to think particles tion in our core ideas about the accumulated in the null zone. Now Suisun Bay is the critical transi- movements of water, salt and sedi- we understand there is not necessari- tion habitat between the river-dom- ments, the sources and biological ly one place of maximum inated freshwater habitats of the effects of contaminants, and the associated with the null zone, but Delta and the downstream marine- productivity in the estuarine food- rather there can be multiple turbidi- influenced embayments of San web. Only 10 years ago, these core ty maxima caused by multiple mech- Francisco Bay, and as such has been ideas included the concepts of: anisms (see Schoellhamer p.41). the focus of scientific study for over (1) a residual circulation pattern three decades, and of numerous dominated by a single gravitational Third, we used to think of Suisun high-priority environmental man- circulation cell with a null zone; Bay as a geographic region with a agement debates and actions. high biomass of clams, worms, fish and other aquatic animals because it had inherent high primary produc- tivity derived from “For scientists, Suisun Bay is a beautiful model system for photosynthesis. In the past decade, we have learned that the rate of pri- studying fundamental properties of estuarine ecosystems.” mary production in Suisun Bay is actually very low (in the bottom 10% of all estuaries world-wide), partly because of strong grazing pressure by the introduced clam Potamocorbula. We have also, as a result, learned that For scientists, Suisun Bay is a (2) accumulations of particles in that null zone; and (3) inherent much of the animal biomass within beautiful model system for studying Suisun Bay derives from the delivery fundamental properties of estuarine high biological productivity because of these high- accumulations of food from outside sources. We ecosystems because it features both now understand Suisun Bay as an horizontal and vertical gradients in (see Primer for an explanation of terms). We now know that these core open system that relies on inputs salinity; responds dynamically to from beyond its boundaries rather fluctuations in river flow; encom- ideas are overly simplistic, flawed, and some are even wrong. than as a closed, self-sustaining, passes complex bathymetry, includ- biological system. ing coupled systems of deep chan- First, our concept of water move- nels and shallow embayments; and ments in Suisun Bay has changed, Beyond these refinements of old exchanges water and materials or more specifically of how gravita- conceptual models, the application of between three systems, an upstream tional circulation works (see dia- integrated science in Suisun Bay is river system, a downstream marine gram p.39). This is a fundamental creating new conceptual models of system, and a lateral marsh system. issue because water movements carry ecosystem attributes previously not things like salt, sediments, contami- considered. For example, we now Water and resource managers, know very precisely how the shape of meanwhile, are seeking new science to nants, and small organisms (from to plankton to larval fish). the Suisun Bay’s floor has changed help them better understand the eco- since the gold-mining era, and how a logical significance of salinity distri- Water movements are caused by slow erosional process is now expos- bution as a broad habitat indicator many interacting forces. Under- ing mercury-enriched sediments (“X2” – see Primer opposite); the standing which forces are most deposited a century ago or longer potential threats of the gold-mining important is essential to understand- (see Jaffe p.42). We know that differ- era legacy of mercury-contaminated ing how salt, plankton, contaminants ent contaminants have their own sediments; the importance of Suisun and biota are transported within the unique sources, fates and ecosystem Bay habitats to fish and bird species of system. These transport processes are effects that must be considered as we special concern; processes that influ- much more complex than we under- develop strategies to enhance living ence the and trophic stood only a decade ago. We now resources. Nickel, for example, is transfer of toxic contaminants within know that residual transports in delivered to Suisun Bay by riverine the estuarine food web; system-level Suisun Bay (that is, transports oper- input and its accumulation in biota disturbance by non-native species; the ating over time scales of days or varies with river flow. However the impacts of manipulating salinity as a longer) are NOT usually driven by a biological availability of cadmium is mode of marsh management; and gravitational circulation, that there controlled by chemical changes that scenarios of response to change in the can be multiple cells of gravitational occur along the salinity gradient (see . circulation (including cells up the Brown p.43). Other new findings,

36 Suisun Bay

based on the integration of environ- of understanding how the ecosystem mental toxicology with ecosystem sci- functions and to provide the founda- ence, illustrate that the ultimate tion of scientific understanding nec- effects of contaminants such as sele- essary to guide management of living nium are strongly regulated by the resources (Cloern, SOE, 2001). feeding pathways between predators and prey. Two distinct pathways exist in Suisun Bay, and the benthic-based MORE INFO? pathway (linking clams to sturgeon [email protected] and diving ducks) is particularly effi- cient at moving selenium into living resources at the top of the (see Stewart p.45). ESTUARINE PHYSICS PRIMER Salinity is greatest near the ocean Our findings illustrate the rapid and smallest near the rivers. This dif- progress that we can make when we Key Terms ference in longitudinal salinity (gradi- attempt to organize our expertise ent) from the river to the ocean can and scientific talents in an integrat- Estuarine scientists use many cause the tidally averaged currents to ed fashion. This research mode terms to describe the complicated flow landward along the bottom and integrates: the study of many differ- physical processes in estuaries, where seaward along the surface (gravita- ent connected processes (such as freshwater from the rivers mixes with tional circulation). The null zone is precipitation, snowmelt, river saltwater from the sea. The salinity of runoff, sediment delivery, sediment the region in an estuary where the freshwater is 0 practical salinity units movements, contaminant inputs, residual, near-bottom, landward cur- (psu) and the salinity of is trophic transfers of carbon, energy rent reverses and flows in the sea- 35 psu. and trace metals); institutional ward direction as a result of river resources (results presented here are The gravitational pull of the sun inflow. In many estuaries, the null most meaningful in the context of zone contains an estuarine turbidity the broader science conducted by and moon generates tides with flood maximum (ETM) where suspended the Interagency Ecological Program (landward) and ebb (seaward) cur- and the academic community); the rents. Tidal currents are strongest sediment concentrations (SSC) and use of diverse tools and approaches during full and new moons, called turbidity are greatest (Schoellhamer, to unravel the complex puzzles of spring tides, and weakest during half USGS). estuarine ecosystems (including sta- moons, called neap tides. This slosh- ble isotopes, moored instruments, ing back and forth is usually much X2 monitoring, mapping, laboratory greater than the tidally averaged X2 is the distance, in kilometers, experimentation, historic recon- (residual) movement of water caused from the to the structions and numerical models); by river inflow or wind. Tidal and and the examination of different tidally averaged near-bed, 2-psu iso- residual currents carry and mix (trans- scales of variability (from the hourly haline (a kind of “contour line” in the scale of tidal currents to the decade- port) salt, sediment, plankton, and Estuary’s waters where the salinity is and century- scales of sediment other constituents. Saltwater is heav- 2 psu). A salinity standard established inputs and reshaping of the geo- ier than freshwater; therefore, saltier under the 1994 Bay-Delta Accord morphology of Suisun Bay. water tends to be near the bottom of requires that freshwater flows be estuaries. The difference in the released from upstream in a way that Our science must continue to amount of salinity between the top maintains X2 within a range of posi- adapt to the Suisun Bay system, which and bottom of the water column is changing before our very eyes in tions in Suisun Bay associated with (stratification) can be great enough to several ways, among them, the con- the abundance of aquatic organisms struction and operation of salinity prevent the top and bottom waters and some threatened and endangered control gates in Montezuma Slough, from mixing. fish. the population collapse of the native mysid shrimp, decade-scale trends of increasing water exports and reduced outflows to Suisun Bay, and large fluctuations in abundance of key- stone species like the non-native clam Potamocorbula. In the meantime, our recent revolution in understanding the critical transition zone between the Delta and the Bay shows how sci- entists from multiple disciplines can work together to attack the challenges

37 RESTORATION

LONG-TERM INFLOW most severe losses AND SALINITY CHANGES LONG TERM MAY SALINITY RISE occurring in the 1930-2000 Cascade and north- 25 NOAH KNOWLES Annual average ern Sierra ranges Scripps Institution of 20 May average (Knowles and Cayan, Oceanography 2001). This would 15 increase winter Changes in estuarine salinity and 10 storm runoff and freshwater inflows over decades and Salinity(psu) reduce the centuries form the climatic context 5 snowmelt-driven for Bay-Delta research and restora- 0 runoff of spring (see tion efforts. Examining past varia- ‘30 ‘35 ‘40 ‘45 ‘50 ‘55 ‘60 ‘65 ‘70 ‘75 ‘80 ‘85 ‘90 ‘95 below). tions and their causes, among them long-term salinity variability in As winter runoff Suisun Bay, can help us understand results and demonstrates their Bay-wide increases and spring this context and assess potential future character. runoff decreases over the coming cen- changes. tury, the watershed might lose its abil- The primary cause of this long-term ity to generate spring flows. Water A reconstruction of seven decades of rise in May salinity is the gradual agencies should prepare for the likeli- estuarine behavior – using a model that development of freshwater manage- hood that they may not be able to mit- successfully replicates observed histori- ment capabilities in the upstream igate for climate change impacts and cal salinity observations throughout the watershed over the last half-century. changes in seasonal flows with today’s Bay (U-P model: Uncles and Peterson, Use of this infrastructure has signifi- freshwater management infrastructure. 1995) — reveals a long-term trend cantly reduced freshwater inflows to The historical long-term rise in May toward higher May average salinities in the Estuary in May, contributing to salinity might continue, and in fact Suisun Bay. This trend represents an the long-term salinity increase. accelerate, in the coming decades, increase of about 5 psu from 1930- Another contributor is the progres- causing more salinity intrusion into present (see above). No statistically sig- sively earlier occurrence of snowmelt the Delta, and potential difficulties nificant trend in annually averaged in the upstream watershed over the last maintaining the X2 standard in Suisun salinity was present. A shorter record of century. Researchers associate the (Knowles, SOE, 2001). observed salinities at Fort Point under trend — originally identified by Roos the Golden Gate Bridge supports these (1991) and subsequently investigated by Dettinger and Cayan (1995) — with MORE INFO? a century-long temperature increase. [email protected] SNOWMELT-DRIVEN The trend is characterized by progres- http://tenaya.ucsd.edu/~knowles/ OUTFLOW CHANGES sively lower May runoff, and by more 4000 runoff coming before May. In this Northern Headwaters 3500 way, the warming trend has con- 1995-2005 flows tributed to the long-term increase of SCIENCE /sec)

3 3000 2050-2069 flows May salinity. 2500 Questions 2000 Though the historical warming • How much of a role have other 1500 trend may be associated with natural modes of climate variability, the effects long-term climate factors, such as 1000 are similar to what may be expected the Pacific Decadal Oscillation, 500 under conditions of human-caused played in shaping riparian and 0 climate change and may therefore estuarine variability? OND J FMAM J J A S offer a glimpse of changes to come. Month • How can we build the current Simulations of changes in snowpack, considerable uncertainties about 4000 streamflow and estuarine salinity pro- Southern Headwaters the nature of future climate 3500 jected by combining models of state- of-the-art global climate change change into our research and 3000 /sec) Unimpaired flow (m

3 (PCM: Washington et al., 2000), management programs? 2500 watershed hydrology (BDWM: 2000 Knowles, 2000) and estuarine water 1500 quality (U-P model) paint a picture of the following potential impact on the 1000 Bay-Delta system by 2060: a projected Unimpaired flow (m 500 average increase of 1.6°C in surface air 0 temperatures over the watershed, OND J FMAM J J A S resulting in the loss of over one-third Month of the total April snowpack, with the (1,000 mfs - 35,000 cfs)

38 Suisun Bay

NEW CONCEPTS materials and biological organisms ual increase in width and depth from OF GRAVITATIONAL within the Estuary. Gravitational the head to mouth of the estuary CIRCULATION AND circulation is caused by salinity dif- (Chesapeake Bay, the Hudson and THE NULL ZONE ferences that occur along the axis of Columbia rivers). In contrast, the the Estuary, and is characterized by a geometry of the northern reach of JON R. BURAU two-layer, tidally averaged flow that San Francisco Bay is characterized by U.S. Geological Survey is landward along the bottom of the a sequence of large, shallow subem- Estuary and seaward along the water bayments (San Pablo Bay, Grizzly Circulation patterns in the bio- surface. The position of the saltwa- Bay, Honker Bay) that are incised by logically productive zone where fresh ter/freshwater interface, known as deep channels. X2, depends upon freshwater inflows and salt water mix in northern San A series of shoals or sills exist (such Francisco Bay — a zone encompass- from rivers upstream. X2 is the approximate upstream limit of gravi- as Pinole ) in the deep-water ing Suisun, San Pablo, Grizzly and channels of the northern reach of Honker bays — are quite different tational circulation, and is statisti- cally related to the abundance of Suisun Bay that can reduce or elimi- from other estuaries, largely as a nate, by topographic blocking, the result of the interaction between certain aquatic organisms (see Primer p.37 and Kimmerer, p.46). landward-flowing near-bed current classic water transport mechanisms associated with gravitational circula- and the North Bay's unusual Hydrodynamic studies in Suisun tion. Thus, a so-called “null zone” — bathymetry (see also Jaffe p.42). Bay show how the position and a region in the Estuary where the Even though tidal currents gener- structure of the salt field, in relation residual, near-bottom, landward cur- ally dominate transport in the North to key bathymetric features, can rent reverses and flows in the seaward Bay, relatively subtle mechanisms, affect hydrodynamic transport by direction — is created at each sill such as “gravitational circulation,” gravitational circulation. In many within the Estuary and at X2. A dis- can play a significant role in trans- drowned-river estuaries the basin tinct gravitational circulation cell porting physical and chemical geometry is characterized by a grad- exists between each sill (see diagram).

TRADITIONAL CIRCULATION MODEL Salty Fresh Net seaward currents

Stratification

z Net landward currents 2 psu (X2) Convergence (Null Zone) Biological maximum Turbidity maximum

REVISED CIRCULATION MODEL

Cell Sill

Net seaward currents Null Zone Entrapment Zone

Net landward currents

Zone of Gravitational Circulation Turbidity 2 psu (X2) Maximum

Carquinez Strait Benicia Bridge Suisun Bay

Gravitational circulation, a two-layer flow pattern (where the bottom current flows landward and the surface currents flow seaward) is shown in the upper panel to occur seaward of X2. In this traditional model, the along-channel salinity differences (gradients that create gravitational circulation cease to exist landward of X2 and thus the vertical structure of the currents is top-to-bottom towards the sea landward of X2. Therefore, at roughly X2, a transition in the vertical structure of the currents occurs which creates a near-bed convergence, which in turn, creates, in many estuaries, a turbidity maximum. The traditional circulation pattern and entrapment mechanism shown in the upper panel is substantially modified in the presence of bathymetric variability, as is shown in the lower panel. Rather than being located at X2, the null zone and turbidity maximum occur in locations of significant changes in depth

39 RESTORATION

In San Francisco Bay and other estuaries, a null zone is often associat- SCIENCE ed with an estuarine turbidity maxi- mum (ETM or “Entrapment Zone” as Questions it is commonly referred to in the San Francisco Estuary) where suspended- • How does the strength of the gravita- solid concentrations and turbidity tional circulation cells change with reach a local maximum (see also the seasons? Schoellhamer, p.41). Thus, whereas Chesapeake Bay and the Hudson and • What are the ecological implications Columbia rivers essentially have a sin- of geographically fixed ETMs ( since gle gravitational circulation cell, null we now know that the ETMs associat- zone, and ETM associated with the 2- ed with sills are much stronger than psu isohaline because of their gradu- the relatively weak ETM that exists at ally sloping bottoms, San Francisco X2)? Bay has a sequence of gravitational circulation cells, null zones, and ETM • What are the ecological implications associated with sills and X2 (Burau, of ETMs associated with large, pre- SOE, 2001). sumably biologically productive, shal- low regions (such as Pinole Shoal in MORE INFO? San Pablo Bay and Garnett Sill in [email protected] Grizzly Bay)? http://sfbay.wr.usgs.gov/access/ flow/drifterstudies/ http://sfbay.wr.usgs.gov/access/ suisunbay/dschoell/contents

REVISED REGIONAL CIRCULATION MODEL

NORTH BAY RESERVE FLEET CHANNEL

0

15

30 Pinole Shoal Benecia Bridge Suisun Cutoff Carquinez Strait Garnet Sill Middle Ground Sill Salty Fresh

?

z ~5cm/s

~20cm/s ~10cm/s 2 psu (X2) Velocity in centimeters per second.

This model recognizes the interaction between the along-channel and vertical salinity differences (gradi- ents) with the bathymetry in the channels of North Bay. Shallow areas in the channels, such as Pinole Shoal, and the change in depth that occurs near the Benecia Bridge and Garnet Sill, significantly reduce or completely eliminate gravitational circulation. Thus, conceptually, gravitational circulation in North Bay occurs as a sequence of gravitational circulation cells, which occur in the deeper channels, bounded by sills.

40 Suisun Bay

SUSPENDED MAY 2000 ESTUARINE TURBIDITY MAXIMUM NEAR GARNET SILL SEDIMENT DYNAMICS

DAVID H. SCHOELLHAMER U.S. Geological Survey

Suspended sediment affects the ecosystem in Suisun Bay by limiting light availability and photosynthesis, carrying food to benthic filter feed- ers such as the clam Potamocorbula amurensis, and providing a transport pathway for contaminants. One objective of freshwater flow manage- ment (i.e., the X2 standard) is to maintain the zone where suspended sediment accumulates (locally known as the entrapment zone), adjacent to the broad, shallow waters of Suisun Bay. To better understand processes affecting suspended sediment con- A frame from a video showing an ETM (dark blue in bottom panel) seen in Reserve Fleet Channel seaward of Garnet Sill (idealized blue bump in middle and centration (SSC), researchers made bottom panels), where it generally remains. The salinity is about 8 psu and the continuous measurements of SCC, current is flooding (white arrows in middle panel). Water level is at a high tide hydrodynamics and meteorology at (intersection of time line and water level line in the top panel). This video frame 19 sites in Suisun Bay between shows the suspended sediment in the ETM deposits at slack tide and resuspends August 1999 and June 2000. These as the current speed increases. sites were concentrated in the shallow A tidal variation in suspended sedi- waters of Grizzly Bay and in the adja- MORE INFO? cent deep tidal channel. ment concentrations in the center of Grizzly Bay often distinguishes two [email protected] Many factors affect the variability water masses—one that has moved into http://sfbay/wr.usgs.gov/access/ of SSC (suspended sediment con- Grizzly Bay during flood tide from the suisunbay/dschoell centrations) in Suisun Bay, includ- turbidity maximum in the channel ing bathymetry, salinity, the and one that has moved during ebb spring/neap tidal cycle, wind, erodi- tide from shallower water in Grizzly ble sediment supply, freshwater flow Bay where wind-wave resuspension is SCIENCE (Knowles), watershed disturbance greatest. (Jaffe), and the semidiurnal tidal cycle (see Primer p.37 for an expla- This work, and other findings Questions nation of terms). (Schoellhamer 2001, Brennan and • How does the bathymetrically con- others in press) has substantially trolled turbidity maximum seaward of When salinity is present, Garnet altered our conceptual model of tur- Garnet Sill affect contaminant trans- Sill in the channel adjacent to bidity maxima in Suisun Bay. One of port and the of Suisun Bay? Grizzly Bay is the terminus of a grav- the rationales for the X2 standard is itational circulation cell (Burau) and to maintain a turbidity maximum at • To what extent do the turbidity maxi- the location of a turbidity maximum. a salinity of 2 psu adjacent to the mum and shallow waters of Grizzly shallow waters of Suisun Bay. As long Bay interact? In this channel, tidally averaged as salinity is greater than zero, how- SSC is determined by the variation ever, a turbidity maximum is located • What are the physical processes that of tidal energy primarily by the adjacent to the shallow waters of account for the turbidity maximum on spring/neap tidal cycle. Energetic Grizzly Bay. The rationale for the X2 the tidal time scale? spring tides resuspend bottom sedi- standard and the explanation of how • How and why does the magnitude of ment and prevent vertical stratifica- the turbidity maximum and shallow tion of the water column, a process the turbidity maximum vary with the waters provide ecological benefit spring/neap cycle and seasonally? that promotes deposition. Thus, should be revised accordingly spring tides increase SSC, compared (Schoellhamer, SOE, 2001). • How is sediment transported within to weaker neap tides. In Grizzly Bay, Grizzly Bay? however, SSC is determined by wind-wave resuspension and the quantity of erodible sediment on the bed.

41 RESTORATION

SEDIMENTATION, EROSION, Bay. These sediments have high mer- AND MERCURY cury concentrations (typically 0.3 to SCIENCE CONTAMINATION 0.5 parts per million) because they contain mercury lost during the Questions BRUCE E. JAFFE gold-extraction process (as much as U.S. Geological Survey 10,000 tons of mercury). • How much of the mercury-contami- nated debris is in a zone where physi- To improve our understanding of cal and biological processes release Understanding long-term sedi- long-term sediment transport pat- mercury into the system? ment movements can help us predict terns and the present 3-D distribu- • How will water management strate- how much debris from upstream tion of mercury-contaminated Gold Rush-era hydraulic mining is hydraulic mining debris in Suisun gies affect the rate at which mercury still in Suisun Bay, its distribution, Bay, researchers undertook quanti- is released from hydraulic mining and whether it is buried or near the tative analysis of historical hydro- debris in San Pablo and Suisun bays? graphic surveys. The data set con- surface where the associated mercury • Is the mercury in the hydraulic min- could be available to the ecosystem. tains more than 150,000 depth soundings collected dur- ing debris bioavailable? ing five surveys from 1867 SUISUN SEDIMENT CHANGES to 1990. Surface models of bathymetry showed pat- 150 As a result of changing sediment terns and quantities of dynamics, most of the hydraulic 100 morphologic change and mining debris has left Suisun Bay, sedimentation between 50 but tens of millions of cubic meters surveys. A more sophisti- of contaminated debris still remain 0 cated model was then at locations both in the Bay and in developed that tracks the the marshes along its . This is -50 fate of hydraulic mining

Million cubic meters in contrast to San Pablo Bay, which -100 debris in Suisun Bay. retains more than a hundred mil- -150 Results of this analysis lion cubic meters of mercury-con- 1867-1887 1887-1922 1922-1942 1942-1990 indicate just how radically taminated debris. Resource man- the Bay’s sediment system agers setting restoration priorities 4 has changed over the past should take into account the higher likelihood of mercury releases from 3 150 years in response to human activities and natu- marshes composed of mercury-con- 2 ral forces. Before the mas- taminated hydraulic mining debris 1 sive input of sediment (Jaffe, SOE, 2001). 0 from hydraulic mining, MORE INFO? cm/year channels were broad and -1 [email protected] more developed in -2 Northern Suisun Bay. -3 During the hydraulic min- 1860 1880 1900 1920 1940 1960 1980 ing period the high deliv- ery rate of sediment over- 80 whelmed erosive forces, 60 resulting in filling of 40 channels. At that time, 20 approximately two-thirds of Suisun Bay was deposi- 0 tional and one-third was -20 erosional.

Million cubic meters -40 -60 Suisun Bay has lost sedi- ment since that era and -80 1867-1887 1887-1922 1922-1942 1942-1990 continues to today as sedi- ment delivery has decreased and natural forces (e.g., tidal currents, Hydraulic gold mining removed wind wave resuspension) continue to more than a billion cubic meters of remove sediment. During the last sediment from the foothills of the period of change analysis, 1942 to Sierra Nevada during the middle to 1990, more than two-thirds of late 1800s. Rivers transported much Suisun Bay was eroding. of this sediment to San Francisco

42 Suisun Bay

TRACE METALS IN SUISUN BAY BIVALVES OUTFLOW CONCENTRATIONS 16 40 CINDY BROWN Nickel U.S. Geological Survey Vanadium 12 30

Outflow -1 g )

Researchers analyzed four metals µ in the clam Potamocorbula amurensis — 8 20 vanadium, nickel, silver and cadmi- um. Each of these has a different (thousands) Delta Outflow (cms) pattern of accumulation and thus 4 10 concentration ( reveals something different about the processes in the Estuary. These patterns tell us where to look for the 0 0 sources of contaminants, what con- ‘91 ‘92 ‘93 ‘94 ‘95 ‘96 ‘97 ‘98 ‘99 trols contaminant availability and how contaminants may affect aquatic (V and Ni); some are influenced by summer flow periods, winds pick up, organisms. internal processes, i.e., resuspen- causing wind/wave resuspension of The non-native clam Potamocorbula sion of sediments (Ni); some have the bottom sediments. This appears amurensis is a useful indicator of trace internal sources in the Estuary and to increase the availability of Ni to metal contaminants because it lives in have an adverse effect on the clams the clam. Thus the primary source of (Ag); and that for others, V and Ni appears to be from the availability for possible uptake rivers, however, unlike V, internal TISSUE CONCENTRATIONS into the food web is driven by processes (resuspension) also make the geochemistry of Suisun Ni available to the clams when river- 100 r=0.79 Bay (Cd). flow into the Bay is low. Regardless, Ni and V do not appear to have an Vanadium (V) and nickel 60 adverse effect on the health of the (Ni) occur naturally in the clam. ultramafic rocks of the water- shed, an external source to Silver (Ag) is naturally rare in the 20 Suisun Bay. Their availability environment. The source of the Ag, to the clams is related to the according to the data, appears to be -20 bay’s hydrodynamics (see internal to the Bay. Highest Ag con- above). The primary sources centrations occur in clams in Suisun Annual gamete index of V and Ni in the tissues are Bay and the Carquinez Strait. The -60 tied to the Delta outflow into data indicate that clams with more the Bay from the Sacramento Ag in their tissues have a lower and San Joaquin rivers. The “gamete index,” in other words, -100 concentrations of these metals there are fewer reproductive clams 0 1 2 3 4 5 are high in the clam coinci- (see left). Clams are not reproduc- µ -1 Annual mean Ag tissue concentration ( g g ) dent with high flows. However, V SUSPENDED SEDIMENT LEVELS in the tissues drops VERSUS NICKEL IN CLAMS salinities ranging from 1-32 parts per to baseline levels 400 40 thousand, and can thus be used to between periods of Suspended Sediment compare a variety of habitats. high flow, whereas Nickel in Clams

Researchers have been collecting and 300 30 -1 Ni increases again g /g ) analyzing about 100 clams monthly at µ in the clams during a number of stations in the North some summer low Bay for this study since 1990. 200 20 flow periods. With Researchers compared the pat- Schoellhamer’s sus- pended sediment terns in variability of trace metal 100 10 Ni Concentration ( accumulation in the clam with the data (see p.42), we patterns of variability of other envi- see that Ni availabil- ity increases with ronmental and biological factors — Suspended Sediment Concentration (mg/L) 0 0 hydrodynamics, sediment dynamics, increasing suspend- ‘91 ‘92 ‘93 ‘94 ‘95 ‘96 ‘97 ‘98 ‘99 reproduction and geochemistry. ed sediment con- The results indicate that some met- centrations in the How the concentration of Ni in the tissues of the clams (right y-axis) relates to als have external sources to the water column (see how much sediment is in the water column (left y axis), indicating that the Ni Estuary, i.e., input from the rivers right). During low in the tissues may be influenced by possible Ni on the sediments and that resus- pension of the sediments may make the Ni more available to the clams.

43 RESTORATION

tively active when Ag tissue concentra- tions are high. Cadmium (Cd) is rare to the natural environment, and its availability is driven by the geochemistry (salinity gradient) of Suisun Bay, unlike any other metal measured. Cadmium is more available in fresher water as free ions. When the river water mixes with ocean water, the Cd combines with the chlorine in the seawa- ter and becomes unavailable to the clams (see below). Lab experiments show uptake of Cd by Potamocorbula is greater at low salinities (<10 ppt) than at higher salinities, and there is some evidence that Cd may have an adverse effect on the clams.

CADMIUM VS. SALINITY

8 7 -1

g ) 6 µ 5 4 3 2 d concentration( C 1 Error bars=1 Std.Dev. 0 30 25 20 15 10 5 0 Salinity(0/00)

These results suggest two important insights: the bioaccumulation and the impacts of one contaminant do not nec- essarily explain the patterns of bioaccu- mulation of other contaminants; and inputs of trace metals cause biological SCIENCE signals that can be detected in the Estuary, as seen with silver and the clam Questions reproduction data. They also underline • How will continued changes in the our ability to integrate trace metal data hydrodynamics and sediment dynam- with data on hydrodynamics, sediment dynamics, reproduction and biogeo- ics affect the availability of metals to chemistry in a way that enables us to bet- the biota in the Estuary? ter understand this complicated ecosys- • What do the effects we see in the tem (Brown, SOE, 2001). biota due to metal uptake mean to MORE INFO? the ecosystem? [email protected] • How do these metals transfer within the food webs?

44 Suisun Bay

SELENIUM IN web. This led THE FOOD WEB to questions SELENIUM IN THE CLAM FOOD WEB regarding the ROBIN STEWART relationship 30 between the U.S. Geological Survey Clam-based food web rise in predator 25 Y=2.79x-20.531 2 Se levels and R =0.7972, P=0.0002 the clam inva- 20

Introduced species may not only g/g) impact the ecology of the estuarine sion in the fall µ Crustacean-based 15 Food web ecosystem, but may also change con- of 1986. Could Y=0.929x-8.357 R =0.3876, P=0.002 taminant dynamics. This research a species inva- Se conc.( 10 identified a link between the intro- sion have duction of the exotic clam implications 5 Potamocorbula, a highly efficient for contami- bioaccumulator of selenium in the nant cycling in 0 North Bay, and elevated Se concen- food webs? 10 12 14 16 18 20 trations in clam-based predators 15 N following the invasion. Prior to 1986, a pelagic Selenium (Se) is an essential ele- (in the water in the increasing selenium levels ment that requires a delicate balance column) food web fueled by a sea- turning up in predators. In order to in nature. Insufficient quantities sonal phytoplankton bloom domi- rule out contributions from other can cause deficiencies, while too nated Suisun Bay. There was also a food sources, researchers conducted much produces a potent reproduc- benthic (on the bottom) food web a study in the fall of 1999 analyzing tive toxin. Selenium’s complex geo- with predators such as sturgeon and invertebrates at the base of both the chemistry and variable patterns of diving ducks, but their benthic food pelagic and benthic food webs for bioaccumulation have made it a supply was unpredictable. The Se. The analysis revealed Se concen- challenge for managers to predict its arrival of Potamocorbula in 1986 virtu- trations in clams (Potamocorbula) that fate and toxicity under variable ally eliminated the seasonal bloom were potentially toxic to predators hydrologic, geochemical and biolog- that fed the pelagic food web and and lower concentrations in crus- ical regimes typically found in estu- was associated with a decline in sev- tacean invertebrates (amphipods, aries. eral species of mysid shrimp and zooplankton and isopods). zooplankton, apparently due to a Laboratory biokinetic studies Selenium studies conducted from lack of food. The energy tied up in showed that clams and crustaceans 1986-1990 by the California the pelagic food web was redirected accumulated Se at similar rates, but Department of Fish and Game to the and into a single clams lost Se from their tissues at found elevated Se concentrations in species of clam. Unlike many bivalve slower rates, resulting in higher Se S.F. Bay diving ducks and sturgeon. species present before the invasion, tissue levels in the clams (Schlekat et Over the same time period the clam Potamocorbula were spatially and sea- al., 2000). Potamocorbula invaded the Estuary sonally abundant, surface dwelling, resulting in significant changes to and palatable due to their soft Researchers then used stable iso- the structure of the North Bay food shells. These factors resulted in topes of carbon and nitrogen to dis- Potamocorbula tinguish between the clam-based becoming a and crustacean-based food webs in the North Bay and to quantify Se SELENIUM IN STRIPED BASS AND STURGEON very impor- tant part of accumulation based on trophic 50 the Suisun position. Although Se was shown to Bay food web. accumulate through both food webs, *** 40 the clam-based food web had a Researchers higher Se biomagnification poten- 30 then found tial than the crustacean-based food g/g) µ * that web (see above). Potamocorbula 20 was a highly Researchers also compared Se conc.( efficient Se absolute Se levels in striped bass and 10 accumulator sturgeon, top predators of both compared to food chains, before and after the 0 previously invasion of the clam (see left). 1986 1990 1999 1986 1990 1999 Significant increases in Se concen- n=5 n=10 n=15 n=10 n=25 n=15 abundant bivalves, high- trations were observed following the introduction of Potamocorbula in stur- n= number of samples lighting the invader’s geon, a clam-based predator, potential role between 1986 and 1990 and 1999,

45 RESTORATION

but not in striped bass, a crustacean- X2 & THE ESTUARY’S species increases with flow or, con- based predator. BIOLOGICAL RESOURCES versely, decreases with X2. These “fish-X2” relationships were used to Continued monitoring of Se levels in WIM KIMMERER justify salinity standards established Potamocorbula will be an important step in S.F. State University in the Bay/Delta Accord of 1994. understanding future dynamics of Se in the Estuary. Se concentrations in clam- Many of the “fish-X2” relation- based predators suggest that dungeness Freshwater flow is the principal ships (see graphs) probably have lit- crab, white sturgeon and splittail are cause of seasonal and longer-term tle to do with the characteristics of potentially at risk for reproductive toxic- variability in estuaries. Increasing low-salinity habitat, as we previously ity. Resource managers should be aware freshwater flow can have many phys- thought, but depend instead on that introduced species may not only ical effects: it can inundate flood other correlates of flow and X2. impact the ecology of a system, but may plains, increase loading and trans- The low-salinity zone does not also change contaminant dynamics port of materials and organisms, appear to work through gravitational (Stewart, SOE, 2001). dilute or mobilize contaminants, circulation (see Burau, p.39). The compress the estuarine salinity field MORE INFO? change in perspective from one in and density gradient, alter the spa- which the X2 relationships derive [email protected] tial distribution of salinity and tem- from the low-salinity zone as habitat perature, increase stratification, and to one in which they derive from decrease residence time. some correlates of flow is based on In the San Francisco Estuary we the fact that there has never been SCIENCE use “X2”, the distance up the axis of any evidence that the low-salinity the Estuary to where the near-bot- zone is a hotbed of flow-related Questions tom salinity is 2 psu, as an index of variability. In fact, phytoplankton the physical response of the Estuary and zooplankton abundance in the • How does the source of food low-salinity zone change rather little particles influence the seasonal to flow. The abundance or survival of several estuarine-dependent with flow. cycle of Se in Potamocorbula amurensis? HOW VARIABLES RESPOND TO INCREASED FRESHWATER FLOWS • Why do Potamocorbula have different Se concentrations than other bivalves?

Greater floodplain inundation

, Density Sacramento

Depth River inflows Salinity Distance Higher river stage velocity Salinity More stratification and gravitational circulation Lower residence time More migration cues

Higher input L of nutrients, S organic matter, Z sediment, fish and X2,and salinty contaminants range used by some species, Decreasing Increased transport move seaward salinity of organisms

San Joaquin River inflows More migration cues Lower proportion of flows diverted

Estuarine species are related to freshwater flow through mechanisms that may involve a variety of flow- related variables occurring throughout the system. This schematic diagram shows what variables increase (blue boxes) and decrease (yellow boxes) with increased flow. LSZ refers to the low salinity zone.

46 Suisun Bay

FISH X2 RELATIONSHIPS

1967-87 1982-2000 (DS) 1988-2000 All Years ring and Sacramento splittail, whose abundance appears to relate to dif- 4 Bay Shrimp 4 SCIENCE 3 3 ferent mechanisms elsewhere in the Estuary. These mechanisms may 2 2 Questions 1 1 include fish transport, by which eggs and larvae are moved more rapidly to • What are the underlying mechanisms 3 5 Herring Am. Shad rearing areas when flow is high than of the fish-X2 relationships? The estu- 2 4 when it is low; movement of larvae arine ecosystem does better when 1 3 into and up the Estuary, which may flow is high than when it is low, 0 2 increase with gravitational circula- tion and therefore with flow; food regardless of the mechanisms, so the 3 5 Delta Smelt Longfin supply, which may increase with main questions are: how much better Smelt 4 2 increasing flow, although evidence does it need to be, for how much of 1 3 for this is weak; water clarity, which the year, and in every year or just 0 2

Log Abundance or Survival decreases with increasing flow, possi- some? 3 1 bly protecting young fish from pre- Splittail Striped Bass 2 0 dation; or habitat space, which may 1 -1 increase with increasing flow for some species. 0 -2 MORE INFO? 50 60 70 80 90 50 60 70 80 90 Given the high cost of water need- [email protected] X2 (km) ed to meet the Bay-Delta standards, continued periodic assessment of the status of the fish-X2 relationships Although some of the fish-X2 remains important (Kimmerer, relationships have changed over SOE, 2001). time, those for some fish and bay shrimp have retained the same slope, that is, the proportional response to X2 (or its correlates) has not changed. GRAVITATIONAL CIRCULATION MECHANISM Rearing Low Flow Habitat Salinity Profiles The mechanisms for the fish-X2 Larvae Move Down Ebb relationships differ by species, and Flood for most species at least two plausible Flood Ebb mechanisms are consistent with the available data. Some species, such as Low Rate of Transport longfin smelt, may have mechanisms more closely related to the low salin- Low High

ity zone than others like Pacific her- Rearing High Flow Habitat Larvae Move Down HABITAT MECHANISM

Longfin Smelt High Rate of Transport 100

80 Low High Ocean Estuary 60

40 Conceptual diagram of changes in gravitational circulation as flow increases. At 20 low flow (upper diagram), the low-salinity zone is in shallow water where gravi-

Spread of Population(km) tational circulation and stratification are inhibited by strong vertical mixing. 0 Transport of sinking particles or larvae that swim downward is relatively weak. 50 60 70 80 90 100 High flow (lower diagram) changes the situation through compression of the lon- Position of Low Salinity Zone (X2, km) gitudinal density gradient, producing a larger density gradient, and through movement of the low-salinity zone into deeper water. Both of these effects increase the tendency for the water column to stratify and for gravitational circu- Longitudinal spread of the population of longfin lation to be strong. This should result in more effective landward transport of smelt as a function of X2. Size of symbols indi- particles and larvae. cates relative abundance. There is no evident ten- dency for longfin smelt to be more spread out in the Estuary when X2 is seaward than when it is landward, suggesting that the area of their habi- tat does not increase with increasing flow.

47 PERSPECTIVE

MODELING: of biological versus physical mecha- seded by the Denton G model, now WHERE IS IT GETTING US? nisms of retention, for example, in built into the DWR model, DWR- Northern San Francisco Bay near X2 SIM, used to represent statewide (see p. 37 & 46), through the water operations. STEPHEN MONISMITH Stanford University Golden Gate, or in the context of evaluating CALFED Environmental Examples of dynamical models Water Account actions. include the several models of net- Much of the focus on under- works of open channels (pioneered standing hydrodynamic processes Three kinds of models have originally by Hugo Fischer) to rep- has come to rest on the use of been used to help us understand resent flows and transport in the numerical models. In an engineer- aspects of the functioning of the Delta. CALFED has made extensive ing context, they are particularly Bay-Delta system and how this use of these to explore how differ- useful for examining how engi- has been changed or will be ent channel configurations may neering or management actions changed by human actions. affect salinity and transport pat- will alter aquatic ecosystems. Such Physical models, such as the Bay terns. More recently, TRIM3D, a management actions might Model in Sausalito, offer minia- three dimensional circulation include the regulation of water ture replicas of the system for model developed by Vincenzo supply and flows; the operation of physical simulations of tidal flows. Casulli of Trento, Italy, and first pumps, water diversions and Statistical models manipulate data applied to San Francisco Bay by other facilities; or the construction to explore relationships such as Ralph Cheng of the U.S. Geological of gates, shallow water habitat or salinity as a function of flow, or Survey, is being used to study runways. Large parts of the cur- species abundance as a function effects on tidal hydrodynamics and rent environmental impact of flow or diversions. Dynamical sedimentation of different pro- research for the San Francisco models are generally based on posed S.F. airport runway expan- Airport runway expansion, for fundamental principles like sions (S. Inagaki), how various example, rely on studies done Newton’s laws of motion or inte- materials (phytoplankton, contami- using two and three-dimensional gration, or on low level empirical nants, etc.) move around under the circulation models. Similarly, eval- relationships like photosynthesis action of tides (Monsen), and most uation of CALFED alternatives for rate as a function of irradiance. recently to examine sediment trans- improving Delta water flows, sup- They are designed to predict cause port in the context of habitat ply and endangered species man- and effect, such as: salinity as a restoration of upland streams agement makes use of a sophisti- function of flow, gate operations (Mike MacWilliams and colleagues cated model of the linked channel or reconfiguration of channels; the at Stanford). network that comprises the Delta. physical movement of salt, parti- To date, models have taught us that we can design facilities and "Models have taught us that we can design facilities and operations in the Delta to achieve operations in the Delta to achieve specific limited goals." specific limited goals. The big challenges for the present are to extend these models to enable Hydrodynamic models can also cles or eggs; and the primary pro- their effective use in real time in be used to help test hypotheses for- duction of plants and animals at support of water project opera- mulated by biologists about physi- the base of the food web and tions, to develop and test cal-biological interactions. These nutrient uptake. improved coupled models of models improve our understanding physics and biology of the Bay- of how the system works, exploring Jassby et al (1995) developed a Delta, and to develop the capabili- factors such as the role of tidal mix- statistical model of X2, for exam- ty of modeling long-term sedimen- ing in the dynamics of the ETM (see ple, which linked flow to abun- tation in the Bay, Delta, and river p. 39-41); the importance of shoals dance of species at all trophic lev- systems. Nonetheless, the to phytoplankton blooms; the vari- els. This modeling work was impor- prospects for using models cre- ability of residence time inside flood- tant to the Bay-Delta Accord of atively to guide management ed islands; and the role of transport 1994, in which EPA set a salinity actions in the future seem excel- in recruitment of organisms or their standard requiring that freshwater lent (Monismith, SOE, 2001). habitat in the Estuary. By inserting flows be managed to maintain X2, particles with "behavior" into a cir- the 2 psu isohaline, within a certain MORE INFO? culation model, for example, trans- range of positions in Suisun Bay [email protected] port of organisms can be predicted associated with species abundance. allowing an assessment to be made The X2 flow model was later super-

48 Suisun Bay PERSPECTIVE SUISUN’S BIOLOGICAL other birds. This abundance of Spring freshwater flows to the RESOURCES waterfowl attracted market hunters marsh, meanwhile, declined sub- to the marsh in the late 1850s. They stantially with mid-1900s damming focused on the western marsh's of the Sacramento and San Joaquin CARL WILCOX California Department many-acre tidal ponds - which yield- rivers and their tributaries. The of Fish and Game ed varied bags of dabbling and div- reduction of inflow during the spring ing ducks, as well as geese and other tends to increase salinity in the Suisun Marsh, prior to the arrival species of commercial value in near- marsh along with subsidence of the of Europeans in western North by cities - and paved the way for the managed marshes, and adversely America, encompassed an extensive first duck clubs in the marsh 20 affects the ability to manage wet- tidal marsh of approximately 60,000 years later. Few examples of tidal lands and tidal marsh species of acres. Dense riparian corridors ponds remain in today's marsh, concern. shrouded tributary streams, such as except in the 3,000-acre Petaluma Suisun and Green Valley creeks in Marsh, the largest extant tidal marsh Managed marshlands, “man- the hills north and west of the on the West Coast. aged” to optimize waterfowl habitat, marsh, and provided habitat for sig- dominate the Suisun Marsh land- nificant runs of steelhead. To the The marsh and adjacent grass- scape today. The marsh provides northeast lay expanses of grasslands lands also supported tule elk, ante- important habitat for ducks and and vernal pools (still visible today lope, deer and visiting grizzly bears shorebirds on the Pacific Flyway, par- north of the Potrero Hills and at the and beavers, as well as enormous ticularly early in the fall and during Jepson Prairie). plant diversity, especially in the tran- drought when water from the Bay is sitions between the tidal marshes available to flood the marsh early in The marsh itself historically con- and the adjacent uplands. These the season. The marsh also sup- sisted of large tidal plains bisected transition zones no longer really ports a reintroduced herd of tule elk, by large channels and containing exist, due to diking and upland and hosts salt-loving pickleweed, an ponds. Tidal flats were relatively rare development. important habitat for the endan- in adjacent Suisun Bay. Freshwater gered salt marsh harvest mouse. But inflows and runoff to the marsh var- Today the Suisun Marsh is a very railroad construction, dredging for ied, depending upon annual rainfall different place — having changed navigation, flood control projects and snow melt patterns, but were from an open tidal marsh to a man- and further reclamation in the marsh not impaired by today's upstream aged marsh within dikes. Efforts to have largely eliminated natural gradi- diversions. Salinity in the marshes reclaim the marsh for agriculture ents from uplands to tidal habitats was fresher in the winter and spring began in the late 1800s, and focused and now threaten, along with inva- and more saline in the summer and on , with the reclaimed sive plants, sensitive flora such as fall, a pattern that varied widely with land used to grow asparagus, wheat the Suisun thistle, soft birds-beak, periods of drought and precipitation, and grapes and to graze dairy cattle. Delta tule pea, and marsh aster. with the eastern marsh being fresher Duck hunters bemoaned the loss of and the western marsh being more marsh to farms. Reclamation in the The dilemma in Suisun Marsh, brackish, as it is today. western marsh lagged behind that in as in other parts of the San the eastern marsh, with the first Francisco Estuary, is how to restore The marsh supported diverse reclamation district not being habitat for listed and sensitive fish, wildlife and plants. The same formed until about 1920. species while balancing the needs of types of fish lived there that exist waterfowl and other species that today, among them delta smelt, By the 1950s, agriculture began depend on managed habitat. The splittail, chinook salmon, steelhead, to fail and farmlands were converted Suisun Charter Process (see p.52) longfin smelt, and to managed marsh — only limited has been initiated to bring scientists tule perch. Even with introductions grazing now remains. Suisun Marsh and stakeholders together to devel- such as striped bass and gobies, the today contains about 54,000 acres op a plan to restore tidal habitats for fishery remains dominated by native of managed marsh. Reclamation sensitive species while maintaining species. The abundance of fish reduced the expanse of tidal marsh the hunting heritage of the marsh, helped sustain a large Native by 79%, to 13,562 acres, much of it which has been the driving force in American population and later a in strips along the edge of tidal the preservation of the largest wet- large fishing industry. sloughs. The largest remaining tidal land in western North America marshes are Hill Slough, Rush (Wilcox. SOE, 2001). The extensive bays, tidal chan- Ranch/Cutoff Slough and Peytonia nels, tidal ponds within the marshes, Slough. Bays and channels account MORE INFO? surrounding seasonal wetlands and for 34,000 acres, shrinking by 17%, [email protected] riparian habitats also supported and tidal flats 1,124 acres, a loss large numbers of waterfowl and of 53%.

49 RESTORATION

SUISUN MARSH FACILITIES MANAGING SUISUN MARSH Compliance Station BARBARA MCDONNELL Monitoring Station California Department Reporting Station

of Water Resources Suisun Marsh Salinity Control Gates

Goodyear Slough Since the mid-1970s, regulatory Outfall requirements and contractual obli- Distribution System gations have required the California Department of Water Resources and the U.S. Bureau of Reclamation to maintain the unique brackish con- ditions of the Suisun Marsh. On the regulatory side, the two agencies were required to mitigate for state and federal water project exports. Instead of mandating that the proj- ects release more freshwater for the marsh, the State Water Resources Control Board chose to set channel water salinity standards for Suisun. A compliance and monitoring net- District in 1987. This contract obli- dard (see p.37). Hydrodynamic work was established. gated the water projects to imple- modeling studies showed that salini- ment the facilities described in the ty in the northwestern marsh would The Plan of Protection, developed Plan of Protection, and it provided not be affected by increased outflow. in the mid-1980s, described a for specific activities to assist Also, physical facilities were not felt phased approach for meeting the landowners. to be effective compared to their standards through the construction environmental impacts. As a result of large facilities including water Monitoring later indicated that of these conclusions, the agencies distribution channels, fish screens completed facilities provided greater stopped work on Phases III and IV and the salinity control gates. The water quality benefits than anticipat- of the Plan of Protection and began Plan served as a guide for marsh ed, and that management activities negotiations on Amendment Three to the Suisun Marsh Preservation Agreement. Amendment Three includes a negotiated series of specific actions “The Charter is like a shotgun marriage, it’s now in and funding to assist landowners in managing their property as water- a rocky honeymoon but we haven’t had to call the marriage fowl habitat. The specific actions counselor yet. It’s not just about waterfowl and clapper were already authorized under the existing Regional General Permit rails and Suisun thistles and killing red foxes, it’s also (RGP) issued by the U.S. Army about the heritage of Suisun Marsh as a historic hunting Corps of Engineers under Section 404 of the Clean Water Act and area. I think we can help both waterfowl and thought to be easy to implement. To address federal fish and wildlife endangered species.” concerns, Amendment Three also established the Suisun Marsh Preservation Agreement Environ- CAY GOUDE mental Coordination Advisory Team U.S. Fish & Wildlife Service and identified mitigation funds for multi-species benefit.

activities until the mid 1990s. In (flood/drain cycles) conducted on In summer 2000, during a joint addition, the two agencies entered private lands by individual landown- Section 7 consultation for into the Suisun Marsh Preservation ers have a big influence on habitat. Amendment Three and renewal of the Agreement with the California In addition, the State Water Board regional permit, the U.S. Fish & Department of Fish and Game and released Decision 1641 increasing Wildlife Service threatened to issue a the Suisun Resource Conservation Delta outflows under the X2 stan- jeopardy opinion. Also at this time,

50 Suisun Bay

the CALFED Suisun Marsh Levee Investigation Team released its draft report describing the effects of uncon- “The western marsh was developed for waterfowl hunting trolled levee breaches in Suisun on Delta water quality. The report recom- and the eastern marsh for agriculture. The Suisun Marsh mended that Suisun levees be included in the CALFED Levee Integrity pro- has 120 years of waterfowl hunting heritage and more than gram. Tensions between the agencies 158 privately owned properties managed as water habitat. grew and stalled the planning and per- mitting process. Also at this time, the These brackish wetlands provide irreplaceable values to the CALFED Record of Decision was resident population of wildlife and migratory birds of the signed, and agency management agreed that a jeopardy opinion was unaccept- Pacific flyway. These resources need to be protected and able. Instead, in November 2000, CALFED stepped in and tasked the enhanced to maintain their current value.” agencies, including U.S. Fish & Wildlife, to come up with a coordinated and comprehensive solution for Suisun STEVE CHAPPELL Marsh and develop a new Charter for Suisun Marsh Resource Conservation District resolving the conflicts that had escalated over Amendment Three, the Regional grams within Suisun Marsh in a implementation plan. The plan will General Permit, the levee investiga- manner responsive to the concerns of likely be a programmatic document tions, and endangered species recovery. stakeholders and based upon volun- with detailed specific actions address- Since fall 2000, the Charter tary participation of private ing different needs on an equal basis, Group has been meeting to address landowners.” as well as integrated provisions for overall improvement to the beneficial the issues in a comprehensive way The Charter agencies acknowledge (see next page). The goal of the uses of the marsh (McDonnell, SOE, that there are difficult issues to deal 2001). Charter, they agreed to in spring with in determining an overall bal- 2001, is to: “Develop a regional plan ance between water quality needs, MORE INFO? that balances implementation of the landowner needs, levee needs and [email protected] CALFED program, the Suisun Marsh endangered species recovery needs Protection Agreement, and other and are developing a long-term management and restoration pro-

SUISUN TIDAL MARSH OWNERSHIP AREAS

Private Navy Dept of Fish & Game Solano County Suisun Resource Conservation District Ownership Boundaries

Grizzly Bay

51 RESTORATION

Habitat Levee Design SYNERGISTIC SOLUTIONS: Habitat levees are designed to fox) where they are not compatible MEETING SUISUN’S re-establish facsimiles of marsh with local management priorities ENDANGERED SPECIES, topographic gradients. They are and endangered species recovery. HERITAGE USE AND WATER lower, wider, and more gently slop- QUALITY NEEDS ing and vegetated than conventional Lower crest elevations and levees, and they may be overtopped vegetated slopes will also: facilitate CHRIS ENRIGHT during storm surges with nominal the dispersal of tidal , an impor- California Department tant natural component of tidal of Water Resources erosion or destabilization. Periodic flooding of lower edges of habitat refugial habitat; minimize levee levees may promote dense, tall, low erosion and eliminate maintenance Until recently there has been a requirements; and slow subsidence deep divide in views about resource marsh vegetation, which provides compared to levees capped at protection needs in the Suisun cover for resident native marsh Marsh. Private landowners in the wildlife. Linear bands of upper higher elevations. Elimination of marsh value the waterfowl hunting marsh vegetation may develop high- the recurrent disturbance cycle heritage and need assurance that er on the habitat levee slope. associated with dike erosion and restoration actions will not diminish Intermittent overtopping by spring maintenance may also reduce the traditional land use through regula- tides will flood out terrestrial preda- competitive advantage of many tion. Regulatory agencies require tor dens (rats, raccoons, skunks, non-native plants. conservation measures that protect endangered species with a high degree of certainty. The water agen- restoration, signals a turning point The synergy among the emerging cies have contractual obligations and in planning the future of the Suisun solutions is exemplified by habitat public trust responsibility to miti- Marsh. levees constructed in concert with gate for the impacts of state and microtidal wetland management on federal projects and protect water Agency and stakeholder partici- subsided land. This integration quality. pants in the Suisun Marsh Charter could provide duck, salt marsh Implementation process are now harvest mouse, and fish habitat, There is growing recognition of a working together to realize this synergy between solutions for the while enhancing flood control and potential. The developing plan will Delta water quality protection, marsh that would exceed all the par- implement CALFED Ecosystem ties’ needs. Emerging wetland controlling subsidence, negating Restoration Program goals for fish screen requirements, stabilizing restoration science is uncovering Suisun Marsh. Everyone agrees that solutions that protect and enhance soil chemistry, and reducing regula- the solution package must co-equal- tion (Enright, SOE, 2001). beneficial uses for everyone. The ly meet the fundamental needs of all integration of innovative habitat parties including endangered species MORE INFO? levee designs, microtidal diked wet- recovery, enhancement of current [email protected] land management, selected intensive uses, and water quality protection. www.iep.ca.gov/suisun/charter management actions, emergency flood planning, and tidal marsh

MICROTIDAL POND MANAGEMENT FEATURES

Exterior side of levee Pond side of levee

Lower elevation Upper elevation WigeongrassTule ( Alkali BulsushCattail( Fat Hen Baltic RushPickleweedSaltgrassAlkali HeathMarsh Gumplant ( ( ( ( ( ( ( ( Ruppia martima ScirpusScirpus acutus maritimus Atriplex triangularisJuncus balticusSolicornia virginicaDistichlls spicataFrankenia salinaGrindelia stricto Mean high spring high tide Typha spp .) ) ) ) ) ) ) ) ) )

~6 ft

~2 ft Habitat Levee ~2 in 7:1 or Greater Slope ~0 in

52 Bay

RESTORATION Bay

“Our economy remains predicated upon the fantasy of infinite urban growth, as mindless as are cancer cells to the ultimate fate of their host. In this case, the victim appears to be the immensely intricate biotic web which shows alarming signs of collapse. We may soon find that we need phytoplankton far more than it needs us.”

GRAY BRECHIN U.C. Berkeley

53 RESTORATION RELATIONSHIP BETWEEN IMPERVIOUS COVER AND STREAM QUALITY WATERSHED MANAGEMENT FOR URBANIZING ESTUARIES Good

TOM SCHUELER Center for Watershed Protection Fair Urbanization poses a strong chal- lenge to watershed managers seeking Stream Quality to maintain the quality of estuaries Sensitive Impacted Urban Drainage and the streams that feed them. The Poor greatest threat to estuaries continues Non-Supporting to be the conversion of natural spaces to car habitat and impervious 10%25% 40% 60% 100% spaces. Watershed Impervious Cover The amount of impervious cover (i.e., concrete and asphalt) in a How 26 different aquatic indicators respond watershed is a good overall indicator to different levels of impervious cover. At 30% of the severity of urbanization’s cover there is a decline in sensitive taxa; at impacts. Stream quality correlates 15-20% cover, a decline in food variety and abundance; at less than 10% cover, chronic SMART directly with the amount of impervi- fecal and coliform contamination. ous cover in the watershed, and a WATERSHED relatively small amount of develop- PRINCIPLES ment can have significant impacts 1. Engage in small watershed on streams (see chart). There are eight primary tools that can be used with varying degrees of restoration planning effectiveness to mitigate the impact REMOVAL RATES FOR 2. Map and analyze subwatersheds TREATMENT PRACTICES (STP) of development. These tools include the development of local watershed 3 Rapid assessment of stream corridors STP Total P Total N TSS plans that adjust zoning to be con- 4. Integrate water quality monitoring sistent with desired stream and estu- Group Dry 19% 25% 47% arine quality objectives, as well as 5. Provide adequate funding for land conservation, stream buffers, programs Ponds Wet 51% 33% 80% better site design to reduce impervi- 6. Conserve natural area remnants Ponds Wetlands 49% 30% 76% ous cover, erosion and sediment control, stormwater treatment prac- 7. Implement watershed retrofits Filters 59% - 81% tices, non-stormwater discharges 8. Implement and watershed education and stew- 9. Eliminate untreated sewage dis- WQ Swales 34% 38% 86% ardship programs. Each of these tools must be adapted to reflect the charges Median nitrogen, phosphorus and total suspended intensity of development within the 10. Engage in watershed forestry solids (TSS-TK) removal rates measured for five kinds of watershed. stormwater treatment practices. Rates are based on 11. Reclaim public lands 134 performance monitoring studies conducted across Restoring urban watersheds is the nation. 12. Implement smart sites principles in challenging. However, even com- municipal construction Source: Center for Watershed Protection munities with watersheds that are more than 25% impervious cover 13. Target education efforts to reduce can restore them using the “smart watershed pollution Impervious cover also contributes watershed” model (see sidebar). 14. Intensively involve community in to coastal runoff polluted with a Whatever the approach, it is impor- restoration planning tant for restoration scientists to variety of contaminants, including 15. Launch nitrogen, bacteria, PAHs and heavy avoid worshipping at the altar of campaigns metals. The impacts of this runoff complexity and to keep things sim- can include sharp increases in ple (Schueler, SOE, 2001). 16. Train municipal employees in nitrogen loads, harmful MORE INFO? pollution prevention blooms, bans on shellfish harvest- [email protected] 17. Maximize opportunities for ing, swimming prohibitions, and www.stormwatercenter.net marina hotspots. Coastal runoff can personal stewardship also affect tidal creeks, creating www.cwp.org salinity fluctuations, declines in aquatic communities and fish, and dramatic increases in nitrogen and bacteria levels.

54 Bay

WATERSHED time of non-native settlement. By reaches on mainstem channels and RESTORATION STRATEGIES evaluating the relative importance of involve entire systems from the hill- different geomorphic processes and sides to the tides, integrating efforts LAUREL COLLINS by establishing historical channel to restore tidal marshes and head- Watershed Sciences conditions, a useful picture of local ward tributary channels with those variation and the impacts of early on mainstem streams. Geomorphic field analyses of land use practices has emerged that A method of prioritization for conditions in streams throughout helps explain current physical con- Bay stream restoration projects Bay Area watersheds can help us ditions and inform restoration could be developed by comparing identify and prioritize watershed approaches. standardized measurements on dif- restoration strategies. Examples Restoration can involve various ferent watersheds. Among the from nine different stream assess- elements such as increasing aquatic prominent factors in Bay watersheds ments illustrate the usefulness of or riparian habitat, removing that continue to create instability such analysis, and report on the sta- migrational barriers, or creating a and sustain degraded habitat are the tus and relative importance of stable self-maintaining system. One loss of tidal marshlands, the loss of processes operating on Bay Area current challenge for land managers capacity in tidal sloughs, diminished streams. and regulators is how to approach base flow in streams, reductions in Researchers studied each of the restoration at the watershed scale, groundwater level, increased peak nine watersheds to determine rather than the reach or lot scale. runoff, loss of riparian trees, head- changes in the supply and distribu- Restoration strategies need to go ward erosion of tributary channels, tion of water and sediment since the beyond piecemeal sections and short and accelerated rates of bed inci- sion, erosion, and sediment supply. EXISTING BANK CONDITIONS FOR MAINSTREAM SITES The physical condition 100 of the nine different watersheds researchers studied is highly varied. 80 For example, Miller Creek, considered to be in relatively good condition along its lower half, has 60 68% of its mainstem bank length measured as stable. Yet many other creeks have Percent Length 40 less than 25% of their banks measured as stable (see left). About 26% of 20 Crow Creek’s 7.4 mile length has artificial bank , the highest 0 San Pedro1 Miller1 Novato1 San Antonio1 Carriger3 Wildcat Crow2 Bolinas4 Norris4 among all the streams 2.6 miles 6.6 miles 6.1 miles 6.6 miles 3.9 miles 8.8 miles 7.4 miles 2.8 miles 1.6 miles studied. Unfortunately, ad hoc construction of artifi-

Stable bank Bank Earthen trapezoidal cial bank revetments in all banks (flood control) i.e., concrete, the streams has been the wood, gabions, etc. usual mitigation for bank Eroding banks Extrapolated Bank retreat erosion, leading, in terms >0.3’ overall of cumulative impacts, to 1 Study site begins upstream of maximum extent of high tides. further loss of natural 2 Study site begins at confluence with Cull Creek, both are tributaries to . stream functions and 3 Study site begins at confluence of Felder Creek. increased rates of bed 4 Study site begins at confluence of Crow Creek. incision. Future restora- tion strategies should give priority to alternative These charts show the various bank conditions of the Bay Watershed Study Sites. Both right and left banks approaches such as were assessed for banks above and below bankfull elevation, thus terrace banks that are influenced by flood biotechnical solutions, flows are included. Dark blue represents banks that show less than 0.25 feet of retreat over the entire bank reconstruction of channel height since the time of non-native settlement, which was established for each site. Dark blue sites are con- geometry, or natural stabi- sidered stable banks. The medium blue represents banks with greater than 0.25 feet of overall retreat. Many banks have had several feet or more of retreat. The light blue represents banks with revetments such as con- lization following efforts to crete, rock rip rap, or other artificial structures. reduce runoff.

55 RESTORATION

Reducing runoff into the head- of the bed surface, toric), amount of dredging, etc. ward tributaries is a key factor for as a result of historical and present Consider pool conditions in Crow reducing channel extension. land use practices, has been as dom- Creek for example. Data show that it Increased runoff from land use inant a process as bank erosion in does not have adequate pool spacing practices has caused side channels to many Bay watersheds. It often leads even though it is a extend upslope into previously to bank erosion and increased sedi- (see pie charts p.57). The number unchannelized hillsides and down- ment supply, creating highly unsta- of pools associated with woody hill into previously unchannelized ble channels during large flood debris, which benefits fish habitat, is alluvial fans, leading to increases in events. In San Pedro and Wildcat relatively small. San Antonio Creek overall and the creeks the amount of sediment sup- has the worst pool spacing, even amount of connection between side plied from bed erosion has exceeded fewer pools associated with wood, channels and the mainstem channel. that supplied from bank erosion by and much of its channel is dry even The increase in drainage density 3 and 7 times, respectively (see though it used to be perennial and (length of channel per unit area) has chart). This factor has been grossly an excellent steelhead fishery. A increased peak floods and flood fre- overlooked as an important sedi- restoration strategy for San Antonio quency. Creation (or restoration) of ment source for many highly Creek, which would increase sum- alluvial fans on small tributary entrenched streams (see also mer base flow and pool spacing, channels, to disconnect them from Williams p.22). could involve restoration of its his- the main streams, could prevent the toric headwater lake. tributary supplies of sediment from Measurements of other channel reaching the mainstem. Such efforts attributes can also be compared The results of these kinds of stud- would also reduce downstream flood including amount and distribution ies, when integrated with other hazards, raise the water at val- of low flows; amount of remaining important channel and watershed ley bottoms, enhance mainstem stable channel, aquatic and riparian attributes, can allow us to develop a , and thus improve riparian habitat; pool and large woody debris ranking system of overall stream and in-stream biological resources. spacing; numbers and types of condition and restoration priorities aquatic species (existing and his- for the Bay region. By assessing the status of each of the important attributes that not only influence physical and biological condition, SEDIMENT SUPPLIES FROM BED INCISION but also that are compatible and AND BANK EROSION SINCE NON-NATIVE SETTLEMENT beneficial to the needs of the com- 200 munity living in the watershed, restoration strategies can be tailored 150 to the individual stream and achieved by planning over the long- term. In the future, it will be 100 important to standardize ways to compare attributes and sediment 50 loads of different streams to provide a regional picture, and to develop a 0 long-term goals process for water- olume, cu.ft./ft. not yet determined sheds as was done for Bay wetlands 50 (Collins, SOE, 2001).

Sediment V MORE INFO? 100 [email protected]

150

200

250 San Miller Novato San Carriger Wildcat Crow Bolinas Norris Pedro Antonio 217 166 166 160 165 167 200 200 200 Study Site and No. of Years Since Non-native Settlement

Normalized volumes of sediment supplied per linear foot of mainstem channel from either bed incision (light blue) or bank erosion (dark blue) since the time of non-native settlement, which is shown as years for each watershed ain the small boxes at the base of each graph.As can be seen, bed incision has been as important (if not more important) as bank erosion to contributing sediment to the San Francisco Estuary.

56 Bay

POOL FORMING MECHANISMS AND POOL SPACING FOR PERENNIAL POOLS GREATER THAN ONE FOOT DEEP FOR STUDY SITES

San Pedro Miller Novato San Antonio Carriger 108’ 145’ 121’ 316’ 644’ >5 ~widths >4 ~widths >3 ~widths >7 ~widths >23 ~widths 63-107’ expected 82-281’ expected 96-224’ expected 190-308’ expected 81 - 189’ expected

Pool Causes Human-Related Natural Wood-Related Undetermined Multiple Wildcat Crow Bolinas Norris 108’ 158’ 123’ 503’ Complex (human-related >3 ~widths >7 ~widths >7 ~widths >38 ~widths with natural or wood 90-210’ expected 60-140’ expected 51-91’ expected 39 - 119’ expected causes)

Note: Expected spacing is based upon 3 to 7 bankfull widths, which allows for a range of morphologic conditions that can include entrenched and confined channels.

These pie charts show the major pool forming mechanisms for the different Bay Watershed Study Sites. Pools formed by flow obstructions from bridge abutments, rock rip rap, or check dams are examples of human-related mechanisms (shown in dark blue). Natural pools are associated with bends, gravel bars, or bedrock abutments (yellow). Wood-related pools, although natural, are separated out to determine the influence of woody debris. This category includes large woody debris, live tree trunks and roots (medium blue). Combinations of these pool forming causes are shown as multiple and complex (light blue and light yellow). Average pool spacing is reported below the pie charts and the distance is compared to the average bankfull width for the study reaches.

QuestionsSCIENCE • Is the contribution of sediment from the Estuary’s local watersheds much larger than thought? Have we underestimated the combined influence of disturbed local watersheds historically, in the early to mid-1800s, compared to the long-thought more important sediment contributions from the Sacramento and San Joaquin system? • Are many of the mainstem channels currently responding to accelerated rates of erosion of tributary channels, particularly in grassland coast range streams and earth flow dominated terrains? • What is the amount of sediment coming from grassland hillslopes from overland flow that is directly supplied to the streams at the channel head in grazed rangelands.? • On appropriate tributary streams, is it possible to create or recreate natural functioning alluvial fans to decrease flood peaks, increase summer base flow, decrease sediment load, and increase biological diversity?

57 PERSPECTIVE

A STREAM RESTORATION mal Joint Powers Authority to bridge PARTNERSHIP FOR THE the political gaps between the two SAN FRANCISQUITO counties and five cities of this small watershed, recognizing that the WATERSHED complex nature and expense of flood protection was beyond the PAT SHOWALTER expertise of a voluntary nonprofit San Francisquito collaboration. After the flood of Watershed Council record on February 3, 1998, local officials remembered the recom- The San Francisquito Watershed mendation of the Watershed Council Council is a voluntary collaboration and worked to form the San among 30 organizations interested in Francisquito Joint Powers Authority. fostering a diverse and healthy water- The Watershed Council is still shed, valued as a natural and com- actively involved in the authority as munity resource, in a manner consis- an Associate Member.

“Recognizing what kinds of projects this voluntary collaboration can accomplish, and those that are beyond its capacity, has been an important success factor.”

tent with public health and safety and In another example, the respecting property rights. The Watershed Council has been work- Watershed Council is sponsored by ing to tackle barriers to steelhead the nonprofit Acterra and its prede- trout migration, a serious problem cessor, the Conservation for this ESA-listed threatened Center Foundation. Over the last species. The Watershed Council seven years, a variety of partnerships secured a grant from the California between the signatory organizations Department of Fish & Game to fund have formed, disbanded and an assessment of barriers to fish reformed to perform various projects migration in the Bear Creek sub- around the watershed. basin. The resulting assessment identified 34 features impeding the Recognizing what kinds of proj- fish, and suggested modifications to ects this voluntary collaboration can about half. Watershed Council vol- accomplish, and those that are unteers modified seven logjams beyond its capacity, has been an soon afterwards, and the Watershed important success factor. In the latter Council wrote a grant to modify case, the Watershed Council func- three other barriers. The most com- tions as a catalyst to inspire a better- plex situation in the sub-basin is a suited organization to take action. water supply diversion dam, where the Watershed Council has served One example of the Watershed as a liaison between the owner and Council's approach addresses the the Department of Water Resources high flood risk in the lower reaches to study possible modifications that of . Due to would improve fish passage the political complexities of the (Showalter, SOE, 2001). watershed, no major flood works or flood risk reduction plan has ever MORE INFO? been implemented. The Watershed [email protected] Council identified the need for a for-

58 Bay

NORTH BAY WETLAND NORTH BAY WETLAND PROJECTS AND BAYLANDS RESTORATION INVENTORY NUMBER OF STATUS TYPE ACRES PROJECTS STUART SIEGEL Wetlands & Water Resources Restoration and Enhancement Projects Constructed Tidal Marsh 1,501 14 Nontidal Marsh 3,560 16 An inventory of North Bay restoration Subtotal, Constructed: 5,061 30 projects provides a new framework for evalu- Planned Tidal Marsh 12,035 13 ating the success of regional efforts to manage Nontidal Marsh 2,758 11 and restore wetlands to benefit fish and Mixed Tidal/Nontidal 2,974 6 wildlife species. Subtotal, Planned: 17,767 30 Total, Projects: 22,828 60 Though wetland restoration has been going on for decades in the North Bay, early proj- Other Baylands Within Historic Margins of the Estuary ects differed from more recent ones in size Existing Wildlife Management Area 3,306 and purpose. Early projects were compara- Tidal Marsh 14,843 tively small, and often involved mitigation for Nontidal 660 wetlands lost to development nearby. Recent Naturally Restored Tidal Marsh 584 projects are comparatively large, and spon- Unprotected Lands Diked Baylands 23,455 sored, in many cases, by agencies and non- Total, Other Baylands: 42,848 profits working to promote recovery of the Estuary’s wetland-dependent fish and wildlife North Bay Baylands – Projects and Other Baylands Combined resources. TOTAL BAYLANDS: 65,676

Researchers compiled an inventory of com- SFO Runway Expansion Mitigation Sites in North Bay Baylands Study Area pleted and pending North Bay tidal, nontidal Planned Projects and Diked Baylands 18,587 and mixed hydrology wetland restoration and enhancement projects within the historic margins of tidal influence. They then mapped PROJECT SPONSORS & SITE OWNERS these projects based on the EcoAtlas GIS and prepared an accompanying database providing NUMBER OF basic information on each (name, sponsor- ORGANIZATION STATUS TYPE ACRES PROJECTS ship, size, type, and status). USFWS Constructed Tidal 306 1 For the inventory and map (see p.60), wet- Nontidal 46 1 Planned Tidal 4,769 4 lands were classified into three groups based Nontidal 90 2 on their hydrologic regime: tidal, non-tidal, 5,211 8 and mixed. Presence or absence of full, unre- stricted daily tidal exchange classifies sites as CDFG Constructed Tidal 873 3 “tidal.” Sites without full exchange are “non- Nontidal 2,509 4 tidal” and have one or more hydrologic Planned Tidal 4,347 1 regimes: muted tidal (restricted daily tidal Nontidal 1,731 4 exchange), managed tidal (periodic tidal 9,460 12 flooding and draining), and freshwater (rain- fall and runoff). Sites combining tidal marsh CSCC Constructed Tidal 322 2 with any type of non-tidal marsh are labeled Planned Tidal 4,535 3 “mixed.” In all cases soil and water salinity Nontidal 1,051 2 levels varied widely within and between sites, Mixed 2,473 3 and seasonally. 8,381 10

Based on the inventory, a total of 30 proj- MAS Constructed Tidal 28 3 ects comprising 1,501 acres of tidal marsh and Nontidal 287 2 3,560 acres of non-tidal marsh had been Planned Tidal 322 3 constructed (see tables). Planned projects will Nontidal 186 1 improve an additional 17,767 acres in a total 823 9 of 30 projects. The study area for S.F. Airport runway expansion mitigation sites in Corps* Constructed Tidal 303 1 North Bay baylands totals 18,587 acres. The Planned Tidal 5,203 3 Habitat Goals project (see p.61) recommends Nontidal 938 2 about 28,000 acres of tidal marsh be Mixed 2,434 2 restored in the North Bay by 2020 to rebuild 8,878 8 ecosystem health –about 65% more than this USFWS = US Fish and Wildlife Service MAS = Marin Audubon Society CDFG = California Dept. of Fish and Game *U.S. Army Corps of Engineers provides federal cost sharing and technical services CSCC = California State Coastal Conservancy 59 RESTORATION

NORTH BAY WETLAND RESTORATION & ENHANCEMENT PROJECTS

Source: Stuart Siegel

60 Bay

NORTH BAY PROJECTS BY WETLAND TYPE SCIENCE NUMBER OF TYPE STATUS ACRES PROJECTS Questions Tidal Marsh Constructed 1,501 14 • How can the sediment deficit needed to Planned 12,035 13 restore marsh plain elevations on diked, Subtotal: 13,536 27 subsided baylands be addressed in an Nontidal Marsh Constructed 3,560 16 environmentally-sound manner? Planned 2,758 11 Subtotal: 6,318 27 • How can we promote open water habitats Mixed Tidal-Nontidal Planned 2,974 6 for migratory shorebirds and waterfowl Total: 22,828 60 while restoring diked baylands to tidal marsh? • How can vital infrastructure lying behind dikes and below sea level, such as roads inventory shows as currently con- tidal wetlands to benefit fish and and rail, be protected at reasonable cost? structed or planned (13,536). The wildlife species. It shows the spatial report also calls for 17,000 acres of relationship between completed, non-tidal restoration, about 6,318 planned, and existing wetland areas of which are constructed or and it identifies diked baylands in planned. Another 2,974 acres of private ownership that could be MORE INFO? mixed hydrology projects are also restored or subject to development. [email protected] planned. Uses of this inventory include site www.swampthing.org selection for regional monitoring www.sfbayjv.org The inventory and map provide a efforts and scientific research, and framework for evaluating the status identification of parcels for acquisi- and effects of regional efforts to tion and restoration (Siegel, SOE, manage and restore tidal and non- 2001). PERSPECTIVE

ECOSYSTEM GOALS shorebirds and waterfowl and to in the coming years. The San PROJECT UPDATE restore and enhance transitional Francisco Bay Area Wetlands habitats, riparian vegetation, and Restoration Program, a partnership seasonal wetlands. of public agencies involved in MICHAEL W. MONROE implementing wetlands action items U. S. Environmental Last year, the Goals Project issued in the S.F. Estuary Project's Protection Agency a companion document to the Goals Comprehensive Conservation & Management Report entitled Baylands Ecosystem Plan for the Bay and Delta and the In June 1999, the San Francisco Species and Community Profiles, which broad recommendations in the Bay Area Wetlands Ecosystem Goals presents information on the life Goals Report, is now underway. The Project released its report entitled histories and environmental program aims to: improve intera- Baylands Ecosystem Habitat Goals. The requirements of many of the plants, gency communication and coordi- report recommended the kinds, fish, and wildlife species for which nation; improve projects through amounts, and distribution of wet- the Goals were developed. early review of design concepts lands and related habitats that are (before they reach permitting); needed to sustain diverse and Nearly 3,000 copies of the Goals reduce delays and project costs; and healthy communities of fish and Report have been distributed, and foster greater understanding and wildlife resources in the San many public and private entities accountability through design review Francisco Bay Area. It was the cul- have embraced the Report’s recom- and improved monitoring (Monroe, mination of more than three years mendations and begun to use them Pers. Comm., 2002). of work by scientists, resource man- as guidance as they seek to improve agers, and other Goals Project par- habitat conditions around the Bay MORE INFO? ticipants. (Monroe, SOE, 2001). [email protected] www.sfei.org/sfbaygoals/index.html The Goals Report calls for restoring Since the 2001 conference, www.abag.ca.gov/bayarea/sfep/ more than 60,000 acres of diked progress has been made in establish- baylands to tidal salt marsh. It also ing a new institutional framework reports/Species.pdf stresses the need to manage large for coordinating sound habitat www.sfwetlands.ca.gov/home.html areas of shallow saline ponds for restoration throughout the Bay Area

61 RESTORATION

PLANT SPECIES IN DECLINE results in new populations that native San Francisco Bay tidal IN THE S.F. BAY ESTUARY behave ecologically like Atlantic marshes, natural Atlantic salt smooth cordgrass. Recent genetic marshes include extensive “short PETER R. BAYE analysis from U.C. Davis indicates form” Spartina alterniflora vegetation U.S. Fish & Wildlife Service progressive interbreeding will assimi- on poorly-drained extensive marsh late and extirpate native Spartina foliosa plains (smaller drainages and creeks Many native wetland plants are on regionally, replacing it with a more choked with cordgrass), and restric- the wane in the S.F. Estuary. Among robust, competitively superior non- tion of “tall form” S. alterniflora to the principal causes are declining native hybrid type (see also p.13). well-drained banks along Atlantic quality of marsh habitats, lack of suit- marsh edges (see below and p.64). Hybrid smooth cordgrass popula- able habitat in restored marshes, and If restoration trends progress tions in San Francisco Bay have the residual effects of past destruction towards Atlantic-type marsh struc- demonstrated that they are potent of both habitats and plant popula- ture and its vegetation patterns, it geomorphic and ecological agents. tions. One threat to local vascular is doubtful whether tidal marsh Unlike native Pacific cordgrass, the plant communities currently stands restoration objectives can be Atlantic-type hybrid cordgrasses rap- out among all others, however, in achieved for a wide range of endan- idly colonize unsheltered intertidal terms of its ability to permanently gered and other native species. flats and marsh pans, and fully colo- change the structure and function of nize the beds and banks of small tidal Other invasive cordgrasses likely all tidal marshes: the rapid invasion creeks and ditches, resulting in a rel- to dominate high tidal marsh zones of the San Francisco Bay Estuary by atively homogeneous marsh. Hybrid have also invaded the Estuary, but nonnative plants. smooth cordgrass may also eliminate have not spread as rapidly as the The most advanced and aggressive estuarine sand spits and beaches. Spartina alterniflora hybrids. These invasion is a hybrid swarm of cord- Estuarine beaches are among the include Chilean cordgrass, S. densiflo- grass derived from a founder popula- rarest remnant habitats in the region, ra, a tough bunchgrass; and salt- tion of smooth cordgrass, Spartina and important for recovery of some meadow cordgrass, S. patens, the alterniflora, from the Atlantic coast. endangered species. Atlantic counterpart to The hybrid swarm interbreeds with, S. alterniflora, which forms extensive In contrast with the more complex and assimilates, native populations of meadows of dense, fine shoots. structure of sinuous, branched Pacific cordgrass, Spartina foliosa, and sloughs and mosaics of pans in

HOW SMOOTH CORDGRASS INVADES BAY TIDAL HABITATS

62 Bay

37 S. patens Introduction RINVush CreeASIVEk SPARTINA DISTRIBUTION Southampton Marsh: S. patens reported here OSP as early as 1968 in Munz’s A California Flora. The San Pablo Bay population has spread widely within marsh since No Introduced Spartina National Wildlife Refuge 29 initial report, and is competing with the endangered Cordylanthus mollis sp. mollis. 680 A complete survey of Grizzly Bay - Grizzly line was conducted by boat. No invasive N Bay a p Spartina species were found. a Vallejo No Hybrids Found R iv e Targeted mudflat and shoreline surveys were conducted r Benicia State Goodyear Slough Unit in North San Pablo Bay and the Napa-Sonoma Marsh. Recreation Area Plants were sub-sampled for genetic analyses. No Marsh S. alterniflora/hybrids were found. However, a single S. densiflora plant was found in Pond 2A by a local botanist.

S. densiflora and San Pablo Bay 80 Point Edith Wildlife Area West Pittsburg S. anglica Introduction State Outlier Populations Lone Tree Marina Park Marin County is host to 3 invasive Spartina species, including 680 Creekside Park: Site of initial Wildlife Point Martinez introduction of S. densiflora Area the only known population of S. anglica. New outlier populations and S. anglica. Plants were of S. alterniflora/hybrids and S. densiflora were found on the 4 transplanted to site in 1976 northern San Rafael shoreline. as part of marsh restoration Martinez Regional Shoreline project. S. densiflora escaped China Camp Point Pinole 4 Creekside Park, and has State Park Point Pinole spread along entire length of Regional McNears Corte Madera Creek, covering Shoreline S. alterniflora/hybrid more than 12 acres of the County Park Northern Limit C creek’s wetlands. o S. alterniflora/hybrids rte M San have spread much a d further north than e Rafael S. alterniflora S. alterniflora Concord r Pa a Albert Park San blo thought prior to this Cr C Pickleweed eek /hybrid Lab Tested* /hybrid Field ID S. densiflora S. patens S. anglica r survey. Emeryville e e k Park Crescent was believed Creekside Park to be the East Bay’s Diameter range Diameter range Diameter range Diameter range Diameter northern limit of in meters in meters in meters in meters range in San S. alterniflora/hybrids, meters Ra 0 - 4.5 0 - 4.5 0.01 - 1.75 0.5 - 4 fael B but scattered populations Piper Park ridge were found as far north Larkspur Corte Madera Marsh 580 Richmond 4.5 - 9.5 5 - 9.5 2 - 15 5 - 19 20 Town Park Ecol. Reserve as and Pt. Pinole in Contra Costa 10 - 65 10 - 65 Miller Knox Walnut Ring county. Introduction Site Shoreline Not Surveyed Mountain Regional Park *S. alterniflora/hybrid Percent cover Creek Preserve verified by lab tests. Point Isabel Paradise <1% Habitat and Land Use Beach Brooks Island Albany 1-1204% Bothin Point 10-30% Mud Flats Public, Privately Protected Blackie's Points represent individual Marsh 30-60% Lands and Wildlife Refuges Pasture 80 Spartina clones or small Deep Bay clusters of clones. 60-90% Undeveloped Land Shallow Bay 90-100% Developed Land Aquatic Golden Gate Park National Recreation Area Emeryville Crescent Treasure Island Oakland Army Terminal 13 ridge y B Naval Ba o Supply 880 sc Oakland 680 ci 80 n Center ra F n a S San Francisco Alameda MLK San Crown Memorial Regional Ramon 580 State Beach Shoreline Shoreline Park Pier 98

Candlestick 280 Bay San Regional Leandro Shoreline 580 eek nzo Cr re o L an S Restoration Sites Impacted 880 Alameda County hosts several of the oldest and South San San Bruno largest S. alterniflora/hybrid invasions in the Estuary. Francisco Colma Point Large restoration projects have been infested along Creek the Hayward Regional Shoreline. 1 Hayward Sam Trans Regional Terminal Shoreline 380 Hayward San Francisco International S. alterniflora/hybrid Transplant Airport San Bruno Slough/Colma Creek: S. alterniflora/ e ridg Union City hybrids reputedly transplanted from “Pond 3” o B Pacifica ate restoration site in Hayward to Colma Creek area Burlingame Coyote n M Sa Alame k in the 1970s. This area now represents one Park Point da Cree S. alterniflora Introduction of heaviest S. alterniflora/hybrid infestations in Bayfront 92 Pond 3: Site of initial introduction of west San Francisco Bay, totaling 55 net acres. Burlingame Shoreline S. alterniflora into San Francisco Bay. Park Seed was sown as part of restoration Bayside Flood Control Channels Joinville project in early 1970s. Plants quickly Redwood Flood control channels became established, and began to Park Shores in the Hayward/Fremont spread along bay shore. 280 Ecological area are filling in with Reserve S. alterniflora/hybrids. Coyote Hills Fremont Regional Park Newark San

Mateo e g 880 Greco id r Island SF Bay Nat'l B 92 n Wildlife Refuge o rt ba SF Bay Nat'l um Wildlife Refuge D

84 San Bayfront Park 0 1 2 3 4 5 Miles Ravenswood Carlos Recreation Area Baylands SF Bay Nat'l Wildlife Refuge Sources: Palo Alto Invasive Spartina Project (2001) and Redwood Scattered Clones Baylands UC Davis Spartina Lab, Spartina data; City Though S. alterniflora/hybrids have spread Preserve further into the South Bay than previously Bay Area Open Space Council (2000), basemap; thought, populations are still sparse south San Francisco Estuary Institute EcoAtlas (2001), of the Dumbarton Bridge, with only scattered Mountain View marsh and mudflat map layers. individual clones found along the shoreline and in sloughs. Shoreline Park Alviso Park

63 RESTORATION

Eradication of Chilean and salt- Numerous plant species of con- SCIENCE meadow cordgrass, and other infre- cern are subject to the same basic quent non-native cordgrasses in the threats as legally protected plant Questions Estuary, is highly feasible, and has species. Some, like Bolander's water been initiated by the regional hemlock (Cicuta maculata var. bolanderi) • Will hybrid smooth cordgrass stands Invasive Spartina Project (see p.13). may be rarer and at greater risk of Eradication of the hybrid smooth extinction than species currently in S.F. Bay generally delay or inhibit cordgrass invasion is also underway, listed. establishment of other native plants but remains complex, difficult, and (including dominants, such as pickle- costly in terms of natural and finan- One of the most basic needs for weed, as well as rare plants) when cial resources. the recovery of rare or endangered suitable substrate elevations have plants of the Estuary is restoration accreted? Or will new (or restored) In contrast, the most serious inva- of suitable tidal marsh habitat. But tidal marshes dominated by hybrid sive plant of plains, tidal marsh restoration without ade- smooth cordgrass be sustained in broadleaf pepperweed (Lepidium lati- quate control of wetland weeds may “arrested development” as persistent folium), has no regional control pro- threaten, rather than promote, gram. The rate and extent of L. lati- recovery of endangered species. cordgrass as sea level rises? folium spread increased alarmingly Therefore, control of the most • Will characteristic geomorphic fea- during the wet years of the late 1990s important nonnative plant invasions tures of S.F. Bay tidal marshes, such when tidal marsh salinities were rela- must have equal priority with wet- as salt pans and small, sinuous tidal tively low. Like invasive hybrid land restoration itself, or restora- creeks, develop under the influence of smooth cordgrass, L. latifolium forms tion efforts will be self-defeating hybrid smooth cordgrass when new extensive dominant cover, often sin- (Baye, SOE, 2001). tidal marshes are restored? gle-species stands, from creeping below-ground parts. MORE INFO? • Will mature hybrid smooth cordgrass [email protected] in S.F. Bay develop single-species Many of the region's endangered www.spartina.org “short form” cordgrass marsh typical plants are threatened by these inva- www.cnps.org of Atlantic marshes? If so, how rapid- sions, as well as by habitat loss and www.cdfa.ca.gov/purpleloosestrife other factors. The most critically ly may this occur? Will California clap- endangered of these listed species is per rails nest successfully in short- Suisun thistle (Cirsium hydrophilum var. form hybrid smooth cordgrass, as hydrophilum). Its habitat is also under they do in young colonies of tall-form rapid invasion by perennial pepper- cordgrass? weed. It survives as a few unstable local sub-populations in northern Suisun Marsh, but little research, management, or restoration has gone into its recovery. ATLANTIC VS. PACIFIC CORDGRASS MARSH STRUCTURE While the popula- tion of endangered soft bird's-beak (Cordylanthus mollis ssp. mollis) continues to fluctuate, its overall distribution has nei- ther declined nor recovered significantly in recent years. Research at U.C. Davis is now underway on reintroduction and restoration of this species. Endangered California sea-blite, long extinct in the Estuary, has been rein- troduced experimen- tally to a restored salt marsh in the Presidio, San Francisco. Not to scale.

64 Bay PERSPECTIVE

SOUTH BAY RESTORATION for Bair Island will be submitted for public review the winter of CLYDE MORRIS 2002-2003. U.S. Fish & Wildlife Service All this progress may be just a Though restoration in South warm-up for long-term restoration San Francisco Bay has been pro- of 15,500 acres of San Francisco ceeding at a slow pace, it may be Bay salt ponds planned for acqui- on the verge of a new era. South sition by federal and state govern- Bay wetlands have succumbed to ments in 2002-2003. This project many of the same pressures found is big enough to offer the exciting elsewhere in the Bay — the devel- possibility of bringing the rails and opment of residential, commer- harvest mice back from the edge cial, transportation and landfill of extinction, but presents signifi- projects. However unlike other cant funding, technical, and man- areas of the region, much of the agement challenges: How do we loss in the South Bay has been to retrofit the ponds to stop making development of commercial salt salt and provide habitat for at ponds. The loss of these tidal wet- least the species who are now lands has been a severe blow to dependent on these saline ponds? the ecosystem, and has placed How do we select which ponds some tidal wetland dependent will become which types of habi- species, such as the California tat? How do we deal with the clapper rail and the salt marsh existing infrastructure, flood con- harvest mouse, on the endangered list. However, because these tidal wetlands were converted to salt ponds, rather than commercial or “The South Bay's tidal wetlands were converted to salt residential development, there is a much greater opportunity for ponds, unlike the commercial or residential development restoration. that claimed wetlands elsewhere in the region, At the Don Edwards S.F. Bay so there is a much greater opportunity National Wildlife Refuge for restoration.” Headquarters in Fremont, several salt pond restorations have already been accomplished. A trol, and treated wastewater flows? number of former salt crystallizers How do we accommodate urban were restored in the 1980s by re- demand for open space recreation establishing the tidal connection (such as jogging, cycling, and dog to the Newark Slough — resulting walking) while protecting sensitive in excellent growth in endangered species and wildlife dependent species numbers. As of the recreation (such as hunting, fish- October 2001 conference, other ing and bird watching)? Where do projects were being planned or we get the funding for the interim built including Deep Water Slough retrofit and operations; and the on Middle Bair Island in Redwood massive planning and design (the City, an S.F. Airport-sponsored restoration itself may cost more project on Outer Bair Island, an than the land purchase)? Eden Landing Ecological Reserve Addressing these issues will restoration project near the San require an unprecedented level of Mateo Bridge, and a 1,400-acre regional cooperation and partner- restoration of former salt ponds at ship among us all (Morris, SOE, Bair Island. Post-conference 2001). progress has been made on many of these projects, notably restora- MORE INFO? tion at Eden Landing is well on the [email protected] way and the draft restoration plan

65 RESTORATION

THE EVOLVING pelagic (open water) communities. Researchers have noted a similar, BENTHIC COMMUNITY These details explain, for example, but much smaller, effect of inter- why the North Bay's phytoplankton annual and seasonal differences in JAN THOMPSON biomass greatly declined with the shallow water P. amurensis grazing on U.S. Geological Survey introduction of P. amurensis, while the the North Bay phytoplankton. With South Bay's phytoplankton biomass the return of freshwater following The composition of the Estuary's did not (phytoplankton are tiny the 1987-1992 drought, shallow- community of clams, worms and drifting plants at the base of the water P. amurensis began to consistent- other bottom-dwelling, or benthic, food web). The different system ly drop to a seasonal low in biomass organisms has been in a near-con- responses to the invasion derive in the early spring. This has resulted stant state of flux since the 1860s from the timing of the phytoplank- in several phytoplankton blooms of due to the introduction of non- ton bloom and the magnitude of short duration (less than a month), indigenous species. The introduc- seasonal cycles of the bivalve in the and varying magnitude. Thus, the tion of the Asian clam Potamocorbula two systems (see graphs). North Bay's phytoplankton bloom, amurensis, for example, not only historically short in magnitude but Biomass of P. amurensis in the South changed the structure of the benthic lasting several months from summer Bay can be of similar or greater community in San Francisco Bay into fall, has now been reduced to a magnitude (20-45 grams dry weight and the Delta, but also brought shorter bloom occurring at a differ- per square meter) to that seen in about ecosystem level responses such ent time of year. The effect this North Bay (10-15 grams), but is as alterations in the food web and in change in bloom dynamics will have more seasonally variable in the the trophic transfer of contami- on the higher trophic levels South Bay where P. amurensis essen- nants. dependent on the phytoplankton for tially disappears in winter in the food remains to be seen. It is in this context that it is shallow water. Due to the high tur- important to explore why some bidity in both the North and South Learning how P. amurensis is affect- invasive species affect ecosystem Bay, the shallow water is critical for ing the Bay ecosystem can help us function and others do not. phytoplankton growth, and thus sea- project system responses to future sonal dif- changes in the benthic community. ferences It can also help us hypothesize if the COMPARISON OF PHYTOPLANKTON BLOOM SUCCESS IN in P.- P. amurensis effect is in any way unique NORTHERN AND SOUTHERN SAN FRANCISCO BAY FOLLOWING ensis graz- or if other introduced species have THE INVASION OF POTAMOCORBULA AMURENSIS ing rates similarly altered the ecosystem. 80 in the North Bay shallow The work of Cohen (1996) indi- water can cates a near continuous import of 40 Potamocorbula have direct benthic species into the system, 10 invaded effects on of which are of the same functional feeding group as P. amurensis, and

g/L) phyto- µ 0 plankton thus might have affected phyto- bloom plankton bloom dynamics if suffi- South Bay 120 magni- ciently abundant. The lack of sea- tude, sonal phytoplankton data from the

Chlorophyll a ( Potamocorbula invaded mid 1800s-1960s makes a thorough 60 duration, and sea- investigation of such historic sonality. changes impossible. Two introduced 0 benthic species offer some clues, ‘79 ‘81 ‘83 ‘85 ‘87 ‘89 ‘91 ‘93 ‘95 ‘97 In the however, because they were cultured Source: DWR,USGS ACCESS South Bay, or harvested in the Bay, and their the sea- biomass and spatial distribution sonal phy- documented. The Asian clam replaced a benthic toplankton bloom has historically People cultured the Eastern oyster community that had few filter feed- occurred, and still occurs, in early (Crassostrea virginica) in San Francisco ers and a low biomass. P. amurensis, as spring during a period of low tidal Bay from 1869 to 1910. As the oys- a large, abundant filter feeder with a energy and high light availability ters never successfully reproduced in seasonally more stable population (see chart opposite). This period the Bay, they were cultured by plac- than the previous community, and a coincides with the annual minimum ing imported “spat” (juvenile wide distribution, had a large effect in P. amurensis biomass. Therefore the that are attached to adult shells) in on the ecosystem. Ecosystem South Bay phytoplankton bloom has localized areas, so the oyster never responses to the introduction of P. not been changed by the invasion of became widely distributed. Record amuerensis show that the effect of the P. amurensis due to the particular keeping on the acreage of oyster benthic community on the food web coincidence of the phytoplankton beds and the pounds of oysters har- is dependent on the details of the bloom with a seasonal minimum in vested suggests that in areas where connection between the benthic and the grazers.

66 Bay THE PHYTOPLANKTON BLOOM IN SOUTH BAY OCCURS DURING PERIODS WHEN SHALLOW WATER BENTHIC GRAZING IS LOWEST 10 60 QuestionsSCIENCE • What epi-benthic community is emerg- ing around invasive aquatic vegetation? 5 30 • What potential invaders are of particu- lar concern in this system?

Chlorophyll a (mg/m3) • Could grazing of Corbicula affect the success of Bay-Delta restoration proj- ects? What factors control the distribu- 0 0 ‘91 ‘92 ‘93 ‘94 ‘95 tion of large filter feeders such as Corbicula? the oyster was cultured, the oysters ton reductions occurred on were likely to have greatly reduced the same spatial scale seen with the phytoplankton biomass. P. amurensis. M. arenaria. The softshell clam, unlike P. amurensis, is intolerant of Estimates have been done of the The second introduced species North Bay's low salinity during number of times in a day that the about which there is distribution non-drought years, and thus the oysters could have filtered the over- and harvest data is the Eastern soft- reduction in phytoplankton was lying water column (expressed as the shell clam, Mya arenaria. Unlike the limited to the drought years. water column turnover rate per day) Eastern oyster, the softshell clam was and compared to the phytoplankton accidentally introduced into the Upstream in the Delta, we find growth rate (about 0.5/day accord- Estuary in the 1870s and spread other examples of how past intro- ing to Cloern et al., 1985, if we rapidly from San Pablo Bay down to ductions may have permanently assume bloom or near-bloom con- the South Bay (Skinner, 1962). altered the ecosystem. Recent studies ditions). In these comparisons, any of the filter-feeding freshwater water column turnover rate in excess Estimated water column turnover bivalve Corbicula fluminea, uninten- of the phytoplankton growth rate rates for this clam, based on harvest tionally introduced in the 1940s, will result in an “overgrazed” system. records in the commercial beds, show that it can be a controlling fac- exceeded 10 times per day prior to tor in phytoplankton biomass on Results from these calculations 1900 and leveled out to rates flooded islands. Given the declines suggest that the water column between one and five times per day in Delta zooplankton and fish pop- turnover rate during oyster cultur- until the 1930s. Due to the softshell ulations in the last half century, we ing varied from a high in the earliest clam's wide distribution and large might ask if this shift in the benthic years of near 10 times per day biomass, it is possible that its graz- community may have, at the least, (assuming a 2-meter-deep water ing did change phytoplankton contributed to changes in the column) to an average of about two dynamics in the Bay. Indeed a paper ecosystem. times per day until 1900. Thus it is published by Nichols (1985) shows likely that phytoplankton was locally that the North Bay's greatly reduced In conclusion, we find that some depleted around the oyster beds, but phytoplankton bloom during the invasive benthic species affect since the beds covered such a small drought of 1976-1977 was likely due ecosystem function more than oth- area, it is unlikely that phytoplank- to the overgrazing of the system by ers, and that the changes to the sys- tem that have been brought about by P. amurensis are probably not unique, WILL CHANGING THE TIMING AND DURATION OF THE PHYTOPLANKTON BLOOM AFFECT THE FOOD WEB? although the persistence of these 40 30000 changes may be unique. We have Apr learned that it is important to know 35 the details of the invaders’ life his- 25000 tories, including feeding mode and 30 the seasonal patterns of growth, 20000 25 reproduction, and predation, if we g/L)

µ are to understand and eventually 20 15000 predict the potential effects of an invasive species on a system 15 10000 (Thompson, SOE, 2001). Jun

Chlorophyll a ( May 10 Jun Sep Apr MORE INFO? 5000 5 [email protected] http://sfbay.wr.usgs.gov/access/ 0 0 ‘93 ‘94 ‘95 ‘96 ‘97 ‘98 ‘99 ‘00 biology.html

67 RESTORATION PERCENTAGE OF NORMAL LARVAE OF NATURAL SPAWN IN FIELD MERCURY IN S.F. BAY ENVIRONMENTAL FACTORS 100 AFFECTING PACIFIC HERRING % Normal Larvae 80 KHALIL E. ABU-SABA S.F. Bay Regional Water GARY CHERR Quality Control Board U.C. Davis 60 The history of mercury in California The S.F. Bay Estuary population of 40 is recorded in the sediments of San herring is California’s largest and Francisco Bay. The Bay is downstream experiences increased variability with 20 of 40 percent of the land area of respect to environmental conditions, California. Three billion kilograms of particularly salinity and spawning 0 PVC Substrate Creosote Piling sediments are annually flushed from substrates (see also p.11). local watersheds and the Central Valley ton and are preyed upon by and deposited in the Bay. salmon, rockfish, lingcod, During and after the Gold Rush, EFFECT OF SALINITY AND CREOSOTE ON birds, and marine mam- LARVAL MORPHOLOGY over seventy thousand tons of mercu- mals. Spawn (developing 100 ry was produced in Coast Range embryos) is a food source % Normal cinnabar mines. Much of this mercu- for birds, crustaceans and 90 ry was used as quicksilver to extract sturgeon. 80 gold from placer formations in the Pacific herring repro- Sierra foothills, and later in the pro- 70 ** duction in the S.F. Estuary duction of munitions, electronics, * * health care and commercial products. 60 ** is dependent on low salini- % ty water, or more specifi- Today the legacy of mining sources, 50 cally, on decreased salini- from both remote and local water- 40 ** ** ties during the winter sheds, is superimposed on air deposi- * * months. Both successful tion, the climate and geography of 30 fertilization and embryo California, heavily managed water supply and flood control projects, 20 ** development require reduced salinities, with the wetland restoration and rehabilita- 10 optimum rates of develop- tion, urbanization, wastewater dis- charge and water reclamation. 0 ment and hatching of 8 ppt 8 ppt + 16 ppt 16 ppt + 28 ppt 28 ppt + embryos occurring at creosote creosote creosote That legacy—combined with more approximately half strength current sources of mercury—is impact- seawater. Larval herring ing beneficial uses of San Francisco * Statistically significant from controls at P<0.01 survival may also be reduced at ele- Bay today. Surveys of contaminant lev- vated salinities. The impacts of Pacific herring is an economically els in fish conducted by the San extreme salinities, which may occur and environmentally important Francisco Bay Regional Monitoring during drought or El Niño condi- marine fish that utilizes San Program (RMP) in 1994 and 1997 tions, have been documented in both Francisco Bay for critical stages of its show that there is too much mercury in lab and field. lifecycle and contributes to the fish caught from the Bay, so the bene- marine and estuarine food web. Although salinity fluctuations can ficial use of commercial and sport Adults and juveniles consume plank- be further modulated by human fishing is not attained. The Bay is an activities such as freshwater diver- important fishery, a food source for sions, other anthropogenic impacts approximately 150,000 anglers, and EFFECT OF CREOSOTE ON habitat for rare and endangered HATCHING SUCCESS AND on reproductive success are more NORMAL LARVAL MORPHOLOGY obvious Herring often use tar cre- species. Monitoring data indicate that 100 osote pilings as spawning substrates, mercury concentrations in popular sport fish exceed acceptable risk levels 90 for example, and researchers have % Normal Larvae found that the survival rate of such for developmental impairment of chil- 80 embryos is extremely low. The effects dren and expectant mothers. Based on 70 * of altered salinities and creosote the latest criteria guidance from U.S. EPA and local consumption surveys, 60 exposures include acute mortality of % embryos attached to the pilings, or mercury concentrations in popular 50 abnormalities in larvae floating in sport fish need to be reduced by two- 40 the creosote-laced water at short fold to fully protect the majority of subsistence fishers. 30 distances from the pilings (Cherr, ** SOE, 2001). 20 Strategies to reduce mercury con- 10 MORE INFO? centrations in aquatic ecosystems must focus both on mercury loads 0 [email protected] Control Control Creosote-treated (1/2 FSW) Wood Wood

68 Bay MERCURY METHYLATION

and mercury methy- SCIENCE lation, because 20 • methylmercury is the Questions primary chemical form that accumu- • Are there ways to create, enhance, lates in biota. Since and manage wetlands that minimize Methyl % the vast majority of 10 the conversion of mercury to mercury in aquatic methylmercury? Adaptive manage- ecosystems is bound ment means systematically trying dif- to particulates, mer- ferent designs, and then seeing which cury loads are assessed one works the best. Factors such as by evaluating how dif- 0 5 10 vegetation type, final elevation, chan- ferent sources affect nel depth, flushing rates, and source mercury concentra- Dissolved Oxygen (mg/L) tions in Bay sedi- water composition are examples of Source: Fairfield-Suisun Sewer District ments. Prior to the the different design factors that could European settlement be considered. of California, the concentration of under permits and waste discharge requirements. • What is the role of atmospheric depos- mercury in Bay sediments was tion in mercury methylization? Is approximately 0.06 ppm. Today, it Recent monitoring data demon- atmospheric mercury more easily con- is approximately 0.4 ppm, a six-fold strates that mercury methylation efficiency in the Bay increases verted to methylmercury than mercury four-fold when dissolved oxy- from mining legacies, and thus a key NUMERIC OBJECTIVES VIOLATED gen drops below contributor of mercury to the food 6 mg/L (see above). chain? How much of the atmospheric load to the Bay comes from local air 0.2 While load reductions can reduce total mercury invento- emissions, and how much is coming

g/L) from long range transport (source is

µ ries by a half over long San Pablo Bay Artesian Slough (decadal) timescales in large key to controllability)? Alviso Slough Lower South Bay 0.1 Guadalupe Slough

Suisun Bay areas, watershed management to

Coyote Creek reduce and Central Bay

Sacramento River anoxia could result in rapid SIP South Bay Basin Plan Total Hg in water ( reductions in tissue concentra- 0 tions in localized areas. median Consequently, the Total South North Maximum Daily Load (TMDL) implementation plan being established by excess compared to pre-settlement SOURCE ASSESSMENT the S.F. Bay Regional conditions. It is projected that con- Water Quality Control 900 trolling all controllable sources will, Board will call for load after decades of equilibration, pro- reductions through duce a steady-state mercury concen- restoration of inoperative tration of approximately 0.2 ppm, 600 mine sites in rural water- or half of the current concentration sheds, pollution preven- in sediments. Hg (kg/yr) Other Loads tion measures in the Guadalupe River

300 Urban Stormwater It is unlikely that fish tissue targets urban environment, and Non-urban Stormwater can be attained over time through adaptive management Air Deposition

strategies to identify and Central Valley load reductions alone, because mer- Wastewater cury bioaccumulation is mainly control factors (e.g., 0 driven by the methylmercury con- nutrient loading, dis- centrations in aquatic ecosystems, solved oxygen) that create rather than total mercury concen- conditions favorable to mercury trations. To reduce mercury con- methylation (Abu-Saba, SOE, 2001 centrations in fish, controllable & Abu-Saba & Mumley, 2002). water quality factors that promote mercury methylation in the aquatic MORE INFO? ecosystem must be considered in [email protected] conjunction with mercury load reductions. Some of these water quality factors (i.e., dissolved oxy- gen) are already subject to regulation

69 PERSPECTIVE

LESSONS LEARNED IN Earth’s crust and those produced ment before their persistence and EIGHT YEARS OF by society must not systematically unintended side effects are CONTAMINANT increase in nature) are violated, known; and it’s a good idea to the regulatory system will remain turn off the tap to the overflowing MONITORING mired in an endless, costly sink before mopping the floor assessment-evaluation- (Hoenicke, SOE, 2001). RAINER HOENICKE remediation cycle. S.F. Estuary Institute

The Regional Monitoring Program for Trace Substances “We have yet to learn (RMP) was established in 1993 as a tool for the Regional Water two lessons: It’s a bad idea to release Quality Control Board to evaluate man-made substances into the environment before their regulatory policies related to the Clean Water Act and the California persistence and unintended side effects are known; and Water Code. The RMP has also it’s a good idea to turn off the tap to the overflowing sink been used by other agencies to evaluate the effectiveness of pollu- before mopping the floor.” tion prevention and reduction actions outlined in the 1993 Comprehensive Conservation and Management Plan (CCMP) for the The implications of these les- San Francisco Estuary. sons are many. We need to place a MORE INFO? greater emphasis on biological www.sfei.org Eight years of RMP data have indicators of pollution impacts. taught us several things: We need to supplement monitor- ing with research to remain rele- 1. Most metals that had been of vant. We need to communicate key regulatory concern no monitoring information more longer need the attention they effectively to legislators and policy once received. makers. Environmental manage- 2. Recovery from pollutant ment agencies and the scientific impacts, especially from per- community are not in all cases the sistent, bioaccumulative con- most important recipients of the taminants, will take decades or monitoring information. longer. In addition, the institutional 3. Synthetic organic contami- framework needs to be better pre- nants, including emerging pol- pared to generate and act on a lutants, are becoming a higher comprehensive picture of ecosys- priority. tem integrity that could be used to 4. Pesticide runoff and its effects focus resources in areas where on non-target aquatic species is relief of pressures on the ecosys- a continuing cause for concern. tem could provide the greatest environmental benefit. Revisions 5. The watersheds surrounding to the legislative framework the Estuary sometimes repre- should also be considered to pre- sent substantial reservoirs for vent new synthetic compounds certain pollutants that will ulti- from becoming emerging pollu- mately be mobilized and trans- tants with unexpected and unin- ported into the Estuary. tended adverse environmental effects. These findings demonstrate that as long as the basic principles In sum, is clear that we have of sustainability, and those specifi- yet to learn two important lessons: cally related to pollution preven- It’s a bad idea to release man- tion (i.e., substances from the made substances into the environ-

70 Bay PERSPECTIVE

A HISTORY Water was also imported by the point, three Berkeley women organ- OF BAY FILL & PERPETUAL private Spring Valley Water ized their friends and others into a URBAN GROWTH Company, first from Pescadero and group called to stop then from San Mateo and Alameda the filling, resulting in the creation Creeks, beginning the destruction of of the S.F. Bay Conservation & GRAY BRECHIN the steelhead runs in the immediate Development Commission (the U.C., Berkeley Bay Area. Freshwater inputs were BCDC), whose first major contest Those who came before and replaced by sewage and industrial was its opposition to a proposed fill during the California Gold Rush wastes which gave the Bay a notori- south of the Ferry Building for a quickly realized that the real for- ous odor. U.S. Steel complex. Democratic tunes were to be made not in Sierra Mayor Joseph Alioto vowed to By the turn of the century, those gravels but in land speculation as weaken the BCDC in Sacramento, who owned land and Bay realized long as people continued to be but did not succeed. that they needed public assistance drawn to the Golden State by its to increase the value of land in The BCDC could not, however, promise of riches. They therefore acquired — by whatever means order to grow more cities....what stop urban growth but only redirect possible — water lots, tidal lands, they called “Greater San Francisco.” it away from the water — views of and the Bay itself with the intention of eventually filling their aqueous properties to create more lucrative “The Bay region, and its transportation planners, real estate for themselves and their descendants. The Bay was thus are trapped in a self-fullfilling prophecy of sprawl seen chiefly as a thing to get rid of, and gridlock, of projections as destiny. The question and the solemn superstructure of Western property titles rose upon a throughout the region, and for the S.F. airport expansion quicksand of epic fraud and theft project, is how can we take control of the demand from the public domain. side of the equation?” Those who sought to profit from urban growth did so by importing energy and water into the city to transform its natural environment, STUART COHEN Bay Area Transportation & Land Use Coalition and in the process, they further transformed those wider hinter- They did so by creating new public which became chief selling points lands from which they took the agencies such as the Bureau of for expensive developments around energy and the water. All cities do Reclamation, the Hetch Hetchy sys- its perimeter. Despite abundant les- this; they are like collective organ- isms that have a metabolism that tem, EBMUD, the Muni, the state sons provided by the Loma Prieta must be sustained by constant Highway Department and the and other seismic events, growth inputs, and they produce waste pro- Department of Water Resources. has continued apace in such haz- portional to those inputs. But, The Reber Plan proposed to use ardous locations as Mission Bay unlike any other collective organism public monies to turn much of the where a massive biotech facility is of which I am aware, a few of the Bay into freshwater reservoirs by being constructed on a prime lique- city's constituent parts profited far building massive dikes. The plan faction site. The economy remains more from its growth by monopo- received enthusiastic support from predicated upon the fantasy of infi- lizing the land than did the mass. the and nite urban growth, as mindless as other business interests that hoped are cancer cells to the ultimate fate Wood was at first used for fuel, to profit from the urban growth it of their host. In this case, the victim sending out a shock wave of defor- would kick off. appears to be the immensely intri- estation whose effects on the Bay cate biotic web which shows alarm- no one has studied. Poor lignite By the latter half of the twentieth ing signs of collapse. We may soon was then imported from Mt. Diablo, century, those nineteenth century find that we need phytoplankton far and then better grades of coal were land claims to the Bay were still more than it needs us (Brechin, brought from as far away as Wales owned by some of the original fami- SOE, 2001). and Australia. In the 1890s, import- lies, but many had passed on to ed oil and hydroelectricity began to corporate interests such as Utah MORE INFO? replace coal. The fossil fuels pro- Mining & Manufacturing (the [email protected] duced wastes which continue to Eccles-Wattis clan), which began to contaminate Bay sediments. fill in vast tracts of the Bay. At that

71 PERSPECTIVE

PLANNING FOR fill, as will some of the options likely Subsequently, SFO released FUTURE AIRPORT NEEDS to be considered for Oakland. additional consultant studies that have addressed the potential contri- These projects bring up two bution of better management of GEOFFREY D. GOSLING important questions: First, to what U.C., Berkeley regional airport resources and an extent will these projects, if imple- Independent Technology Panel con- mented, meet the long-term air vened by SFO and BCDC has under- The San Francisco Bay Area is transportation needs of the Bay taken an assessment of the poten- currently struggling with the environ- Area? Second, to what extent can tial capacity gains that might be mental issues posed by the need to future air traffic management tech- achieved through new air traffic expand the capacity of the commer- nology, better management of exist- management technology. While cial airport system serving the ing airport resources, or the devel- potential capacity gains from new region. The region is facing the opment of a fourth air carrier air- air traffic management technology prospect of continuing long-term port in the region minimize the appear promising in the long term, growth in the demand for air travel. need for Bay fill? the implications of the Panel’s find- While the full implications of the for future levels of air traffic A recent update of the Regional events of September 11 and subse- delay remain to be determined. quent developments are not yet Airport System Plan (Metropolitan clear, it seems unlikely that the Transportation Commission, 2000) Alternative strategies to meet social and economic forces that attempted to address these ques- the future air transportation needs have been driving the worldwide tions. Unfortunately, limitations in of the region involve difficult trade- growth in air travel in the past will the scope of the analysis undertak- offs between Bay fill, airport capaci- disappear. en for the Plan make the answers ty, and user convenience. These trade-off decisions are not primarily technical, but revolve around the “We need to better manage the ballet of planes crossing the runways. To do this, we've value that our society places on looked at many options, ranging from building a 400-1,200-acre new runway to environmental and other goals. In expanding the airport upland and using new technology and better demand manage- order to have an informed public ment. As a result of public input about minimizing Bay fill, we've developed some new debate about these trade-offs, it is hybrid runway alternatives which will create about 600 acres of new land in the Bay. important not only that the techni- We're still investigating related issues of where to dispose of dredged material, where cal studies of the complex issues to get fill material, and how to mitigate for loss of aquatic habitat.” involved be performed in an open, unbiased manner, but that appropri- ate efforts are undertaken to explain LEE HALTERMAN the significance of the findings to SFO decision makers and the public at large (Gosling, SOE, 2001). Since the 2001 conference, SFO has San Francisco International that it provides of limited value in released the Final Report on Airfield Airport (SFO) recently opened its addressing these questions. For Development Planning (March new International Terminal, which example, the forecasts upon which 2002), but the only new air traffic has significantly expanded the Plan is based looked only 20 management technology consid- its terminal and landside capacity, years into the future, less than 10 ered in the capacity and delay analy- soon to be further enhanced by the years beyond the earliest date sis it presents is the use of opening of the Bay Area Rapid when the proposed new runways Simultaneous Offset Instrument Transit extension to a station in the are likely to become operational. In Approach procedures, which SFO airport terminal complex, and is addition, the Plan gave only the has already committed to imple- currently considering a major recon- most superficial attention to the ment. With the drop in traffic and figuration of its runway system. San potential contribution of new air revenue at the airport since Jose International Airport is in the traffic management technology September 2001, almost all work on process of implementing its master and did not perform any quantita- the Airfield Development Program plan expansion, and Oakland tive analysis of the potential role has been suspended (Gosling, International Airport is planning that a fourth airport could play in Pers.Comm. 2002). additional terminal facilities and the future regional system or how considering its future needs for a air traffic would be distributed MORE INFO? new runway. The proposed new run- among the region's airports under [email protected] way configurations at SFO will different air service or demand involve significant amounts of Bay management assumptions.”

72 STATE OF THE ESTUARY Big Picture

“The best available science has always been an essential feature of our Estuary programs, but there is a compelling need to move the science into the mainstream of public dialogue and activism.”

JOHN WISE U.S. Environmental Protection Agency (retired)

73 PERSPECTIVE

SCIENCE AND POLICY: and its advisory committee be habitats, restoration of urbanized ESSENTIAL TO ESTUARY responsive to scientific develop- creeks and baylands, Delta RESTORATION ments and base decisions on restoration, climate change, etc. sound science as well. Bringing together outstanding scientists, policy makers, regula- RICHARD KATZ The CALFED Science Program tors, elected and appointed offi- Member, State Water Resources will bring world-class science to all Control Board cials and the concerned public will elements of the program — advance and enhance future deci- ecosystem restoration, water sup- sions to keep the Estuary protect- Background: 2001 marked the ply reliability, water use efficiency ed and improve the quality of life beginning of the CALFED imple- and conservation, water quality, not only in the Bay Area but also mentation process. It follows and and flood management. for all of California (Katz, SOE, builds upon the Comprehensive Performance measures and indica- 2001). Conservation and Management tors for each program element will Plan for the Bay and Delta that track progress. Incorporation of MORE INFO? was approved by the Governor peer review into the science pro- www.swrcb.ca.gov and U.S. EPA Administrator in gram ensures a strong and credi- 1993. The task ahead is daunting, ble scientific component in all namely launching the largest, programs. most comprehensive water man- Role of Legislature and agement program in the world. It SWRCB: Much of the need for sci- is the most complex and extensive ence review is focused on habitat ecosystem restoration project ever restoration efforts, and experience proposed.

“Good science leads to good policy, but the environmental and scientific community attending this conference has to do its homework. You have to explain to newly elected legislators how this ecosystem is also the drinking water supply for 20 million Californians, how this ecosystem affects the state, their constituents, and the state's ability to create jobs. Good science will not lead to good policy without political action and education.”

Science-based Program: A cen- in the legislature tells me that, fre- tral feature of the program is sci- quently, legislation follows when ence-based adaptive management. new and irrefutable information There is a strong commitment to demands change. Of course, the assure that decisions and actions SWRCB has continuing interest are based on well-grounded sci- and jurisdiction on both water ence and a $1 billion science-driv- quantity and quality issues and ini- en ecosystem restoration pro- tially, will count on the first annual gram. Science CAN inform policy science report due by the end of and using it is the obligation of this year and the Independent decision-makers, from the State Science Board for information. Water Resources Control Board Role of the Conference: This (SWRCB), and its nine regional State of the Estuary Conference boards, to the state and federal provides invaluable information to agencies, which have statutory confront the challenges of urban- responsibility for implementing ization of the Estuary by focusing some aspect of the CALFED pro- on topics related to contaminant gram. It is imperative that the new loads, biological resources and CALFED governance commission

74 Big Picture PERSPECTIVE

ECOSYSTEM stakeholder buy-in and collabora- ture watersheds, areas with repre- COMPLEXITY & tion between government and non- sentative impediments and a scat- RESTORATION governmental stakeholders. tered baseline of projects. Rational institutional response to Allocation of the investment knowledge about how to effectively between engineering, monitoring, SAMUEL N. LUOMA accomplish restoration may and developing new knowledge CALFED & U.S. Geological Survey depend upon a social environment might also vary with the category. of trust. Effective prioritization demands The of ecosystem structure and function by human activities is widely documented, threatening important values that “Rational institutional response to knowledge about how include preservation of biodiversi- ty and prevention of species to effectively accomplish restoration may depend upon extinctions. Restoring ecosystems a social environment of trust.” is an important goal of modern environmental management, including the CALFED Bay-Delta Program. However, a growing Priorities are essential in an appreciating ecological complexity, body of evidence suggests that ecosystem restoration program if ecosystem restoration is to live restoration of ecosystem structure because finances are always finite. up to its potential (Luoma, SOE, or function, and restoring popula- In the Bay-Delta Program, we are 2001). tions of threatened species, can be identifying “signature opportuni- a substantial challenge. In addi- ties” for restoration. Some criteria MORE INFO? tion, sustaining successful restora- for such opportunities might [email protected] tion can require on-going invest- include a strong biological justifi- ments that few programs antici- cation for investment and a high pate. These observations mean likelihood of the investment hav- that an ecosystem restoration pro- ing a short-term, detectable bio- gram requires: logical impact at a reasonable scale. Success is more likely if res- • A sophisticated investment olution of institutional impedi- strategy, ments has at least begun. A histo- ry of prior investment might also • Careful documentation of what be an advantage. In an ecological- works and what does not, and ly complicated setting, no pro- • An institutional system that gram should prioritize all its fund- responds to the evaluations of ing to a few projects, however. effectiveness. Some localities or subject areas could have long-term potential for Effective investment in ecosys- restoring species or functions, but tem restoration requires allocating impediments or potential con- resources among investments in straints to restoration need to be new projects, investments in better understood (deeply sub- enhancing the effectiveness of sided islands in the Delta are an existing projects, and investments example). Investment in under- in sustaining successful efforts. standing impediments could reap Documentation of what works immense benefits in the long- requires more than routine moni- term. Similarly a baseline of toring. Necessary ingredients investment in smaller or more iso- include interdisciplinary study of lated projects, and in general existing efforts, creative retrospec- ecosystem understanding, across tive approaches and development the system, is also critical. We of new knowledge about pressures, should not expect that we know ecosystem state and response at where the all the best opportuni- multiple levels. We are fast learning ties exist. Rational prioritization that ecosystem restoration rarely might involve investing equally in succeeds without pre-established the three categories: a few signa-

75 PERSPECTIVE

FUTURE OPPORTUNITIES We need to re-energize this We need to bring adaptive manage- process of re-engaging the public ment, based on the goals and indi- JOHN WISE by organizing around the following cators, explicitly into the realm of U.S. Environmental Protection four themes: public engagement. Agency (Retired) Ecological science: The best Restoration: Restoration must available science has always been proceed simultaneously on a land- The major overarching chal- an essential feature of our Estuary scape scale and on a local water- lenge, or opportunity, facing the programs, but there is a com- shed scale. It will be a challenge to San Francisco Estuary is to re- pelling need to move the science mobilize public involvement in engage the public in an active pro- into the mainstream of public dia- restoring the Sierra headwaters gram to ensure that the long-term logue and activism. “Ecological sci- and the major Valley rivers. On the integrity of the Estuary ecosystem ence” means a multi-disciplinary other hand, people often have a is sustained for future generations. approach to the science of the passion for a “place.” Restoration ecology of the Estuary: the myriad projects within their neighborhood, The public has been significant- interrelationships among the physi- their watershed, their community ly and meaningfully engaged for cal attributes, the chemical and can be a compelling basis for pub- well over 40 years, as Save the Bay biochemical and geochemical lic engagement. And, in turn, such led to the creation of the S.F. Bay processes, and the biological project-based involvement can be Conservation & Development dynamics of life forms at every mobilized in service of the restora- Commission (BCDC), which in level — the beautiful chaos, the tion of the entire Estuary. turn led to the Porter-Cologne extraordinary variability and com- Basin Plans, the Comprehensive plexity of the system. All of this is Vision of sustainability: The Conservation and Management of course a heroic task, pushing Estuary is an essential element in Plan, Bay-Delta water quality stan- the limits of our knowledge. But to the “interconnectedness” of the dards and the Bay-Delta Accord, the extent that we can unify our sci- environment, the economy and the creation of CALFED and the ence and knowledge, we can social equity—the mosaic of rela- S.F. Estuary Institute, and the organize a public engagement tionships that will determine the checking in on our progress every process to benefit from such sustainable future of the Bay Area. few years with these State of the knowledge, and in turn support the Therefore, progress toward sus- Estuary Conferences and the Bay- continued development of such tainability and progress in protect- Delta Environmental Report Cards. knowledge. ing our Estuary are intimately con- Continuous public involvement has nected. Both will directly depend been essential in driving the Goals and indicators: Goals and on how well we are able to infuse process forward; time and again indicators—framed by the best our ecological science into the fab- contentious issues have been over- available science—are the driving ric of our schools, our institutions, come by engaging the public in the force of progress and public our governmental systems and our process. engagement. What gets measured daily lives. The ultimate vitality of gets done. The Ecosystems Habitat our democratic society depends on Yet the distractions of modern Goals Project (see p. 61) is an science-based, knowledge-based life—the prevalence of internation- excellent example of how goals and and information-rich policies driv- al tensions and terrorism, the ups indicators drive involvement. ing a comprehensive public and downs of our economy, the engagement process. Public educa- performance of our schools, afford- As we measure and assess our tion and public involvement are the able housing, traffic congestion— indicators of progress towards our essential foundation to secure the all command our attention. This, goals, we must also utilize the integrity of our Estuary, and to along with the public’s ingrained emerging management technique guide us on our journey toward a complacency, call for renewed vigor known as “adaptive management.” sustainable future. in public engagement and public We often do not know the course, action. Moreover, we may have hit or the impact, of our policies. As These four themes, individually the “green wall” of communica- we measure our indicators, we and collectively, form the core of tions. We are comfortable talking must be prepared to modify, adapt our opportunity, indeed our obliga- to ourselves (to the faithful inside or change direction. Adaptive man- tion, to ensure the integrity of the experts); but because of our lan- agement is of course implicit in Estuary for present and future gen- guage, our message is not getting how we currently seek to manage erations (Wise, SOE, 2001). out to a broader audience – a the Estuary. Notably, CALFED has broader community of interest. embraced this approach in its MORE INFO? plans and investment decisions. [email protected]

76 Bibliography

STATE OF THE ESTUARY Katz, Richard, SWRQB. Science and Policy – Amweg, Erin L. and Donald P. Weston, U.C. CONFERENCE BIBLIOGRAPHY Essential to Restoring the Estuary. P.74 Berkeley. Toxicological Effects of Complex Kimmerer, Wim, Romberg Tiburon Center. Pollutant Mixtures: Organophosphates and KEY ON P. 80 Continuing Saga of the Effects of Flow and X2 on Alkylphenols in Larval Chinook Salmon. the Estuary's Biological Resources. P. 46 Anderson, B., J. Hunt, B. Phillips, P. Nicely, R. PRESENTATIONS* Knowles, Noah, Scripps Institution of Tjeerdema, U.C. Davis; J. Sericano, Texas A&M Oceanography. Long-Term Changes in Inflow and University; B. Thompson, R. Hoenicke, SFEI. Salinity: Suisun Bay’s Climate Context Over the Investigations of Causes [of?] Sediment Toxicity in Abu-Saba, Khalil E., SFBRWQCB. The View from Past 70 Years. P. 38 San Francisco Bay Sediments. Downstream: The Past, Present and Future of Luoma, Samuel N., CALFED & USGS. Ecological Barad, Michael F., S. Geoffrey Schladow, U.C. Mercury in San Francisco Bay. P. 68 Complexity and Ecosystem Restoration. P. 75 Davis; John C. Warner, David H. Schoellhamer, USGS. San Pablo Bay Coastal Intensive Site Anderson, Susan, U.C.Davis, Tracking Pesticide Margolin, Malcolm, Heyday Books & Bay Nature Effects on Native Fish with Biomarkers P. 30 Network (CISNet) of Environmental Stress Magazine. San Francisco Estuary: A Historical Indicators: Hydrodynamic Database. Baye, Peter R., USFWS. Recent Status and Perspective. P. 5 Barbata, Steve, Delta Science Center; John Cain, Assessment of Plant Species in Decline in the San Monismith, Stephen, Stanford University. Francisco Bay Estuary. P. 62 Jim Robins, Natural Heritage Institute. The Marsh Modeling: Where Is It Getting Us? P. 48 Creek Watershed Science Program: An Integrated Brechin, Gray, U.C. Berkeley. Enclosing the Monroe, Michael W., USEPA. Overview and Approach to Watershed Stewardship. Commons: The History of Bay Privatization. P. 71 Update of the San Francisco Bay Area Wetlands Bergamaschi, Brian A., Miranda S. Fram, USGS; Brown, Cynthia L., USGS. Trace Metal Variability Ecosystem Goals Project. P. 61 Ramunas Stepanauskas, University of Georgia, in Bivalves Reveals a Lot about the Estuary. P. 43 Morris, Clyde, Don Edwards S.F. Bay National Athens; Roger Fujii, USGS; Richard F. Losee, Brown, Larry R., USGS. Shallow-Water Habitat: Wildlife Refuge. Restoration in the South Bay. P. 65 MWD; James T. Hollibaugh, University of Georgia, What Is It and Is It Any Good for Fish? P. 31 Mount, Jeffrey F., U.C. Davis. Restoration of Athens. Variation in the Composition and Brown, Randall, CALFED. Can You Hear the Reciprocal Relations Between Rivers and Reactivity of Natural Organic Material in the Canary Sing? P.7 Floodplains in the Central Valley. P. 27 Sacramento-San Joaquin Delta and the San Francisco Estuary. Burau, Jon R., USGS. Sills and Cells: A New Moyle, Peter B., U.C. Davis. Fluctuating Conceptual Model of Gravitational Circulation and Coexistence: The Ever-Changing Status of Native Brastow, Peter, GGNRA. Restoration: the Null Zone Concept in Suisun Bay. P. 39 and Alien Fishes in the San Francisco Estuary. P. 9 A Status Report on Successes & Challenges, Monitoring & Management. Carlson, Ernie, USACOE (retired). 30 Years on Nichols, Frederic H., USGS (retired). San the Bay. P. 2 Francisco Bay Estuary: Today’s Challenges. P. 18 Brown, K.J. and G.B. Pasternack, U.C. Davis. Paleoenvironmental Assessment of a Pending Cavallo, Bradley, DWR. Salmonid Life Histories: Reed, Denise J., University of New Orleans. Delta Sacramento Delta Restoration Site. Freeway Fliers or Sunday Drivers. P. 29 Wetland Restoration Principles. P. 32 Cady, Mark and Claire Murray, The Community Chappell, Steven, Suisun RCD; Cay Goude, Schmutte, Curt, DWR. Integrating Solutions for Alliance with Family Farmers. Protecting the San USFWS; Barbara McDonnell, DWR; Carl Wilcox, Restoring the Bay/Delta Estuary. P. 34 Joaquin River through Outreach and Education to DFG. The Debate Over the Future of Suisun Schoellhamer, David H. and John C. Warner, Stanislaus County Walnut Growers: The BIOS Marsh. PP. 49-51 USGS. A Turbidity Maximum and Flood/Ebb Approach. Cherr, Gary N., U.C. Davis & Bodega Marine Asymmetry of Suspended Sediment. P. 41 California Reclamation Board and U.S. Army Laboratory; Carol A. Vines, Frederick J. Griffin, Schueler, Tom, Center for Watershed Protection. Corps of Engineers. Findings and Planning for Bodega Marine Laboratory. Environmental Factors Watershed Management for Urbanizing Estuaries. P. 54 Flood Damage Reduction and Ecosystem Affecting Reproduction of Pacific Herring in the Restoration in California’s Central Valley. San Francisco Bay Estuary. P. 68 Showalter, Pat, San Francisquito Watershed Council. Stream Restoration in the San Francisquito Watershed: Castellini, Laura, S.F. State University. Stream Cloern, James E., USGS. An Example of Integrated A Story of Partnership. P. 58 Bioassessment in Presidio Watersheds as a Baseline Science Applied in Suisun Bay. P. 36 Siegel, Stuart W., Wetlands and Water Resources. for Riparian Restoration Plans. Cohen, Andrew N., SFEI. Status of Biological Inventory and Status of North Bay Wetland Chan, Yvonne, Nadav Nur, Hildie Spautz, Diana Invasions. P. 12 Restoration Projects. P. 59 Stralberg and Julian Wood, PRBO. Spatial and Collins, Laurel. Watershed Restoration Strategies. Stewart, A. Robin, USGS. Understanding Selenium Temporal Heterogeneity in Reproductive Success P. 55 in the Grizzly Bay Food Web: It Takes a Village of for Tidal Salt Marsh Song Sparrows (Melospiza de Vlaming, Victor, Laboratory. Scientists. P. 45 melodia): The Significance of “Edge Effects.” The Saga of Organophosphorus Insecticides in Thompson, Janet K., USGS. The Evolving Benthic Chun, Stephanie N., Paciencia S. Young and Aquatic Ecosystems of the Central Valley. P. 32 Community and Its Effects on Estuarine Fish and Joseph H.Cech Jr., U.C. Davis. Temperature Dettinger, Michael, USGS; Daniel Cayan, Their Food. P. 66 Preference and Metabolic Rate of the Threatened Delta Smelt. USGS/Scripps Institution of Oceanography; Noah Warnock, Nils, Gary W. Page, Nadav Nur, PRBO; Knowles, Scripps Institution of Oceanography. John Y. Takekawa, USGS; Janet T. Hanson, Clark, Ross and Vanessa Metz, California Coastal Floods, Droughts and Planning for San Francisco SFBBO. Bird Populations in San Francisco Bay: Commission. Bringing the Model Urban Runoff Bay – A Sierra Nevada Perspective. P. 19 What Does the Future Hold? (not included) Program to the Estuary. Enright, Chris, DWR. The Synergy of Integrated Williams, Philip B., Philip Williams & Associates. Is Dake, Stuart, San Francisco International Airport. Solutions to Meet Endangered Species, Heritage There Enough Sediment? P. 22 Pesticide Reduction at San Francisco International Use, and Water Quality Needs in the Suisun Marsh. Airport. P. 52 Wise, John, USEPA (retired). Looking to the Future – Opportunities. P.76 Davis, J.A., SFEI. PCBs in the San Francisco Freyberg, David L., Stanford University. The Delta- Estuary: Achievements, Trends, and the Future. Central Valley Setting: Hydrologic Complexity and Zoback, Mary Lou, Western Earthquake Hazards Team. Downing, James, Steven Osborn, Dan Watson, Pete Restoration. P. 26 The Role of Earthquakes in Shaping the Physical and Fiscal Environment of the Bay Area. P. 20 Schafer and David Tucker, City of San Jose. High Gleick, Peter H., The Pacific Institute. Water and Quality Monitoring Enhances Regulatory Decision- Energy: Challenging Connections. P. 21 Making in South San Francisco Bay. Gosling, Geoffrey D., U.C. Berkeley. Planning for POSTERS* Drexler, Judy Z., Robin L. Miller, Gail Wheeler Future Airport System Needs for the San Francisco and Roger Fujii, USGS. Reversing Subsidence Bay Area. P. 72 Ach, Jay A., . Fisherman's through Wetland Restoration on , Gunther, Andrew, Center for Ecosystem Wharf EQAC and San Francisco's New Hyde Street Sacramento-San Joaquin Delta. Management and Restoration. Determining the Harbor: A Model for Environmental Input into Feliz, Dave, DFG; Robin Kulakow, Yolo Basin Health of the Estuary. P. 6 Public Agency Policy and Projects. Foundation. Wildlife Abounds at the Vic Fazio Yolo Hieb, Kathryn, DFG. Status and Trends of the Ach, Jay A., Port of San Francisco; Len E. Cardoza, Wildlife Area after Four Years of Managing Estuary's Aquatic Resources – Zooplankton to Fish. P. 9 ; Norman Chan, Port of Wetlands in the Yolo Bypass Floodplain. Hoenicke, Rainer, SFEI. Lessons Learned from Richmond. Recycling Mud: Reusing Dredged Fleck, Jacob A., California State University Eight Years of Contaminant Monitoring. P. 70 Sediment for Environmental Cap Construction in Foundation; Roger Fujii, USGS; Deborah A. Bossio, International Centre for Research in Jaffe, Bruce E., Richard E. Smith, Robin Bouse and the San Francisco Bay Area. Agroforestry. Effects of Land Management on Peat Sam Luoma, USGS. Sedimentation, Erosion, and Afentoulis, , DFG. Effects of Fish Handling Soil Biogeochemistry in the Sacramento-San Mercury Contamination: The Story of Hydraulic Gold and Transport at the Skinner Fish Salvage Facility Joaquin Delta: Implications for Disinfection Mining Debris in North San Francisco Bay. P. 42 1999-2000. Byproduct Precursors.

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Foxgrover, Amy and Richard Smith, USGS. Delta Johnson, Michael L., Donald G. Huggins, John Messer, Cindy and Jody Sears, DWR. An Evaluation Bathymetry: Progress on the Development of a 10- Muir Institute of the Environment; Kaylene Keller, of the Potential Impacts of the Chinese Mitten Crab Meter Grid of Delta Bathymetry. Michael Byrne, Chad Shook, Laura Legacki, U.C. on the Benthic Community in the Sacramento-San Fujii, Roger, USGS; Jacob A. Fleck, California Davis. Modeling Loads to the San Francisco Bay- Joaquin Delta. State University Foundation; Gail Wheeler, Judy Z. Delta Estuary Using SIMPLEX. Miles, Susan Lee, Cal State University, Hayward. Drexler, USGS. Assessment of Water Quality in a Jones, Paul, USEPA; Joshua N. Collins, SFEI. Bay Avian Diversity Increase in a Small, Restored Rehabilitated, Non-Tidal Wetland in the Area Wetlands Regional Monitoring Program. Wetland: Regulatory Implications. Sacramento-San Joaquin Delta: Focus on Dissolved Josselyn, Michael and William Martin, Romberg Moon, Edward and Kathryn M. Kuivila, USGS. Organic Carbon and Disinfection Byproduct Tiburon Center. Yosemite Wetland Restoration Effects of Salinity on the Abiotic Hydrolysis of Precursors. Feasibility Study Candlestick Park, San Francisco, Select Pesticides. Fults, Dan and Bill Johnston, San Joaquin River California. Moran, Kelly, TDC Environmental. Water Quality Group Authority. Implementation of the San Kellogg, Michael G., San Francisco Public Utilities Implications of Diazinon & Chlorpyrifos Product Joaquin River Agreement. Commission. Sediment and Biological Community Formulations and Uses. Gewant, Darren and Stephen Bollens, Romberg Patterns at the Mouth of the Estuary. Nelson, Kent, DWR; Marcia Brockbank, SFEP; Tiburon Center. Community Composition and Kern, Doug, Urban Watershed Project. Tennessee Gilbert Cosio, MBK Engineers; Ed Littrel, DFG. Abundance of Macrozooplankton and Micronekton Hollow Riparian Corridor Restoration Project. Demonstration Project for the Protection and of San Francisco Bay: Effects of Hydrology and Enhancement of Delta In-Channel Islands. Trophic Interactions. Kuivila, Kathryn M., Theresa L. Pedersen, Jacqueline R. Houston, Patricia D. von Phul and Newhouser, Mark, Sonoma Ecology Center. Goldbeck, S., B. Goeden, SFBCDC; T. Lawrence A. LeBlanc, USGS. Pyrethroid Arundo donax Eradication and Coordination Gandesbery, California Coastal Conservancy; S. Insecticides in the San Francisco Estuary: II. Project – Coordinating Arundo donax Eradication Nicholson, USACOE; M. Orr, Philip Williams & Sampling and Analytical Challenges. Projects in the Bay-Delta Region. Associates. Hamilton Wetlands Restoration Project, San Pablo Bay, CA. Leatherbarrow, Jon, Rainer Hoenicke and Lester Nicholson, Scott, USACOE; Nadine Hitchcock, McKee, SFEI. Contaminant Contributions from Amy Hutzel, California Coastal Conservancy; Jim Grieb, Thomas, Tetra Tech; David Drury, Santa the Guadalupe River and Coyote Creek Watersheds Swanson, Larry Wyckoff, DFG. Napa-Sonoma Clara Valley Water District. Guadalupe River to the Lower South San Francisco Bay. Marsh Restoration. Watershed Total Maximum Daily Load for Mercury. LeBlanc, Lawrence A., Kathryn Kuivila, USGS; Norton, Elizabeth C., NMFS. Feeding Habits of Grigg, E.K., D.E. Green, S.F. State University; Jonas Gunnarsson, Donald Weston, U.C. Berkeley. Outmigrating Juvenile Chinook Salmon S.G. Allen, S.F. State University & Point Reyes Sediment-Associated Pesticides in the San Francisco (Oncorhynchus tshawytscha) in the San Francisco National Seashore; H. Markowitz, S.F. State Bay-Estuary: I. Concentrations and Desorption Estuary and the of the Farallones. University. Population Status and Trends of Harbor Kinetics of Suspended and Bedload Sediment. Seals (Phoca vitulina richardsi) in San Francisco Nur, Nadav, Hildie Spautz, Yvonne Chan, Julian Bay, CA, 1970-2000. Lee, Diana, Alyce Ujihara, Daniel Smith, Martha Wood and Diana Stralberg, PRBO. Conservation Harnly, Bob McLaughlin, DHS; Ian Walker, Debbie Biology of Tidal Marsh-Dependent Songbirds in Grossinger, Robin, Laurel Collins, SFEI; Elise Goldberg, Gloria Cardona, Lauren Wohl-Sanchez, the San Francisco Estuary: Status, Trends, Brewster, Kallos Design Arts. Bay Area Historical Impact Assessment; Rainer Hoenicke, Michael May, Distribution, and Abundance in Relation to Ecology Project: Wildcat Creek Example. Patricia Chambers, SFEI. San Francisco Bay Significant Habitat Features. Grosso, Cristina, Rainer Hoenicke, Donald Yee, Seafood Consumption Study. Oldland, Susan, DWR. Preserving Floodplains, Sarah Lowe and Jung Yoon, SFEI. Managing Lesen, Amy E., U.C. Berkeley. Don't Forget the Restoring Habitat, Protecting People. Regional Monitoring Data for Accessibility. Little Guys: A Monthly Study of the Relationship of Olson, Brad L., East Bay Regional Park District. Gunnarsson, J. S., U.C. Berkeley; L. LeBlanc, Benthic Foraminifera (Single-Celled Protists) with East Bay Regional Park District Resource USGS; D.P. Weston, U.C. Berkeley; K.M. Kuivila, Food Resources in South San Francisco Bay. Enhancement Program. USGS; L. Deanovic, U.C. Davis. Sediment- Lincoff, Andrew and Amy Wagner, USEPA. Associated Pesticides in the San Francisco Bay Orlando, James L. and Kathryn M. Kuivila, USGS. Volunteer Monitoring Results for E. coli and Pyrethroid Insecticides in the San Francisco Estuary: II Toxicity and Bioavailability of Suspended Diazinon in East Bay Creeks. and Bedload Sediment. Estuary: I. The Increasing Use of Pyrethroids. Lingl, Herb, Aerial Archives. Aerial Photography of Orman, Larry, GreenInfo Network. Envisioning Hammersmark, Christopher, Dr. S. Geoffrey the Estuary. Schladow, William Fleenor and Stephen Blake, Wetland Change in the San Francisco Bay, 1850s to U.C. Davis. Modeling Tidal and Floodplain Lundquist, Tryg, U.C. Berkeley. Algal Bacterial 1990s. Inundation for Restoration on the McCormack- Selenium Removal Facility. Oros, Daniel R., Rainer Hoenicke, SFEI; Robert Williamson Tract. Lynch, Lisa M., Johnson Wang, Lenny Grimaldo W. Risebrough, Bodega Bay Institute. Identification Hammond, J., PRBO; S. Bakeman, K.M. and Brent Bridges. Developing a Key to Identify and Evaluation of Previously Unknown Organic Chouinard, USFWS; Geoff Geupel, PRBO. Larval Delta Smelt and Wakasagi in the San Contaminants in the San Francisco Bay-Delta Songbird Status and Productivity along Large-Scale Francisco Estuary. Estuary. Riparian Project within the Macias, Sue and Janet Hanson, SFBBO. Nesting Orr, Michelle, Jeffrey Haltiner, Robert Battalio, San Joaquin River National Wildlife Refuge. Gulls and Terns of South San Francisco Bay. James Kulpa, Philip Williams & Associates; Michael Harrison, Callie, Chris Enright, Curt Schmutte, Mager, Randall, DWR. The Restoration of Riparian Rafferty, S.S. Papadopulos & Associates. Tidal DWR; Peter Baye, USFWS. Demonstration of a Habitat, Channel and Floodplain on the Merced Wetland Restoration at Cooley Landing: A Pilot Microtidal Marsh and Lagoon System: Endangered River. Project for South Bay Salt Pond Restoration. Estuarine Species Recovery and Waterfowl Mahan, Leah and Steven Thompson, NMFS. The Parsons, Lorraine and Jessica Martini-Lamb, Management in Suisun Marsh. National Oceanic and Atmospheric Administration Sonoma County Water Agency. The Use of Hartwell, S. Ian, Ed Long, Jawed Hameedi and (NOAA) Community-Based Restoration Program. Reclaimed Water for Wetlands Restoration and Michelle Harmon, NOAA/NOS National Centers Enhancement: Hudeman Slough Mitigation and Malamud-Roam, Karl Patrick, Contra Costa Enhancement Wetlands Case Study. for Coastal Ocean Science. Preliminary Results of Mosquito & Vector Control District. Nodical Tides Biological Effects Associated with Sediment in the San Francisco Estuary. Pawley, Anitra, Gary Bobker, Tina Swanson and Contamination in San Francisco Bay. Peter Vorster. Developing Indicators for the Bay McDowell, Miles and Denise Reed, University of Delta System. Hogue, V.E., A.M. Lassiter, A. Marchi, F.P. New Orleans. How Hydraulic Mining Debris Has Wilkerson and R.C. Dugdale, Romberg Tiburon Impacted the Marshes of San Pablo Bay. Pedersen, J.A., UCLA & USEPA; J.W. Anderson, Center. Phytoplankton and Nutrient Dynamics in D. McCoy, Columbia Analytical Services; I. the North and Central San Francisco Bay (Suisun, McGann, Mary, Rendy Keaten and Jonathan J. Hartwell, NOAA; T.S. Fleming, USEPA; J. San Pablo, and Central Bays). Kolak, USGS. Carbonate Production in San Hameedi, NOAA. Distribution of Dioxin-Like Francisco Bay Altered by the Proliferation of the Compounds in Surficial Sediments of the San Hopkins, Todd E., Romberg Tiburon Center. The Non-Indigenous Foraminifer Trochammina hadai. Proposed San Francisco Bay National Estuarine Francisco Bay. Research Reserve. McGinnis, Samuel M. and Hillary Hodge, Cal State Peterson, Heather, USGS & S.F. State University. University, Hayward. Potential Adverse Impacts to Irving, Judy, Independent Documentary Group. Long-Term Benthic Community Change in a the Endangered Salt Marsh Harvest Mouse Highly Invaded Estuary. “Traveling Environmental Film Festival” and “San (Reithrodontomyes raviventris halicoetes) Posed by Joaquin River Oral History Film.” Tidal Marsh Restoration Projects within Diked Phillips, R. Lawrence, USGS. Sedimentation on the Johnson, Bill, SFBRWQCB. Developing a Total Pickleweed Stands. Flood Tidal Delta of San Francisquito Creek, South San Francisco Bay, California. Maximum Daily Load for Diazinon in Urban McGinnis, Samuel M. and Jonathan Koehler, Cal Creeks. State University, Hayward. The Use of Restored and Partially Restored Tidal Marshes by Native and Introduced Fishes in the Lower Delta Region.

78 Bibliography

Rogers, Laurette, Chris Choo, John Parodi, Ruth Sommer, Ted, Bill Harrell, Gavin O'Leary, Louise Waller, Scott, Cindy Messer, Casey Ralston, Karen Hicks, Delia Hitz, ; Sandy Conrad, Fred Feyrer, DWR; Dave Feliz, DFG; Gehrts, Shaun Philippart, Stephen P. Hayes, Anke Neumann, Center for Ecoliteracy. STRAW: Elizabeth Soderstrom, John Cain, Natural Heritage Mueller-Solger, Zach Hymanson, Mike Dempsey, Students and Teachers Restoring a Watershed: A Institute; Robin Kulakow, Yolo Basin Foundation. Hank Gebhard, DWR; Heather Peterson, Joint Project of The Bay Institute and the Center Managed Inundation of Floodplain to Support USGS/DWR; Jim Orsi, Mecum Lee, DFG. The for Ecoliteracy. Splittail Spawning and Rearing. DWR and USBR Rollwagen Bollens, Gretchen and Deborah L. Spautz , Hildie, Nadav Nur, PRBO; Jules Evens, Program: A Thirty Year History of Water Quality Penry, U.C. Berkeley. Copepod Feeding Avocet Research Associates; Diana Stralberg, and Biota in the Bay-Delta System. Preferences in San Francisco Bay and Potential Elizabeth Brusati, PRBO. California Black Rail Watson, Elizabeth B. and Frances Malamud-Roam, Impacts on the Planktonic Food Web. Distribution, Abundance and Nest Site U.C. Berkeley. Environmental History of the San Rosenkranz, Philipp, Linda Deanovic and Inge Characteristics in the San Francisco Estuary. Francisco Estuary: Contributions from Paleoecology Werner, U.C. Davis. Using the Estuarine Starratt, Scott W., USGS & U.C. Berkeley. A to Conservation and Restoration Biology of Coastal Amphipod Gammarus daiberi in Toxicity Testing. 3,000-Year Record of Salinity Variation in a Wetlands. Rudnick, Deborah and Vincent Resh, U.C. Brackish Marsh at Rush Ranch, Northern San Watters, Diana L., DFG; Heather M. Brown, U.C. Berkeley. Burrowing Habits of the Invasive Chinese Francisco Bay, California. Davis; Eric J. Larson, DFG; Frederick J. Griffin, Mitten Crab in San Francisco Bay: Monitoring Steere, John, S.F. Bay Joint Venture. Poster for the U.C. Davis; Kenneth T. Oda, DFG; Gary N. Population Dynamics and Quantifying Impacts to San Francisco Bay Joint Venture: Partnership Tools Cherr, U.C. Davis. Use of the San Francisco Bay Bank Integrity. for Restoring the Estuary. Estuary for Spawning by Pacific Herring, Clupea pallasi: 1973 to Present. Sanders, Alison M. and Stephen M. Bollens, Stepanauskas, R., M.A. Moran, University of Romberg Tiburon Center. Condition Indices of Georgia, Athens; B.A. Bergamaschi, USGS; J.T. Webster, Sara E., Christopher L. Kifting and Julia Larval Pacific Herring (Clupea pallasi) in the San Hollibaugh, University of Georgia, Athens. Links A. Norton, Cal State University, Hayward. Francisco Estuary. Between Bacterioplankton Composition and Water Statistical Comparisons of Physical Factors, Associated Marsh Zooplankton, and Small Schemel, L.E., M.H. Cox, S.W. Hager, USGS; Chemistry in the Sacramento-San Joaquin . Common in Restored Marsh Habitats throughout A.B. Muller-Solger, T.R. Sommer, W.C. Harrell, the Upper San Francisco Bay Estuary. DWR. Influences of Local Streams on Water Quality Stralberg, Diana, Nadav Nur and Hildie Spautz, in the Yolo Bypass Floodplain of the Sacramento PRBO. Landscape-Level Predictors of Songbird Werner, Inge, Linda A. Deanovic, John D. River. Abundance in San Francisco Bay Tidal Marshes. Henderson, Georgino H. Oliveira, Barry W. Wilson, B. T. Angermann, Wes W. Wallender, Sellors, Mike, National Audubon Society. Audubon Swanson, Christina and Gary Bobker, The Bay David E. Hinton, William Krueger, Mike N. Oliver San Francisco Bay Restoration Program White Paper Institute. New Approaches to Water Management and Frank G. Zalom, U.C. Davis. Toxicity of on Mitigation for Public Works Projects. and Fisheries Protection in the Estuary: Evaluating Dormant Spray Pesticide Runoff from California Shah, Shefali, Estuary Action Challenge. Estuary CALFED's Environmental Water Account. Orchards. Action Challenge: A Project of Earth Island Swanson, Christina, Paciencia S. Young, Joseph J. Werner, Ingeborg, Juergen Geist, Mark Okihiro, Institute. Cech Jr., Stephanie Chun, Trilia Chen, Teresa Philipp Rosenkranz, U.C. Davis; David E. Hinton, Shanks, Lisa Woo, USDA Natural Resources MacColl, Leslie Kanemoto, U.C. Davis; Geir Duke University. Effects of Aqueous and Dietary Conservation Service; Amy Evans, Alameda County Aasen, Tim Mussen, Rachel Kussow, Vanessa Exposure to the Pyrethroid Pesticide Esfenvalerate RCD; Lisa Anich, Contra Costa RCD; Jennifer Metcalf, DFG. Improving Fish Screens in the on Medaka (Oryzias latipes). Allen, Southern Sonoma RCD; Nancy Scolari, Sacramento-San Joaquin Watershed: Applied Research Using the Fish Treadmill. Weston, Donald, U.C. Berkeley; Inge Werner, U.C. Marin County RCD; Joy Zyskind, San Mateo RCD. Davis; Kathryn Kuivila, USGS; Michael Lydy, Equine Facilities Assistance. Teh, Swee J., Xin Deng, Foo-Ching Teh and Silas Wichita State University; William Jennings, Shouse, Michelle K., USGS. Mudflat Community 0. Hung, U.C. Davis. Selenium-Induced DeltaKeeper. Assessment of Pesticide Effects on Trends Compared with Decreasing Trace Metal Teratogenicity in Sacramento Splittail Fish and Their Food Resources in the Sacramento- Loading in South San Francisco Bay. (Pogonichthys macrolepidotus). San Joaquin Delta. Siegel, Stuart W., Wetlands and Water Resources. Thomas, Molly and Summer Morlock, Institute for Winton, Bryan R., USFWS. Transportation Impacts Inventory, Status and Map: North Bay Wetland Fisheries Resources. The Klamath Resource to Wildlife on Route 37 in Northern San Pablo Bay, Restoration Projects. Information System [KRIS] Supports Northern Solano and Sonoma Counties, California. California’s Watershed Assessment Efforts. Siegel, Stuart W., Wetlands and Water Resources. Wittner, Eric, Lester McKee, SFEI; Vicki Lukas, Tidal Channel Network Evolution at the Restored Topping, Brent R., James S. Kuwabara, Francis Bill Kaiser, USGS. Building a Regionally Carl’s Marsh, Sonoma County, California. Parchaso, Stephen W. Hager, Andrew J. Arnsberg Consistent Base Map for the San Francisco Bay and Fred Murphy, USGS. What Regulates Area: The National Hydrography Dataset. Simenstad, Charles, University of Washington; Dissolved-Nickel Distributions in the South Bay? Denise Reed, University of New Orleans; Philip Yee, D., J. Leatherbarrow and J. Davis, SFEI. Williams, Michelle Orr, Philip Williams & Tsai, P., R. Hoenicke and D. Yee, SFEI. Measurement of Trace Organic Contaminants in Associates; Steven Bollens, Romberg Tiburon Atmospheric Deposition of Mercury to the San Municipal Wastewater . Francisco Estuary. Center; Nadav Nur, PRBO; Jason Toft, Jeff Young, Paciencia S., Christina Swanson, Stephanie Cordell, University of Washington; Sean Avent, Tsai, P., SFEI; E. Hansen, K. Lee, City of San Chun, Trilia Chen, Teresa MacColl, Leslie Tammie Visintainer, Romberg Tiburon Center; Jose; D. Yee, SFEI; D. Tucker, City of San Jose; R. Kanemoto, Joseph J. Cech Jr., U.C. Davis; Rachel Hildie Spautz, PRBO; Zachary Hymanson, DWR. Hoenicke, SFEI. Atmospheric Deposition of Trace Kussow, Timothy Mussen, Vanessa Metcalf, Geir Understanding Tidal Marsh Restoration Processes Metals in the San Francisco Bay Area. Aasen, DFG. Which Approach and Sweeping and Patterns: BREACH II Research in San Pablo Tsai, P., SFEI; H.A. Bamford, Chesapeake Velocities Near a Fish Screen Are Stressful to Delta and Suisun Bays. Biological Laboratory; R. Hoenicke, SFEI; J.E. Smelt? Slotton, Darrell G., Thomas H. Suchanek, Shaun Baker, Chesapeake Biological Laboratory. M. Ayers, Ron D. Weyand, Anne M. Liston, Atmospheric Concentrations and Fluxes of Organic Chance E. Asher and Douglas C. Nelson, U.C. Contaminants Across the San Francisco Estuary. *Titles within the Presentations and Posters sections Davis. Methyl Mercury Trends Throughout the based on abstracts submitted prior to the confer- Veldhuizen, Tanya and Lenny Grimaldo, DWR. ence. Some details may have changed since then. Sacramento-San Joaquin Delta – In Relation to Spatial and Temporal Distribution of the Chinese Wetlands Restoration. Only those posters submitted by authors for publi- Mitten Crab in the Sacramento-San Joaquin Delta. cation after the conference were included in the Smith, Debra, Shannon Klohr, Katy Zarema and Veldhuizen, Tanya, Cindy Messer, DWR; Deborah Posterbook appendix. Maxene Spellman, S.F. Estuary Invasive Spartina Rudnick, U.C. Berkeley. Evaluation of Sampling Project. Introduced Spartina in San Francisco Bay: Methods for the Chinese Mitten Crab. 2000-2001 Survey and Findings. Vincik, Robert F., DFG. An Overlook of Telemetry Smith, Richard E., Bruce Jaffe, Laura Z. Torresan, Studies at the Suisun Marsh Salinity Control Gates. Seth Carbon and Amy Foxgrover, USGS. San 1993-1999. Francisco Bay Bathymetry – An Interactive Web Site for Bathymetric Display and Analysis. von Flue, Ray, USFWS. Chinese Mitten Crab Reporting System and Monitoring Program. Soderstrom, Elizabeth A. and John Cain, Natural Heritage Institute. Furthering Restoration Science: Walkling, Rich and John Cain, Natural Heritage An Adaptive Management Plan for Dutch Slough. Institute. Subsided Island Restoration as a Means to Combat Levee Fragility and Seismic Vulnerability in the Delta.

79 STATE OF THE ESTUARY

SUPPORTING BIBLIOGRAPHY Pillai, M.C., T.S. Shields, R. Yanagimachi and Vines, C.A., F.J. Griffin, M.C. Pillai and G.N. G.N. Cherr. 1993. Isolation and partial characteri- Cherr. 2000. The effects of soluble creosote- zation of the sperm motility initiation factor from derived compounds on development of Pacific her- Abu-Saba and Mumley, 2002. The View from eggs of the Pacific Herring, Clupea pallasi. Journal ring embryos. Aquatic Toxicology 51:225-239. Downstream: A TMDL Strategy to Attain Water of Experimental Zoology 265:336-342. (Gary N. (Gary N. Cherr) Quality Standards for Mercury in San Francisco Cherr) Yanagimachi, R., G.N. Cherr, M.C. Pillai and J.D. Bay. Water Environment Federation: 2002 TMDL San Francisco Bay Area Wetlands Ecosystem Goals Baldwin. 1992. Factors controlling sperm entry into Science and Policy Conference; November 13-15, Project. 2000. Baylands Ecosystem Species & the micropyles of salmonid and herring eggs. Phoenix, AZ Community Profiles: Life Histories and Development, Growth, and Differentiation Alpine, A.E. and J.E. Cloern. 1992. Trophic inter- Environmental Requirements of Key Plants, Fish & 34:447-461. (Gary N. Cherr) actions and direct physical effects control phyto- Wildlife. plankton biomass and production in an estuary. San Francisco Estuary Institute. 2000. The Pulse of and Oceanography 37:946-955. the Estuary – 2000 Update, Monitoring and Baxter, R.D. 1999. Osmeridae. Pages 179-216 in J. Managing Contamination in the S.F. Estuary. ACRONYM KEY Orsi, editor. Report on the 1980-1995 fish, shrimp San Francisco Estuary Project. 1992. State of the and crab sampling in the San Francisco Estuary. Estuary: A Report on Conditions and Problems in CALFED: CALFED Bay-Delta Program Interagency Ecological Program for the the S.F. Bay/Sacramento-San Joaquin Delta Sacramento-San Joaquin Estuary. Technical Report DFG: California Department of Fish and Game Estuary. 63. DHS: California Department of Health Services San Francisco Estuary Project. 1993. Baylands Ecosystem Habitat Goals, A Report of DWR: California Department of Water Resources Comprehensive Conservation & Management Plan Habitat Recommendations Prepared by the S.F. Bay for the Bay & Delta. GGNRA: Golden Gate National Recreation Area Area Wetlands Ecosystem Goals Project. 1999. San Francisco Estuary Project. 1997. State of the MWD: Metropolitan Water District of Southern Brennan, M.L., D.H. Schoellhamer, J.R. Burau Estuary, 1992-1997, Vital Statistics, New Science, California and S.G. Monismith. In press. Tidal asymmetry and Environmental Management. variability of bed shear stress and sediment bed flux NMFS: National Marine Fisheries Service at a site in San Francisco Bay, USA: Proceedings of San Francisco Estuary Project. 1999. Bay-Delta NOAA: National Oceanic and Atmospheric the Sixth International Conference on Nearshore Environmental Report Card. Administration and Estuarine Cohesive Sediment Transport San Francisco Estuary Project. 2000. State of the NOS: National Ocean Service Processes, Delft, The , September 4-8, Estuary 2000: Restoration Primer. 2000. PRBO: Point Reyes Bird Observatory Schlekat, CE, P.R. Dowdle, B.G. Lee, S.N. Luoma RCD: Resource Conservation District Cloern, J.E., B.E. Cole, R.L.J. Wong and A.E. and R.S. Oremland. 2000. Bioavailability of Alpine. 1985. Temporal dynamics of estuarine phy- Particle-Associated Se to the Bivalve Potamocorbula SFBBO: San Francisco Bay Bird Observatory toplankton: A case study of San Francisco Bay. amurensis. Environ. Sci. Technol. 34 (21): 4504- SFBCDC: San Francisco Bay Conservation and Hydrobiologia 129:153-176. (Janet Thompson) 4510. Development Commission Cohen, A.N. 1996. Biological invasions in the San Schoellhamer, D.H. 2001. Influence of salinity, SFBRWQCB: San Francisco Bay Regional Water Francisco Estuary: A comprehensive regional bottom topography, and tides on locations of estu- Quality Control Board Analysis. Ph.D. thesis, University of California arine turbidity maxima in northern San Francisco SFEI: San Francisco Estuary Institute Berkeley, 186 p. (Janet Thompson) Bay, in McAnally, W.H. and Mehta, A.J., ed., Griffin, F.J., C. Vines, M.C. Pillai, R. Yanagimachi Coastal and Estuarine Fine Sediment Transport SFEP: San Francisco Estuary Project and G.N. Cherr. 1996. Sperm Motility Initiation Processes: Elsevier Science B.V., p. 343-357. SWRQB: State Water Resources Control Board Factor (SMIF) is a minor component of the Pacific Schoellhamer, D.H. and J.R. Burau. 1998. USACOE: United States Army Corps of Engineers herring egg chorion. Development, Growth, and Summary of findings about circulation and the USBR: United States Bureau of Reclamation Differentiation 38:193-202. (Gary N. Cherr) estuarine turbidity maximum in Suisun Bay, USDA: United States Department of Agriculture Griffin, F.J., M.C. Pillai, C.A. Vines, R. California, U.S. Geological Survey Fact Sheet FS- Yanagimachi and G.N. Cherr. 1998. Effects of 047-98, 6 p. USEPA: United States Environmental Protection salinity on sperm motility, fertilization, and devel- She, J. et al. 2002. PBDEs in the San Francisco Bay Agency opment in the Pacific herring, Clupea pallasi. Area: Measurements in harbor seal blubber and USFWS: United States Fish and Wildlife Service Biological Bulletin 194:25-35. (Gary N. Cherr) human breast adipose tissue. Chemosphere 46(5): USGS: United States Geological Survey Grosholz, E.D., G.M. Ruiz, C.A. Dean, K.A. 697-707. Shirley, J.L. Maron and P.G. Connors. 2000. The Simenstad C., J. Toft, H. Higgins, J. Cordell, M. impacts of a nonindigenous marine predator in a Orr, P. Williams, L. Grimaldo, Z. Hymanson and California bay. Ecology 81: 1206-1224. D. Reed. 2000. Sacramento/San Joaquin Delta Jassby, A.D., J.E. Cloern and B.E. Cole. 2002. Breached Levee Wetland Study (BREACH). Annual primary production: patterns and mecha- Preliminary Report. Wetland Ecosystem Team, nisms of change in a nutrient-rich tidal ecosystem. University of Washington, School of Fisheries, Limnology and Oceanography, v. 47, in press. Seattle, WA. (Larry Brown) Matern, S.A., P.B. Moyle and L.C Pierce. 2002. Skinner, J.E. 1962. A historical review of the fish Native and Alien Fishes in a California Estuarine and wildlife resources of the San Francisco Bay area. Marsh: Twenty-One Years of Changing Department of Fish and Game Water Projects Assemblages. Transactions of the American Branch Report No. 1, 226 p. (Janet Thompson) Fisheries Society 131:797-816. (Larry Brown) Sommer, T.R., L. Conrad, G.O Leary, F. Feyrer Middaugh, D.P., M.E. Shelton, C.L. McKenney and W.C. Harrell. 2002a. Spawning and Rearing of Jr., G.N. Cherr, P.J. Chapman and L.A. Courtney. Splittail in a Model Floodplain Wetland. 1998. Preliminary observations on responses of Transactions of the American Fisheries Society embryonic and larval Pacific herring, Clupea pal- 131:966-974. (Larry Brown) lasi, to neutral fraction biodegradation products of Sommer, T.R., M.L. Nobriga, W.C. Harrell, W. weathered North Slope oil. Archives Batham and W.J. Kimmerer. 2002b. Floodplain Environmental Contamination and Toxicology rearing of juvenile chinook salmon: evidence of 34:188-196. (Gary N. Cherr) enhanced growth and survival. Canadian Journal of Moyle, P.B., R.D. Baxter, T. Sommer, T.C. Foin Fisheries and Aquatic Sciences 58:325-333. (Larry and R.R. Abbot. 2001. Sacramento Splittail White Brown) Paper. CALFED, Sacramento, California. Sommer, T., B. Harrell, M. Nobriga, R. Brown, P. Nichols, F.H. 1985. Increased benthic grazing: an Moyle, W. Kimmerer and L. Schemel. 2001. alternative explanation for low phytoplankton bio- California's Yolo Bypass: Evidence that flood con- mass in Northern San Francisco Bay during the trol can be compatible with fisheries, wetlands, 1976-1977 drought. Estuarine, Coastal and Shelf wildlife, and agriculture. Fisheries 26:6-16. (Larry Science 21:379-388. (Janet Thompson) Brown) Pillai, M.C., R. Yanagimachi and G.N. Cherr. Sommer, T., R. Baxter and B. Herbold. 1997. 1994. In vivo and in vitro initiation of sperm Resilience of Splittail in the Sacramento-San motility using fresh and cryopreserved gametes from Joaquin Estuary. Transactions of the American the Pacific herring, Clupea pallasi. Journal of Fisheries Society 126:961-976. Experimental Zoology 269:62-68. (Gary N. Cherr)

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