S tate of the the of tate E stuary 2008 2008 stuary

A Greener Shade of Blue? state of the -delta 2008

A Greener Greener S hade of of hade B lue?

San Francisco Estuary Project & Calfed October 2007 State of the Estuary Conference Proceedings

San Francisco Estuary Project 1515 Clay Street #1400 Oakland, 94612 A Greener Shade of Blue? ta b E L OPENING REMARKS ...... 3

EXECUTIVE SUMMARY ...... 5 F O

VITAL STATISTICS ...... 18 S T N E T N O C

IMPORTANT CHANGES IN THE STATE OF THE ESTUARY Tom Mumley The State of the Estuary and the 2007 CCMP...... 40 Matt Kondolf Watersheds and Land Use...... 40 Michael Carlin Climate Adaptation Strategies...... 41 Richard Looker Pollution Prevention and Reduction...... 42 Josh Collins Wetlands: Links Between Watersheds and the Bay...... 43 Steve Goldbeck From Spoils to Beneficial Reuse...... 44 Ted Sommer The Collapse of Pelagic Fishes...... 45 Bruce Herbold The Collapse of Pelagic Fishes...... 45 Susan Ellis Aquatic Invasive Species...... 46 Kathy Hieb Response of the Estuary’s Aquatic Biota to Changing Conditions...... 47 Cordylanthus maritimus subspecies palus- Joelle Buffa Response of Two Mammals to tris. Extirpated in South Bay, remaining Natural Events and Management...... 48 mostly in and Richard- son Bay. Its stronghold is west Marin’s John Takekawa Challenges in Conserving Migratory Birds ...... 49 marine tidal marshes. It can become very abundant locally. Photo and cap- THE DELTA tion courtesy of Peter Baye. Ellen Hanak The Changing Delta...... 52 Michael Healey Old Uses for a New Delta...... 53 Dan Cayan Assessing Scenarios of Change...... 54 Les Harder The Fragility of Levees...... 55 Steve Chappell : The Forgotten Link...... 56 Roger Fujii Subsidence Reversal...... 57 Phil Williams How Delta Decisions Affect San Francisco Bay...... 58

INTEGRATING ECOLOGICAL RESTORATION INTO WATERSHED MANAGEMENT Mark Stacey The Connection Between Estuary and Perimeter Habitats...... 60 Wendy Eliot Wetlands Restoration in the North Bay...... 61 Letitia Grenier Biota Without Borders...... 62 Peter Baye Native Plant Diversity...... 62 Arthur Feinstein Putting it Back Together...... 63 Richard Thomasser A Living River Case Study...... 64 Bruce Wolfe Controlling Pollution ...... 65 Steve Ritchie Integrating Wastewater, Stormwater, Floodwaters, and Restoration...... 65 Maura Moody Salmon and Steelhead Recovery...... 66 Eric Cartwright The Bottleneck in the Creek Flood Control Channel...... 67 Andy Gunther Restoring Steelhead...... 68 Jeff Miller When Will Steelhead Return to ?...... 69 State Of The Estuary 2008 ta b E L LAND USE

F O Kamyar Guivetchi California Water Plan Update 2009...... 72

Steve Raney Efficient Cities...... 72 S T N E T N O C Kristina Ortez Cost-effective Strategies to Ensure Water Supply...... 73 Richard Harris New Conservation Trends...... 74 Michelle Pla The Importance of Recycled Water...... 75 Jeff Loux Better Land Use Planning...... 75 Elizabeth Patterson Linking the Ahwahnee Principles...... 76 Linda Fiack The Convergence of Urban and Rural Land Uses...... 77 Dave Burch Air and Water Quality; Land Use and Transportation...... 78

Beavers in , downtown POLLUTANTS Martinez. Photo courtesy of Cheryl Reynolds (www.martinezbeavers.org). Denise Greig San Francisco Bay Harbor Seals...... 80 Collin Eagles-Smith Mercury Risk to Birds...... 82 Kevin Kelley Environmental Endocrine Disruption...... 83 Tracy Collier Protecting from Contaminants...... 84 Steve Weisberg Statewide Assessment of Embayment Sediment...... 85 David Lewis Targeting Trash...... 86 Steve Moore Sources, Amounts, and Patterns of Trash in Bay Area Streams...... 87 Lesley Estes Oakland’s Programs to Reduce Trash...... 88 Mark Cuneo Structural Trash Removal...... 89 Lester McKee Sources of Pollutant Loads...... 90 Gayle Tupper Success and Opportunities in Pollution Prevention...... 91 Jim Scanlin Stormwater Drainage System Maintenance Practices...... 92 Mike Stenstrom Structural Control ...... 93

RESTORATION Jeremy Lowe Managing Wetland Habitats as Sea Level Rises...... 96 Naomie Feger Dredged Sediments and Wetland Restoration...... 97 Tom Parker Effects of Inundation and Salinity...... 98 Peggy Olofson Invasive Spartina Control...... 99 Stuart Siegel Determinism, Chaos, and Randomness...... 100 Robin Grossinger Planning Ecosystems Based on Historical Landscapes... 101 Clyde Morris Restoration in South San Francisco Bay...... 102 Christy Smith Tidal Restoration in ...... 103 Howard Shellhammer Small Mammals and Salt Marsh Restoration...... 104 Nadav Nur Avian Demographic Parameters and Marsh Restoration...... 105 Nancy Schaefer Upland Habitat Goals...... 106 Carl Wilcox Where Do We Go with the Baylands Ecosystem Habitat Goals?...... 106 Korie Schaeffer The Subtidal Habitat Goals Project...... 107 Eric Tattersall Turning Conflict into Cooperation...... 108

BIBLIOGRAPHY ...... 110

*Individual abstracts listed by first author only. Some titles have been shortened in the Table of Contents; please cite as shown on the abstract page. A Greener Shade of Blue?  E V I G T N U I C N E X P E O

Opening remarks

How green—or ecologically sustainable—is the Estuary and its watershed? S K R A M E R

How much progress has been made since the CCMP, the Comprehensive RY A M M U S Conservation and Management Plan for the Bay-Delta Estuary, was first signed in 1993? This was the question posed in many guises—with many different answers—at the October 2007 State of the Estuary conference on the 15 an- niversary of the CCMP. The vital statistics and abstracts in this report present data, opinions, and the latest science about pressing issues and “to do” lists for the Estuary. And below, several Estuary thinkers share their thoughts on how well Snowy plover by Bob Lewis we are doing at accomplishing the CCMP goals of restoring wetlands, improving conditions for wildlife and aquatic organisms, achieving sustainable water and land use, preventing and cleaning up pollution, dealing with dredging, and educating the public about issues affecting the Estuary.

Marc Holmes, I think the question mark in “A Greener Shade?” is merited. Right now, almost every assumption that we made ten years ago about the future is in serious doubt, from the value of tidal wetland restoration with rising sea levels, to our ability to sustain Estuary fish in the face of drought and ongoing excessive water diversions. Add to those the unpredictable impact of thousands of pollutants on the ecosystem and, with these variables alone, it is becoming increasingly clear that we don’t have much of a clue about how to proceed. As an environmental community, we certainly should be having frank conversations about this unpre- dictable future. Whereas in the past, we thought we were struggling only with the question of how to sustain the ecological vitality of the Estuary in the face of wildlife declines, since Katrina, the POD, and sea level rise, we now are faced with the reality that we also are unable to sustain California’s traditional economic activities related to the Estuary. We now must consider not simply tweaking the plumbing to increase fish numbers, but retooling the entire Central Valley land use map, as well as the activities of all of urban California that relies on Estuary water. That is to say, the California way of life requires complete overhaul. Even if we agreed to sacrifice threatened and endangered species, we can’t afford to the Delta and other low-lying areas against sea level rise, for instance. This new awareness has stunned policy makers who believed that the Califor- nia dream could continue indefinitely. Not only have they failed to plan for this new environmental world order, they continue to defend the old way of life. They can’t have it both ways.

Leo Winternitz, CALFED Bay Delta Program Clearly we’re worse off than 15 years ago. We have the pelagic organism decline (POD); we have toxic algae in the environment, more invasive species, greater urbanization in the Delta. We’re not better off, and those are the symptoms. The big symptoms are the numbers of lawsuits being filed once again in this arena: they are indicative of problems we’re facing and haven’t been able to resolve. In terms of our thinking, we’re better off. We understand more; we know bet- ter what we don’t know. Perhaps we’re a bit more sophisticated in recognizing that we don’t have the answers and that therefore our plans have to be able to accommodate mistakes or things we don’t know. For instance, we’ve recognized over the last 15-20 years the immense values of floodplain attenuation and the values of floodplains for the ecosystem.  State Of The Estuary 2008 O G N I N E P

We’ve come to recognize that water is a very limited resource, and that the system is probably overappropriated in terms of water diversions as we look at

their effects on the environment. We’ve become smarter not just at doing things S K R A M E R but in recognizing uncertainties in what we do and acknowledging those, so in that sense we’re a lot greener. Can we put this knowledge to use, to action in the near future and for the long term? I don’t know; we’ll have to find out.

David Lewis, In some areas we’ve made significant improvements, and in other areas I think we’ve lost ground. We’ve made the most progress meeting wetlands and habitat goals; 15 years ago we still had to convince people that wet- lands were important; 5 and 10 years ago we still had to convince them that wetlands needed to be acquired and protected. Now we have almost 40,000 acres waiting to be restored. Save the Bay’s polling shows strong support for helping pay for that work. Proposing to destroy wetlands on the Bay shore- line is pretty close to impossible these days—that’s a big change in 15 years. Is there more work to do? More places to acquire? Obviously a lot. And there is increased to expedite the pace because of sea level rise. We will be able to restore more and restore more easily and with more benefits the sooner we do it; the longer we wait the harder it will be to get it started, and the harder it will be to have a maximum benefit. I’m optimistic, though, because of public attitudes and institutions. We’ve also made big progress in 15 years on water quality, and we’re on the verge of making more. Most of that progress has been in point source regulation. Where there hasn’t been as much progress is on non-point source—trash and other pollutants. But there is growing public understanding, and potential for significant effective regulation. If something dramatic doesn’t happen with the Bay Area storm- water permit and soon, I think the Bay Area will go the route Los Angeles did—with litigation.

Black-necked stilt Photo courtesy of Jean Matuska. Tom Mumley, Chair, CCMP Implementation Committee, S.F. Bay Regional Water Quality Control Board There is heightened communication and awareness of Estuary issues, and we have much improved monitoring and planning. There is greater appreciation of the Estuary’s values and the challenges in sustaining and improving them. We have stopped the loss of wetlands and we are now restoring them. We see benefits of pollution prevention and control actions resulting in continued decline of legacy pollutants such as mercury and PCBs and much improved management of cop- per and pesticides. We now manage dredging and disposal of dredge material in an environmentally beneficial way, and we are seeing more and better watershed- protection based land use. That said, we face major challenges with the continued emergence of new chemical pollutants and influx of invasive species, and as we make progress managing water use and floods, we must account for the future consequences of climate change. Fortunately, we have created partnerships and collaboration forums to give us cause to be optimistic that we will successfully conquer these challenges. A Greener Shade of Blue?  E V I T U C E X E

fifth-largest port in the United States chemistry, species, to do proactive Executive Summary and as a provider of blue-collar jobs. management. The issue is not whether A version of this summary appeared “The has tremen- we are playing God—we are already as a December 2007 ESTUARY news- dous expansion capabilities consistent doing that—but how to get it right.” RY A M M U S letter article. with the environmental sustainability Isenberg addressed the Estuary’s of the Bay,” Wunderman declared. political geography. “Why are the The stated theme of this year’s “It’s underutilized as a transportation Bay and Delta two different political State of the Estuary conference was mechanism.” Wunderman concluded regions despite being connected? I “A Greener Shade of Blue,” and the by assuring the crowd that the busi- say it is a pure artifact of notions of conference returned a mixed verdict ness community sees the health of regional self-importance—it’s human on whether or not the Estuary and the Bay-Delta as critical. nature that each of us is the center of its watershed are in fact “greener.” On BCDC’s Travis jumped right to the universe.” Isenberg told the largely an unusually rainy October morn- climate change. He predicted that Bay Area crowd “your strength is ing, Oakland city council president all of the Bay previously lost to fill your weakness. You agreed on what it Jean Quan welcomed a crowd of meant to save the Bay, playing to the nearly 600 people to the Scottish Rite strength of regional importance.” But Center on Lake Merritt’s shores, re- “The issue is not whether now, the forgotten Delta must take minding them that water quality and we are playing God— center stage, said Isenberg. restoration are a priority for Oak- we are already doing The Delta Vision Task land, which was recently named the was charged with creating a plan country’s fifth-most-sustainable city that—but how to get to protect and improve the Delta and has passed Measure DD, which it right.” ecosystem, said Isenberg, while at the provides $200 million to restore Lake same time protecting and improving Will Travis, BCDC Merritt and Oakland’s creeks. Follow- the state’s water supply system. “The ing Quan, ABAG’s Henry Gardner, the Delta ecosystem is going to hell. Not Bay Area Council’s Jim Wunderman, will eventually be reclaimed by Bay one person or organization has said NRDC’s Barry Nelson, Delta Vision waters. Other manifestations of that the Delta is in good shape. [The Blue Ribbon Task Force’s Phil Isenberg, climate change will include more fre- Delta issue] is collectively much more BCDC’s Will Travis, and Redefining quent storm surges, heavy rains, high than the Bay Area because it’s the Progress’s Michel Gelobter brain- , and high winds, plus extended transfer point of all the water that stormed about the role of the Delta droughts and wildfires, he warned. comes in. Where should the state go in the future of the Bay Area. “[Climate change] will have pro- on the question of the ecosystem?” “How can we balance social jus- found local impacts. We need a plan Isenberg pointed out that it is not tice, sustainable development, and the that anticipates that.” But the devil just the swimming pools of Southern environment while moving forward is in the details, he admitted. “How California and Coachella Valley taking with the Bay-Delta?” asked Gardner. do we plan a region and a Bay that water from the Delta; it is also—and “We will have a continuing challenge will surely get bigger? We are going has been for a long time—the Bay in providing housing for all of those to have to build a lot of levees that Area. “It can’t be ‘our water projects who need it. Many cities granted con- are big enough and strong enough to are good, and theirs are bad.’” ditional use permits in the communi- hold back floods around the airports. NRDC’s Nelson presented himself ties closest to the Bay in low-income We also need to take a hard look at as the “panel historian,” taking the and minority communities to support where it might be most cost-effective crowd through key dates in the a variety of business activities. That to remove existing developments and Bay’s history and how its role has had a devastating impact on some of replace them with wetlands, which changed from when it was discovered those communities, conditions that absorb floods and sequester carbon.” by Europeans to mining and com- persist today.” Also on Travis’s to do list: “abandon mercial interests to the building of Wunderman spoke of the Bay’s any future plans to develop low-lying the Central Valley Project, which he importance, both as a draw for tour- areas.” Said Travis, “We need a plan for christened “the dawn of the golden ists, with 260,000 area jobs devoted the Estuary that is bold and audacious. age of the hydraulic frontier. We to tourism, and as a major attractor of We’ve got to stop talking about how built the highest dam in America, the new residents. He also spoke of the to restore it to the way it was; we most elaborate plumbing system, Port of Oakland’s importance as the need to design for different elevations, and the largest pumps on the face  State Of The Estuary 2008 E V I T U C E X E

of the planet. It was an astonishing “We need to ask “The Delta region is growing faster accomplishment.” But the frontier has than Mexico. Housing below sea level closed, said Nelson. “We’ve operated ourselves whether we will inevitably flood.” Kondolf also

on the assumption that we can always pointed out that a 100-year flood (a RY A M M U S are entering the era take out more water this year than of sustainability or 1% chance every year) is not the only the last. But there are real limits to flood that could occur. “We could how much water we can take out. collapse.” also get a 200- or 400-year flood,” he The entire Colorado River has been Barry Nelson, NRDC warned. captured; there are signs that we are SFEI’s Josh Collins said scientists hitting that limit in San Francisco Bay.” need to come up with a new set possibly affecting water quality, the The end result? “It’s not a surprise of tools for simulating habitat re- state should consider adopting a that fisheries are down as diversions sponse to climate change, in order “California product stewardship are up,” said Nelson. “It’s hard to make to make choices among scenarios. council” that would require manufac- the case that we can take more water “Tracking change is not enough,” said turers to adopt a “cradle-to-cradle” out.” There are alternatives—cheaper Collins. “With the increased rate of approach for their products in order ones—to pumping more water, said change, wetlands won’t be protected. to reduce waste and pollution. The Nelson. “We could divert less, invest Wetlands should be viewed in their Board’s Richard Looker built on in recycled water, and save energy and watershed context. There’s a logical that theme, pointing out how many greenhouse gases. We need to ask progression from watershed-based societal benefits have a parallel envi- ourselves whether we are entering wetland planning to protection.” ronmental impact: controlling pests the era of sustainability or collapse.” One positive change in Estuary can equal aquatic toxicity; preventing Redefining Progress’s Gelobter management, according to BCDC’s fires can lead to PBDEs in the Bay drew parallels between Hurricane Steve Goldbeck, is the progress made and its wildlife; health and beauty Katrina and New Orleans and the in using dredged spoils for beneficial products not removed in wastewater potential for similar disaster in the uses—i.e., wetland restoration proj- treatment can disrupt endocrine and Delta if we don’t take action to ects. Since the Long Term Manage- other functions in fish; the products prevent it. If we were to be pro-active ment Strategy (for dredged materials) and processes leading to economic in fixing the Delta, said Gelobter, “we was implemented in 1993, said Gold- health have often led to long-lived could be a model for the world.” The beck, the volume of material disposed environmental contaminants. panel session concluded with Gardner of in the Bay has been reduced by Another emerging challenge for asking what the business community 50%. “Our long-term goal is to have Estuary resource managers is climate can do to help protect the Bay and no more than one million cubic yards change (and associated sea level Delta. Wunderman responded that per year of in-Bay disposal,” said Gold- rise). The SFPUC’s Michael Carlin we need to focus on better integrat- beck. “We are halfway there.” discussed how urban water manag- ing transit and development. “We And Cal Fish & Game’s Susan Ellis ers are trying to cope. “The San made a mistake,” said Wunderman. described another positive change, Francisco water supply is going to “We screwed it up by not having the exemplified in how her agency re- be rain dominated instead of snow proper balance between housing and sponded rapidly to the quagga mussel dominated,” said Carlin. The SFPUC public transit. But we’re beginning to invasion. “We had a unified response plans to diversify its water sources, he get it. It’s time to focus on the urban using incident command with state said, by becoming part of a Bay Area- core and develop a transit system and federal agencies, Metropolitan wide regional desalination project, by that supports it. We have to figure Water District, the City of San Diego, relying more on groundwater, and by out how to overcome the resistance and a multi-state quagga team. We using graywater to flush toilets. to change that is inherent in the busi- have them contained in Southern U.C. Berkeley’s Matt Kondolf also ness community.” California right now.” discussed the impacts climate change The late morning and afternoon The afternoon session focused will have, particularly on the Delta, sessions were devoted to presenta- on important changes to aquatic which he warned could be “New tions on important changes in the resources and wildlife—fish, mammals, Orleans East. We have created the Estuary and how they will be man- and birds—in the Estuary. DWR’s Ted same conditions for a similar disas- aged. The S.F. Regional Board’s Tom Sommer reviewed the state of the lat- ter in California,” he said, describing Mumley suggested that with new est science on the “pelagic organism how levees raise the flood stage. pollutants constantly emerging and decline” (POD) of Delta and longfin A Greener Shade of Blue?  E V I T U C E X E

smelt, threadfin shad, and striped bass. back and forth between the Bay and have long-term data, it is very hard to Probably the most pressing—and as the ocean to spawn and rear, respond make sense of complex phenomena,” yet unanswered—question is whether poorly to El Niño years. “They prey said Takekawa. He and his colleagues

Delta smelt have dropped below on zooplankton,” said Hieb. “When are now studying the movements RY A M M U S critical population levels. As far as the the ocean is warmer, there’s less of individually marked birds. One cause of the decline, said Sommer, zooplankton.” With warmer ocean surprise was that the South Bay’s scientists are asking themselves where , Hieb predicted, there Colma Creek, surrounded by industry, anything has changed in the Delta, will be poor recruitment of cold is one of the most important spots and how and why. In 2007, there was species and migration to for clapper rails in the entire Bay. With increased toxicity in the Delta from the Bay of more warm water tropical multiple restoration projects taking contaminants and toxic algae that species. She also predicted more place around the Bay, said Takekawa, moved into core habitat, “dead zones” from toxic algal blooms, we need to keep looking at all of the a decline in recruitment and habitat caused by the increase in nutrients projects from a bird’s eye view to quality, reduced food availability due resulting from warmer water. evaluate their effects. He added that to invasive species, and increased U.S. Fish & Wildlife’s Joelle Buffa migratory birds responded quickly mortality. There was also more smelt switched the focus to mammals, dis- to South Bay salt pond restoration, mortality at the pumps in recent with overall numbers increasing at winters when pumping increased to the ponds. “But will mudflat values be the point of creating negative flows in “A small change in the decreased?” he asked. “A small change Old and Middle rivers, said Sommer. in the elevations of mudflats could “At this very moment, scientists from elevations of mudflats make a different to shorebirds if we all over the world are trying to figure could make a different start having sea level rise. Their time [the POD] out,” said Sommers. to shorebirds if we start for foraging could be decreased, along U.S. EPA’s Bruce Herbold built upon with a corresponding decrease in Sommer’s talk, telling the audience that having sea level rise.” population.” “scientists have found a lot of what John Takekawa, USGS The morning session of Day caused the POD, but that’s not going Two refocused on the Delta. The to solve the problem. Everything else CALFED Science Program’s Michael is secondary to the fact that there’s cussing the state of the endangered Healey said that as sea level rises, new not many fish out there.” Herbold salt marsh harvest mouse and harbor development will need to be better said that genetic diversity in the seals at South Bay refuges. Buffa planned to reduce the risk of flooding. smelt population may be so low at described how managers have taken “The Delta of the future is not going this point that the viability of their various actions, including acquiring to be the same as today,” said Healey, offspring is affected. Another problem land, removing fill, reintroducing tidal echoing Travis’s comments about the is that their fall habitat has shrunk and action, and conducting other water Bay. “We need to plan and design for moved eastward. Why? “We’ve stabi- management activities, to aid the a Delta that will deliver the services lized flows,” said Herbold. “They used mouse. In one instance, they created we value.” Healey also stressed the to be very variable.” Herbold suggest- a “mouse pasture,” transplanting mice need to “monitor and massage” ed that the Delta has become more from a proposed development site what’s happening in the Delta. “There like a lake. “This means less estuarine and tracking them afterwards. “We are no right or wrong solutions; just fish. The POD may have been a tip- learned that the mice do colonize better or worse. We need to take a ping point—from a variable estuarine new habitats, and that salinity is much more adaptive approach. As system to a steady state/lake-lagoon important [to encourage pickleweed soon as you impose one , the type of system.” growth],” said Buffa. “Translocation system changes in response, and you Fish & Game’s Kathy Hieb broad- can be successful where the popula- have a whole new set of problems to ened the focus from the Delta to the tion is low and where you create high deal with.” Pacific Ocean, describing how changes refugia.” The Public Policy Institute’s Ellen in ocean temperatures and nutrients USGS’s John Takekawa presented Hanak gave an overview of the are affecting the Estuary’s aquatic crit- an avian perspective on the Bay— Delta’s value to society—water supply, ters. In warm water years, Dungeness which, because there are so many agriculture, ecosystems, infrastructure, crab have poor embryo and larval species of birds with such different recreation, and hunting, among others. survival, while Pacific herring, which go lifestyles—is complicated. “If you don’t With the housing market slowing  State Of The Estuary 2008 E V I T U C E X E

down at least temporarily, said Hanak, found in Phase 1. So far, said Svetich, four inches per year. By increasing ac- there might be a short-term oppor- the preliminary phase 1 results show cretion rates to nine inches per year, tunity to make changes in the system. a risk of island inundation in flood the Delta’s accommodation space

“There’s the real possibility that we events, with a high probability of could be reduced by 70% in five RY A M M U S could encounter big problems in the failure for western and central Delta years, said Fujii. The amount of carbon Delta before a new management islands, a finding that closely matches dioxide sequestered would equal strategy is in place. There’s a two- U.S. Army Corps models. the reduction in emissions if all the thirds risk of a catastrophic failure The Suisun Resource Conser- SUVs in California were swapped for over the next 50 years, with earth- vation District’s Steve Chappell Priuses, said Fujii. quakes and sea level rise. What this reminded the audience of the impor- The afternoon session broadened means in terms of those services is the focus to the question of how to that the holes [described by PWA’s “The Delta’s fragility is integrate restoration into manag- Phil Williams, see below] in the Delta ing watersheds for flood protection, would be filled with water coming California’s central water recreation, water supply, and a laundry from the Bay. We would have to shut management challenge.” list of other beneficial human uses. down the pumps for a while. We can’t First up was PWA’s Phil Williams, who Ellen Hanak, PPIC go back to the Delta of 150 years stressed that any management actions ago, but we can’t stand still either,” taken to improve the Delta will also said Hanak. “The Delta’s fragility is tance of Suisun Marsh, the “forgotten affect the rest of the Estuary. “We’ve California’s central water manage- link” between the Bay and Delta. created a massive hole—up to 20 ment challenge.” Hanak concluded by Chappell described the river otters, feet below sea level—on 340,000 predicting that “everyone will not get salt marsh harvest mice, short-eared acres of farmland behind levees in the better together in the Delta of the owls, Suisun thistle, and other native Delta,” said Williams. “I don’t believe future.” and non-native species, including fish, we’ve fully grasped how this will affect USGS’s Dan Cayan told the crowd that live in and around the marsh, physical processes and how that will that sea level rise in S.F. Bay has fol- and the many migratory waterfowl affect the rest of the Estuary.” lowed the historical patterns of global and diving ducks that use it. Chap- That huge hole is subsiding about sea level rise, predicting that “we pell also described the programmatic six times faster than sea level is rising, can expect both a drier and a more CEQA/NEPA process underway for a said Williams, which means that, in a hazardous water future, and a saltier Suisun Marsh management plan that “doomsday” scenario, a large por- Bay-Delta environment compared includes some tidal marsh restora- tion of this volume could end up in with the historic environment.” Cayan tion. “Opportunities are better in tidal waters. “The whole tidal Estuary also predicted that a sediment deficit Suisun Marsh for restoration than in could get a lot bigger,” said Williams. will probably be a critical part of the the Delta,” said Chappell. “It is not as “The area of San Francisco Bay would future Delta and said that warming subsided.” Of course all restoration is be doubled, but just as important, temperatures are approaching lethal predicated on willing sellers, stressed the physical processes—the tides, the limits for fish. “For some fish species Chappell. “Salinity intrusion is a big movement of saltwater and sedi- in the Delta, an increase of a couple issue,” said Chappell. “As are mercury ment that sustains the Bay—could be of degrees could catapult the situation and carbon. We have to consider significantly altered.” into catastrophe.” those in plan implementation.” U.C. Berkeley’s Mark Stacey DWR’s Ralph Svetich described Following on the carbon theme, moved south, to the salt pond resto- the ongoing Delta Risk Manage- USGS’s Roger Fujii described how ration project, discussing its possible ment Strategy study examining the a pilot project at effects on the rest of the South Bay. In fragility of the Delta’s levees. Phase flooded tules to encourage decom- a study of the island ponds adjoin- 1 examined the risk to Delta levees position, and rebuilt subsided soils at ing Coyote Creek, Stacey found that from earthquakes, floods, sea level the same time. As the tules die and as more water moved up the creek rise, subsidence, and a combination of decay, the marsh sequesters carbon through the breaches into the ponds, all of those occurrences. An inde- dioxide at higher rates than agricul- there was an increase in the tidal pendent review panel was critical of tural fields. With microbial decom- prism, but the effects of the changes the report, and a revision is pending. position offset by biomass accretion, were different across different phases Phase 2 will evaluate individual risk the land surface builds back up. Fujii of the tides. “When you open up the reduction strategies based on risks reported elevation gains of up to restoration sites to tidal action, it dis- A Greener Shade of Blue?  E V I T U C E X E

sipates the funnel effect that charac- equal stance with flood protection diverse habitats,” concluded Feinstein, terizes the far South Bay, which could and clean water supply in our quest “we also need to control us.” change the inundation regime for high to restore the “physical, biological, and Coastal plant ecologist Peter Baye marsh habitat,” said Stacey. A decrease chemical integrity of the Estuary” as addressed the fact that many of our RY A M M U S in amplification is good for diminishing set forth in the CCMP. “It’s all part of tidal marsh restoration projects to flooding, but bad for marsh habitat. the same goal,” said Grenier. “Wildlife date have not included rare plants “The changes in tidal prism increase inhabit landscapes. What we do in the that could be collected from remnant water velocity locally, but also change Bay affects the whole flyway. There sites and propagated, helping to en- dissipation and reduce inundation are four to five million birds com- sure their survival as species. One ex- at a much larger scale,” said Stacey. ing through here. How can we act ample is a rare salt marsh owl’s clover And because sources of sediment on a landscape scale to keep them that still exists in Whittell Marsh near for the restoration project are “down here?” Our modern landscape has Point Pinole. “Almost none of these Estuary,” the restoration sites are not seen a huge loss of connectivity, she rare species are finding homes in tidal going to capture much sediment, said said. “We have the tools to plan for marsh restoration sites,” said Baye. Stacey. There is very little sediment providing better connecting habitat “Even where there are well-devel- coming in directly from the water- for wildlife, but we lack a common vi- oped marsh plains and channels, 30 shed; instead the sediment reaching sion. We haven’t really specified what years later [these restoration projects] the restoration sites is likely to be our wildlife goals are. Instead, we are still support only the most common coming from the far South Bay via stuck waiting for a crisis. How can we recycling by tides and winds. invest earlier in landscapes for wildlife? Moving to the North Bay, the Conserving wildlife is like a lot of the “Almost none of these Sonoma Land Trust’s John Brosnan other ecosystem functions we are rare species are finding discussed the realities of trying to interested in. We need to think and homes in tidal marsh integrate watershed and wetlands plan on a landscape scale.” restoration planning. Brosnan said his Citizens Committee to Com- restoration sites,” agency is trying to achieve the goals plete the Refuge’s Arthur Feinstein Peter Baye, Coastal Plant Ecologist set forth in the Baylands Ecosystem offered a pragmatic perspective of Habitat Goals Report and the CCMP. wildlife conservation around the Bay. Yet, using the ongoing Sears Point “What’s not to be thrilled about?” tidal marsh species.” Discussing the Restoration Project as a case study, asked Feinstein. “We have over 100 restored Muzzi Marsh, Baye pointed he showed how constraints like flood species of wildlife and plants listed as out that no uncommon species have protection, invasives control, remedia- endangered or threatened. No Bay dispersed from nearby Heerdt Marsh, tion, multiple users, sea level rise, and Area species has yet been delisted.” the oldest prehistoric marsh in the physical infrastructure—in this case As solutions, Feinstein suggested that area, to colonize Muzzi. Baye ended Highway 37 and a rail line—are not we need to focus on habitat diversity, with a series of recommendations for only splitting up the landscape, but links between habitats, bigger areas restoring diversity, including designing also “dictating what we can and can’t of habitat, and freedom from human restoration marshes more creatively. do with integrating wetlands and tidal harassment. Creativity has been critical in restor- wetlands.” Having a rail line there Public access has had a negative ing the , according to Napa triples the cost of restoration, said impact on wildlife, said Feinstein, citing County Flood Control’s Richard Thom- Brosnan. “Once the agricultural levees birders who harass the birds they are asser, who described the history of this are taken down [for restoration], we watching and boaters who disturb multi-year, multi-stakeholder, multi-ob- have to build bigger, stronger levees resting ducks on the Bay, and develop- jective ongoing effort. After the Army for the railroad and Highway 37 be- ment near sensitive areas, such as the Corps presented a plan to channelize cause of sea level rise.” Despite “huge least tern habitat at the old Alameda the river in concrete in the 1960s buy-in” from neighbors, ranchers, and Naval Air Station. “Once you get peo- (and again in the 1990s), the com- farmers, said Brosnan, “the highway ple into wild areas, even urban areas, munity demanded that any plan for and railroad line [which refuses to you’re going to lose your diversity,” flood control also be a plan for a “living help defray the costs] are driving the said Feinstein. “Even in very dense river” that would connect the river to outcome.” areas, if you keep people away, there its historical floodplain. As a result, the SFEI’s Letitia Grenier stressed the are nice wildlife effects. If we want full consensus-based project includes both need to give wildlife conservation environmental restoration and large a geomorphic channel design that will 10 State Of The Estuary 2008 E V I T U C E X E

return proper sediment transport bal- Services’ Maura Moody started off The Alameda Creek Alliance’s Jeff ance and the creation of 650 acres of by describing the recovery plan being Miller gave an historical overview of wetlands. Five major bridges are being drafted for Central California Coast steelhead presence in the watershed,

made higher and longer to free up hy- salmon and steelhead. The Center for describing how Calaveras Dam, built RY A M M U S draulic constrictions, and to span the Ecosystem Management and Resto- in 1925, cut off access to the best channel and the new marshplains, said ration’s Andy Gunther said that while habitat. The watershed also supported Thomasser; two bridges were com- the Bay Area does possess a massive coho and Chinook salmon at one pletely rebuilt. “The river and habitat greenbelt, the creeks that connect to time, said Miller, and remnant steel- now have some room to move.” the Bay are under increasing pressure. head runs persisted until 1964. Today, The S.F. Bay Regional Board’s “Choosing restoration will require steelhead are still trying to make it up Bruce Wolfe gave an overview of that we conduct experiments on how the creek, despite its obstacle course. his agency’s efforts to protect both to restore steelhead trout. Their fight But attitudes have changed during riverine and marsh wetlands. “We’re upstream is both mysterious and in- the last two decades, and during the better regulating development of up- last decade, 27 fish were successfully land areas,” said Wolfe. “We are now caught and moved upstream by vol- trying to manage flows better than “Returning these wild unteers, dramatizing the need for fish we have and the changes in runoff passage improvements. “We’re poised patterns that development causes.” creatures provides to restore these fish,” said Miller. Wolfe said his agency no longer takes something to us as well.” “Their visibility and persistence in water quality-based effluent limits showing up every year has galvanized Andy Gunther, CEMAR from a national list, but instead tackles us.” The Alliance now has more than them on a statewide and regional 1,500 members and more than 15 (Baylands) basis. “TMDLs are really spiring. Returning these wild creatures agencies cooperating in restoration. watershed plans,” said Wolfe. “We are provides something to us as well,” Genetic analysis of landlocked fish now looking at wetlands and streams said Gunther. The lifecycle and impact and anadromous fish below the dams as a physical unit. Wetlands are really these fish have had over time, said show their genes to be closely related. the deltas of riparian systems.” An- Gunther, give them the cultural status “The biggest question is whether other change at his agency, said Wolfe, of “charismatic megafauna. Steelhead there will be enough water left in is recognizing that riparian zones have can drive ecosystem management: the stream,” said Miller. “Right now, many benefits. They use an entire watershed in their none of the agencies release flows for The Coastal Conservancy’s Steve lifecycle. They can help preserve the fish. The draft EIR [for the Calaveras Ritchie built upon the “deltas” idea. landscape for future generations.” Dam replacement] does not allow for As the salt pond restoration project The Alameda County Water minimum flows for fish. We’re hoping nears the end of its five-year planning District’s Eric Cartwright described to work with the SFPUC to address process, said Ritchie, “what about the some of the physical barriers that the impacts of these dams.” ponds’ connection to local water- will need to be addressed to restore sheds?” But making that connection passage for these fish. “The question is POLLUTION: might be complicated. “It’s flood pro- how to provide passage through the Can We Clean It Up? tection with restoration, not just a fun flood control channel while keep- little restoration project,” said Ritchie. ing the existing benefits the channel Thursday’s pollution session Key challenges are: The Guadalupe provides,” said Cartwright. When the focused on legacy and emerging pol- River watershed is the single worst Army Corps built the channel, it did lutants and their impacts on wildlife, source of mercury in the Bay, and dry not provide for fish passage, said Cart- as well as the trash epidemic in the weather runoff contributes to poor wright. However, the District has de- Estuary and its watersheds, and the water quality. cided after conducting several studies challenges and solutions involved— Perhaps the most poignant exam- that it can remove the lowest rubber here and elsewhere—in cleaning up ple of trying to integrate restoration dam and keep it out of the channel our mess. into watershed management and wa- permanently. At the upper rubber First off on Thursday morning, the ter supply was that of the long-term dam, the District will build a fish lad- Marine Mammal Center’s Denise efforts to restore steelhead to Alam- der and install fish screens at several Greig described her studies of Bay eda Creek, the focus of the afternoon intake structures. Other challenges harbor seals and emerging contami- session. The National Marine Fisheries include funding and instream flows. nants. “They eat at the same trophic A Greener Shade of Blue? 11 E V I T U C E X E

level humans do,” said Greig. “PBDEs fish species.” Kelley is now looking Project Authority, wrapped up the in San Francisco Bay seals increased beyond estrogenic effects to wider session on the biological effects of between 1989 and 1998. They also physiological impacts and perfor- pollution. Bay showed how his project have mercury, lead, PCBs, and DDT mance. “We consistently find impair- uses a “multiple lines of evidence” ap- RY A M M U S in their bodies.” Between 1989 and ment near publicly owned treatment proach to integrate chemistry, toxicity, 1998, the PBDE levels were higher works sites,” said Kelley. and benthic fauna data to provide even than those of contaminated Tracy Collier of NOAA and Sandie an overall assessment of sediment Baltic Sea seals, said Greig, adding O’Neill of the Washington Depart- conditions in California. Most of S.F. that PCB in healthy ment of Fish & Wildlife described Bay fell into the “possibly impacted Bay seals appear to be decreasing, their agencies’ collaborative work on category. We were surprised; we were while DDT metabolites are increas- toxics in Puget Sound, pointing to expecting to see 60% of Bay sediments ing. “So even though they are banned the need for a biological observation as having ‘little or no evidence of now, they get stirred up from the system for toxic contaminants. “If you impact,’” said Bay. “Instead, a very high sediment, are present in harbor seals, just look at the sediment community amount turned out to be possibly im- and passed from mother to pup,” profile relative to other estuaries and pacted.” Eighty percent of monitoring explained Greig. The latest worry is bays, Puget Sound is not that con- stations showed significant sediment PFOS—perfluorooctane sulfonate— taminated,” said Collier. Yet biologically toxicity, said Bay. another flame retardant. “We only based monitoring has shown con- Midday, talk turned to trash, spe- have a small sample so far, but the lev- tamination of the pelagic food web, cifically to the overwhelming plastic els are high compared to Artic polar including PCBs in herring, said Collier. problem in the Estuary, its creeks, and bears and ringed seals,” said Greig. “You would not have predicted that the ocean. Moderator Larry Kolb esti- Greig was followed by Collin from sediment and water measure- mated that the number of plastic bags Eagles-Smith, who described the risk ments.” (which frequently end up in the Bay to Bay birds from mercury. Eagles- He also showed results of their and its creeks and stormdrains) used Smith examined mercury concentra- work on a syndrome they have by the public averages out to one bag tions in surf scoter, American avocet, termed “pre-spawn mortality” that per person per day. In the Bay Area, black-necked stilt, Forster’s tern, and is being observed in coho salmon with seven million people, said Kolb, Caspian tern adults, chicks, and eggs, returning to spawn in Puget Sound if only one in 1,000 people uses a finding mercury concentrations to streams. “We’re spending millions to plastic bag, that would still amount to be highest in Forster’s terns, followed restore ecosystem attributes that 7,000 bags per day. by stilts, Caspian terns, scoters, and should be sufficient to support life, Save the Bay’s David Lewis avocets. Risk to hatching success was but 60% to 90% of these salmon die described the overall potpourri of found to be greatest in the South Bay, before spawning,” said Collier. The trash in the Bay. “It’s not from ships, and 58% of breeding Forster’s tern but from us,” said Lewis, adding that adults and 46% of their eggs ex- only 20% of water-borne trash comes ceeded toxicity thresholds established “Ninety percent of [the from boats. Lewis said big sources of for other birds, raising the question plastic debris] will trash in Bay creeks are overflowing whether population impacts might take years or decades or inadequate trash receptacles and be occurring. “This is striking and direct littering and dumping of house- concerning,” said Eagles-Smith. to decompose; when hold garbage. But Lewis emphasized Kevin Kelley from CSU Long Beach it reaches the ocean, that the biggest problem is plastic. moved from birds to fish, describing “Ninety percent of it will take years the results of his studies on Pacific cold saltwater tends to or decades to decompose; when it staghorn sculpin and shiner perch. preserve it.” reaches the ocean, cold saltwater He has found PCBS, PAHs, and tends to preserve it.” David Lewis, Save the Bay chlorinated pesticides in the livers of Possible partial solutions include both species, as well as evidence of Governor Schwarzenegger’s newly endocrine-disrupted states. “Endo- bottom line, he said, is that “com- formed Ocean Protection Coun- crine disruptors serve as biomarkers pared to monitoring sediment and cil (tasked with tackling trash) and of environmental perturbations,” said water, the animals can tell you more.” Coastal Cleanup Days (in 2006, more Kelley. “We have indeed seen endo- Steve Bay, of the Southern than 686,000 pounds of trash were crine disruption in the Bay in different California Coastal Water Research removed from the Bay shoreline in a 12 State Of The Estuary 2008 E V I T U C E X E

single day). Save the Bay is using ad trash, or three pieces for every foot trash. The city recently banned non- campaigns to try to change people’s of stream. Half of the trash was plas- biodegradable takeout containers and behavior while some cities are tic, followed by glass and paper. The established an “excess litter” fee for all

implementing source reduction, ban- highest trash deposition rates were food facilities. It tried to implement a RY A M M U S ning plastic bags and Styrofoam food found in both wet and dry weather. plastic bag ban like San Francisco’s but containers. But changing individual be- was sued. It has also installed a boom havior will take some time to have an across the mouth of Damon Slough impact, said Lewis, who would like to “It shows you that if you (a trash “hot spot”) and is targeting see the S.F. Bay Regional Board imple- care about the Bay, other known polluters upstream of ment stronger stormwater permits the slough, like the Oakland Coliseum regarding trash. Trash separators and you have to care about and flea market. But nothing is simple, booms will work but not unless they the creeks. says Estes. To install the boom, they are mandatory, said Lewis. “The Water Steve Moore, Nute Engineering, had to build a road to service it and Board could require significant trash S.F. Bay Regional Water Quality buy a truck to hold a crane. After the reduction. Save the Bay has presented Control Board member first flush, says Estes, as much as 6,000 thousands of petitions asking the pounds of trash is removed from the Board to do so.” Lewis also described boom, an act that requires several “end-of-pipe” capture nets used in “We have to address trash in the dry days of cleanup. The city received $4.5 places like Southern California that season, too, not just after the first million from Measure DD to install help divert trash before it ends up flush,” said Moore. “It’s either being structural controls at Lake Merritt. in the ocean. Lake Merritt is one of tossed, washed, or blown in.” Not sur- “This is our jewel, and it’s trashed,” the few places around the Bay where prisingly, the worst sites tended to be said Estes. “In addition to the envi- vortex separators (mechanical de- located at the bottoms of watersheds ronmental impacts, what economic vices) are being used to collect trash. that receive runoff from an entire wa- impact does that have?” The city The lack of effort to do so elsewhere ter- or pipe-shed. “As the low point in is also installing drain inlet baskets around the Bay “should be an intense the landscape, these streams are sticky (which need frequent maintenance) source of shame,” said Lewis. “We places,” said Moore. and stormwater separators in various need much stronger controls.” “It shows you that if you care watersheds. But these projects, says Lewis was followed by Nute about the Bay, you have to care Estes, “are a big deal and mean big Engineering’s Steve Moore, formerly about the creeks. Streams are the construction.” Oftentimes, construc- of the S.F. Bay Regional Board, who, likely main pathway of floatable plas- tion interferes with underground while working there, designed and tic to marine waters, and our trash utilities, and being an old, built-out undertook a “trash rapid assessment” levels are not improving but perhaps city, Oakland is full of surprises in study to examine the sources, pat- getting worse,” said Moore, who that regard, said Estes. Her conclu- terns, and amounts of trash in Bay added that he found trash in water- sion? “We would like to find the key Area waterways. “We certainly noticed sheds across all socioeconomic strata. answer but I believe the solution is a the elephant in the watershed and felt “We need to invest in structural or combination.” compelled to come up with a method other solutions and address it in a Estes was followed by Mark to measure it,” he said. With Board co- systematic way,” concluded Moore. Cuneo of Santa Monica, who, after workers, Moore surveyed 26 creeks “Trash is today’s sewage.” assuring the largely Bay Area audi- around the Bay, from Petaluma to San The next trash talker, the City of ence that, unlike the stereotype of Mateo, looked for longitudinal patterns Oakland’s Leslie Estes, described her- a Southern California water-sucking in the watersheds they surveyed, and self as a “visitor from the real world.” city, Santa Monica plans to be 80% performed return surveys to deter- Oakland has a toolbox of strategies independent from imported water mine the trash return rate. Oakland’s for dealing with trash, Estes explained, by 2010, described his city’s efforts Peralta Creek scored the worst of all from anti-littering programs in to tackle stormwater pollution. Santa of the sites, polluted with human waste schools where street sweepers get to Monica only receives 14 inches of and syringes. “We had to stop out of interact with kids, to “adopt a spot” rain per year, but, surrounded on concern for our own health at one cleanup programs with citizens, to three sides by Los Angeles County, it point,” recalled Moore. enforcing penalties for illegal dumping, nonetheless receives plenty of trash On 93 site visits, Moore’s team conducting clean creeks campaigns, in runoff. Ballona Creek and the Los picked up more than 25,000 pieces of and hiring kids to go out and pick up Angeles River have been put on the A Greener Shade of Blue? 13 E V I T U C E X E

303(d) list of impaired waterways EBMUD’s Gayle Tupper described RESTORATION: Diverse due to trash (their mouths have had her agency’s successes in working Ecosystems And Challenges trash booms installed), and a trash with dental offices to install amalgam

TMDL has been put in place. “If you separators that remove mercury, and Assessing progress on the Bay- RY A M M U S can avoid litigation over TMDLs and in collecting mercury thermometers lands Ecosystem Habitat Goals, Carl regulations, you’re way ahead of the from residents, hospitals, and schools. Wilcox of Cal Fish & Game recalled game,” he advised. Over the past 10 a colleague’s optimism in 1995: “We’ll years, Santa Monica has spent $120 do this in six months and 50 pages or million installing catch basin insets “Because so many less.” Four years and countless meet- and screens, and a state-of-the-art ings later, the goals—a biologically stormwater treatment plant. In dry heavy metals and based vision for ecosystem restora- years, the city also “boards over” other urban pollutants tion—launched a new era in Bay storm drain inlets to keep trash out. lodge in sediment, we conservation, providing guidance for “But trash doesn’t magically disappear the S.F. Bay Joint Venture, the South out of these things; we have to do the ought to be looking at Bay Salt Ponds Restoration Project, maintenance,” said Cuneo. getting sediment out of and county-level Habitat Conservation The afternoon session segued from stormwater.” Plans. Next step: linkage with antici- trash back to other pollutants and pated Subtidal, Upland, and Streams what to do about them. SFEI’s Lester Mike Stenstrom, UCLA Habitat Goals, and with CALFED’s McKee reported on our state of Ecosystem Restoration Program. knowledge about pollutants in the Bay, NOAA Fisheries’ Korie Schaeffer citing PBDEs here as among the high- Seventy-five pounds of mercury was gave an update on the process of est in the world. Pollutants in stormwa- collected from East Bay residents in establishing goals for managing and ter continue to prevent the Bay from take-back events last year, said Tupper. restoring S.F. Bay’s “hidden” subtidal achieving better water quality, said An ongoing challenge is the pharma- habitat. “The focus will be on habi- McKee, and though recent TMDLs call ceuticals that make their way into the tats we want to see more of or in for significant reductions in mercury Bay from being flushed or dumped better condition,” she said. Her group and PCBs, we do not have enough down drains. “We’re looking for ways is factoring in human stressors. “We information about where the highest to control these substances and raise can’t just wave our arms and come concentrations occur and how they awareness to convince people [the up with some goals without realizing cycle through the urban environment. substances] shouldn’t go down the past impacts are still active,” she said. However, he added, recent, first-of- drain,” said Tupper. A final goals document is expected by their-kind studies have demonstrated Concluding the pollution ses- December 2008. that PCBs probably linger in greater sion, UCLA’s Mike Stenstrom told Nancy Schaefer of Land Conser- concentrations in older industrial areas the crowd that “for better or worse, vation Services, Stuart Weiss of the in the Bay Area, a clue that can tell TMDLs are the driving force” be- Center for Earth Observation, and regulators where to focus. hind cleanup efforts. He described Ryan Branciforte of GreenInfo Net- Alameda Countywide Clean Water modeling tools and data being used work discussed another goal-setting Program’s Jim Scanlin spoke of the to evaluate alternatives for meeting project, this one for upland habitat. challenges in trying to comply with TMDLs in the upper Ballona Creek Phase 1 involves identifying how much the new TMDLs for mercury and watershed. Because so many heavy land in what kind of condition will be PCBs. To do its part in reducing total metals and other urban pollutants needed to conserve the Bay Area’s mercury inputs to the Bay by 50%, lodge in sediment, said Stenstrom, upland biodiversity, racing against Alameda would need to reduce its “we ought to be looking at getting urban sprawl. Vegetation mapping is mercury inputs by 78 kilograms per sediment out of stormwater.” To that already completed. Weiss said goals year; similarly it would have to reduce end, he described some of the low- include preserving 90% of globally PCBs by about nine kilograms per tech, green, “biofiltration” solutions rare habitat and allowing room for year. “Can we get there from here?” that places like Seattle have imple- ecosystems to change. “We set high asked Scanlin, adding that his agency mented using vegetation—swales and goals because we can,” he said. He has found frequent street sweeping stormwater planters (aka “infiltration foresaw partnerships with private to be more effective than is generally trenches”), among others. landowners, including ranchers. “In thought at removing mercury. grassland, a moderate amount of 14 State Of The Estuary 2008 E V I T U C E X E

grazing is really the key to manage- dredge soil. Lowe discussed tradeoffs marsh development would help, as ment over large areas,” he said. between leaving levees in place for would connectivity between mouse U.S. Fish & Wildlife’s Eric Tattersall wave protection and reconnecting habitat sites. “We think we can meet

took on the contentious subject of marsh and mudflat, and possible these architectural guidelines in the RY A M M U S habitat conservation planning. “If re- engineering fixes. next few decades,” Shellhammer said. gional HCP is done the right way, we Naomi Feger of the S.F. Bay PRBO Conservation Science’s end up preserving large functioning Regional Board and Roger Leventhal Nadav Nur reviewed birds as indica- ecosystems,” he said, while project-by- of FarWest Restoration Engineering tors of marsh restoration success, project approaches lead to frag- titled their joint presentation “Sedi- measured by demographic metrics: mented habitat. Tattersall described ment—the Good, the Bad and the reproductive success, recruitment of recently permitted plans in Santa Buried.” Feger presented case studies juveniles, survival of adults, emigration, Clara County and east Contra Costa of three remediation efforts using and immigration. He said local-scale County, and a pending plan in Solano dredged material: Hamilton Marsh, data is important. “There’s concern County. “Every successful plan has a Peyton Slough, and the Peninsula that restoration sites are ecological political champion who can bring it to Sportsmen’s Club (the last a lead- traps—sinks, not sources.” Nur docu- fruition,” he concluded. “Consensus? shot contamination site). Leventhal mented different patterns for different Forget it! There’s too much conflict. noted some “regulatory discomfort bird species. Mature marsh sites had What we’re after is informed consent. with using fill at all; it’s not a normal a 1,500% higher density of salt marsh It’s not all you want, but better than mouse-hugging kind of wetland proj- common yellowthroats than restora- the status quo.” ect.” But he argued that if you know tion sites. However, song sparrow Turning to the past, SFEI’s Robin your contaminants, dredged sediment nestling survival rates were highest in Grossinger looked at historical eco- can benefit restoration with “no some of the restored marshes. Biolo- systems as guides to restoration. “The net degradation.” He said economic gists are also looking at demographics historical landscape may be even constraints must be overcome in of California clapper rails, great blue more directly relevant than we had order to increase beneficial reuse of herons, and upland songbirds. realized,” he said. “Our society took sediments and reduce ocean disposal. Christy Smith of the San Pablo Bay over this landscape quite suddenly. We Next up was San Jose State Uni- reported on didn’t ask for the owner’s manual.” versity professor emeritus Howard tidal marsh restoration and enhance- Using old maps and written records, ment projects at , Tubbs Grossinger is attempting to identify Island, and Cullinan Ranch, each the wet and dry places, the intermit- “Sea level rise will presenting its own set of challenges. tent streams, and the overlooked accelerate. Will the At Cullinan Ranch, for example, partial “B-side” habitat types, like sycamore marshes keep up?” or full restoration would require new alluvial woodland. Remnant seasonal levees to protect Highway 37 from wetlands in Santa Clara and Napa Jeremy Lowe, PWA flooding. Smith stressed adaptive counties “are tiny fragments of former management (“measure three times, perennial wetlands. If you’re interested cut once”) and the need to keep in wetland restoration, historic wet- Shellhammer, now with H.T. Harvey, restoration partners involved. lands show you where to look.” who has spent 50 years studying Smith’s South Bay counterpart, If ecological history can be ob- the endangered salt marsh harvest Clyde Morris of the Don Edwards S.F. scure, the future of estuarine environ- mouse. He discussed small mam- Bay National Wildlife Refuge, looked ments is up for grabs—with climate mals—the mouse and the elusive back on seven restoration projects change a prime source of uncertainty. salt marsh wandering shrew—in spanning 20 years. “It must have been PWA’s Jeremy Lowe said the S.F. tidal marsh restoration projects. The really fun back in the 80s to restore Bay’s marshes have handled historic shrew may or may not still exist in things,” he said. “You didn’t worry sea level rises well. “But sea level the Bay’s marshes; if it’s there, it will too much about permits, and plans rise will accelerate. Will the marshes benefit from mouse conservation were something you did on the back keep up?” he asks. As the waters rise, measures. Both need mature marshes of an envelope.” But he’s seen things mudflat and marsh systems tend to with internal escape cover and high improve—with the South Bay Salt move landward—if enough sedi- marsh tidal refugia, but very little high Pond Restoration, “for the first time ment is available. In the long-term, we marsh remains. Reducing the slope in my career we’re doing adaptive may need to recharge mudflats with of outboard dikes to allow for high management instead of knee-jerk A Greener Shade of Blue? 15 E V I T U C E X E

management.” Still there have been Project reported on the ongoing war will dictate the need for better tran- surprises, like the challenge of dealing against aggressive hybrid cordgrass sit,” said ABAG’s Dave Burch. with dissolved . “You don’t strains (see ESTUARY, October Municipalities and regional bodies always know what you don’t know,” 2007). She called for the develop- are trying to focus growth in specific RY A M M U S said Morris. “We need to commit not ment of best practices for regional areas to direct planning and invest- to do more restoration without fund- agencies. “Monitor and remove it—just ments into “priority development ing for adaptive management, because areas,” said ABAG’s Ken Kirkey. A key without that we won’t be successful.” element of priority development In his talk on restoring Delta “Monitor and remove it areas is proximity to transit, so that ecosystems, Stuart Siegel of Wetlands —just monitoring has driving can be reduced to create what and Water Resources called this huge Cities 21’s Steve Raney called a “low- area “a case study in complexity.” gotten us nowhere.” miles community.” Manmade changes—diking islands, Peggy Olofson, The projections for the Bay Area’s shortening channels—complicate the Invasive Spartina Project growth mean that managers and goal of maintaining “viable populations policymakers will need to get creative of desirable species. In the Delta, we about where to put people and how don’t say ‘native’; there are some non- monitoring has gotten us nowhere,” to make those living places more natives people like to have, like striped she said. “Don’t open a new marsh sustainable, the topic of a panel discus- bass.” Climate change introduces too early near existing hybrid Spar- sion in the afternoon session. “We further complexities. “Wetlands can tina. And be careful with equipment want to make it so that people get move up gentle slopes as sea level and dredge sediment.” to as much as they can on foot,” said rises, but not with levees,” Siegel said. the ’s Marla Wilson. He sketched ideas emerging from LAND USE: Making To accomplish that, cities must build planning efforts, including new Connections compactly and have walkable streets floodplains and “green” levees. and neighborhoods, and they need to When S.F. State University’s Tom That land-dependent creatures— write these ideas into their general Parker took the podium, it was late in and the farms and other upland plans. “That gives elected officials the the day. “When I go to conferences, areas they inhabit—are in some will to do it,” said Laurel Prevetti of the usually by this time I’m out drink- way related to estuaries was once a City of San Jose. ing somewhere,” he quipped. But his foreign concept. But now, said U.C. Prevetti noted that in the 1970s, message was no joke: global climate Davis’s Jeff Loux at the land use San Jose officials drew a line around change imperils the Estuary’s marshes. session of October’s conference, “It’s the city, indicating its boundary for Temperature increase may decrease self-evident that water and land use growth. That forced later administra- primary production; inundation and planning are linked.” And as the state tions to recycle land—developing infill flooding will increase, with restored population grows, that link will need on grayfields like underused parking marsh sites inundated more than natu- to tighten, requiring multiple agen- lots. Much of the development of ral sites. Rising salinity will reduce spe- cies—city planning departments, the 1970s and 1980s also resulted in cies diversity. “Given temperature and utilities districts, water agencies, and office parks—large buildings sur- salinity increase and marsh accretion transportation departments—at rounded by huge parking lots. One rates failing to keep up with sea level local and regional levels to work way that nature has been brought rise, what’s the scenario?” he asked. together more closely. back to such environs, said Prevetti, “The winner is pickleweed,” which “The region will add five more is through greenways and restored occurs now in a variety of salinity and Oaklands by 2035,” said the Joint urban streams. inundation conditions. But it’s more Policy Committee’s Ted Droettboom, The topic of creek restoration sensitive to salinity in poorly drained commenting that growth will have brought insight from the S.F. Bay sites. So an increase in salinity and inun- to be planned much more carefully Regional Board’s Ann Riley, who de- dation will significantly reduce wetland to mitigate the additional traffic and scribed how creeks can be creatively productivity, “especially in pickleweed, its effects on air and water quality. integrated into cities, such as in San the one species most likely to expand Regional bodies like ABAG are finally Luis Obispo. When it comes to under those conditions.” looking into the nexus among air restoring streams in cities, said Riley, Closing the restoration session, quality, land use, transportation, and one of the most common problems Peggy Olofson of the Invasive Spartina water quality. “Our land use patterns is negotiating for more room for the 16 State Of The Estuary 2008 E V I T U C E X E

stream—which often means nego- “We’re at the end of the using water once and spending a half tiating for fewer parking spaces in a billion dollars to treat and put it conjunction with development or road of the system of back,” said Pla.

redevelopment. Even a small reduc- DWR’s Kamyar Guivetchi sum- RY A M M U S using water once and tion in the number of parking spaces spending a half a billion marized his agency’s efforts to work can often make a critical difference hand-in-hand with federal and state for a city stream. Riley’s lesson: “Don’t dollars to treat and put agencies, tribal governments, local accept a plan as given.” it back.” governments, and members of the But one given is that cities have public to update the California Water infrastructure—like stormdrains—that Michele Pla, BACWA Plan. Among the key changes from greatly affects their watersheds, so the current plan—last updated in planners are finding ways to reduce Bay is starting to use less freshwa- 2005—is the inclusion of impacts pollution through greener solutions. ter and more recycled water for from global warming. The SFPUC’s Rosey Jenks spoke of irrigation. Palo Alto and other cities Linda Fiack of the Delta Protec- her agency’s efforts to reduce the have been testing ecoroofs, cisterns, tion Commission compared the number of impervious surfaces that and permeable pavers. Said Bobel, Delta and its water supply to the carry pollution to watersheds. When “What’s innovative about this? The country cows that provide milk for roads are repaved, for example, Babylonians were doing cisterns.” city folks. “Most people don’t know their impermeability can be reduced The NRDC’s Kristina Ortiz said where their water comes from,” she so they can act as filters. Jenks also lots of little gadgets that might not noted. “The Delta is that cow in the described how green roofs—like the seem so innovative, incorporated into country.” But regional and county new one at the California Academy of planning, can collectively save a lot of planners do know where their water Sciences —are helping reduce runoff. water. Using technology and comes from, and they’re planning The idea of green building is cur- sensors can help with water savings, for it now. Fiack explained how the rently popular among architects and particularly in landscaping, where five Delta counties of Contra Costa, developers, noted Paul Okamoto most urban water is used. Another San Joaquin, Sacramento, Solano, and of Okamoto Saijo Architecture. But big consumer of water is the toilet: Yolo—all revamping their general more needs to be done in light of New dual flush models can save gal- plans—are including a Delta element. the consequences of global climate lons. “It’s to the point where turning And Benicia mayor Elizabeth Pat- change. Three design concepts should off the tap is like turning off the light,” terson, who said her city has inte- be integrated into green building. Ortiz said, noting that people need grated watershed restoration into its First is the 2030 Initiative (a standard to become as attuned to conserving general plan, wrapped up the session where all buildings shall be carbon- water as they are to energy. To that by describing the importance of con- neutral by 2030), which has already end, EBMUD and PG&E have teamed necting small grassroots groups with been adopted by the U.S. Conference up to offer rebates and tiered pricing movers and shakers. “We need to get of Mayors and American Institute as incentives to get customers to save. their ideas to where the power is.” of Architects. Second is analyzing EBMUD bills now include a water intensity of transportation as part of budget that not only presents con- a green building analysis. “We need to sumption, but also provides climate understand how much energy is spent information to show customers how on transportation due to the location to cut down on landscape watering. of buildings and our current land-use “It’s the low-hanging fruit, but it helps,” patterns,” said Okamoto. Third, build- said EBMUD’s Richard Harris. ings should incorporate the design Using recycled water can save concept of “passive survivability”—in energy and reduce stress on the which buildings are still functional Bay, said Michele Pla of the Bay Area when services like electricity, water, Clean Water Agencies. Pla explained and sewer are interrupted. that using more recycled water low- Water management for all new ers the need to treat water, brings development must also be consid- down energy consumption, and curbs ered, and Phil Bobel of the City of pollutant loads to the Bay. “We’re at Palo Alto discussed how the South the end of the road of the system of A Greener Shade of Blue?

Vital Statistics 1818 State Of The Estuary 2008 AL TA I V

A S C I T S I TAT S Water PERCENT OF INFLOW DIVERTED

60 Recent Inflows

Normal or above normal rainfall 50 has meant improved Delta inflows in recent years, but the dry winter of

2006-2007 ran counter to that trend. 40 Inflows to the Delta and Estuary were 25.6 million acre-feet (MAF) in

water-year 2006 (October 1, 2005 30 - September 30, 2006) and 6.7 million acre-feet (MAF) in water-year 2007 (October 1, 2006 - September 30, 20 2007). Delta outflows were 22 MAF in 2006 and 2.9 MAF in 2007 (Inter- agency Ecological Program, 2008). 10 97 98 99 00 01 02 03 04 05 06 07 MORE INFO? www.iep.ca.gov/dayflow/index.html

Diversions for Beneficial Use Water Use Efficiency has pioneered the use of recycled water for non-agricultural purposes, Water is diverted both within the Water use efficiency, conserva- including car washes and commercial Delta and upstream in the Estuary’s tion, and recycling projects within laundries, and several Bay Area cities, watersheds to irrigate farmland and the Bay-Delta region aim to provide including Novato, Petaluma, and Santa supply cities. Total exports were 3.2 a “drought-proof” source of water Rosa, have their own programs. Many MAF in water-year 2006 and 6.7 to help meet the needs of cities, other Bay Area agencies are forging MAF in water-year 2007. The average industries, and agriculture. At the local ahead with the design, construction percentages of total Delta inflows level, the Bay Area Water Recycling and operation of water recycling diverted were 34.4 in water-year Program’s (BAWRP) Master Plan, now projects. The East Bay Municipal Utility 2006 and 54.3 in 2007 (Interagency complete, calls for recycling 125,000 District has set a water recycling goal Ecological Program, 2008). af/year in the Bay Area by 2010, of 14 mgd by 2020. The Dublin San MORE INFO? and about 240,000 af/year by 2025. Ramon Services District (DSRSD) www.iep.ca.gov/dayflow/index.html The Marin Municipal Water District recycling facility’s current treatment

FRESHWATER FLOWS TO THE SAN FRANCISCO ESTUARY, 1980-2007 IN MILLIONS OF ACRE FEET Total Delta Inflow Net Delta Outflow (after export and in-Delta use) 70

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50

40

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0 80 82 84 86 88 90 92 94 96 98 00 02 04 06 A Greener Shade of Blue? 19 AL TA I V

capacity is 3 mgd, with 10 miles of addition to parks and industrial users

Fish and Fisheries S C I T S I TAT S distribution installed. Planned capac- (including Pixar and Novartis), the ity for this facility is 9.6 mgd. DSRSD project will supply recycled water for Dungeness Crab and EBMUD have jointly developed toilet flushing to EBMUD’s Oakland the San Ramon Valley Recycled Water headquarters and another Oakland Program (SRVRWP), serving areas of highrise. The EBRWP will ultimately Blackhawk, Danville, Dublin, and San include nearly 30 miles of pipeline Ramon. When complete, this multi- through parts of Alameda, Albany, phased 6.7-mgd project is expected Berkeley, Emeryville, and Oakland and to deliver 3.3 mgd to DSRSD’s ser- will save 2.5 mgd (2,800 acre-feet/ vice area and 2.4 mgd to EBMUD’s year) once all recycled water custom- service area with 1 mgd available to ers are hooked up to the system. The The Dungeness crab (Cancer either. DSRSD has been delivering first phase will supply up to 0.7 mgd. magister) is a valuable sport and com- recycled water since November 2005. Eventually, EBWRP water may be mercial species that reproduces in the EBMUD customers including the used in wetlands restoration. EBMUD ocean in winter and rears in nearshore City of San Ramon, the San Ramon is also planning additional recycling coastal areas and estuaries. Small Valley Unified School District, and projects for industrial users in Rich- juvenile Dungeness crabs immigrate Chevron’s world headquarters began mond and Rodeo and for irrigation in to the Estuary in spring, rear for 8-10 receiving recycled irrigation water in San Leandro. A bill sponsored by Rep. months, and then emigrate from the February 2006. Meanwhile, EBMUD George Miller (D-Martinez) to autho- Estuary at approximately 4” carapace currently produces over 5 mgd of rize a federal role in water recycling width. Estuary-reared crabs grow faster recycled water. EBMUD’s multi- projects elsewhere around the Bay than ocean-reared crabs, mainly due phased East Bayshore Recycled Water (Palo Alto, Mountain View, Pittsburg, to warmer water temperatures and Project (EBRWP) is expected to Antioch, Redwood City, and San Jose) increased prey density in the Estuary. begin delivery to some Oakland and passed the House of Representatives Estuary-reared crabs reach legal size Emeryville customers in the spring in July 2007. at the end of their third year, 1-2 years of 2008, subsequently expanding to MORE INFO? before ocean-reared crabs. Albany, Berkeley, and Emeryville. In [email protected]

AGE-0 DUNGENESS CRAB ABUNDANCE INDICES FROM THE SAN FRANCISCO ESTUARY, 1980-2007

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12

x 10

8

6

Abundance Inde 4

2

0 80 85 90 95 00 05 Year 20 State Of The Estuary 2008 AL TA I V

The 2006 abundance index of the fishery consecutively through the U.S. Fish & Wildlife Service decision A S C I T S I TAT S age-0 Dungeness crabs was near 2006-07 season. Landings decreased in January 2005. A listing petition for record low in the Estuary, similar to dramatically in the 2007-08 season, four western lamprey species had the low abundance observed in previ- with less than 1 million pounds landed been submitted two years earlier by ous years with strong El Niño events. in Central California through January the Center for Biological Diversity Abundance rebounded to a modest 2008. and 10 other conservation groups. level in 2007. Neither winter 2005- MORE INFO? USFWS claimed the petitioners had 06 nor 2006-07 had strong El Niño [email protected] not provided specific information on events, with sea surface temperatures threats to the Kern brook lamprey in the Gulf of the Farallones near Kern Brook Lamprey and another nonmigratory species, average. However, frequent winter the western brook lamprey. storms in winter 2005-06 resulted in Endemic to the San Joaquin Valley, the Kern brook lamprey (Lampetra MORE INFO? a strong northward-flowing Davidson [email protected] Current. This surface ocean cur- hubbsi) is a primitive eel-shaped vertebrate with an unusual life cycle. rent likely transported Dungeness Green Sturgeon crab larvae north of the Gulf of the Typical lampreys are predators, attach- Farallones. Since the San Francisco ing to fish with suckerlike mouths, The southern Distinct Population Estuary is near the southern limit of rasping a hole with a tongue covered Segment (DPS) of North American Dungeness crab distribution, there is with sharp plates, and feeding on the green sturgeon (Acipenser medirostris) no large population to the south to victim’s blood and body fluids. How- was listed as threatened under the replace this larval loss. The planktonic ever, several species have evolved Endangered Species Act on April 7, larvae transported north were not a nonpredatory lifestyle. Instead of 2006, and represents the southern- able to return to the Gulf, resulting migrating to sea as larvae (ammo- most breeding distribution for this in poor Dungeness crab recruitment coetes), Kern brook lampreys and species. Its current spawning habitat here in 2006. Nearshore currents other nonpredatory species spend appears to be limited to the upper and ocean temperatures were more their entire lives in their natal streams. mainstem , though favorable for Dungeness crab larvae Their larvae subsist on algae and recent sightings in the Yuba River in winter 2006-07, resulting in higher detritus; after metamorphosing in the (Gary Reedy, SYRCL, pers. comm.) fall, adults spawn in spring in gravelly suggest adult sturgeon cryptically abundance. Low to modest Dunge- riffles and die without feeding. occupy other Central Valley rivers. ness crab abundance in the Estuary First collected from the Friant-Kern Recent modeling of spawning habitat from 2005 to 2007 was preceded by suggests only 4.6% of the available 4 years of very high abundance from Canal in 1976, Kern brook lampreys Central Valley habitat has character 2001 to 2004. These high abundance were later found in the lower Merced, - indices resulted from cooler than Kaweah, Kings, and San Joaquin Rivers. istics similar to spawning habitat of average ocean temperatures and As larvae, they occupy silty back- northern DPS green sturgeon (Klam- favorable nearshore currents (less waters of foothill streams, prefer- ath and Rogue rivers), and 44.2% of northward flow) during the crab’s ring cool, shallow pools and other their historic spawning habitat in the larval period. low-flow environments with sandy or Sacramento-San Joaquin system has The recent strong Dungeness muddy substrates. Many such habitats been lost over the past century (Neu- crab year classes in the Estuary were have been eliminated by channeliza- man et al. 2007). reflected in the commercial landings tion. Known populations are scattered Sacramento River green sturgeon for several years. Central California through the San Joaquin drainage and are late-maturing and exhibit exten- Dungeness crab landings surpassed 5 isolated from each other. With one sive marine migrations along the west million pounds annually in the 2002- exception, all populations are below coast, constituting the primary stock 03 to 2006-07 fishing seasons, the dams where sudden changes in flow present in summer aggregations in may strand the larvae. Larvae have the Columbia River and Willapa Bay first time landings last exceeded 4 mil- also been drawn into the siphons of (Israel 2007; Lindley et al. in press). lion pounds here since the late 1950s. canals from which they are unable to Spawning fish enter San Francisco Bay The 2001 year class of San Francisco return to the spawning grounds. between March and May, pass through Estuary-reared crabs reached legal size A California Species of Special the Estuary in a few weeks, and then and became available to the fishery Concern, the Kern brook lamprey ascend the Sacramento River to reach in the 2003-04 season, and the 2002 was denied federal protection in a fast-flowing turbulent habitats with through 2004 year classes entered A Greener Shade of Blue? 21 AL TA I V

optimal temperatures. If these fish agement and increasingly intensive remained low. Then in 2006-2007, the arrive at the Red Bluff Diversion Dam monitoring of Southern DPS green estimate plummeted to 10,935 tons, S C I T S I TAT S (RBDD) prior to its gates closing, sturgeon. Regulatory efforts continue even lower than 1997-1998, and San then they appear to spawn in areas to move forward, including a draft Francisco Bay landings fell to 292 tons, above RBDD (Heublein 2006). Green 4(d) Rule outlining permitted activities with an historic low in the percent- sturgeons are observed below RBDD and take for green sturgeon. Collab- age of 2- and 3 year old fish. The following its closure, and this barrier orative research is underway to assess 92% drop in the spawning biomass eliminates upstream passage for these green sturgeon productivity, evaluate estimate appears related to another later migrating adults. Under certain threats, and characterize habitats. El Niño event and an unusually dry conditions, green sturgeon successfully MORE INFO? winter. Dive surveys in emigrate underneath RBDD’s gates, [email protected] found sharp declines in the density although in 2007, 10 green sturgeon of the subtidal plants (Zostera and were observed to have been killed Pacific Herring Gracilaria) to which the herring attach under the RBDD gates in late May. their eggs, suggesting that spawning This may represent a significant por- Between the 1997 El Niño and fish may have been displaced to more tion of the annual spawning popula- the 2004-2005 season, the spawning favorable habitat. The quota for 2007- tion, which, using genetic estimation biomass of Pacific herring (Clupea 2008 was 1,057 tons, divided among methods, was determined to range pallasi), which supports the Bay’s larg- three platoons of herring boats. between 10 and 54 spawners above est commercial fishery, has remained below the long-term (since 1978) MORE INFO? RBDD from 2002 to 2006 (Israel [email protected] 2007). Adult green sturgeons occupy average of 52,234 short tons. In response to this decline, the Fish and the Sacramento River’s deepest holes Delta Smelt as late as November (Richard Corwin, Game Commission, which manages USBR, pers. comm.). the fishery, lowered catch quotas. The Delta smelt (Hypomesus Recent laboratory research has Although ocean productivity has been transpacificus), a 55-70 mm long os- focused on understanding the green favorable for herring over the last merid, is endemic to the upper San sturgeon’s ability to tolerate thermal several years, a large recruitment of Francisco Estuary. Once quite com- young fish to the spawning popula and salinity gradients. Water tem- - mon, a dramatic decline in the 1980s peratures above 17.5°C constituted tion has yet to occur, and older age led to the federal and state listing of the upper thermal optima for green classes have been declining. Following this fish as a threatened species in sturgeon embryos, and temperatures record high biomass levels of 99,050 1993. It is the annual life cycle, lim- >22°C resulted in mortality (Van short tons in 1995-1996 and 89,570 ited diet, low fecundity, and restricted Eenennaam et al. 2005). Young green short tons in 1996-1997, spawning distribution within the Estuary that biomass plunged to 20,000 short tons sturgeon are more temperature tol- makes Delta smelt environmentally following the 1997 El Niño. Between erant and their growth was not nega- sensitive. Possible reasons for the 1997 and 2003, estimates fluctu tively impacted between 19 and 24ºC - decline of Delta smelt include stock- (Allen et al. 2006). Juvenile green ated between 27,400 and 39,500 recruitment effects, declining habitat short tons. The 2004-2005 spawning sturgeon develop critical osmoregula- quality, increased mortality rates biomass estimate was 58,934 short tory capacities between their first and (largely related to water exports), tons, the first estimate to exceed the second years that permit them to en- and reduced food availability due to long-term average of 51,825 tons ter saltwater by 1.5 years (Allen and invasive species. used to set fishery quotas since the Cech 2007). Dissolved oxygen is also To reduce the impact of Delta 1996-1997 season. That was also the a critical parameter for juvenile green pumping operations on Delta smelt, first season since the 1997 El Niño sturgeon, since they have high oxygen CALFED developed the Environ- in which the number of 4 year old consumption (Mayfield and Cech mental Water Account (2000), which and older herring increased. 2005- 2004), and suboptimal conditions helps to reduce Delta smelt take by 2006 saw a record high of 145,054 likely represent a chronic stressor. shifting the timing of pumping. Despite tons, more than twice the 27-year The information scientists have gained this measure, Delta smelt abundance average. Since 85% of the spawning about habitat loss, limited spawner indices have reached all time lows for activity occurred in Richardson Bay, abundance, and risks associated with two of California Department of Fish which is closed to the commercial current water management activities and Game’s (DFG) long-term moni- fishery, the catch for that season support the precautionary man- toring surveys, the Summer Townet 22 State Of The Estuary 2008 AL TA I V

Longfin Smelt A S C I T S I TAT S SUMMER TOW-NET SURVEY – DELTA SMELT 1959-2007 Longfin smelt (Spirinchus thaleich- 70 thys) in the San Francisco Estuary

60 represent the southernmost spawning population in North America. The 50 Estuary is not as hospitable to longfin smelt as it once was. Abundance of 40 longfin smelt continues to be a posi-

30 tive function of Delta outflow during its December-May larval period (Bax- Abundance Index 20 ter 1999), but this relationship has changed over time. The first change— 10 a decline in the intercept but no

* * * change in the slope of the outflow- 0 59 64 69 74 79 84 89 94 99 04 abundance relationship—occurred Year subsequent to the 1986 introduction of the over-bite clam, Corbula amu- rensis, which changed the upper Survey (TNS, since 1959) and the Fall ing negative flows in Old and Middle Estuary food web (Kimmerer 2002). Midwater Trawl (MWT, since 1967), Rivers and opening the Delta Cross After 2000, the longfin smelt outflow- even in fairly plentiful water years like Channel gates to improve transport abundance relationship appeared to 2006. For example, TNS indices from of juvenile smelt beyond the influence change again, this time in concert 2005-2007 were 0.3, 0.4, and 0.4 re- of the export pumps. with abundance declines of three spectively, compared with an average Meanwhile, in response to a other upper Estuary pelagic fishes, of 6.4 for 1991-2001. MWT indices suit by the California Sport Fishing Delta smelt, young striped bass, and for the same years were 27, 41, and Protection Alliance, Alameda County threadfin shad (Sommer et al. 2007). 28, compared with an average of 545 Superior Court Judge Frank Roesch Even though longfin smelt abundance for 1991-2001. ordered DWR in March 2007 to increased following high winter-spring Such abrupt decreases in Delta reduce smelt mortality through outflows of 2006, the outflow-abun- smelt and other pelagic fishes (longfin entrainment in the Delta pumps, dance pattern for years 2003-2006 smelt, striped bass, and threadfin resulting in the temporary shutdown was lower than expected and hints at shad) prompted studies led by the of the Harvey O. Banks pumping a second decline in the relationship. Interagency Ecological Program to station. In August 2007, U.S. District In addition, some evidence indicates address this Pelagic Organism Decline Court Judge Oliver Wanger ordered that survival from their first to their (POD). Research so far has included state and federal water agencies to second winter has also declined since analysis of changes in the estuarine either reduce pumping or release 1994 (Rosenfield and Baxter 2007). food web (with the introduction of more water upstream of the Delta In August 2007, concern about the overbite clam and several cope- to maintain sufficient flow to prevent the decline and numerous potential pod species, and low phytoplankton entrainment. He subsequently set stressors led several environmental productivity), in water conditions September 25, 2008 for a new groups to petition the California Fish (salinity, , temperature), in wa- Biological Opinion from state and and Game Commission (Commis- ter export patterns, and in the Delta federal wildlife agencies. sion) and the U.S. Fish and Wildlife smelt’s fecundity and growth rate. A On yet another track, UC Davis’ Service to provide emergency Threat- final POD report is expected by the Fish Conservation and Culture Lab, ened or Endangered Species status end of 2008. which has raised smelt in captivity for longfin smelt (The Bay Institute Early in 2007, data from the DFG for the past 15 years, is attempting et al. 2007). At its October 11, 2007 20 mm survey of larval Delta smelt to establish a captive population as a meeting, the Commission rejected the showed an 89% reduction from 2006 hedge against the species’ extinction. emergency listing request, opting in- levels. In response, the Delta Smelt MORE INFO? stead to evaluate the petition through Working Group recommended [email protected]; standard rulemaking procedures and emergency actions including address- [email protected] directing the Department of Fish and A Greener Shade of Blue? 23 AL TA I V

Game to proceed with the standard The winter-run Chinook salmon, 2001, for example, changing the need rulemaking as quickly as possible. On with the lowest population, has been to reduce pumping and use EWA re- S C I T S I TAT S November 30, 2007, the DFG submit- listed as both a state and federal sources to protect fish. The winter-run ted its initial evaluation of the petition endangered species since 1994. As population was 5,299 in 2005; 7,513 to the Commission, concluding that a result of more regular interagency in 2006; and 6,144 in 2007. the petition incorporated sufficient, scrutiny of operations, a new count- The next most sensitive stock, the accurate, and pertinent up-to-date ing method for Chinook winter-run spring-run, was state listed as threat- information on longfin smelt popula- salmon critical to assessing “incidental ened in 1998 and federally listed in tions, habitat and threats, and recom- take limits” is now in place. Federal 1999. The method used to estimate mending the petition be accepted incidental take limits for winter-run the spring Chinook return to the for consideration. At its February 7, allow up to 2% of “juvenile produc- Feather River Hatchery was changed 2008 meeting, the Commission voted tion” to be lost at the pumps. The in 2005, with a subset of tagged fish to designate the smelt a candidate formula for setting take limits com- being used for the estimate of spring species for formal listing under the bines the number of offspring pro- escapement. The spring-run popula- California Endangered Species Act. duced (“juvenile production”) with tion was 15,900 in 2005; 12,567 in The Commission also approved the number of adult fish returning 2006; and 11,950 in 2007. interim regulations to require reduc- to spawn each year (“adult escape- Sacramento fall-run have histori- tion of water exports from the Delta ment”). The latter number—based cally been the most abundant Chi- when longfin smelt are present in on how many fish passed through nook stock. Their population dropped areas where they could be entrained the Red Bluff Dam fish ladders—be- from 839,956 in 2002 (the estimated at the pumps. came questionable in recent years population for Battle Creek was MORE INFO? as the dam gates remained open for the highest on record) to 383,500 [email protected] longer periods and fewer fish had in 2005 and 270,224 in 2006. The to use the ladders. An alternative preliminary 2007 estimate of 90,414, Central Valley method, counts of spawned female second-lowest since 1973, forced Chinook Salmon carcasses upstream, backed up by curtailment of the 2008 salmon sea- earlier surveys, revealed a variation son. The Pacific Fishery Management Central Valley Chinook salmon up to a factor of five in the total es- Council’s minimum conservation goal (Oncorhynchus tshawytscha) occur timates of spawning adults. The new for this run is 122,000. The estimate in four discrete runs—winter-run, higher estimates of adult escapement of 2,021 two-year-old spawners in spring-run, fall-run, and late fall-run translated into a higher estimate of 2007 was far below the 36-year aver- (run refers to the season in which juvenile production and meant that age of 40,000. adults return to their native streams the take limit was never reached in to spawn).

SALMON RUNS OF CONCERN Winter-run To Upper Sacramento River IN THOUSANDS OF ADULT FISH RETURNING TO SPAWN Spring-run To Upper Sacramento River Fall-run To

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A S C I T S I TAT S STRIPED BASS INDEX 1961-2007

FMWT Index

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0 61 63 65 67 69 71 73 75 77 79 81 83 85 87 89 91 93 95 97 99 01 03 05 07

TNS Index 120

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0 61 63 65 67 69 71 73 75 77 79 81 83 85 87 89 91 93 95 97 99 01 03 05 07

The Sacramento late fall-run Striped Bass The striped bass is one of the four (distinct from fall-run) population was species involved in the recent Pelagic Native to eastern North America, 17,035 in 2005; 23,134 in 2006; and Organism Decline (POD) phenom- the striped bass (Morone saxatilis) 18,593 in 2007. enon, along with Delta smelt, longfin was introduced to California in 1879, Returns of the San Joaquin fall-run smelt, and threadfin shad. See the when fish from New Jersey’s Na- in 2005, at 23,000 were above the Delta smelt account for a summary of vasink River were released in the San 1967-1999 average annual return of POD activity to date. Francisco Estuary. The species did well 20,470. However, the return fell to Abundance indices of striped bass in its new environment, supporting a 12,184 in 2006 and 2,572 in 2007. in their first year of life (young-of- commercial fishery from 1888-1935, Since 1986, San Joaquin spawner re- the-year or YOY) remain at very low and is still the basis for an important turns have constituted less than 10% levels. On a scale where the peak sport fishery. However, the popula- of the total Central Valley escapement Midsummer Townet Survey (TNS) tion began to decline in the 1930s, for fall run Chinook. index was 117 in 1965, the 2005 prompting tighter regulation of sport index was 0.9. The TNS index of 0.8 MORE INFO? www.pcouncil.org/ fishing and intensive research. salmon/salsafe.html in 2004 was the lowest in the 45-year A Greener Shade of Blue? 25 AL TA I V

history of the survey. The indices were entire plant. Human health risks from These invasive species have the po- even lower in 2006 (0.5) and 2007 imazapyr are reported to be low, and tential to disrupt estuarine food webs. S C I T S I TAT S (0.3). On a scale where the peak the herbicide is less toxic to aquatic The exotic shimofuri goby has been Fall Midwater Trawl Survey (FMWT) organisms than glyphosate; however, reported to feed on C. caspica, but the index was 20,038 in 1967, the 2006 there is a high risk of damage to non- three hydromedusae have no known index was 363, up from 121 in 2005. target plants if inadvertently applied. predators in the Estuary and contrib- The 2007 index fell to 82. Following two years of treatment, the ute nothing to the food web until they MORE INFO? Invasive Spartina Project manager die off in winter. Their prey, captured [email protected] reported excellent control and very with tentacles loaded with stinging ne- little grow-back. In 2006 the control matocysts, includes copepods, barnacle Invasives program treated 1,450 acres of Spar- nauplii, crab zoea larvae, and larval fish. tina (94% of the Bay-wide popula- Researchers at UC Davis are study- Cordgrass tion, 107 of 134 known locations), ing prey selectivity, including selectivity reporting 60 to 95% killed. Treatment among copepod species, and dietary Species of Spartina (cordgrasses), at two locations was delayed because overlap with POD fish. At this point introduced into the Estuary in the of the presence of the endangered their potential contribution to the 1970s, have spread rapidly and pose a California clapper rail. Spot treatments POD phenomenon remains unclear. serious threat to the success of future will continue from 2009 forward. The hydromedusae are especially tidal marsh restoration throughout Meanwhile, the plant has colonized abundant in Suisun Marsh. They also the Estuary. The impacts associated two recent East Bay restoration sites occur in the Napa, Sonoma, and Peta- with the spread of Atlantic cordgrass and a small portion of the Petaluma luma Rivers. Overall abundance varies (Spartina alterniflora) include hybrid- River within the last two years. Bar- with salinity and temperature; numbers ization with and likely local extinction ring additional expansion, the Invasive fell in 2005, a low-salinity year, com- of native Spartina foliosa, regional Spartina Project expects to control pared with 2004. For all three, catches loss of unvegetated tidal flat habitat, the invasive Spartina by 2011. in Suisun marsh were highest in Sep- elimination of small tidal channels, and MORE INFO? tember. In a recent study, Moerisia sp., loss of pickleweed habitat essential [email protected] which can occur in particularly dense to the endangered salt marsh harvest concentrations, was shown to have mouse. The rate of spread is greatest Invasive Hydrozoans more predatory effect on copepods on mudflats and restored tidal marsh, than the other species (Schroeter where soft sediment and quiescent Three species of hydromedusae 2007). One concern is that swarms of hydrology provide ideal habitat. The (popularly known as “jellies”) from medusae may deter fish from exploit- invasion no longer consists of the the Black and Caspian Seas have ing local prey resources. pure parent genotype; many hybrid colonized the brackish waters of the MORE INFO? morphologies have been observed. upper San Francisco Estuary: Maeotias [email protected]; Hybrids are more vigorous and re- marginata, Moerisia sp., and Blackfordia [email protected] productively fit than either of the par- virginica. They probably reached our area in ships’ ballast water. M. mar- ent species. Although genetic tests can Overbite Clam be cryptic, UC Davis researchers have ginata may have been present since at developed these tests to distinguish least 1959, which Moerisia sp. was first The overbite (Asian) clam (Corbula hybrids from natives. In 2005, the collected in 1993. All three alternate amurensis, previously Potamocorbula previously used herbicide glyphosate between a sedentary, asexually repro- amurensis) continues to be the domi- (AquamasterR, the aquatic version of ducing polyp form and a free-swim- nant benthic organism in the North RoundupR) was largely replaced by a ming, sexually reproducing medusa Bay. Seasonal decline of the bivalve new agent, imazapyr (HabitatR), only form. Polyps may produce either occurs throughout the North Bay in recently registered for use in Califor- medusae or more polyps; medusae winter of most years, and is followed nia. Unlike glyphosate, treatment with produce polyps. M. marginata was by peaks in density after reproduc- imazapyr does not require a 6-to-12- originally believed to be an all-male tion in spring and fall. There have hour post-application period without population, but females have been been some short duration phyto- tidal inundation. Glyphosate also tends detected. A fourth exotic hyrdrozoan, plankton blooms in the northern Bay to bind to sediment and become in- Cordylophora caspica, occurs only in during early spring of some years, activated, and requires coating of the the polyp form. when Corbula biomass is at an annual 26 State Of The Estuary 2008 AL TA I V

minimum. These blooms have been years may have created more favor- course of the study, the green crab A S C I T S I TAT S earlier and shorter in duration than able conditions for them. severely reduced the abundance of historic blooms. Corbula was first seen C. gigas, an efficient filter feeder, three common invertebrate species, in the South Bay in 1988 and had has been known to outcompete and but did not impact the shorebird food become a dominant bivalve by 1990. overgrow mussels and other bivalve web (Grosholz et al. 2000). The Na- Unlike in the North Bay, however, the species. Its presence may complicate tional Green Crab Management Plan South Bay phytoplankton bloom has efforts to restore the native Ostrea includes several recommendations not been depleted by Corbula filter- conchaphila. The major concern, for local population control strategies. feeding. This is partially due to the however, is that its impact on estuarine These include early warning methods seasonal cycle of Corbula and other food resources may contribute to the for new range expansions, preven- shallow water bivalves in that part decline of pelagic organisms. tion measures against new introduc- of the Bay—during the spring bloom MORE INFO? tions, and coordinated monitoring period, clam biomass is very low and [email protected] of population trends, new outbreaks, thus the clam’s grazing pressure is and losses to commercial fisheries. In too low to restrict phytoplankton Green Crab Bodega Bay, an intensive sampling and bloom formation. (Thompson, pers. removal effort in 2006 removed over comm.2004). The European green crab (Carcinus 67% of initially marked green crabs, maenas) is now established in every MORE INFO? and appears to have reduced green significant Bay and estuary between crab predation on the native shore [email protected] Monterey, California, and Gray’s crab Hemigrapsus oregonensis (De Harbor, Washington. It appeared in Pacific Giant Oyster Rivera et al. 2007). The results indicate South S.F. Bay in the early 1990s and that local eradication may be feasible. Also known as the Japanese or has spread north at least as far as the Miyagi oyster, Crassostrea gigas is the . Salinity limits the MORE INFO? most common oyster species grown crab’s distribution: crabs have been [email protected] commercially on the West Coast. collected from water ranging from Chinese Mitten Crab Farmed in and Drakes 5-31 parts per thousand (ppt) salt Estero, it was not detected in San to water, but few have been col- The Chinese mitten crab (Eriocheir Francisco Bay until 2004. In a 2006 lected from water with less than 10 sinensis) population rapidly increased survey by SFEI’s Biological Invasions ppt. A 10-year study in Bodega Bay after it was first reported in the San Program, over 260 were collected found that in contrast to their slow Francisco Estuary in the early 1990s. between the Dumbarton Bridge and growth rates in Europe, green crabs Numbers of downstream migrating the San Leandro Marina. No new sites here grew rapidly and reached sexual adult crabs peaked at the USBR fish were detected in the 2007 survey. maturity in their first year. Over the facility in the south Delta in 1998 and Several possible sources for the popula- tion have been suggested, USBR including an illegal planting MITTEN CRAB STATUS CDFG near San Rafael, larvae 1000000 6 drifting in from rearing 100000 5 sites or arriving in ballast

water, and three RMP h 10000 4 programs that used this tc 1000 3 species in bioaccumula- CDFG CPUE USBR Ca tion studies. Although they (thousands) 100 2 had previously spawned 10 1 in the Bay, these oysters had not settled in at an 1 0 05 effective rate until recently. 96 97 98 99 00 01 02 03 04 06 07 Year The higher phytoplankton concentrations reported Total catch of adult mitten crabs at BurRec’s fish facility (bars) and catch per unit effort (CPUE) of in the South Bay in recent adult mitten crabs from Cal Fish & Game’s S.F. Bay Study otter trawl survey (line), 1996-2007. A Greener Shade of Blue? 27 AL TA I V

1999, in northern Bay (Central Bay to May 1999, about a year after more the western Delta) trawls in 1998 and than a million trout were planted S C I T S I TAT S 2001, and in Suisun Marsh trawls in and the lake had reopened, the pike 1999. All data sources support a popu- reappeared, possibly intentionally lation decline since 2002, with only a reintroduced. With CALFED funding, few crabs reported in the northern control efforts resumed. Biologists had portion of the Estuary, including the pulled approximately 55,000 pike from Delta, in 2006 and none in 2007. the lake by September 2005. During U.S. Fish & Wildlife Service the summer of 2007, approximately monitoring for juvenile mitten crabs in 2,000 pike were electrofished from Delta tributaries detected no mitten the creeks feeding the lake. This was crabs in 2006 and 2007. No reports followed in September by a second of mitten crab sightings or bait steal- Rotenone treatment, during which the ing were made by the public to the tributary creeks were screened off. Ecological Reserve, West , toll-free reporting line in either 2006 Drinking water for the city of Portola, and Sears Point. Nearly 300 other or 2007. When numbers are low, the which now uses wells and springs, projects to protect and restore wet- mitten crab’s only detectable impact is was not affected. Nearly 50,000 lands and riparian habitats are also in stealing bait from sport anglers in the pounds of dead fish were removed progress. SFBJV’s habitat goals call for Delta and Suisun and San Pablo Bays. from the lake following treatment, of the acquisition of 63,000 acres of Bay What controls mitten crab popula- which over 80% were bullhead and habitat, 37,000 acres of seasonal wet- tion in the Estuary is not understood, about 6% were pike (Sacramento land, and 7,000 acres of creeks and although winter temperatures and Bee 2007). Water quality sampling by lakes, to be followed in most cases by outflow are hypothesized to control the California Department of Public restoration or enhancement. survival and growth of larvae and tim- Health through December failed to The Central Valley Joint Venture ing of juvenile settlement. Since larvae detect Rotenone and its breakdown updated its Implementation Plan in hatch in winter in the lower Estuary product. Restocking with trout began 2006, enlarging its previous focus on and have no retention mechanisms, in December and will continue in the waterfowl by adding objectives for winter ocean conditions may control spring of 2008. DFG is also working shorebirds, non-game waterbirds, and larval survival in addition to Estuary with community leaders to prevent riparian songbirds. conditions. A “boom-and-bust” cycle another reintroduction, a criminal of- The South Bay Salt Ponds Restora- has been reported for some intro- fense with penalties including a fine of tion project, affecting 16,000 acres of duced species, although this may not up to $50,000 and up to a year in jail. former Cargill Salt property, has com- be universally true for all introductions. For current status, visit http://www.dfg. pleted its Initial Stewardship Plan and MORE INFO? ca.gov/lakedavis. is moving to implement Phase 1. This [email protected] MORE INFO? will entail six projects totaling 2,800 [email protected] acres in the Eden Landing, Alviso, and Northern Pike Ravenswood areas, with the breaching of pond levees to restore tidal marsh The voracious Northern pike Wetlands & Wildlife habitat and the reconfiguration of (Esox lucius), native to Canada and existing managed ponds. Elsewhere the Midwest, was illegally planted Wetlands in the South Bay, restoration of the in the 85,000-acre-foot Lake Davis 1,500-acre site began reservoir in the early 1990s. In 1997, Current efforts by San Francisco in July 2007. The California Coastal the California Department of Fish and Bay Joint Venture (SFBJV) partners Commission provided $1.5 million Game treated the lake with Rotenone include restoration projects for the for restoration of seasonal wetlands to eradicate pike from the lake. The South Bay salt ponds, Petaluma and at the Berkeley Meadows and the pike were significant predators on Triangle marshes, Simmons Slough, cleanup of the nearby Brickyard, both rainbow trout and also presented a Pacheco Marsh, Hamilton Air Force in Eastshore State Park. potential threat to the Delta ecosys- Base–Bel Marin Keys, Napa-Sonoma Several North Bay restoration tem. The treatment temporarily shut Marshes, Cullinan Ranch, Napa River projects also moved forward. At the the lake to all recreational uses and Flood Control Project, American Hamilton Wetlands site, the US Army compromised local water supplies. In Canyon, Dutch Slough, Eden Landing Corps of Engineers began pumping 28 State Of The Estuary 2008 AL TA I V

sediment from nearby Bel Marin Keys Suisun Thistle Despite these encouraging results, A S C I T S I TAT S onto the 700-acre former airfield in major threats to the short and long April 2007. Following a judicial ruling term viability were observed, includ- against further dredging, Marin Audu- ing 1) the pernicious and invasive bon is soliciting bids for the restora- perennial pepperweed (Lepidium tion project while awaiting permits latifolium; associated with 85% of from the Corps of Engineers and the subpopulations); 2) presence of a City of Novato for the first phase non-native, phytophagous, biocontrol of restoration of the Bahia Wetland. weevil (Rhinocyllus conicus, capable Marin Audubon has also completed of reducing seed set by 86% in other work at Triangle Marsh and breached Cirsium species); 3) habitat destruction a levee at Petaluma Marsh. by feral pigs (Sus scrofa, damaged 34% A final Environmental Impact of subpopulations); and, 4) potential Report for another former Cargill hybridization with another non-native Suisun thistle (Cirsium hydrophilum property, the Napa Plant Site on the congener (Cirsium vulgare, co-oc- var. hydrophilum) is an herbaceous, Napa River, was issued in 2006. A final curred with 45% of subpopulations). short-lived perennial restricted to preliminary plan for Cullinan Ranch As a consequence of both natural moist or wet habitats of the Estuary, was released in February 2007, calling and human influences, the remaining specifically salt and brackish marshes for tidal marsh restoration south of tidal marshes of the Estuary are both of the Suisun Marsh ecosystem. the railroad line and enhancement degraded and threatened. Current Presumed extinct until it was redis- of seasonal wetlands north of it. In restoration efforts targeting habitat covered on in 1989, it Suisun Marsh, 507 acres of diked improvement for Suisun thistle and was federally listed as endangered in seasonal wetlands near Hill Slough are reducing threats to its persistence are 1997 due to its narrow distribution, being restored to tidal habitat. in the planning stages, pending funding low population numbers, and threats Over the last decade, state and for Rush Ranch to develop various to its existence (i.e., altered hydrol- federal agencies have spent $370.5 conceptual restoration plans. Suisun ogy, competition from native and million to acquire and/or begin res- thistle populations currently are pro- non-native plants, seed predation by toration on 13 sites totaling 36,176 tected at Grizzly Island Wildlife Area, both the thistle weevil, Rhinocyllus acres. A 2007 report by Save the Bay Peytonia Slough Ecological Reserve, conicus, and larvae of the butterfly, proposed investing $1.43 billion to and Rush Ranch. Phyciodes mylitta). restore an additional 36,000 acres of Prior to extensive surveys at Rush MORE INFO? wetlands, doubling the extent of San Ranch in 2003, Suisun thistle was [email protected] Francisco Bay’s tidal marsh. known to exist at three locations: For a comprehensive list of wet- less then 10 plants at Grizzly Island Wildlife land restoration projects that have Wildlife Area, less than 100 plants at been implemented around the Bay, Peytonia Slough Ecological Reserve, California Red-Legged Frog see the database and maps compiled and 2,000 to 3,000 plants at Rush by Wetlands and Water Resources Ranch. 2003 surveys across the 1,050 (www.swampthing.org). For wetlands acres of high marsh at Rush Ranch creation, restoration, mitigation, and demonstrated a distribution that far enhancement projects, see the San exceeded previous estimates; a total Francisco Estuary Institute’s Wetland of 47 subpopulations were mapped Project Tracker (www.wrmp.org/proj- with a total geographic extent of 8.55 ectsintro.html), San Francisco Bay Joint acres, all of which belong to a large, Venture (http://www.sfBay.jv.org/), and single population of approximately Central Valley Joint Venture (http:// 137,500 (22,300 – 873,200) individu- www.centralvalleyjointventure.org). The once-abundant California als. Preliminary size class distribution For information about restoration of red-legged frog (Rana aurora dray- data suggested that recruitment of the Cargill property, see http://www. tonii) federally listed as threatened, new individuals likely was sufficient to southBayrestoration.org/. has disappeared from approximately maintain the population size. 70% of its historical range. It is now A Greener Shade of Blue? 29 AL TA I V

found only in coastal wetland areas Greater and Lesser Scaup western lesser scaup since the 1980s and freshwater streams from Marin (Anteau and Afton 2004). Poor spring S C I T S I TAT S County south to Ventura and in scat- condition may result from declining tered streams in the Sierra Nevada. habitat quality and reduced prey base Range-wide, only four populations at migratory stopover sites. contain more than 350 adults. Contaminants are also a concern. Habitat loss, stream sedimentation, Both greater and lesser scaup in pesticides, and predation all threaten San Francisco Bay continue to show the frog, the largest native to the high selenium concentrations, above western United States. In spring levels known to cause reproductive 2004, the U.S. Fish & Wildlife Service problems in female mallards. Because renewed a proposal to declare of their feeding habits, lesser scaup The greater scaup (Aythya marila) 4.1 million acres across California, may have greater selenium exposure: and lesser scaup (A. affinis) are blue- including parts of the Bay Area, as overbite clams (Corbula amurensis), billed diving ducks that nest in interior critical habitat for the frog. Follow- which bioaccumulate selenium, form a wetlands and northern boreal forests, ing litigation, the Service issued a higher proportion of their winter diet and winter in coastal waters including revised proposal in November 2005 in Bay waters. Greater scaup have a the San Francisco Estuary. The two that eliminated 82% of the area in more varied diet, including other mol- species are impossible to distinguish in the original proposal, including many lusks and amphipods. aerial surveys, so data for both scaup of the core areas delineated in the Changes on the breeding grounds are combined in U.S. Fish & Wildlife 2002 recovery plan. In the Bay Area, may also be contributing to the less- Service and US Geological Survey the new proposal eliminates almost er’s decline. A recent study (Corco- reports. About 45% of scaup in the all critical habitat in eastern Contra ran et al 2005) found low duckling lower Pacific Flyway winter in the San Costa County based on a habitat survival in Alaska’s Yukon Flats, which Francisco Bay. Greater scaup may be conservation plan. The revision also lost 18% of its wetland area between more abundant on the Bay itself, and exempts routine ranching activities 1952 and 2000. Lesser scaup nesting appear to have been more impacted on private land from federal cover- on small wetlands and creeks may be by the Cosco Busan spill. Lesser scaup age. In 2007, the Service announced hardest hit. use salt ponds as winter habitat more it will reverse the final critical habitat than greater. MORE INFO? decision for the red-legged frog as Midwinter Waterfowl Survey [email protected] well as rulings that denied six other estimates for San Francisco Bay scaup endangered species increased pro- have held largely steady since the Northern Harrier tection, after an investigation found 1950s. This database may not capture the actions were tainted by politi- trends in lesser scaup, many of which cal pressure from a former senior appear to move out of the Bay and Interior Department official. Also in into the Delta and Central Valley by 2005, a court decision required the early January when the survey takes Environmental Protection Agency to place. Continent-wide, scaup popula- consult with U.S. Fish & Wildlife on tions have been declining steadily. Af- the registration of 66 pesticides with ton and Anderson (2001) report this potential impacts on the frog, and trend may be largely due to reduc- imposed interim restrictions on the tions in the lesser scaup population. use of these 66 pesticides in core One hypothesis suggests that frog habitats around the Bay Area female lesser scaup are arriving on and California. their northern breeding grounds in MORE INFO? poorer physical condition. They may A long-winged hawk of open [email protected] forego nesting or may nest later in country, the northern harrier the season than usual, with reduced (Circus cyaneus) occurs in the Bay- nestling survival. This is supported by Delta region as a spring breeding studies showing declines in body mass species, winter visitor, and migrant. and reserves in northbound Mid- Atypically for hawks, northern har- 30 State Of The Estuary 2008 AL TA I V

riers are polygamous; males may suggesting the need to remove linear estimate may be an average density A S C I T S I TAT S have two to five mates. Territorial features from plover nesting ponds of 2.13 birds/hectare in high value males court females with a spec- (Tucci et al 2007). habitat (Evens and Nur 2002). Key tacular sky-dancing display. Harriers MORE INFO? predictive factors in black rail distribu- are also unusual in that they nest on [email protected] tion are vegetation height, absence the ground. Their prey base consists of amphipods (indicators of lower largely of rodents, especially voles California Black Rail elevation marsh), and, in San Pablo (Microtus); birds, mainly passerines and Bay, presence of Frankenia (an indica- small waterbirds; reptiles; and frogs. A tor of high-elevation marsh habitat) harrier’s owl-like facial ruff enables it (Evens et al. 1986). Other contrib- to locate concealed prey by acoustical uting variables include: marsh size cues alone. (rail abundance tended to increase A California Species of Special as the size of the marsh increased); concern, northern harriers are marsh distribution (the distributional dependent on declining wetland and relationship of each marsh to other upland grassland habitats. Requiring marshes likely influences rail presence ground nest sites safe from humans and abundance); marsh configuration and predators, they are vulnerable to (broader marshes tended to sup- development and recreational use of port rails in higher abundance than these environments. Locally, data from Tidal marshlands of the S.F. Bay linear marshes); predator populations the Raptor Observatory region supports the preponderance (sites bounded by levees or riprap of the California black rail ( shows an increase in harriers migrat- Laterallus provide access and habitat to mam- ing through the Marin Headlands jamaicensis coturniculus) population malian predators); hydrological cycles since 1996. From an earlier average of in the western United States (Evens (tidal marshes with full tidal influence 0.2 hawks per hour, the harrier count et al. 1991, Evens and Nur 2002). provide the best habitat for rails); and has risen to 1.5 hawks per hour in State listed as threatened, breeding fluctuations in water level (inundation recent years. This may reflect either black rails are confined mostly to above a certain depth may exclude prey population cycles or a distemper remnants of historic tidal marshlands habitat to black rails). Threats to black epidemic in the 1990s that eliminated in the Estuary’s northern reaches, rail populations within San Francisco gray foxes and other mammalian primarily those associated with San Bay include loss of refugial habitat competitors for rodent prey (Fish Pablo and Suisun Bays (Manolis 1978, along the marsh upland edge, habitat 2008, pers. comm.). Trulio and Evens 2000, Evens and loss due to rising sea level, predation, Nur 2002). Black rails occur in the Banding records and radiotrack- and contamination. South Bay as well, but mostly during ing studies indicate a very sedentary winter, and with breeding limited to MORE INFO? Bay-Delta harrier population that very few locations (e.g., Dumbarton [email protected] ranges from the coast to the Sacra- Marsh). Small numbers have also mento River and from Petaluma to California Clapper Rail been discovered recently in small Alviso. They are joined in winter by wetlands in the Sierra foothills and at migrants from the far north. One a few isolated marshes in the Delta harrier banded on Whidbey Island in (Ainger et al. 1995). A 1996 study Washington was recovered two years estimated approximately 14,500 black later in Petaluma. rails in the entire S.F. Bay system, with Ironically, northern harriers have approximately 7,200 black rails in the been identified as a key predator of San Pablo Bay system and a similar western snowy plovers in the South number in and Carquinez San Francisco Bay salt ponds, respon- Strait (Evens and Nur 2002). Be sible for record high nest depredation - in 2006, and the species has been cause detection probability is based on a statistical model, and there are added to the avian predator manage- many factors that may bias estimates, ment program. Harriers in the South the true number may be substan Bay were observed hunting along - Although small satellite populations levees as well as over marsh habitats, tially higher or lower; a more reliable of the California clapper rail (Rallus A Greener Shade of Blue? 31 AL TA I V

longirostris obsoletus historically oc- that have been invaded by non-native birds in California and less than 50 curred in tidal marshes along the out- Spartina alterniflora. At Central Bay birds in Oregon and Washington). In S C I T S I TAT S er coast, (Tomales Bay, Bolinas Lagoon, locations such as April 2006 the Bush administration ), the entire population and San Bruno Marsh, there appears issued a proposed regulation to allow is now restricted to San Francisco to be strong association between counties unlimited “take” of all plovers Bay. The population estimates within increase in vegetation cover provided over the county’s recovery goal, the Bay have fluctuated widely over by Spartina alterniflora and increase in primarily from development and the last four decades. In the 1970s clapper rail densities. off-road vehicle impacts. Since some Gill (1979) estimated 4,200-6,000 MORE INFO? counties are already over their recov- birds within the Bay. By the 1980s, the [email protected] ery goal, this plan will likely cause a population had plummeted to a low decline in the total plover population of 300-500 individuals. In the 1990s Western Snowy Plover in the short-term. It may produce a clapper rail numbers were estimated slight increase in the long-term, but is at 1,040 to 1,264, with up to 564 in very unlikely to ever actually recover Suisun and San Pablo Bays (1992-93 the species. The recovery plan also data) and up to 700 in South San relies heavily on volunteer activity and Francisco Bay (1997-98 data). The voluntary cooperation of county and results of more recent Bay-wide state agencies, rather than provid- surveys, 2004 to 2007, are not yet ing adequate funding for recovery available, but the consensus among or regulatory protections. While the rail researchers is that numbers have Bay did not historically support 500 remained stable or increased some- snowy plovers, managing salt evapora- what over the last decade, especially In the Bay Area, the federally tion ponds for plovers is an opportu- in the South Bay. It is clear, however, threatened Pacific Coast western nity for it to play a significant role in snowy plover ( that there have been shifts in distri- Charadrius alexandrinus the recovery of this species, especially bution among the disparate habitat nivosus) is primarily associated with because many of the plover’s his- parcels available within the Bay. The commercial salt evaporation ponds toric coastal breeding and wintering recent multiyear study (2005) found and levees, which means that land sites have been degraded by human that the species had declined or managers have not to date been able disturbance and urban development. been extirpated in some areas of the to actively manage habitat or re- Off-leash dogs also pose a significant North Bay since the early 1990s. In sources for this species. However, the threat to snowy plovers at coastal 2005, no clapper rails were detected recent purchase of more than 15,000 breeding sites. Snowy plovers were at any of the nine Suisun Bay sites, acres of salt ponds in south S.F. Bay among the bird species killed by the by U.S. Fish & Wildlife and Cal Fish & or at the mouth of November 2007 oil spill in San Fran- Game could aid in plover recovery. where the previous survey found ap- cisco Bay. Future pond management will include proximately 25 individuals. However, Based on surveys in May 2006, the managing several of these ponds as in 2007 rails were again detected breeding population for San Francisco plover nesting and foraging habitat, as at those San Pablo Bay sites, but in Bay was estimated as 99, a decline well as conducting predator control lower numbers than in the 1990s. Two from 124 in 2005. Hatching success and minimizing human disturbance. former low-density sites, Richardson at two South Bay sites was estimated These actions are outlined in Fish & Bay and Point Pinole, also had no as 85% in 2005 and 5% in 2006. The Wildlife’s 2007 final recovery plan for detectable rails in 2005, but low- decrease was attributed to high nest the plover, which calls for increasing numbers were detected in 2006/7. predation rates at the Eden Landing the S.F. Bay breeding population from The population at White Slough near Ecological Reserve. Common ravens, its current level of 150-200 individu Vallejo also showed a sharp decline - northern harriers, and California gulls in 2004/5 but a modest rebound in als to 500. The recovery plan sets a were the predominant nest predators 2006/7. The causes of these declines low bar for recovery and delisting of (Robinson et al 2007). the species (delisting would occur and rebounds are unclear, although MORE INFO? predation by the non-native red fox when 3,000 breeding plovers are maintained over a 10 year period— [email protected] has been a contributing factor. Num- after an increase of only 510 adult bers have increased in some sites 32 State Of The Estuary 2008 AL TA I V

California Least Tern plover colony, was discovered last endangered subspecies has suffered A S C I T S I TAT S year in Solano County, Suisun Marsh. from loss of habitat and from brood In 2007, Montezuma Slough biologists parasitism by the brown-headed observed 32 breeding pairs and at cowbird, a relative newcomer to least 5 fledglings. Hayward Regional California. Unlike songbirds that Shoreline, approximately 20 km south co-evolved with cowbirds, the vireo of Alameda Point, had terns for a third lacks an effective nest defense. Female year in a row with 35 breeding pairs cowbirds destroy or eject the hosts’ that produced 49 fledglings. For the own eggs and replace them with their first time, least terns were observed own, leaving the victims to raise a nesting at Eden Landing, located clutch of cowbirds rather than vireos. just south of Highway 92 on the By the time the least Bell’s vireo was east shore of San Francisco Bay. Six federally listed in 1986, the California nesting attempts were observed, but population had fallen to 300 breeding California least terns (Sternula antil- no fledglings produced. The Albany pairs, mostly in San Diego County. larum browni), state and federally listed colony on CalTrans property has not With effective cowbird control as endangered, continue to nest at hosted least terns since 2001 and and riparian restoration, the vireo Alameda Point, formerly the Naval Air CalTrans has stopped monitoring this began to regain portions of its lost Station Alameda. The Alameda Point area indefinitely. Pittsburg Power Plant range. Appropriate nesting habitat California least tern colony represents reported to the California Depart- had been created at the San Joaquin the largest California least tern colony ment of Fish and Game that there River refuge in a project coordinated in the San Francisco Bay Area. While were seven least tern nests on the by the U.S. Fish & Wildlife Service, disturbances from gulls and raptors property, but no chicks were ob- involving PRBO Conservation Science have increased, human disturbance served. Tern numbers have decreased and River Partners. In addition to wil- from trespassers has decreased to from 13 pairs in 2001 to 4 in 2005, lows and other streamside trees, River almost none. none of which were successful. Least Partners planted a herbaceous under- The number of tern pairs using the terns have abandoned the Oakland story of mugwort and other spe- base had been increasing each year, Airport as a breeding site probably cies to attract songbirds such as the until 2006. It is believed that some of due to predation by feral cats and yellow warbler. The second vireo nest these terns chose one of two more the non-native red fox (last reported (a presumed second brood attempt), recently established nesting sites close breeding attempt in 1995). discovered by PRBO Conservation by: Montezuma Slough, east of Suisun Science’s Julian Wood, was in an ar- Bay or Hayward Shoreline (EBRPD). MORE INFO? royo willow screened by mugwort. As in past breeding seasons, [email protected] In 2006, despite extensive flood- the number of successful fledglings ing on the refuge, the banded male continues to fluctuate. In 2006, 409 Least Bell’s Vireo vireo returned with a mate; three breeding pairs produced an average A small grayish neotropical migrant young were successfully fledged. But of 79 fledglings, a very poor season songbird, the least Bell’s vireo (Vireo no male was detected the following due to high avian predation pressure bellii pusillus) made national headlines year. A female vireo built a nest and and an inadequate food supply of in 2005 when a pair nested at the San laid 4 eggs, then abandoned the nest; chick-sized fish in the Bay. In contrast, Joaquin River National Wildlife Refuge, the eggs were apparently removed 2007 had 355 breeding pairs that apparently rearing two broods. The by a predator, and the female was not produced an average of 247 fledglings, birds were first detected by PRBO observed again. Intensive monitoring very close to the production in 2005 Conservation Science biologist will continue during the 2008 nesting with 260 fledglings from 424 breed- Linette Luna, who recognized the season. ing pairs, and down from the previous male’s distinctive song. This was the all-time high of 320 in 2001. Those first confirmed breeding record for MORE INFO? fledglings represented between 8 the San Joaquin Valley since 1919, and [email protected] and 18% of the state’s total fledgling an encouraging sign of the effective- population. ness of riparian restoration. Montezuma Slough, a new north Once common in riparian areas Bay least tern and western snowy throughout the Central Valley, the A Greener Shade of Blue? 33 AL TA I V

Salt Marsh Song Sparrows individuals; of Suisun song sparrows fairly stable over the past decade, and (Melospiza melodia maxillaris), found are estimated to be >600. Approxi- S C I T S I TAT S in Suisun Bay, from 43,000-66,000; mately 15 haul-out sites are known in and of San Pablo or Samuel’s song the Bay, with sporadic reports of ad- sparrows (Melospiza melodia samu- ditional sites being used. Harbor seals elis), found in San Pablo Bay, from are found in the greatest numbers 81,000-90,000. Population densities throughout the year at three sites: of the Alameda subspecies generally , , increased from 1996-2003, then de- and . Mowry Slough, still creased from 2003 to 2006. Surveys the largest pupping site in the Bay, is in the Hayward area in 2006 detected used predominantly during the pup- very low numbers. Density indices ping (mid-March-May) and molting for San Pablo and Suisun song spar- (June-mid-August) seasons. Since rows have been declining since the 2000, approximately 300 harbor seals Reproductive success of salt marsh late 1990s and reached historic lows and >100 pups have been counted at song sparrows has been increasing in 2006. The presence of salt marsh Mowry Slough each pupping season. slowly since 1998, which was the song sparrows is not strongly linked Monitoring of three haulouts on poorest year recorded to date. De- to any one, or even several, species of the Don Edwards San Francisco Bay spite this increase, the overall success plants, though the three subspecies of National Wildlife Refuge documents observed at most marshes (usually song sparrows do appear to respond a dramatic upward trend at Coyote only between 15% and 20% of nest- positively to gumplant and coyote Creek (Alviso) due to increased ing attempts result in any fledged brush and negatively to rush. Nev- pupping success (Buffa 2007). In the young) may be below the level neces- ertheless, the population density of winter (mid-November-mid-March) sary to ensure a stable population. song sparrows is well correlated with months, when Pacific herring (Clupea Reproductive success varies among landscape features. Density is great- pallasi) spawn in the Bay, the num- marshes, with landscape characteris- est where land adjacent to the marsh ber of seals at Yerba Buena Island tics (such as proximity to the water’s contains less urbanized areas and less increases to 200-300 harbor seals edge) being good predictors of nest agriculture and a greater extent of (1998-2004). Additionally, the number survival. The greatest cause of nest natural uplands. Conversely, density is of seals using Castro Rocks, a chain of failure is predation by both native lowest in small, isolated marshes. All rock clusters just south of the Rich- (gopher snake, northern harrier, com- three song sparrow subspecies are mond Bridge and the second-largest mon raven, American crow, raccoon, state Species of Special Concern. pupping site in the Bay, has increased river otter) and non-native (house greatly during the winter season since cat, red fox, Norway rat) predator MORE INFO? 2000, with a maximum of 300-600 species; rodents are likely the most [email protected]. seals recorded during recent years. common predator in most marshes. The increase in seals hauling out at In addition, about 10% of nests fail Harbor Seal Castro Rocks in the winter may be each year due to flooding during related to shifts or increases in her- the highest tides. Nesting success ring spawning closer to Castro Rocks. data for 2005 showed an unusually Castro Rocks is used by an average high rate (31%) at Pond 2A (San of 100 seals year-round (2000-2004). Pablo Bay) and lower success rates Seismic retrofit work began on the in other San Pablo Bay marshes, and Richmond Bridge in early 2001, and relatively high rates in Suisun Bay. In researchers from San Francisco State 2006, nesting success was extremely University monitored what effect the low at Benicia (Suisun Bay) due to construction had on seal numbers predation and at China Camp (San and behavior. Despite an early shift in Pablo Bay) due to flooding. Estimated site use to rocks located farther from numbers of breeding Alameda song the bridge when construction was sparrows (Melospiza melodia pusil- underway in the immediate area, and lula), restricted to Central and South San Francisco Bay harbor seal (Ph- an increase in disturbances due to S.F. Bays, range from 13,400-20,000 oca vitulina) numbers have remained construction activity; seals maintained 34 State Of The Estuary 2008 AL TA I V

use of the Castro Rocks haul-out site Salt Marsh Harvest Mouse tidal wetlands (Sustaita 2004). Other A S C I T S I TAT S for the duration of construction work recent studies in the Don Edwards (2001-2005). San Francisco Bay National Wildlife Contaminant levels in San Fran- Refuge have documented the effect of cisco Bay harbor seals have been a management activities on the southern concern since the 1990s. The authors subspecies (raviventris), documenting of a 2005 study reported that poly- that the mice colonize restored habitat chlorinated biphenyl (PCB) residues quickly and that translocation can be in harbor seal blood had decreased successful in augmenting low popula- during the past decade, but remained tion levels (Buffa 2007). at levels great enough that adverse MORE INFO? reproductive and immunological It is not known whether the [email protected] effects might be expected. They also population of the Bay’s endangered salt reported associations between PBDE marsh harvest mouse (Reithrodontomys Riparian Brush Rabbit (polybrominated diphenyl ether) con- raviventris) has changed significantly centrations, high leukocyte counts, and over the past three years. Population low red blood cell counts, suggest- studies are conducted only when ing that seals with high contaminant development projects or changes in burdens might be subject to increased land use threaten the mice, and few rates of infection and anemia (Neale such studies have been required during et al. 2005). An emerging contaminant this time. When such studies are con- found circulating in blood samples ducted, their piecemeal nature makes from harbor seals is perfluorooc- it difficult for scientists to get a take tane sulfanate (PFOS), a compound on overall population trends. Several used in a variety of stain-resistant marsh restoration projects that could and water repellent coatings. These Populations of the federally listed impact mice populations are underway chemicals have been detected in the (endangered) riparian brush rab- in the North Bay, and the South S.F. marine environment worldwide, but bit (Sylvilagus bachmani riparius) are Bay Marsh Restoration Project has preliminary work done by the Marine largely restricted to riparian habitat begun in the South Bay, but it will take Mammal Center’s Denise Greig in along the Stanislaus River in Caswell years to decades for new marshes collaboration with San Francisco Memorial State Park, the San Joaquin to be produced and hence increase Estuary Institute suggests that levels in River National Wildlife Refuge, and mouse populations. Meanwhile, recent seals from San Francisco Bay may be two small parcels of private land along surveys document that there is very two to three times higher than levels the San Joaquin River. The rabbits little mouse escape cover left in the reported in seals from the Baltic Sea were thought to be restricted to the South Bay, where what was once miles or Norwegian Arctic. habitat in Caswell until surveys discov- of high marsh vegetation has been ered the two additional populations MORE INFO? reduced to a maximum width of 8 to (one of which was recently found to [email protected] 9 feet or eliminated completely (Shell- be more extensive than first thought), [email protected] hammer, pers. comm. 2005). and a cooperative state/federal effort [email protected] Although the mouse has been began a breed-and-release program considered a pickleweed specialist, into the refuge. The numbers in research on its northern subspecies Caswell were extremely low in 2001, (calcoides) in Suisun Marsh indicates but rebounded slightly in 2002 and that mixed halophyte growth (rushes, 2003. The population remains too sedges, saltgrass, fat hen) is also used. small to allow population size estima- When tidal habitats were compared, tion tools to function properly, so the the percentage of females in repro- exact size of the Caswell population ductive condition was higher in the is not known. Efforts are underway mixed-halophyte zone than in pick- in the park to improve the habitat leweed. The study also found viable for rabbits, as well as for federally mouse populations in diked as well as listed (endangered) riparian wood A Greener Shade of Blue? 35 AL TA I V

rats (Neotoma fuscipes riparia). The • Propose for Board consideration

Delta and Upstream S C I T S I TAT S captive breeding program was begun Contaminants a comprehensive long-term in early 2002, with three male and Delta-wide monitoring program to three female rabbits released into Delta smelt and several other provide data on contaminants in an enclosed pen during the winter. pelagic fish species in the Bay-Delta sediment, water, and aquatic organ- isms. The monitoring program will The rabbits successfully bred, and 49 Estuary have experienced popula- be integrated with monitoring young rabbits were later released into tion declines in recent years. The already conducted by other groups natural riparian habitat at the refuge. Interagency Ecological Program (IEP) including the Interagency Ecological The program was expanded in 2003, determined that at least three general Program (IEP.) with two additional enclosures and factors might be acting individually or • Execute contracts to conduct 194 young rabbits released into the in concert to lower pelagic productiv- screening studies of potential refuge. Overall, since 2002 a total of ity: toxic contaminants, exotic species, inhibition of primary productivity 671 rabbits have been released from and water project operations. The and toxicity to fish associated with the captive breeding program into State and Regional Water Boards ambient ammonia concentrations the wild, another 62 are currently have authority over water pollu- and, if impairments are found, take scheduled for release once they have tion and water project operational appropriate regulatory controls to matured, and 204 wild-born rabbits requirements. protect beneficial uses. have been identified through the In December 2007 the State • Require characterizations of dis- ongoing studies. The rabbits are not Water Resources Control Board and charges to and from Delta Islands released into the wild until they are Central Valley Regional Board passed for water quality purposes. large enough to successfully survive joint resolution No. 2007-0079 to • Encourage the Department of the translocation. All rabbits are ensure protection of beneficial uses Pesticide Regulation (DPR) to screened by a veterinarian before and equitable administration of water expedite their pyrethroid pesticide being released. rights in the Bay-Delta and its tribu- re-registration process and provide Flooding in 2006 along the San taries. The San Francisco Bay Regional Agricultural Commissioners with Joaquin River inundated much of the Board adopted a similar resolution guidance on pesticide use restric- rabbits’ habitat, and was a setback (No. R2-2008-09) at their January tions that could be implemented for the program. Through an adap- 2008 Board meeting. Among other in the interim. The Water Boards tive management process, the federal, things the resolution committed Water will work with DPR and Delta state, and private entities involved have Board staff to prepare a strategic county Agricultural Commission- learned a great deal about the specific work plan for joint Board consider- ers to consider the feasibility of habitat needs in of the species, and ation. The plan will describe the scope special restrictions on pesticide use on Delta Islands and lands on the have worked extensively to create of individual pollution control actions, periphery of the Delta. the habitat structure needed by the relative priorities, timelines, and rabbit. The risks of flooding, wildfire, resources needed to carry them • Develop and implement regulatory and other events can never be entirely out. Some specific actions that will controls in coordination with the eliminated, but actions such as the be addressed by the Strategic plan State Lands Commission and the U.S. EPA to address the introduc- construction of higher elevation refugia include: tion of invasive species in ballast (“bunny mounds”), revegetation of • Execute a contract to compile and water and hull biofouling. burned areas, and riparian restoration assess available data on contami- • Take the following actions to de- are helping to alleviate the nant concentrations and toxicity velop or implement TMDLs (Total facing the species. as measured in bioassays for all Daily Maximum Load) or other monitoring programs in the Delta MORE INFO? actions addressing water quality during the last 5 years to deter- [email protected] impairments. mine whether contaminants are a likely contributor to the pelagic o To implement the organo- organism decline or are impacting phosphate (OP) pesticide aquatic beneficial uses. Contractor TMDL, the Water Boards will will also provide recommenda- require management plans tions on integrating and improving to address exceedances of ongoing monitoring. OP pesticide water quality objectives in discharges and 36 State Of The Estuary 2008 AL TA I V

evaluate water quality impacts The forecast for PCBs and dioxins

A S C I T S I TAT S Bay Contaminants from replacement products, is for slow progress toward recovery such as pyrethroid pesticides. The Bay contains a complex soup over the next 20 years, with concen- o The Water Boards will con- of pollutants that vary in the severity trations likely to remain above risk tinue to negotiate a manage- and types of risks they pose, and in thresholds. The outlook for mercury ment agency agreement with their sources, spatial distributions, and is unclear, and depends on whether the U.S. Bureau of Reclama- trends over time. Enforcement of the effective management actions can be tion to implement a real-time Clean Water Act and other environ- identified and implemented. For exotic salinity management program mental laws over the past 35 years species, the rate of introductions could by August 2008 as required by has resulted in tremendous improve- be reduced significantly through the San Joaquin River salt and ments in overall Bay water quality, management actions. The future looks boron TMDL. solving serious problems related to brighter for other pollutants (selenium, o The Water Boards will devel- organic waste, nutrients, and silver PAHs, and legacy pesticides) whose op and adopt salt and boron contamination. Contamination due concentrations do not exceed risk water quality objectives in the to toxic chemicals in general has also thresholds by much or at all, or it is not San Joaquin River upstream declined since the 1950s and 1960s. entirely clear if they pose significant of Vernalis and an associated Several significant water quality risks in the Bay at present concentra- TMDL. threats remain, however, including tions. Concentrations of selenium and o The Water Boards will de- mercury, PCBs, dioxins, and exotic PAHs could fall below risk thresholds velop and adopt a selenium species. A fish consumption advisory in 20 years depending on manage- TMDL for the Delta and remains in effect due to concentra- ment of sources. For legacy pesticides, northern San Francisco Bay. tions of mercury, PCBs, dioxins, and concentrations should fall below risk o The Water Boards will adopt organochlorine pesticides of potential thresholds in 20 years through natural a TMDL for mercury in the human health concern in Bay sport breakdown, with lingering concerns Delta and begin implementa- fish. A duck consumption advisory is only for effects in combination with tion along with the existing also in effect due to selenium con- other pollutants. For nickel and copper, TMDL for mercury in San centrations of potential human health concentrations are below thresholds Francisco Bay. concern. There are also indications and management plans are in place to o Pathogen counts in a number that current levels of contamination make sure they stay there. of Delta waterways in the are harming the health of some wild- Concern for another group of City of Stockton urban area life species. Mercury concentrations pollutants is growing, due to either exceed applicable numerical are high enough to reduce the hatch- increasing rates of input into the Bay criteria. In March 2008, the or advances in scientific understand- Central Valley Regional Board ing rate of Forster’s terns, and also approved a pathogen TMDL appear to be high enough to cause ing of the magnitude of specific for these waterways. embryo mortality in clapper rails, an water quality threats. For PBDEs and endangered species found in Bay tidal pyrethroids the 20-year outlook is The U.S. EPA approved the marshes. PCB concentrations may be currently unclear, and will depend Basin Plan amendment for control of high enough to also cause low rates heavily upon management decisions. mercury in Cache Creek in February of embryo mortality in Bay birds and Concentrations of both of these pol- 2007, the nutrient Basin Plan amend- to affect immune response in harbor lutants would be expected to drop ment for Clearlake in July 2007, and seals. Selenium concentrations appear rapidly in response to reduced inputs the OP pesticide Basin Plan amend- to be high enough to cause abnor- to the Bay. If use of these chemicals ment for the Delta in October 2007. malities in early life stages of Sacra- is curtailed, the Regional Monitoring The Sacramento-Feather River OP mento splittail and white sturgeon. Program (RMP) should be looking pesticide Basin Plan amendment was Pollutant mixtures appear to similarly ahead to evaluate the risks associated readopted for diazinon in May 2007. affect early life stages of striped bass. with the next generation of flame-re- The OP amendment now includes Assessments of benthic communities tardants and insecticides, which hope- water quality objectives for chlorpyrifos. in the Bay indicate that some areas fully will be less of a threat to Bay wa- MORE INFO? may be impacted by pollutants. The ter quality. The outlook for sediment [email protected] frequent occurrence of sediment tox- toxicity will be unclear until the causes icity is another indicator of pollutant of this toxicity can be identified. Too impacts in Estuary sediments. many unknowns surround the issue A Greener Shade of Blue? 37 AL TA I V

of risks due to pollutant mixtures to Surf scoters accounted for 36% of persistence of bunker oil, although characterize current status, much less birds found alive, 20% of birds found it has been shown to damage the S C I T S I TAT S the status in 20 years. dead, and 26% of all birds collected. reproductive systems of laboratory Progress is being made on cleanup Significant numbers of Clark’s mink. Bunker oil varies chemically plans (TMDLs) for pollutants of con- grebes, horned grebes, western gulls, from batch to batch, so generaliza- cern in the Bay. The San Francisco Bay northern fulmars, double-crested tion is difficult. One study found that Regional Water Board has completed cormorants, and ruddy ducks were major oil spills in western Europe TMDL projects addressing mercury also collected. Except for the gull and doubled the winter mortality of com- in the Bay, pesticides in urban creeks, fulmar, all these birds forage by diving mon murres whether the culprit was and pathogens in several Bay tribu- from the surface of the water. Grebes, crude or bunker oil. taries. TMDL projects are scheduled cormorants, and murres are fish-eat- Endangered species affected by for completion in 2008 for PCBs in ers, while the three ducks eat benthic the spill include marbled murrelet, the Bay, pathogens in Richardson Bay, mollusks and other aquatic inverte- western snowy plover, and brown nutrients in Napa River and Sonoma brates. Other foraging guilds—for pelican. Several Important Bird Areas, Creek, and sediment in Sonoma example, plunge-divers like terns and including Richardson Bay, East Shore Creek. Other TMDL projects are pelicans—appear to have been less Wetlands, and Brooks Island were planned for selenium and legacy pes- affected. impacted; Brooks Island’s breeding ticides in the Bay. Information on TM- Caspian terns were not home. DLs is available at: www.waterboards. UC Davis researchers headed by ca.gov/sanfransciscoBay/tmdlmain.htm. Michael Ziccardi and Greg Massey are Continued monitoring and advanc- using the catastrophe to learn more es in scientific understanding will be about care and survival of oiled birds. essential in refining the forecasts for They have analyzed blood samples to the Bay’s assortment of pollutants of determine the best predictors of sur- concern, and in tracking the response vival and clarify the causes of anemia of the ecosystem to management in spill victims, and studied infrared actions taken to continue the general scans as indicators of waterproofing. trend toward improvement of Bay A group of surf scoters had radio water quality that has occurred over transmitters implanted so their travels the past several decades. and survivorship after release could be monitored. Two control groups More Info? Photo courtesy of U.S. Coast Guard. [email protected] were also radio-tagged for com- parison. There is little existing data on Cosco Busan Spill post-spill survivorship of rehabbed The surf scoter is one of the most waterfowl, most of it from hunters The Cosco Busan spill claimed the abundant birds in San Francisco Bay who report the bands of birds they lives of at least 45 species of birds, in fall and winter. But local Audubon have shot. According to IBRRC Ex- ranging from the pelagic northern Society Christmas Bird Counts report ecutive Director Jay Holcomb, bands fulmar and parasitic jaeger to the higher totals for greater scaup than from six of 175 ducks released after shorebound fox sparrow. Some were for scoter, along with substantial num- a spill on the Santa Clara River were hit harder than others. First impres - bers for ruddy duck and bufflehead. reported over a six-year period. sions that most of the oiled birds Location may account for some ap- Susan De La Cruz and other were surf scoters are supported parent patterns. Southern Marin had USGS biologists are also looking at by data from the International Bird the highest CBC numbers for western over-winter survival of oiled scoters Rescue Research Center. More surf grebe, which ranked second to surf compared to non-oiled birds in a scoters were collected alive than any scoter among spill victims; eared study with UC Davis, DFG, and Hum- other species, followed by western grebes, concentrated in the South Bay, boldt State. Effects on adult survival grebe, eared grebe, and greater scaup. had fewer spill casualties. in a species like surf scoters can have The scoters also headed the list of Other variables may include how long-term effects on the popula- species found dead, followed again by susceptible different species are to tion. Scoters are a long-lived sea western grebe, common murre, and bunker oil. Compared with crude oil, duck species with low reproductive Brandt’s cormorant. little is known about the toxicity and potential, and are particularly sensi- 38 State Of The Estuary 2008 AL TA I V

tive to changes in adult survival. Such A S C I T S I TAT S species may have the most difficulty recovering from oil spills (Samuels and Ladino 1984). Additionally, many sea ducks show high winter site fidelity and pair on wintering areas; thus, factors that affect survival rates in the Bay could have disproportion- ate effects on local subpopulations. Since San Francisco Bay supports an average of about 45% of the lower Pacific Flyway surf scoter, the numer- ous mortalities here could potentially impact the Pacific Coast population. De La Cruz and colleagues are also looking at differences in foraging behavior and movement patterns between oiled and control birds, to determine whether oil exposure has Photo courtesy of Ron Sullivan. influenced their physiology such that they are not foraging and/or using Estuary habitats in the same manner had been returned to oil-free shore- as non-oiled birds. lines in San Mateo and Marin Coun- There are also long-term, chronic ties. The IBRRC said 1,858 had been effects to be considered. Scoter and found dead in the field (939 visibly scaup may continue to be exposed oiled); another 653 had died or been to residual oil through their prey in euthanized at the rescue center. Many subsequent winters. Studies after the others may have sunk in the Bay or Exxon Valdez have shown that sea the ocean, or been eaten by preda- duck survival is lower in chronically tors and scavengers. If, as is likely, only exposed (nine years after the spill) one of every ten casualties is being individuals and that chronic oil expo- retrieved, deaths resulting from the sure affects shorebird reproduction. spill could exceed 22,000. In some cases, residual oil may Marine mammals appear to have influence the food scaup and sco- been less impacted. The deaths of two ters eat by eliminating or changing northern fur seals and a harbor seal dominant prey species, and thereby were attributed to the spill. changing the energy available to diving ducks. Changes in the amount and MORE INFO? type of prey available could poten- www.ibrcc.org/Cosco_Busan_ tially influence the number of birds spill_2007.htm; the Estuary can support over winter. www/vetmed.ucdavis.edu/owcr There are also indirect effects in which a change in some key organism in the system due to oil exposure can trigger a cascade of delayed long-term ecosystems effects (S. De La Cruz, pers. comm. 2008). A total of 1,084 oiled birds ware taken to the IBRRC’s Cordelia facility in the aftermath of the spill. As of January 2008, 421 rehabilitated birds A Greener Shade of Blue?

Important Changes I n t h e S tate of t h e E st u a r y 40 State Of The Estuary 2008 T T N RTA O P M I

in-Bay disposal of dredged sediments quality (such as nutrient loading) may The State of the by 50%. Over 9 million cubic yards improve locally, but loads of pesticides Estuary as Reflected has been “beneficially” re-used in and automobile-related contaminants

wetland and upland restoration proj- can be higher. When urbanization S E G N A H C in the 2007 CCMP ects, levee rehabilitation, and landfill displaces agriculture from prime THOMAS E. MUMLEY cover. Yet there are long-lived “legacy” farmland to marginal lands, water San Francisco Bay Regional Water contaminants that will take decades quality impacts increase on a regional Quality Control Board to clean up. And while we have come scale because marginal lands typically a long way in conserving water supply, require more fertilizers and have

The newly revised Comprehensive N I we need to do more, and to diversify steeper slopes and more erodible Conservation and Management Plan sources of supply and take regional soils, thus yielding more sediment.

E H T (2007 CCMP) of the San Francisco approaches to water management. With intense population growth Estuary Project is a reflection of One of our biggest challenges is pressure in urban areas, urban growth

the current state of the Estuary and A E TAT S land use—to better manage wa- has spilled into low-lying areas such provides a vision for the future of tersheds at local levels and multiple as the Sacramento-San Joaquin Delta. the Estuary. This is the first review watershed scales. And to address all Although the Delta Protection Act and revision of the original CCMP

of these issues, we must do a better has prevented urbanization of deeply- F O established in 1993. Over the past job of getting scientists and resource subsided central parts of the Delta,

two years, over 80 stakeholders re- managers to communicate, and a bet- outside of this core, thousands of E H T viewed the 1993 CCMP actions and ter job of educating the public about houses are now being built in deep accomplishments, identified current the Estuary. floodplains—lands that lie below sea

RY A U T S E and future challenges, revised 70 of MORE INFO? level or more than 10 feet below the the 145 actions, and developed 61 [email protected] level of the 100-year flood. Ironically, new actions. federal flood control policies con- Although much has been ac- spire with financial pressures on local complished, we still have far to go. jurisdictions to encourage develop- We have one of the best pollution ment on these deep floodplains. monitoring programs in the world in Watersheds and However, even if they are “protected” San Francisco Bay and TMDLs for salt, by 100-year levees, the residual risk of pesticides, oxygen, mercury, selenium, Land Use: Trends flooding from larger floods remains and PCBs. Yet new contaminants and Implications surprisingly high: more than 25% over are emerging all the time, including the life of a 30-year mortgage. The personal care products and pharma- for the Estuary water quality implications of levee ceuticals, and flame-retardants, some MATT KONDOLF failure and inundation of vast areas of which have been banned. Marine University of California, Berkeley of the Delta are sobering to con- debris is a huge problem in the Bay template. Management of the Delta and the ocean. The biggest change in land use in for water supply and ecosystem has We have made huge strides in northern California is urbanization: been hotly debated for over three restoring habitat for salmon on Battle, of upland watersheds from which decades, but options to address these Butte, and Deer Creeks, and also in runoff is generated, and of low-lying resources are rapidly being foreclosed wetlands acquisition and restora- lands that receive floodwaters from by uncontrolled urbanization. tion throughout the Estuary, yet we the watersheds. There is now greater MORE INFO? continue to lose seasonal and riparian awareness of the hydrologic effects [email protected] wetlands to poorly planned develop- of urbanization on watersheds, and ment. The Estuary remains a major stormwater management for new coastal wintering and migratory stop- urban developments has greatly im- over for waterfowl; yet mercury in the proved. Nonetheless, the rapid pace Bay food chain is contaminating some of continued urbanization tends to species of birds and their eggs, pos- counteract the reduction in impact sibly affecting reproduction. We have a of each new development. When Long Term Management Strategy for prime agricultural lands become ur- Dredged Materials that has reduced banized, some components of water A Greener Shade of Blue? 41 T T N RTA O P M I

and the state, diversification becomes temperature and precipitation effects Climate Adaptation increasingly important as the region’s are needed, as are better data on Strategies for Urban population continues to grow and stream flow and snow pack. Providing

supplies are stretched thinner. The for more regional coordination among Water Management Department of Water Resources land use agencies is necessary to meet S E G N A H C MICHAEL CARLIN California Water Plan involves meet- future growth and prepare for the ef- and SUSAN LEAL ing statewide goals for groundwater fects of global climate change. San Francisco Public Utilities development, water recycling, and MORE INFO? Commission conservation. Local urban water man- [email protected]

agement plans involve water agencies N I Historically, Bay Area water continuing to pursue local projects to management agencies have worked meet the state’s and their own supply E H T together on integrated water issues in diversification goals. San Francisco SFPUC EARLY an attempt to diversify water supplies, ADAPTATION TO CLIMATE Public Utilities Commission has its E TAT S reduce wastewater discharges, and own diversification plan that includes CHANGE STRATEGIES: protect the health of ecosystems. More investigation of potential options such • Develop local water supplies to recent integrated and regional water

as desalination and recycled water rely less on imported snow-depen- management initiatives include the use, as well as increased groundwater dent supplies. F O

Bay Area Integrated Regional Water use and conservation. The Bay Area • Explore desalination—the SFPUC E H T Management Plan, inter-ties among Bay Integrated Regional Water Manage- is part of the Bay Area Regional Area water agencies, recycled water ment Plan provides a regional context Desalination Project.

efforts, regional desalination projects, RY A U T S E for water supply diversification. • Diversify water sources, including and watershed management plans. As our understanding of the ef- the use of groundwater. While water supply diversification fects of global climate change evolves, • Use graywater to flush toilets. has been a goal of many water supply water, wastewater, and flood protec- agencies throughout the Bay Area tion agencies are faced with additional • Learn from other water agencies. challenges. Future • Engage ratepayers: In the summer challenges that of 2007, SFPUC customers were HETCH HETCHY RUNOFF: may need to be able to reduce water use by 12% BASE vs. 3ºF considered by wa- through voluntary conservation ter management measures. People can reduce their Median Inflow to Hetch Hetchy Reservoir agencies include water use, and continue to do so. 250 reduced snow Ba s e • Develop better science and techni-

200 3 De g Ad j pack, precipitation cal tools. and temperature 150 • Focus on adaptation while leading changes, localized in mitigation. 100 flooding, sea level • Strengthen communication with rise, and more regulatory agencies. 50 frequent droughts. 0 In San Francisco, • Interact with wastewater agencies. O c t N o v D e c J a n F e b M a r A p r M a y J u n J u l A u g S e p wastewater treat- • Provide opportunities to reduce ment facilities are wastewater and flooding while The black line shows the current runoff at risk from sea offsetting potable demand through pattern. The teal line shows the predict- level rise, and we will need to decide water recycling, stormwater capture. ed runoff pattern with a 3˚ Fahrenheit warming. The results in terms of water whether to move or protect them. • Support local/state regulatory supply are that peak runoff moves up 1 The effects of climate change reform that encourages new de- month; there will be less snowpack later inspire integrated urban water man- velopment standards that reduce in the season and reduced carryover storage at the end of the drawdown pe- agement and a renewed interest in resource needs. riod (May-October). The greatest danger reducing demand, diversifying water • Update local and state planning, to supply will be early runoff coupled supply, and changing the way com- plumbing and building codes to with below normal precipitation the following year. These effects will be com- munities are designed and developed. support the use of greywater, mon to all snow-fed systems in the West. More robust tools to understand stormwater, rainwater, and recycled water. 42 State Of The Estuary 2008 T T N RTA O P M I

Pollution Prevention and Reduction: TAKE HOME POINTS Familiar Foes and Emerging Enemies • We must have better lead-

S E G N A H C RICHARD E. LOOKER ership and more protective San Francisco Bay Regional Water Quality Control Board product legislation at the national and state levels. Water quality managers have had ents or degradation products. More- • Citizens need to be modest success over the last decade over, improved analytical techniques educated to not misuse or

abuse products that could N I in gaining an understanding of the allow us to detect the presence of sources of a number of pollutants, chemicals at very low concentrations result in the discharge of

E H T such as copper, fats/oils/grease, and so we know about the presence (in pollutants. some forms of mercury. In fact, water, sediments, and biota) of many • Local agencies must provide

A E TAT S because of long experience work- potential chemical , but we the “last line of defense” by ing on some of these issues, source may know very little of the conse- enacting appropriate poli- control has become routine and quent biological risk. These pollutants cies and through intelligent commonplace. However, even some of concern for which we do not design and operation of

F O commonplace pollutants (like trash) have enough historical monitoring wastewater and stormwater infrastructure.

continue to be serious water qual- information to assess trends and are E H T ity concerns. While new chemicals not captured within existing water and products usually benefit society, quality regulatory frameworks are

RY A U T S E there is almost always an associated called emerging contaminants. They to continue learning about the sourc- environmental impact. include polybrominated diphenyl es and pathways of both familiar and New products and chemicals ethers (PBDEs), used as flame-retar- emerging pollutants so that manag- enter the market at a very fast pace, dants in many consumer products, ers can develop and employ effective and there is not an infallible process and perfluorinated chemicals, used in control strategies. in place for determining the ultimate non-stick or stain-resistant coatings. MORE INFO? environmental fate of active ingredi- The challenge of the next decade is [email protected]

EVERYTHING vs. THE ENVIRONMENT

Pest Control/Nuisance on vs. Aquatic Toxicity Land and Water (Pesticides)

Preventing fires vs. PBDEs in our water, sediment, and (PBDEs) tissues, resulting in possible harm

Health and beauty vs. Endocrine disruption in wildlife and (Pharmaceuticals and possibly humans, other health effects personal care products) Economic health vs. Legacy Contamination (PCBs, Mercury)

Air quality vs. Groundwater contamination (MTBE) A Greener Shade of Blue? 43 T T N RTA O P M I

riparian habitats past and present, Wetlands: assess their status, track the progress Take Home Points Links Between of programs and projects designed to We need to “give way” to protect all wetlands, and set wetland • Watersheds and goals at the watershed scale. The the Bay. The Bay will continue S E G N A H C needed coordination among public to grow into local water- the Bay and private interests is possible with a sheds. JOSH COLLINS growing capacity to commonly visual- • Climate change will affect San Francisco Estuary Institute ize local wetlands and related projects local runoff and erosion

in the context of all the others in the (sediment and freshwater N I Much is being done to protect region, and to assess the effects of our supplies), not just sea level

wetlands around the Bay. The Baylands E H T cumulative efforts to assure healthy rise. Goals are being met by many efforts wetlands for the future. The devel- that are more adaptive, collaborative, • While we can’t manage sea

oping plans envision our lakes and level rise, we can manage E TAT S and better coordinated than ever streams, coastline and Bay, hillsides runoff and erosion. before. This will help us meet the and valleys, and the wetlands between challenge of protecting these lands, so • Given the uncertainties of

as one integrated circuitry of physi- the future, wetland protec- dangerously situated between rising F O cal and biological processes essential Bay waters and widening cities. Saving tion means going beyond

to our survival. And the vision has to static habitat goals with a set the Bay in the new world might mean E H T accommodate change. Given all of the of tools for simulating habitat doing things we’ve never done before, economic and ecological uncertain- response to land use and cli- like filling the Bay to give it places to ties before us, protecting ourselves mate change and for explor- RY A U T S E grow new marsh if the old washes requires forecasting the consequences ing alternative management away, or moving people out of the scenarios. of alternative plans. Watersheds are Bay’s way. But in the meantime, we natural templates for comprehensive • Watersheds are natural can’t neglect the other wetlands, the protection of the Bay, the Bay Area, templates for comprehensive ponds and wet meadows, springs and and the life they should support. protection of wetlands and seeps, and lakeshores and riparian ar- related habitats. eas that dot and cross the landscape MORE INFO? from the Bay’s shore to the ridge [email protected] tops. These wetlands help protect the Bay by providing nutrients, filtering pollutants, and lessening floods. They link the terrestrial and aquatic worlds together, sharing attributes of both worlds while being worlds unto them- selves. Most of the wildlife in the Bay Area relies on these wetlands, which have more indigenous biological diversity than any other habitat type. They are also the celebrated center- pieces of the local aesthetic. They are the shady creek, the song sparrow by the frog pond, the dragonflies on the lakeshore. And they are vulnerable to many of the same kinds of problems that threaten the Baylands: pollution, climate change, habitat fragmenta- tion. Protecting these wetlands will How far inland will the Bay shore migrate? The answer depends on the rate require no less effort than protecting of sea level rise (white arrows pointing inland), existing topography (the inland migration will be shorter in steeper areas), and the amount of sedi- the Baylands and the Bay. A regional ment provided by local watersheds (the outlined arrows pointing Bay-ward). approach is needed. New efforts are As the watersheds erode, they build new topography by raising streambeds, underway to map the wetlands and floodplains, and tidal marshes that slow the upstream migration of the Bay. 44 State Of The Estuary 2008 T T N RTA O P M I

Since then, the Long Term Man- ing maintaining staffing, funding, and From Spoils to agement Strategy (LTMS) for the the support of stakeholders. New Beneficial Reuse placement of dredged material in listings of sensitive species like the

the San Francisco Bay region was green sturgeon present ongoing chal- S E G N A H C STEVE GOLDBECK developed and implemented. Today lenges. The use of multiple reuse sites San Francisco Bay Conservation and we are halfway through the transition around the Bay must be coordinated. Development Commission to low in-Bay disposal volumes and Impacts of sand mining need to be BRIAN ROSS significant beneficial reuse. There is a assessed. Sea level rise and changes in U.S. Environmental Protection Agency designated deep-ocean disposal site. Bay sediment dynamics must be taken

N I The Sonoma Baylands project was into account. When the original CCMP was constructed using dredged material, MORE INFO? E H T signed in 1993, almost all dredged the Montezuma Wetlands project material was disposed of in the Bay. [email protected] is accepting material, the Hamilton

There were no multi-user ocean or

A E TAT S Wetlands project is coming online, upland disposal sites, and the main dis- and dredged sand is being used to posal site near Alcatraz was filling up. directly nourish Ocean Beach. There is Disposal in the Bay was highly contro- BENEFICIAL

a comprehensive testing program for RE-USE PROJECTS F O versial and opposed by fishermen and dredged material, and an interagency environmentalists; dredged material • Sonoma Baylands: 322 acres, Dredged Material Management Office E H T was widely considered to be useless, reused over 2.5 million cubic coordinates permit applications. The toxic spoil. There was little coordina- yards. LTMS agencies meet regularly with

RY A U T S E tion of permits, dredging projects stakeholders and support an ongoing • Carneros River Ranch (ag- were often delayed, and the Port of science program. Environmental work ricultural reuse): 540 acres, Oakland’s 42-foot deepening project reused 0.7 million cubic yards windows help protect sensitive spe- had taken 20 years to get underway, to date, 2 million cubic yard cies. The Port of Oakland completed with no dredging in sight. The Dredging capacity for ongoing reuse. its 42-foot project and is now dredg- and Waterway Modification section ing to 50 feet. • Middle Harbor Habitat Area of the CCMP called for actions to ad- Hurdles remain to completing the (subtidal habitat, including dress and resolve these issues. eelgrass): 180 acres, reused 6 transition to beneficial reuse, includ- million cubic yards. • Montezuma Wetlands: 1,800 THE PLAN: acres, capacity 12 million cu- bic yards; has already reused MINIMIZE IN-BAY DISPOSAL over 3 million cubic yards. MAXIMIZE BENEFICIAL REUSE • Hamilton Wetlands: 700+ 0 acres, capacity over 8 million In -B a y cubic yards, will have reused 8 0 O c e a n over 3 million cubic yards by the time the Oakland -50 7 0 U p la n d /R e u s e foot Deepening Project is

6 0 completed in 2008. • BMK “Unit V” will expand 5 0 Hamilton to 2,000+ acres, 25 million cubic yards capacity. 4 0 • Ocean Beach: ~1 million 3 0 cubic yards sand placed near shore for beach nourishment. 2 0 • South Bay Salt Ponds repre- 1 0 sent a potential for additional reuse opportunities in the 0 future. P re - LT MS LT MS A Greener Shade of Blue? 45

Quick Answers T N RTA O P M I

Change Mechanism? Population with POD? Impact? to court orders to limit water The Collapse of Stock Yes Yes Yes project operations, to forced re-consultations under the Pelagic Fishes in Habitat Yes Yes Yes

Endangered Species Act, and S E G N A H C the Upper San Food Some Yes Yes to heightened concern among many groups and agencies. This Francisco Estuary: Mortality Yes Yes Yes high level of concern has led An Update to intense scientific work in contaminants, disease, entrain-

TED SOMMER ET AL.

ment, habitat loss, trophic N I 1. Did anything change at the same California Department of effects of introduced species, and many time as the Pelagic Organism Water Resources E H T Decline? other factors. Although the pelagic fish commu- This broader ecosystem approach

2. How and why did these factors nity of the upper San Francisco Estu- in science is being reflected in real- E TAT S change? ary historically has showed substantial time operations and in the re-consul- variability, a recent collapse of pelagic 3. Did these factors affect popula- tations for water project operations. tions of pelagic organisms? fishes has captured the attention of Evidence suggests that sensitivity of F O resource managers, scientists, leg- Preliminary, unpublished results are these species involves year-round

conditions and a number of interact- islators, and the general public. The shown above. E H T consequences of the decline are most MORE INFO? ing, human-induced stressors. Fall serious for Delta smelt (Hypomesus Delta smelt habitat has shrunk and [email protected] transpacificus), a threatened spe- moved eastward. Flows in the Delta RY A U T S E cies whose relatively narrow range have stabilized, whereas they used to overlaps with large water diversions be variable in all but drought years. that supply water to over 25 million This may have helped the overbite people and a multi-billion dollar agri- claim to become established farther cultural industry. Other pelagic fishes The Collapse of upstream, and possibly contributed showing a similar decline include the Pelagic Fishes in to less nutritious phytoplankton, native longfin smelt (Spirinchus tha- particularly the spread of the toxic leichthys), and two introduced species, the San Francisco blue-green algae Microcystis. It is pos- striped bass (Morone saxatilis) and sible that the pelagic organism decline threadfin shad (Dorosoma petenense). Estuary: What Does could represent a tipping point from a The declines occurred despite recent the Future Hold? variable estuarine system to more of moderate hydrology, which typically a steady lake/lagoon system. results in at least modest recruitment, BRUCE HERBOLD ET AL. Simultaneous with the current and investments of hundreds of mil- U.S. Environmental Protection Agency concern for pelagic fish is widespread lions of dollars in habitat restoration In the early 1990s Delta smelt concern about the stability of the and environmental water allocations and winter-run salmon were listed structure of the Delta and the likely to support native fishes. Moreover, under the California and Federal impacts of climate change. Under the initial results suggest that fishes in Endangered Species acts. Biological governor’s direction this is leading to upstream, downstream, and littoral Opinions to protect these species grand re-envisioning of how this engi- habitats are not in a similar state of prompted the adoption of new water neered ecosystem will look in the fu- decline. In response to the pelagic fish quality standards. These regulatory ture. Short-term protective measures collapse, an ambitious multi-agency efforts focused on flow and habitat for pelagic fishes are being included in research team has been working since conditions in the Delta from February the work of several groups charged 2005 to evaluate the causes of the through June. These new regulations with determining the long-term needs decline, which likely include a combi- and other restoration efforts appear of the Delta. Understanding manage- nation of factors: stock-recruitment to have greatly benefited salmon. Rad- ment and protection of our native effects; a decline in habitat quality; ical declines in both Delta and longfin fish in the short-term is an essential increased mortality rates; and reduced smelt abundances in recent years led element in the future restoration of a food availability due to invasive spe- to petitions to list longfin smelt as sustainable Delta. cies. The three big questions questions threatened and to downgrade the MORE INFO? we are looking at are: status of Delta smelt to endangered, [email protected] 46 State Of The Estuary 2008 T T N RTA O P M I

Aquatic Invasive DON’T MOVE A MUSSEL! Species: Planning How do mussels hitch a ride?

S E G N A H C and Implementation By contaminating recreational watercraft and commercial haulers from infested waters: l Many Southern California freshwaters l Most waters east of the Continental Divide l Waters along the Colorado River drainage l Lake Mead, NV/AZ and waters it feeds SUSAN ELLIS and l All of the Great Lakes and their tributaries DOMINIQUE NORTON Don’t let them ruin your boat or California’s waters! California Department of Fish and Game When leaving the water: l Inspect all exposed surfaces - small mussels N I feel like sandpaper to the touch. Over the past five years, the Cali- l Wash the hull of each watercraft thoroughly.

E H T fornia Department of Fish and Game l Remove all plants and animal material. has worked with other agencies and l Drain all water and dry all areas. l Drain and dry the lower outboard unit. stakeholder groups to develop an A E TAT S l Clean and dry all live-wells. Aquatic Invasive Plan that includes l Empty and dry any buckets. over 160 actions for addressing l Dispose of all bait in the trash. aquatic invasive species issues in the l Wait 5 days and keep watercraft dry between

launches into different fresh waters. F O state. The vectors for introduction 866-440-9530 For more information

highlighted in the plan include com- www.dfg.ca.gov/quaggamussel E H T mercial shipping, commercial fishing, recreational equipment and activities,

LOOK FOR MUSSELS HERE

RY A U T S E trade in live organisms, construc- tion in aquatic environments, and water delivery and diversion systems. The objectives for the Plan that were identified during stakeholder meetings are as follows: coordina- tion and collaboration, prevention, early detection and monitoring, rapid response and eradication, long-term CHECK YOUR BOAT, TRAILER AND VEHICLE control and management, education Fish and Game efforts to control new invaders include public outreach. and outreach, research, and laws and regulations. The Plan identifies lead and cooperating agencies for each ac- tion within these objectives and sets AQUATIC NON-NATIVES IN S.F. BAY up a timeline for completing actions and revising the Plan. The Plan also In 2005, we sampled 70 sites in S.F. Bay for non-native aquatic species. includes a draft Rapid Response Plan Target habitat types were intertidal rocky, intertidal sandy, subtidal fouling, that provides generic guidance for and subtidal infaunal communities. 514 total species were identified: agencies responding to suspect infes- • 103 non-natives (20% of all identified species) tations. Using a Rapid Response Plan • 81 cryptogenic (neither demonstrably native nor non-native) and an Incident Command system, the recent quagga mussel invasion has • 330 native to California been contained in southern California. • 285 unresolved taxa (could not be identified to species level) MORE INFO? Supplemental zooplankton sampling in 2006-2007 revealed an addi- [email protected] tional 10 non-native and 4 cryptogenic species.

• At one site—Port Sonoma in the —76% of all species identified were non-native. • Three species are probable new invaders to S.F. Bay. • Another two species are probable new invaders to California waters. A Greener Shade of Blue? 47 T T N RTA O P M I

Response of the common cold-temperate species, including the Dungeness crab, English LIKELY CHANGES Estuary’s Aquatic sole, speckled sanddab, and several With Global

rockfishes, increase in abundance Climate Change Biota to Changing while less common cold-temperate S E G N A H C species reappear. • Ocean temperatures will increase. Ocean Conditions The frequency and duration of KATHY HIEB et al. warm and cold-water events and the • Summer could California Department of Fish associated changes in ocean condi- increase.

and Game tions are well documented in the • There will be a deeper N I eastern Pacific over the last century, and upwelling of

Many biological and physical E H T but human-mediated changes on nutrient-poor water. factors influence the abundance, a global scale may result in new distribution, and community composi- • The Davidson Current will

trajectories. Most ocean scientists E TAT S tion of the Estuary’s aquatic biota. For increase with more frequent predict that the physical environment species that reproduce and rear in storms. will be more variable and change at the upper Estuary, the importance of • Variation in temperature

an unprecedented rate in the near water exports, food supply, contami- will increase with shorter F O future. There are several scenarios or nants, and invasive species has been regimes and more frequent

predictions of future changes in ocean the focus of recent directed studies. El Niño events. E H T climate, but all agree that there will be However, species that reproduce • There will be poor recruit- increased variability on the interannual in the nearshore ocean and rear in ment of cold-temperate spe- (1-3 year) scale. Although we cannot RY A U T S E the Estuary are subject to a different cies; adults will migrate north. predict the precise changes in ocean suite of factors in early life, including conditions, we can hypothesize how • More warm-subtropical spe- ocean temperature, nearshore surface cies will migrate here with the Estuary’s biota would respond to currents, and upwelling. Important local recruitment of warm- certain types of short and long-term ocean factors that affect biota include subtropical species. changes. Marine species here have a temperature, strength and onset of wide range of responses to changes • There may be more dead coastal upwelling, strength of the in ocean conditions. zones (as in Oregon 2002- wintertime Davidson Current, and 2006) and toxic algal blooms. productivity. MORE INFO? The San Francisco Estuary is situ- [email protected] ated in a transitional zone between two ocean faunas: a cold-temperate fauna to the north and warm-sub- tropical fauna to the south. In this zone, we have observed relatively rapid responses of some nearshore species to changes in ocean condi- tions. Ocean temperature is a leading indicator of ocean conditions; warm- water and cold-water periods can be relatively short in duration, such as El Niño and La Niña events, or on longer multi-decadal or century time scales. During warm-water periods, warm-subtropical species such as the California halibut, white croaker, Cali- fornia tonguefish, and white seabass increase in abundance or make an appearance here after many years of absence. During cold-water periods, 48 State Of The Estuary 2008 T T N RTA O P M I

Most investigations of salt marsh Response of Two harvest mouse population numbers TAKE HOME POINTS Estuarine Mammals in the Estuary have been conducted

in response to proposed develop- • Salt marsh harvest mice S E G N A H C to Natural Events ment projects or changes in land use colonize newly restored and Management that threaten mice. In contrast, small habitat relatively quickly. mammal studies conducted on the • Translocating mice can be Activities Refuge have focused on monitoring successful in augmenting the effects of management actions low mouse populations

JOELLE BUFFA, NORTON W. BELL,

N I undertaken to increase the amount (where habitat is below and WILLIAM PURCELL of available habitat or improve habitat carrying capacity).

E H T San Francisco Bay National Wildlife conditions for the mice. The establish- • Water management in Refuge Complex ment of Don Edwards S.F. Bay Na- diked pickleweed marshes

A E TAT S The San Francisco Bay National tional Wildlife Refuge (NWR) in the is important. Wildlife Refuge Complex (the Ref- South Bay and San Pablo Bay NWR • Salinity of pickleweed uge) manages habitat for two estua- in the North Bay included specific marshes is important.

rine mammals: harbor seal (Phoca objectives to protect and contribute F O • Natural events can have vitulina) and salt marsh harvest mouse to the recovery of this federally listed unexpected effects on

(endangered) species. Management E H T (Reithrodontomys raviventris). Harbor mouse recovery efforts. seal monitoring has been conducted actions undertaken in seven marshes weekly since 1998 at Mowry Slough, (Mayhew’s Landing, La Riviere Marsh, • Restoration sites need to

RY A U T S E include high tide refugia for which is the largest of the three major Entry Triangle Marsh, New Chicago mice. haul-out sites in San Francisco Bay, Marsh, Mouse Pasture, and also the largest pupping site in Setback, and Tolay Creek) have the Bay. Monthly monitoring has also included land acquisition, removal of been conducted since 1999, weather fill, reintroduction of tidal and muted permitting, at Alviso Slough, which is tidal action, other water management a smaller haul-out and pupping site activities, and, in one case, the translo- located in the South Bay. Our data cation of a population of salt marsh show daily, seasonal, and annual pat- harvest mice from an area slated for terns in seals using these haul-out ar- development. While numbers of mice eas. Two seasonal peaks in harbor seal have generally increased following numbers have been well documented: management actions, there have been April, which coincides with peak pup- setbacks caused by design flaws, lack ping, and June, which coincides with of staff/funding causing inconsistent the molting season. The number of plan implementation, and natural seals at Mowry Slough haul-out in- events. Still, adaptive management, creased during the earlier portion of and resiliency in the rodent popula- the survey period and has remained tion indicate that this story is headed stable more recently. The Alviso site toward a happy ending. The Refuge, has experienced a steady increase in cooperation with many other in total numbers and number of partners, is implementing the initial pups. Explanations for these patterns phases of the South Bay Salt Pond include tidal cycle, physiological needs Restoration Project. Results of our of the seals, and other natural and monitoring are being used to design anthropogenic factors. The Refuge is project components to benefit har- also cooperating with San Jose State bor seals and mice. University on a study of recreational MORE INFO? boating impacts to the harbor seal [email protected] haul-out on Bair Island. A Greener Shade of Blue? 49 T T N RTA O P M I

but these areas may decrease with Challenges in Conserving Migratory Birds restoration and sea level rise. The Es- as Estuary-wide Restoration Takes Place tuary plays a critical and complex role

in conservation of waterbirds from JOHN TAKEKAWA et al. local to Estuary scales that must be S E G N A H C Usgs Western Ecological Research Center considered for all levels of restoration NILS WARNOCK planning. PRBO Conservation Science MORE INFO? [email protected]

San Francisco Bay has become a studies have shown that most species N I focus for wetland restoration on the exhibit strong site fidelity to local areas.

Pacific Coast. Multiple restoration For example, species such as California SCIENCE QUESTIONS: E H T projects are taking place throughout clapper and black rails have very small • Bird numbers have increased at

the South Bay Salt Ponds. But the Estuary, but there has been little home ranges of less than a hectare E TAT S will mudflat values decrease in effort to look at the impact of all of during the breeding season, but they response to restoration? A small these projects together. also may move among subregions. change in the elevation of mud-

The goal of most Bay restora- We also discovered that one of the flats could make a difference to F O tion projects has been to return tidal most important Clapper rail sites in shorebirds as sea level rises: their flow to diked baylands and to restore the whole Bay—Colma Creek—is sur-

time for foraging could be de- E H T vegetated marshes for endemic tidal rounded by industry. creased—and their populations marsh species. Shallow open bays Ground-nesting birds like Forster’s could decrease. and ponds in the Estuary support a and Caspian terns may be negatively • Have dunlin decreased because RY A U T S E large number of migratory birds in the affected by avian predators, such as of changes in the South Bay? Can Pacific Flyway. Migratory birds respond California gulls, that can unexpectedly in- we look at the effects of restora- quickly to changes in habitat, yet with- crease as a result of restoration actions. tion and see if restoration activities out long-term data it can be difficult to This raises difficult management issues. affect bird use of the Flyway? make sense of complex phenomena. Diving ducks and shorebirds are • How does the Estuary relate to By summarizing population informa- found in most subregions, but the nesting areas in the Northwest tion and movement studies of selected South Bay is especially important Territories? There is a direct link migratory and endemic birds, we dem- for shorebirds, while the North and between remote areas and other onstrate how individual restoration Central Bays support large numbers areas in the south. projects, large restoration programs of waterfowl. Within the flyway, the • Can we use the movements of within subregions, and overall Estuary Bay is the wintering refuge for clapper migratory birds as a proxy to un- restoration changes may affect avian rails and black rails. The majority of derstanding restoration? communities. Our avian movement lesser and greater scaup, canvasback, and surf scoters counted on the Pacific coast occur in the TAKE HOME POINTS SHOREBIRD RESPONSE Bay during the midwinter. TO EBB AND FLOOD TIDES Western sandpip- · To understand changes in mi- ers spend more gratory birds caused by local time staging at the restoration, regular adaptive Bay during the monitoring must be conduct- spring migration ed through transitional stages. than at any other · Determining species’ carrying site along the capacity would help to assess Pacific coast. Mud- restoration success regionally. flats and shoals · Effects of Estuary changes are especially may be evident in redistribu- important habitats tion of populations. used for forag- · For migratory bird popula- ing by waterfowl Small shorebirds stayed <100 m of tideline. Their large popula- tions, broad scale restoration tions may be most affected by changes in mudflat elevations and shorebirds, effects should be evaluated at with restoration. a flyway level with calibration to other coastal sites. An example of rare remnant brackish tidal marsh with large pans, grading into lowland native wet rush- sedge meadow, grassland, and oak woodland, China Camp. Photo and caption courtesy of Peter Baye. A Greener Shade of Blue?

The Delta 52 State Of The Estuary 2008 E H T

LTA E D are increasing the pressures on Delta operated at reduced capacity to limit The Changing Delta: levees. One recent study put the risk harm to the smelt. What it Means for of a catastrophic levee failure—mul- In our Envisioning Futures re- tiple failures on multiple islands—at port,* we suggest the need for a Californians roughly two-thirds over the next 50 new long-term management system ELLEN HANAK years. Such a failure would cause mas- for the Delta, because the system’s Public Policy Institute of California sive flooding and salt water intrusion increasing fragility makes current prac- into the Delta, disrupting key infra- tices unsustainable. We consider the The Sacramento-San Joaquin Delta structure, including the pumps that consequences of changing—or failing has long been an important resource deliver water supplies to urban and to change—on the range of Califor- for California, providing agricultural agricultural users from the Bay Area nians who depend on the Delta. Most and recreational uses, wildlife habitat, to the Mexican border. stakeholders have considerable ability infrastructure pathways, and water Meanwhile, an ecological crisis is to adapt to a changing Delta. Mitiga- supply services throughout the state. brewing, with precipitous declines in tion is appropriate for those likely to The Delta is in poor health today. Its the endemic Delta smelt, a protected lose ground in the Delta of the future. levee system is fragile, many of its na- species. As the summer of 2007 MORE INFO? tive species are declining, and it lacks demonstrated, failure to resolve this [email protected] strong governing institutions. crisis is also a threat to the state’s Sea-level rise, increased floods water supplies. State Water Project associated with warmer winters, seis- * Jay Lund, Ellen Hanak, William Flee- pumps were temporarily shut down, nor, Richard Howitt, Jeffrey Mount, micity, and continued land subsidence and both federal and state pumps and Peter Moyle, 2007. Envisioning Futures for the Sacramento-San Joa- Delta Management Alternative #5: quin Delta, Public Policy Institute of South Delta Restoration Aqueduct California, San Francisco, California. www.ppic.org

TAKE HOME POINTS

• The Delta could experience a catastrophic failure of its levee system as a result of a large earthquake or higher flood flows before a new manage- ment system is put in place. • Demand to build housing in the Delta is great due to the Delta’s proximity to several metro- politan areas, and its relatively inexpensive land. The recent housing market slowdown offers a window of opportunity to make changes in the system. • The Delta’s fragility is California’s central water management chal- lenge. • We can try to work with the of nature pushing on the Delta and foster habitat for desirable species. • Adaptation will have to occur one way or another. The ques- tion is whether we choose to work with the system or not. A Greener Shade of Blue? 53 E H T

tion of some critical habitat types and supply, agriculture, urban develop- LTA E D Old Uses for ecological processes that have been ment, recreation, and transportation. a New Delta lost over the past 150 years. Habitat The Delta of the future is not going types that need to be expanded to be the same as today. We need to MICHAEL HEALEY include saltwater and freshwater plan and design for a Delta that will Calfed Science Program tidal marsh and seasonally inundated deliver the services we value. The established principles of water floodplain, as well as the hydraulic and MORE INFO? and environmental management in morphodynamic processes that sus- [email protected] California are being restructured, and tain these habitats. Also necessary will an important focus is the Sacramen- be changes in Delta geometry and flow patterns to increase variation in to-San Joaquin Delta. Multiple listings TAKE HOME POINTS of Delta species as endangered or water residence time and heteroge- neity in open water habitat. threatened have highlighted the failure • Environmental management of the established principles to pro- In anticipation of sea level rise, de- in the Delta is a wicked tect ecological integrity. In 2007, the velopment needs to be directed away problem. governor appointed a high level task from the margins of the Delta so that • Sustainable management of habitat types on the margin can ad- force to develop a sustainable vision the Delta is a complex, ever vance upslope as sea level rises. While for the Delta; their Vision Plan was changing problem. There is released and is available at www.delta- these changes reflect a reestablish- no one-shot fix. vision.ca.gov. Now the Vision must be ment of habitats and processes that • All solutions are temporary. implemented. Since the Vision places were more typical of the Delta prior significant emphasis on biodiversity to 1850, the new Delta will also sus- • Every solution creates new conservation, greater land and water tain a broad spectrum of social and conditions and problems. allocation for environmental purposes economic services that were not part • There are no right or wrong will be needed, as well as the restora- of the historic Delta, including water solutions, only better or worse solutions. • Management never ends: Minimum the future is uncertain but Area Point changing. • We need to choose solu- tions for the Delta that are robust to change: today’s so- lutions will soon be obsolete. • The Delta is a landscape and should be managed as such. As sea level rises, land in the Delta has the potential to be inundated. Protecting infrastructure raises ques- tions about where to put new development to reduce the risks of flooding. • The size and arrangement of land and water types defines the ecosystem. • Drivers of change impose a The nature, size, and arrangement of habitat or ecosystem patches is very impor- new standard of adaptability tant to how the Delta functions. Large patches support more species. Adjacent on managers. patches exchange materials and organisms easily; distant patches do not. In think- ing about a sustainable Delta environment we need to think about how it is struc- • Society and economy are not tured in terms of ecosystem patches. Different kinds of species respond differently on hold. to different sizes and shapes of land and water patches. Connectivity between the Delta and upland habitats is also important. 54 State Of The Estuary 2008 E H T

LTA E D climate models to compute, through Assessing a cascading series of linked models, CASCADE Scenarios of precipitation, runoff, river discharge, CHALLENGES temperature, salinity, sediment • Working across and transport, geomorphology, primary Change in the Delta amongst disparate production, incorporation of contami- disciplines Ecosystem nants into food webs, expansion of DAN CAYAN invasive species, and habitat quality • Downscaling global to regional-local scales Scripps Institution of for native fishes. CASCADE is still a & U.S. Geological Survey work in progress; however, it can help • Climate uncertainties: provide visions of the future Delta e.g., sea level rise and JIM CLOERN across a range of plausible scenarios. precipitation U.S. Geological Survey Early predictions are that we can ex- • Constructing realistic California’s Delta is the interface pect a saltier Bay-Delta environment biological models between the largest estuary on compared to that of the past, and a • Uncertain social, regulatory, North America’s west coast and lack of sediment supply will probably operational environment a vast watershed that produces be a critical part of the Delta’s future. • Non-linearities: invasives, runoff from winter storms and spring In terms of climate change, for some levee breaks snowmelt. It is the hub of California’s species of fish, a couple of degrees water-delivery system, a region of increase in temperature could be rapid population growth, a subsided catastrophic. landscape protected by fragile levees, MORE INFO? and habitat for endemic species [email protected] of plankton, smelt, and salmon whose Contaminant conceptual model (Stewart and Luoma, usgs) populations are at risk of extinction. The challenge of sustaining native biological com- munities demands in- novative approaches for assessing how habitats and their life-supporting func- tions will be altered by global change. With support from CALFED and USGS, we have launched a three-year research project (CASCADE) to assess how the Delta ecosystem might evolve into the 21st century in response to pre- scribed scenarios of climate, sea level rise, levee failures, and water operations. This contaminant conceptual model describes the critical physical, chemical, and biological processes and The project uses their interactions that determine the fate and effects of contaminants in the San Francisco Bay and Delta. Outputs from submodels that characterize individual processes are incorporated in successive submodels outputs from global to determine bioaccumulation and effects in different levels of the food web. A Greener Shade of Blue? 55 E H T

response, and alternative conveyance LTA E D The Fragility approaches) are being evaluated for of Levees their potential to reduce risk of levee failure. In addition, three trial scenarios in the Delta have been developed that would LES HARDER include different combinations of risk California Department of reduction building blocks. Water Resources Recently, Governor Schwarzeneg- ger called for the Department of California’s water supply is depen- Water Resources to carry out $120 dent upon water conveyance across million in immediate actions to im- the Delta and by water exports prove conditions in the Delta. Part of from the Delta. In recent years, many this effort is intended to help restore researchers have become concerned the Delta’s natural habitat. Other ac- about the vulnerability of local levees tions are related to improving emer- in the central Delta to both sea level gency preparedness and planning. The rise and earthquake shaking. Such Governor’s actions represent some concerns have called into question the of the very first steps towards risk long term sustainability of the levee reduction. system and current water conveyance MORE INFO? approaches. Future levee failures, par- [email protected] ticularly during the dry season, have the potential of drawing saltwater into the Delta from San Francisco Bay. If a future earthquake caused a Costs to maintain current level of levee large number of islands to suddenly performance over the next 100 years (to ~2100) flood during the dry season, water export could be significantly curtailed, perhaps for years. There would also be major impacts to the Bay-Delta highway and rail transportation sys- tems, and unknown impacts to Delta habitats and fisheries. To better define such risks, the Delta Strategy (DRMS) is being carried out. The Phase 1 portion of DRMS is a risk management study that examines both the current and future risk of levee failure, and considers the effects of climate change and other stressors on the system. A draft Phase 1 report has been completed and is now under review. It shows that Delta levees will be at significantly higher risks in the future from both flood and seismic events. The Phase 2 portion is beginning and is intended to examine alternative risk reduction measures. Several separate measures, or building blocks (e.g. improved levees, emergency preparedness and 56 State Of The Estuary 2008 E H T

LTA E D Historical land uses have reduced Suisun Marsh: Suisun’s tidal wetlands by 90%. Now HISTORY OF The Forgotten Link the primary type of wetland is sea- PROTECTION & sonal wetland managed for resident PRESERVATION Between the Bay and migratory wildlife under the ACTIONS auspices of 158 private owners and

and Delta numerous public agencies. A charter 1963 Suisun Soil Conservation STEVE CHAPPELL group of seven local, state, and federal District formed by landowners Suisun Resource entities came together to develop a Conservation District long term approach for tidal restora- 1970 tion and managed marsh enhance- The Suisun Marsh is the largest Suisun Resource Conservation ments that balances the recovery of brackish wetland in the western Unit- District (SRCD) formed listed species with maintaining the ed States, situated between the fresh- 1974 marsh and levees for waterfowl and water ecosystem of the Sacramento- Suisun Marsh Preservation to meet water quality objectives. The San Joaquin Delta and the saline Act passed by California traditional NEPA/CEQA planning pro- ecosystem of greater San Francisco Legislature cess has been expanded to include a Bay. Suisun Marsh’s water quality af- Science Integration Strategy, concep- 1976 fects and is affected by diversions that tual models, enhanced public involve- Suisun Marsh Protection supply water to 23 million Americans ment, and a science-based adaptive Plan completed by DFG and and to farms and businesses account- management program for imple- BCDC ing for over $500 billion in economic mentation that will address multiple benefits. The marsh is home to a wide 1977 objectives of the CALFED Program variety of plants, fish, and wildlife that Assembly Bill 1717 passes the and guide Delta Vision considerations depend upon balancing of fresh and Suisun Marsh Preservation Act for Suisun Marsh. saline waters for their survival. MORE INFO? 1978 [email protected] Water Rights Decision 1485 1987 Suisun Marsh Preservation Agreement signed by SRCD, DWR, USBR, DFG 2000 Suisun Marsh Habitat Management, Preservation, SuisunSuisun Marsh Marsh Habitat Habita Mt Maanagementnagement, Preservation, and Restoration Plan Preservation, and Restoration Plan and Restoration Plan (PEIR/ PrograMmatic EIR/EIS PEIR/EIS EIS) begins

Draft Tidal Restoration Targets

REGIONS

1 2 3 4

Alternative A 500–1,000 460–920 860–1,720 180-360 2,000 – 4,000 acres Alternative B 1,000–1,500 920–1,380 1,720–2,580 360-540 4,000 – 6,000 acres

Alternative C 1,500–2,250 1,380–2,07 0 2,580–3,870 540-810 6,000 – 9,000 acres

A Greener Shade of Blue? 57 E H T

per year from 1997 to 2005; however, LTA E D Subsidence Reversal through Wetland different conditions within the wet- Restoration and Carbon Sequestration lands led to as much as 9.2 centime- ters per year gain in some locations. in the Delta This rate of carbon sequestration ROGER FUJII, ROBIN MILLER, and KIM TAYLOR is much greater than published rates U.S. Geological Survey for many other land uses, suggesting that permanently flooded, shal- low wetlands may meet criteria for failure, and overcoming ongoing sub A serious threat to the Sacra- - greenhouse gas emission credits. Pin- mento-San Joaquin River Delta is the sidence and increasing risk ultimately ning down precisely why some areas deeply subsided central and western requires raising land surfaces. gained nearly 10 centimeters per year, islands. These islands’ land surface One effective approach to increas - more thoroughly assessing green- elevations have subsided by as much ing land-surface elevation, while house gas fluxes, developing carbon as 8 meters since the late 1800s, and sequestering greenhouse gases, is accounting methods, and evaluating continue to subside 2 centimeters establishing shallow wetlands on these the potential for mercury methylation per year due to microbial oxidation of subsided islands. Using our knowledge and production of dissolved organic peat soils. As subsidence progresses, that keeping fields under water will carbon are needed to further test drainage ditches are deepened, mitigate the oxygen-driven decompo- the viability of this approach. If this increasing the hydraulic head between sition of peat soil and that consistent evidence bears up under further scru- the channel water surface and the shallow water depths spur the growth tiny, managed wetland systems show island’s shallow groundwater table. of emergent marsh vegetation, in promise as an alternative farming This increases seepage of water under 1997 we established two wetlands practice in the Delta. and through the levees, making them (25- and 55-centimeters deep) on more vulnerable to failure. Many of Twitchell Island. Average land-surface MORE INFO? the desired functions of the Delta will elevation gains across both wetlands [email protected] be lost during a catastrophic levee were approximately 4 centimeters potential Change In Delta Accomodation Space Through Carbon Sequestration

Dark gray indicates land below sea level. 58 State Of The Estuary 2008 E H T

LTA E D How Delta Decisions and functioning of San Francisco Bay, as they could induce major changes TAKE HOME POINTS Affect San Francisco in the hydrology, hydrodynamics, es- tuarine circulation, salinity distribution, · We have created a massive Bay sediment budget, sediment dynam- hole in the Delta, up to 25’ PHIL WILLIAMS and ics, and geomorphic evolution of the below sea level, as a result of agricultural practices that have DAVID BREW Bay’s bathymetry. Over the next 50 induced subsidence. PWA Ltd. years these changes would coincide with other man-made and natural · In a “Doomsday” scenario, The San Francisco Estuary is physical changes occurring in San with a complete levee failure, artificially divided into two geographic Francisco Bay, including sea level rise, the Estuary would double parts, the Delta, and San Francisco shoreline erosion, habitat restoration, in area; the volume of water Bay. These parts are managed by dif- and dredging. The cumulative effect of in the Delta would increase ferent government entities, located these changes will in turn affect eco- by four times what it is now, in different cities, addressing different system processes and habitat distribu- and the volume of the whole San Francisco Estuary would management questions. Since the tion throughout the entire Estuary. At increase by 50%. Katrina disaster, the impossibility of present, because of the institutional continuing “business as usual” policies isolation of the two parts of the Estu- · The tidal prism of the Delta in the Delta in the face of continued ary, these cumulative Estuary-wide could increase by six times land subsidence and the impacts of impacts are not being systematically what it is now. global warming has become gener- considered. However, over the last 20 · We have not fully grasped— ally recognized. Now, state and local years we have significantly advanced or analyzed—how this will governments are actively considering our understanding of how the physi- affect physical processes and an array of more sustainable future cal Estuary functions and evolves. We habitats in the rest of the scenarios for Delta management. have the tools available to generate Estuary. The most feasible scenarios include projections of what the whole Estuary · As saltwater moves upstream, returning tidal action to significant will look like in 50 or 100 years to Suisun Bay could become portions of the Delta, with conse- help inform Delta and San Francisco more like San Pablo Bay, and quent increases in the tidal prism and Bay decisions. San Pablo Bay more like the tidal volume of the entire Estuary. Central Bay. MORE INFO? These increases could have significant [email protected] · There will be significant implications for the future evolution impacts on San Francisco Bay marshes with sea level rise and saltwater intrusion: marshes will be saltier, brack- The Doomsday Scenario: An ish marsh and mudflats could Estuary Twice as Big be lost. · A higher low tide would decrease mudflat area. · Less mud in circulation will make tidal marshes harder to restore. · There could be increased shoreline erosion with a higher mean tide; and an increase in the tidal prism will increase channel scour. · We need to recognize that there will be significant chang- es in the physical system when we abandon Delta islands. A Greener Shade of Blue?

Integrating Ecological Restoration I n to W ate r s h ed m A n age m e n t 60 State Of The Estuary 2008 TING ECOLOGICAL RESTORA WTERSHED MANAGEMENT N E M E G A N A M D E H S R E WAT O T N I N O I AT R O T S E R L A C I G O L O C E G N I AT R G E T N I

The Connection Between Estuary and Perimeter Habitats: Implications for Tidal Marsh Restoration MARK STACEY and LISSA MACVEAN University of California, Berkeley

The to-be-restored South Bay salt flowing into the ponds will be sourced ponds represent a surface area compa- from along the perimeter of the Estu- rable to the adjoining far South Bay, ary down-estuary from the restoration and the nature and magnitude of the site. Finally, the outflow from the re- connection between them is critical stored habitats creates a large pool of for both the Estuary itself and the re- relatively saline waters sitting adjacent stored habitats. Through a combination to the restored ponds at the end of of analytic approaches and the analysis the ebb tide. During the ensuing flood, of observations collected adjacent to these waters are swept upstream in breached ponds along Coyote Creek, Coyote Creek, with an abrupt frontal we examined the details of exchange transition evident between the pond between Coyote Creek and the “Island waters and the ambient creek waters. Ponds” and identified several impor- During the following ebb tide, at a tant features of the exchange. station across Coyote Creek from the First, flow into the restored habitats ponds, the salinity variation is altered appears to be from waters sourced from the expected, with a slightly along the margins of the Estuary, with elevated salinity near the end of the dominant sediment inflows occur- ebb. These results quantify the effects ring late in the flood tide. Secondly, of “tidal trapping” on the ambient salin- the outflow from the restored sites ity for this site, with an increase in the is scouring a subtidal channel through average salinity intrusion into the creek. the intertidal zone that adds vertical MORE INFO? variability to the exchange flow. From [email protected] these results, it appears that sediment

The scale of the restoration area (light gray) is comparable to the surface area of the far South Bay (the region south of the Dumbarton Bridge, dark gray), which will modify tidally-driven currents locally as the restored regions fill and drain, and has the potential to modify tidal dynamics more broadly due to the interaction of the tidal wave with the perimeter of the Bay. A Greener Shade of Blue? 61 TING ECOLOGICAL RESTORA WTERSHED MANAGEMENT N E M E G A N A M D E H S R E WAT O T N I N O I AT R O T S E R L A C I G O L O C E G N I AT R G E T N I

tive projects across the watershed. In Wetlands 1996, the Sonoma Baylands Wetlands Restoration in the Restoration Project was completed. At 289 acres in size, Sonoma Baylands North Bay was the largest planned tidal wet- WENDY ELIOT and lands restoration project at the time JOHN BROSNAN construction was completed. Progress Sonoma Land Trust since then has been steady, and proj- ects continue to expand in scope and Historically, nearly 80,000 acres of size, totaling thousands of acres that tidal marshes and mudflats fringed have been restored or are on track San Pablo Bay. Most of these tidal to restoration, including Hamilton, Bel marshes were diked for agricultural Marin Keys, Bahia, Carl’s Marsh, the reclamation during the 1890s, result- Sears Point Restoration Project, Tolay ing in the loss of over 82% of the Creek, Cullinan Ranch, the Napa Plant North Bay’s historic tidal wetlands Site, and the Napa-Sonoma Marshes, and dramatic reductions in the wildlife which includes restoration of almost populations that depended on the 10,000 acres alone. Partners are look- marshes. Over the past 20 years, ing ahead to additional wetland and conservationists, landowners, and upland restoration projects, including agency managers from the region the 1,737-acre Tolay Lake Regional have set ambitious goals for restoring Park and the 1,600-acre Roche Ranch the North Bay’s wetlands. The efforts, acquisition, which will preserve and including the San Francisco Estuary restore nearly all of the Tolay Creek Project’s Comprehensive Conserva- watershed. Together, numerous pri- Castilleja ambigua from Point Pinole, tion and Management Plan and the vate and public partners are restoring extirpated in SF Bay tidal marshes, and Baylands Ecosystem Habitat Goals nearly extirpated in the North Bay as large landscapes within the 50,000 well. Photo courtesy of Peter Baye. Report, provide the consensus for acres of restorable tidal wetlands supporting grand-scale restoration across the San Pablo Bay watershed. and offer roadmaps to achieving res- MORE INFO? toration goals. Since the early 1990s, [email protected] wetlands restoration has occurred in significant individual and collec-

TAKE HOME POINTS

Constraints to integrating wetlands and tidal wetlands include:

· The need for flood protection · Invasives control · Remediation · Multiple users of the site · Sea level rise · Physical infrastructure 62 State Of The Estuary 2008 TING ECOLOGICAL RESTORA WTERSHED MANAGEMENT N E M E G A N A M D E H S R E WAT O T N I N O I AT R O T S E R L A C I G O L O C E G N I AT R G E T N I

identification and protection of existing Biota Without Borders unstable refuges of high native marsh LETITIA GRENIER and JOSH COLLINS species richness; (b) linking restoration San Francisco Estuary Institute with protection of native plant popula- tion “capital” in species-rich refuges; and Boundaries and barriers that humans place on the landscape are new in evolu- (c) active adaptation of marsh restora- tionary time. Most wildlife have not evolved to recognize the boundaries or pass tion and management to recover viable the barriers that we create. The landscape as viewed through the human perspec- populations of non-dominant native tive is very different from that which wildlife experience. Wildlife need to link plants in restored tidal marshes. uplands, baylands, and the Bay through their movements each day, by season, and for juvenile dispersal. As wildlife move through the landscape according to the rhythm MORE INFO? of the natural history that has evolved for each species, they encounter resistance [email protected] (and sometimes assistance) from human endeavors. Similarly, as we try to under- stand and conserve wildlife, we may also be thwarted by human constructions. Bar- TAKE HOME POINTS riers to wildlife movement can be apparent, such as a busy freeway, but there are other barriers that are subtle to human perception: loss and degradation of habitat • In constructing wetlands, and change in the configuration of habitat patches. The structure of human institu- avoid homogeneity. Embrace tions, which often divide watersheds from Bay wetlands, can hinder wildlife conser- heterogeneity in substrates vation as well. Changes in the connectivity of the landscape for wildlife will continue and topography, and work as the Bay Area urbanizes further and sea level rises. We will better conserve our with designers to allow for it. natural heritage if we predict and prepare for these changes by imagining them • Accidents often deliver through the perspective of wildlife. biodiversity—uncommon and MORE INFO? rare species often become [email protected] established along the edges of restored tidal marshes. Give Native Plant Diversity less common natives a chance and introduce them early on TAKE HOME POINTS In Restored North when they still have a chance.

· One of the goals of the Bay Tidal Marshes • All remnant populations of rare tidal marsh species that Comprehensive Conserva- PETER BAYE do not have legal protection tion and Management Plan Coastal Plant Ecologist for the Estuary is to restore should be identified and saved. the physical, biological, and Most of the North Bay’s tidal chemical integrity of the marshes are young (post-reclamation Estuary. This means that era) and deficient in native estuarine clean water, water supply, plant species diversity. Areas rich in un- flood protection, and wildlife common or rare native tidal marsh and conservation all have to be ecotone plant species are widely scat- part of the same goal. tered in the region. Many are associated · Our modern landscape with pre-reclamation marsh remnants shows a huge loss of habitat or unusual soil conditions. Diked, non- connectivity from what was tidal marshes in some cases harbor here historically. species-rich refuges of tidal marsh · We need a common vision ecotone species. Some uncommon to of how to restore and be rare plants are capable of long-distance stewards of wildlife on a dispersal into restored tidal marshes, landscape scale, and to invest but most have rather weak colonizing early in conserving land- and dispersal ability, and are usually scapes for wildlife. Since we overwhelmed by native or non-native haven’t yet specified what dominant tidal marsh pioneer plants Symphiotrichum subulatum (Aster subu- our wildlife goals are, we are when new tidal marshes are restored. latus), locally abundant in Suisun Marsh stuck waiting for a crisis. (mostly in diked marshes now), rare in Recovery of the North Bay’s estuarine South and North Bay tidal marsh edges. plant species diversity will require (a) Photo courtesy of Peter Baye. A Greener Shade of Blue? 63 TING ECOLOGICAL RESTORA WTERSHED MANAGEMENT N E M E G A N A M D E H S R E WAT O T N I N O I AT R O T S E R L A C I G O L O C E G N I AT R G E T N I

native plants? Or do the ecological Putting it Back functions we hope to replicate in such TAKE HOME POINTS Together: a restoration project require land- scape components that go beyond · Once you allow humans into Are We Leaving out the wetland or streambed itself? Do an restored area, even an wetland and riparian ecosystems also urban area, species diversity Essential Pieces of require transition zones and adjacent gets diminished. If full envi- Ecosystem uplands if we are to replicate the full ronmental restoration with suite of ecological functions present large diverse habitats is the goal, people must be con- Restoration? in natural aquatic systems? Recent sci- trolled. If we are everywhere, ence indicates that the answer is yes. ARTHUR FEINSTEIN then the wildlife species we Citizens Committee to Complete But how do we achieve these are restoring habitats for the Refuge holistic, multi-habitat projects when won’t be. undertaking pure restoration projects? · We need to provide for The San Francisco Bay Area is one What are the hurdles such restora- quality public access—not of the most exciting places to be if tion projects face? In the regulatory quantity. you are interested in wetland and world, can we preserve such existing riparian habitat restoration. Nowhere habitats when they are threatened · The larger, and the more else in the country are wetland and by development or demand such varied the habitat, the better it is for sustaining biodiver- riparian restoration projects taking expansive habitats when imposing sity (although small habitats place with the size, complexity, and mitigation on developments that variety of those in the Bay Area. aimed at specific species can destroy streams and other wetlands? be very valuable). But what does wetland/riparian When we are fortunate enough to restoration mean (and in this context undertake restoration projects that I include the restoration that results incorporate a full range of habitats, from mitigation projects)? For pure, there other issues that must be non-regulatory, restoration projects, addressed to ensure that the restora- is it simply recreating the specific tion provides all the desired functions. footprint and hydrology of an historic Those issues include restricting human Preening Alert Behavior marsh, or for a mitigation project access to protect wildlife. creating a wetland of some specific Locomotion MORE INFO? acreage, or for a riparian area simply [email protected] digging a channel and lining it with

Feeding Resting

During the day, a typical duck may spend 57% of its time resting, 28% of its time feeding, 11% in locomotion, 4% preening, and 1% in alert behavior. What is the impact of human recreation if it increases a duck’s locomotion or alert time? Energy reserves for migration are particularly important for water- fowl. Pacific populations of brant lose one-third of their body (about 1.87 lb. of fat) in just a few days during their 3,000-mile journey from Alaska to Mexico. Photo courtesy of Jean Matuska. 64 State Of The Estuary 2008 TING ECOLOGICAL RESTORA WTERSHED MANAGEMENT N E M E G A N A M D E H S R E WAT O T N I N O I AT R O T S E R L A C I G O L O C E G N I AT R G E T N I

A Living River The Living River Design Case Study RICHARD THOMASSER Napa County Flood Control and Water Conservation District The Napa County Flood Control and Water Conservation District and the U.S. Army Corps of Engineers are implementing the Napa River/Napa Creek Flood Protection Project along approximately 7 miles of the Napa River and approximately 1/2 mile of Napa Creek in the city of Napa. The objective of the project is to provide an economically-feasible and environ- mentally-sensitive method of protect- ing the city of Napa from 100-year Key elements of the design include reconnecting the river to its natural flood- plain and restoring the significant wetlands in the southern reach of the project. storm events. The plan called for cleaning up contaminated sites rather than avoiding them. The project will achieve flood One of the key flood protection elements is a dry bypass which will stop flood- protection and habitat enhancement ing in the downtown reach but not cut off the river’s natural flow through its downtown oxbow. by using environmentally beneficial methods such as the creation of wetlands, marshplain, and floodplain terraces, selective removal of exist- Geomorphic Channel Design ing levees, use of open space as the floodway, construction of setback levees, floodwalls, and bypass chan- nels, and biotechnical bank stabili- zation. Environmentally damaging measures such as deepening the river by excessive dredging will be avoided. The project was developed through a two-year community-wide coalition process, which was coordinated by the District. The Community Coalition has been a cooperative process among a wide ranging group of stakeholders with diverse interests. The Community Coalition, with the assistance of the Corps, resource agencies staff, and outside consultants, developed the major concepts in the project to meet the dual objectives of reducing flood The project includes a geomorphic channel design, which creates marsh and flood- damage and maintaining and enhanc- plain terraces, and is designed to maintain more natural sediment transport, while ing environmental quality. Through the creating significant additional emergent marsh and riparian habitat along the river, Community Coalition, the “Living River right into the downtown reach. Guidelines” were created, which is the design guide for the project. MORE INFO? [email protected] A Greener Shade of Blue? 65 TING ECOLOGICAL RESTORA WTERSHED MANAGEMENT N E M E G A N A M D E H S R E WAT O T N I N O I AT R O T S E R L A C I G O L O C E G N I AT R G E T N I

providing increased flood protection, patterns. We also want to begin to Controlling habitat, and recreational opportuni- recognize the social and economic Pollution to Protect ties while protecting water quality and benefits of restoration projects and to preventing pollution on a watershed include all of the regulated community. Water Quality basis. Key Water Board programs and We are now addressing pollutants BRUCE WOLFE projects designed to integrate and on a statewide and Baylands basis: San Francisco Bay Regional support multiple uses include the TMDLs are really watershed plans. Water Quality Control Board Total Maximum Daily Load (TMDL) We are trying to recognize the many program; a Wetland and Stream Policy benefits of riparian zones that haven’t The San Francisco Bay Water currently being developed; the Surface been spelled out yet, and have begun Board continues to move beyond Water Ambient Monitoring Program; to view wetlands and streams as a the classic pollutant-by-pollutant ap- the Regional Monitoring Program; physical unit. To quote Josh Collins, proach to water quality protection beneficial reuse of dredged materials “wetlands are really the deltas of ripar- that was our agency’s initial focus through the Long Term Management ian systems.” In the future, we will look after adoption of the federal Clean Strategy; and large scale wetland more closely at flood attenuation and Water Act in 1972. Our regulatory restoration projects. storage when projects are permitted, efforts are now designed to not only We are learning that we need as well as cumulative impacts, and ways protect, but also restore water qual- to better regulate development of in which we can provide incentives for ity through collaboration with other upland areas, and in some cases, to watershed-based planning. agencies and stakeholders, as we try treat “flow” as a pollutant—i.e., where MORE INFO? to accomplish multiple goals, such as developments cause change in runoff [email protected]

sometimes too limiting for good deci- Salt Pond Restoration Integrating Waste- sion-making. Using unnatural plumbing A five-year planning process is as an organizational framework—i.e., water, Stormwater, nearing completion. The plan inte- a county, city, or special district—can grates habitat restoration, flood pro- Floodwaters, and sometimes work. We don’t have to use tection, and public access. But what the same approach everywhere. Here about the connection to adjacent Restoration are some examples. areas and local watersheds? We need STEVE RITCHIE to reinforce watershed connections, South Bay Salt Pond Restoration Lake Merritt and Channel particularly steelhead restoration, Project This project restores a flood con- mercury TMDL decisions, and storm- The systems developed around San trol basin and has good public access. water management. Francisco Bay to manage wastewater, Yet is important to connect to the MORE INFO? stormwater, and flooding have been Estuary. The lake and upper channel [email protected] largely independent activities driven by restoration is funded, and the interest a variety of laws and regulations as well in restoring the lower channel is there: as funding considerations. The resulting this should be approached in con- municipal plumbing is not being used junction with Sewer District 1 Clean TAKE HOME POINTS optimally for the benefit of the com- Water Act compliance. munity and the Bay. With the increas- • We need to always think about restoration/integration ing investment in habitat restoration Damon Slough of wastewater, stormwater, both in creeks and around the margins The recent Damon Slough project and floodwaters control of the Bay, new opportunities pres- is a nice piece of work: it has good from financial, scientific, and ent themselves for re-management public access to the tidal fringe, but regulatory standpoints. of these systems to provide multiple controlling trash upstream is essential We should do these things benefits and guide investment in the • to achieving the full value of the proj- in chunks that make sense to future. We need to think about the ect. The project should be approached manage. Bay differently—it’s a big estuary with via stormwater permit compliance myriad challenges. Natural plumbing— in conjunction with Sewer District 1 i.e., watersheds—can work, but is Clean Water Act compliance. 66 State Of The Estuary 2008 TING ECOLOGICAL RESTORA WTERSHED MANAGEMENT N E M E G A N A M D E H S R E WAT O T N I N O I AT R O T S E R L A C I G O L O C E G N I AT R G E T N I

The North Central California Salmon and Steel- Coast Recovery Domain (showing head Recovery, northern and southern boundaries) North Central California Coast MAURA EAGAN MOODY NOAA Fisheries NOAA Fisheries (NOAA) aka the National Marine Fisheries Service is the federal agency with regulatory ju- risdiction over anadromous salmonids listed under the Endangered Species Act. NOAA is responsible for develop- ing recovery plans for these species. The North Central California Coast Recovery Domain includes salmon and steelhead from several populations— Central California Coast coho salmon, Central California Coast steelhead, California Coastal Chinook, and North Central California steelhead. Key com- ponents of the recovery plan include: (1) developing criteria for popula- tion/species viability; (2) assessing population and habitat-based threats; (3) developing recovery criteria and technical documents that form the variety of data as background for the site-specific management actions foundation of the plan, multiple public draft recovery plans, which will present that will reduce or eliminate identi- workshops will be held across the a blend of scientific and policy/manage- fied threats; and (4) assessing costs of north coast of California to facilitate ment recommendations for recovering implementation. Beginning with Central public involvement in the process. these listed fish. California Coast coho salmon, NOAA Draft materials are available at http:// MORE INFO? hopes to complete draft recovery swr.nmfs.noaa.gov/recovery/index.htm. [email protected] plans for these salmonids in 2008. In NOAA is currently requesting review addition to developing numerous and comment on draft materials and a

A Sample Recovery Strategy For Alameda Creek Steelhead Our analysis ranks channel modification as a high or very high threat in the Alameda Creek watershed. Strategies to address this threat could include: • Providing fish passage over the BART weir • Installing fish screens at key diversions • Enhancing the riparian corridor • Providing adequate bypass flows • Developing partnerships for implementation of fish passage measures A Greener Shade of Blue? 67 TING ECOLOGICAL RESTORA WTERSHED MANAGEMENT N E M E G A N A M D E H S R E WAT O T N I N O I AT R O T S E R L A C I G O L O C E G N I AT R G E T N I

drop structure owned by the Alam- ladders past the remaining barriers, The Bottleneck in eda County Flood Control and Water and a recent agreement between the Alameda Creek Conservation District (ACFC&WCD). ACFC&WCD and ACWD provides ACWD and ACFC&WCD have for a cooperative approach to ad- Flood Control been working cooperatively to ad- dress passage past the flood control dress these barriers. Fish screens are drop structure and the middle inflat- Channel under construction for a portion of able dam. ERIC CARTWRIGHT the unscreened diversions, and plans MORE INFO? Alameda County Water District are underway for the removal of one [email protected] of the inflatable dams. Conceptual With a drainage area of almost 700 designs have been developed for fish square miles, Alameda Creek has the largest watershed draining to San Fran- cisco Bay aside from the Sacramento- San Joaquin River Delta. The size of the Concept for Fish Passage improvements drainage, the pristine habitat, the protected status of large por- tions of the upper basin areas, and the presence of native rain- bow trout make the watershed a high priority area for restora- tion of steelhead trout. Although the upper Alam- eda Creek watershed con- tains an estimated 15 miles of steelhead trout spawning and rearing habitat, like many Bay Area watersheds this one has passage barriers that must be addressed to restore the fish- ery. These barriers have all been assessed as part of watershed planning efforts, and the own- ers of all the barriers are working co- operatively with the Alameda Creek Substantial Progress is Being Made Fisheries Work Group to make them passable to steelhead trout. Some barriers have already been removed, will be removed soon, or have modifi- cations in the planning process. Barriers remain in the lower 12-mile portion of Alameda Creek that was channelized by the U.S. Army Corps of Engineers as part of a flood control project in the 1960s and 1970s. These barriers include the Alameda County Water District’s (ACWD) groundwater management facilities (three inflatable rubber dams, and unscreened diversions) and a 68 State Of The Estuary 2008 TING ECOLOGICAL RESTORA WTERSHED MANAGEMENT N E M E G A N A M D E H S R E WAT O T N I N O I AT R O T S E R L A C I G O L O C E G N I AT R G E T N I

Restoring Steel- working relationships and engendered trust among parties and institutions TAKE HOME POINTS head Trout to that was previously scarce. Working together with professional support, · The creeks that connect to Alameda Creek participants have attracted several the Bay are under increas- ANDY GUNTHER million dollars for high priority proj- ing pressure. Yet steelhead, which use the entire Center For Ecosystem Management ects to remove barriers to migration watershed during their and Restoration and screen a key water diversion. One the most important aspects lifecycle, can drive ecosys- Alameda Creek is the largest of restoration is deciding the magni- tem management and be the impetus for preserv- watershed draining to San Francisco tude, timing, location, and source of ing landscapes for future Bay, and with large tracts of protected water flows in the creek to support generations. habitat containing healthy rainbow restoration while minimizing the trout populations has long been of impacts on water supply operations. · Restoration is a choice and interest for steelhead restoration. The Stakeholders have recently signed a requires conducting ex- periments on how to best most recent effort began in 1999 Memorandum of Understanding to restore steelhead trout. It with the formation of the Alameda address this issue, and have pledged Creek Fisheries Restoration Work gives us a chance to “think funds to conduct the joint fact-finding globally, act locally.” Group, the first effort since the fish required for credible and legitimate were listed as threatened pursuant to restoration plans. · The upstream fight of steel- the Federal Endangered Species Act. head is both mysterious MORE INFO? Restoring anadromous fish to a and inspiring. The return [email protected] significantly urbanized watershed is of these wild creatures restores something in us as an exceedingly complicated task that well. will require the coordinated, sustained action of local, state, and federal agen- cies, working cooperatively with land- owners and other concerned citizens. These interested parties must define a vision of restoration, determine the necessary actions and their sequence of implementation (including provision of in-stream flows), and a mechanism for monitoring success and adjust- ing future activities to better achieve restoration goals in the light of urban development, climate change, and other unforeseen future environmen- Alameda Creek Steelhead tal perturbations. These activities must be integrated with existing public and private activities, including flood control and water supply projects. The Work Group prepared a peer- reviewed assessment of the potential to restore steelhead (2000), and a draft Restoration Action Plan (2003). These efforts have helped build solid Photos courtesy of Jeff Miller, Alameda Creek Alliance. A Greener Shade of Blue? 69 TING ECOLOGICAL RESTORA WTERSHED MANAGEMENT N E M E G A N A M D E H S R E WAT O T N I N O I AT R O T S E R L A C I G O L O C E G N I AT R G E T N I

When Will Steel- tion flows to sustain a viable steel- head run. Adequate stream flows TAKE HOME POINTS head Return to are needed to allow steelhead to again thrive in the creek, particu- · The visibility and persistence Alameda Creek? larly late-summer cold water rearing of these fish in showing up JEFF MILLER flows and flows for out-migration of every year has galvanized Alameda Creek Alliance steelhead smolts to reach the Bay. the Alameda Creek Alliance. Eighty-six percent of the stream flows · We now have over 1,500 After an absence of almost half a of upper Alameda Creek above the members in the watershed, century, salmonids are poised for a Sunol Valley are currently diverted and over 15 agencies coop- comeback in Alameda Creek. Volun- for water supply demand, and none erating. teers rescuing fish below barriers in of the watershed’s reservoirs release · Genetic analysis of steelhead lower Alameda Creek during the past any minimum flows for fish. With ef- trout below the dams shows decade have documented at least forts to provide fish passage under- their genes to be most 100-150 wild adult steelhead. The way, much of the hope for restoring closely matched to resident persistence of these fish offers a glim- Alameda Creek’s anadromous fish fish of Alameda Creek. mer of hope and has galvanized public runs now hinges on the city of San · Landlocked trout can be a support for restoring Alameda Creek Francisco’s project to replace the seis- source population for re- and its native fishes. The restoration is mically challenged Calaveras Dam. storing steelhead below the gaining momentum with over a dozen Discussions have begun over dam. local, state, and federal agencies work- required water flows and potential ing cooperatively on planned fish pas- · The biggest question is habitat enhancement projects in whether the SFPUC will sage projects and a draft restoration the watershed. All of the watershed leave enough water in the plan. Three dams have been removed stakeholders recently agreed to jointly stream. with a fourth dam coming out in conduct studies to estimate the range, · We hope the restored 2008. Two fish ladders have been built magnitude, timing, duration, frequency, and three more major fish passage South Bay salt ponds can and location of stream flows neces- provide improved rearing projects are in the planning stages. sary to restore steelhead trout to the habitat for steelhead at the The biggest unanswered question Alameda Creek watershed. mouth of Alameda Creek. is whether sufficient water will be MORE INFO? available to provide suitable habitat, · The potential for steelhead [email protected] water temperatures, and out-migra- restoration has captured the imagination of Bay Area resi- dents. Restoring steelhead to Alameda Creek could be a model for successful urban stream restoration.

Photos courtesy of Jeff Miller, Alameda Creek Alliance.

Volunteers carry fish past barriers on Alameda Creek. Eastern Petaluma Marsh shoreline along Lakeville Highway, south of Papas Taverna, where the high marsh has a rare connection to the natural old alluvial fans of Sonoma Mountain, washing terrestrial sediments over the upper edge of brackish marsh. This spot has a rare display of salt marsh annual wildflowers—particularly smooth goldfields (Lasthenia glabrata)—that are now better known from vernal pools, but which co-dominate with pickleweed and toad rush at the high marsh edge here. Photo and caption courtesy of Peter Baye. A Greener Shade of Blue?

Land Use 72 State Of The Estuary 2008 D N A L

• An advisory committee of about E S U California Water 38 statewide organizations repre- Efficient Cities: senting a spectrum of interests will Plan Update 2009 Easy on the CO2 provide input on statewide policy and H O KAMYAR GUIVETCHI issues and initiatives. 2 It is politically impossible to California Department of • Regional workshops and multi-re- Water Resources gion forums will focus on regional jump directly to 2050 sustain- ability, but we can progress The California Water Plan is a water issues and management through three “change stages” strategic plan for managing California’s strategies with an emphasis on integrated regional water manage- to get there: populist, funda- water resources and systems, and is a ment. mental (2020), and profound key element in the Governor’s Strate- (2050). The Bay Area has too gic Growth Plan. It is required by the • Through the extended review many people consuming too California Water Code and is updated forum, people can follow the much land. Our suburbs are the every five years. Water Plan process without direct involvement in work activities. world’s least sustainable places. Water Plan Update 2005 took a Members will receive regular infor- How do we create efficient hu- substantially new approach by de- mation updates and public meeting man settlement patterns, mini- scribing short and long-term actions notices. mizing the distance between that can be implemented at the state work, home, and activities? The and regional levels, and identifying a • The Statewide Water Analysis Network (SWAN), a voluntary solution: pioneer green settle- portfolio of 25 resource management network of scientists and engineers ments and use the capitalist strategies to sustain California’s com- from the public, private, and non- imperative to spread them like munities, economy, and environment. governmental sectors, will hold a virus: Water Plan Update 2009 will public workshops on technical build on Update 2005 by emphasiz- topics. • change the culture (via ing comprehensive and integrated sociological persuasion); More information is available at regional management of water • new and better transit www.waterplan.water.ca.gov resources and flood management technology (PRT); MORE INFO? systems. Update 2009 will integrate • comprehensive door-to- [email protected] information about California’s water door mobility using GPS cell uses and supplies, conservation, water phones; quality, environmental stewardship, • move people closer to their and flood management; and it will jobs; lay the groundwork for addressing climate change impacts on California’s Photo courtesy of Heidi Perryman • develop “auto hostility” by charging for parking; water resources and systems. (www.martinezbeavers.org). Water Plan Update 2009 will be • grow walkable places. developed in a collaborative process —Steve Raney, Cities21 with broad public input and multiple [email protected] opportunities for participation. Annual plenary meetings will bring all partici- pants together. • A steering committee composed of 18 state government agencies is guiding plan development. The steering committee is coordinating with federal agencies, consulting with tribal governments, and en- gaging statewide and local agen- cies and organizations, technical experts, and the public. A Greener Shade of Blue? 73 D N A L

Benefits of Alternative Water Management Strategies

Cost-effective • Investments in alternative strategies decreasing the risk to California’s E S U produce water at approximately economy from potential Delta Strategies to Ensure one fifth the cost of water from levee failures. In contrast, Sites Long-term Water Temperance Flat. Reservoir would increase our reli- • Almost 20% of California’s electric- ance on the Delta, and increase Supply Reliability ity use, and over 30% of its natural risks to the state’s economy. gas use, are associated with the • Alternative water management KRISTINA ORTEZ use of water. Water use efficiency tools can deliver benefits far faster Natural Resources Defense Council and recycling can generate sub- than dam projects that can take The Bay-Delta Estuary is facing a stantial energy savings and reduc- more than a decade to build. crisis. Numerous species are listed tions in greenhouse gas emissions. • Climate change is likely to reduce as threatened or endangered, or • Investing in water efficiency and the potential yields of Temperance proposed for listing. The Delta smelt groundwater cleanup will improve Flat and Sites Reservoirs. In contrast, is on the verge of extinction. The water quality by reducing urban many alternative water manage- status quo is not sustainable for any runoff from lawns and gardens ment tools will be as effective, or of the Delta’s users, including farm- and by delaying or reducing the even more effective, in the future. size of water system expansions. ers, commercial and sport fishermen, • State investments in alternative Delta residents, and the 23 million • Investments in surface stor- water management strategies will Californians who rely on the Delta for age could harm the Bay-Delta be far more effective in attract- a portion of their water supply. Invest- ecosystem by reducing flows to ing water user matching funds. ments to improve water supply reli- the Delta and increasing diver- Water users are eager to invest sions from the Delta. In contrast, in conservation, reclamation, inte- ability must also improve conditions in alternative water management grated regional plans, and other the Delta. Despite proposed spending tools would decrease our reliance tools—but not new dam projects. to build two new surface storage on the Delta. projects in California—Sites and Tem- • Temperance Flat is designed to perance Flat dams—in virtually every • A massive levee failure in the provide water to a small number Delta could jeopardize the water of farmers near the San Joaquin area, alternative water management supply for 23 million Californians. River. In contrast, investments in tools provide superior performance Investments in alternative water conservation and reclamation and broader benefits when compared management tools will reduce re- would produce benefits for the with proposed surface storage proj- liance on Delta diversions, thereby taxpayers who pay for state bonds. ects. The 2005 California Water Plan Update contains extensive, detailed estimates of the water supply poten- Cost and Potential Yields From Selected tial of a range of proven water supply Water Sources tools. The bar chart presents many of $1,800 3,500 those totals, ranging from low to high $1,600

3,000 year) per acre-feet thousand (in yield estimates. We believe that the $1,400 2,500 Yield Water Potential more ambitious estimates are realistic, $1,200 and that aggressive targets and ambi- $1,000 2,000 tious programs will assure Californians $800 1,500 a reliable water future. $600 1,000 Cost (per acre-foot) MORE INFO? $400 500 [email protected] $200

$0 0

y t ion t anup gemen erva ecycling Cle s Efficienc R r na on er Ma er Ag C Wat Temperance Flat High Cost Estimate

Urban Water Groundwate Low Cost Estimate Groundwat Potential Water Yield Water Management Strategy Sources: Department of Water Resources, California Water Plan Update, Bulletin 160-05, Vol. 2, Chapter 3, p. 7. Department of Water Resources, California Water Plan Update, Bulletin 160-05, Vol. 2, Chapter 22, p. 5. Water Recycling 2030 Recommendations of California’s Recycled Water Task Force, June 2003. DWR Water Desalination – Findings and Recommendations. This is an average cost according to Bulletin 160-05. Department of Water Resources, Role of Surface Storage in the Governor's Comprehensive Water Plan, September 2007. 74 74 State Of The Estuary 2008 D N A L

Indoor Water Efficiency Requirements E S U New Conservation Trends and Possibilities For Water Savings RICHARD HARRIS East Bay Municipal Utility District Resource efficiency has been a growing area of interest for utilities, resource management agencies, non- governmental organizations, and the development community for many years. Water supply reliability, energy consumption, environmental steward- ship, sustainable development, and economic viability all have played a Outdoor Water Efficiency Requirements strategic role in helping shape past, present, and future communities. EBMUD’s new water efficient service requirements went into effect July 1, 2007. They promote the rewards and benefits of water efficiency, and apply to all new water services and meter upsizing. Recom- mended water-efficient products have been performance rated by a third party, have been proven to achieve measurable water savings, and are readily available at a reasonable cost to consumers. Average Customer Costs and Benefits MORE INFO? [email protected] A Greener Shade of Blue? 75 D N A L

The Importance of Recycled Water E S U to the San Francisco Bay Area MICHELLE PLA Bay Area Clean Water Agencies

Population growth and climate Recycled Water can reduce Bay Discharges change are predicted to reduce the reliability and sustainability of the water supply for the Bay Area. Com- municating the growing importance of recycled water to the Bay Area, its role in regional water management objec- tives, the regional economic benefits of recycled water, and ways to ensure its safety and allay public concern is an important task for Bay Area water resource managers. The Bay Area Clean Water Agencies recently commis- sioned a White Paper on the “The Importance of Recycled Water to the San Francisco Bay Area,” the purpose of which was to provide a digest HOW CAN BETTER LAND USE PLANNING of factual information about water HELP THE ESTUARY? recycling, including specific information (What Does Smart Growth Have To Do With Water?) developed over many years through many studies. Three main topic areas • Compact urban form means a smaller footprint for population and, in were covered: (1) the importance of theory, more protected watershed lands, recharge areas, natural drain- recycled water to regional water man- ages, and less impervious surface. agement; (2) economic considerations • Higher density (especially residential use) means less landscaping per of recycled water; and (3) recycled capita and therefore significantly less water use (and pollutants) per water implementation opportunities capita. and challenges. The paper asserts that • Public open spaces, parks, and plazas offer opportunities for large land- recycled water: scape water conserving design and space for innovative surface runoff • Helps address growing water management. demands and dependence on vul- • Narrower streets and less surface parking lots result in less impervious nerable imported water supplies; cover per capita; less vehicle miles traveled should result in less pollut- • Helps mitigate risks of long-term ants per capita. climate change; • Has a smaller energy footprint than —Jeff Loux, U.C. Davis most other water supply options; • Can be used to simultaneously address multiple regional water management objectives. Using recycled water can also re- duce mass loadings of pollutants into the Estuary. MORE INFO? [email protected] 76 State Of The Estuary 2008 D N A L

resource conservation that enables E S U Linking the a built environment to be designed Ahwahnee Water Ahwahnee at the human scale while not at the Principles expense of natural communities. • Start with the watershed. Principles to Cities’ Many communities within the Bay Area have adopted the Principles • Use a systems-based General Plans as part of their General Plans. In approach. ELIZABETH PATTERSON addition, the Association of Bay Area • Utilize and protect natural City of Benicia Governments, the Bay Area Water infrastructure. Forum, and the League of California Sustaining the long-term viability of • Use resources—land and Cities have endorsed the principles. our communities begins with a vision water—efficiently. Adopting the principles shows a of stewardship actions to preserve all • Use integrated, multi-purpose community’s commitment to sustain- of our resources, including precious solutions. able growth and responsible water water resources. Cities currently face stewardship. • Solve root causes of major challenges with water pollu- problems, not just symptoms. tion, stormwater, flood damages, and MORE INFO? ensuring a reliable water supply for [email protected]; www.lgc.org current residents and new develop- ments. In response to these challenges and the impacts that local land use decisions can have, the Ahwahnee A Watershed Perspective on Development Principles for Resource Efficient Land use were developed by the Local Government Commission, with a grant from the State Water Resources Control Board, to provide opportuni- ties to reduce costs and improve the reliability and quality of our water resources. The Ahwahnee Principles establish specific guidelines for communities to create a sustainable built envi- ronment. A sustainable community protects natural resources and open space, balances housing and jobs, and provides many transit alternatives. The Ahwahnee Water Principles ensure This conceptual drawing illustrates how much open space or watershed land is left if compact development is used instead of sprawl, and the difference between the protection of water resources permeable and impermeable surface. Permeable surfaces allow water to infil- by maintaining natural floodplains, trate; impermeable surfaces promote rapid runoff, increasing the volume and encouraging open space and pervious velocity of stormwater and the amount of pollutants flowing into the Estuary or other receiving water bodies. surfaces, and employing water conser- vation and recycled water technolo- gies. The Principles, when incorporat- ed into city and county general plans, encourage and help facilitate “smart growth” land use development by arming planners, planning councils, and decision makers with tools to control and shape growth in the commu- nity. The Principles link livability with A Greener Shade of Blue? 77 D N A L

consistency with the Management E S U The Convergence Plan in land use planning approvals is of Urban and Rural subject to appeal relative to projects in the Primary Zone. Land Uses in the The Act and the Management Plan have significant influence over land Delta use and water management in the LINDA FIACK Delta. These documents, and addition- Delta Protection Commission al information about the Commission, can be viewed at delta.ca.gov. The Delta Protection Act was enacted pursuant to legislative action MORE INFO? and the signature of the Governor in [email protected] 1992 (subsequently amended, most recently in 2007). The Act states that West Sacramento YOLO COUNTY 80 Sacramento CALIFORNIA the Sacramento-San Joaquin Delta 50 is a natural resource of statewide, DELTA national, and international significance, Delta Primary Zone N containing irreplaceable resources, Delta Secondary Zone and that it is the policy of the state Freeport County Boundaries Clarksburg 0 2 4 6 to recognize, preserve, and protect SOLANO COUNTY scale in miles 84 those resources of the Delta for the use and enjoyment of current and Hood SACRAMENTO 99 COUNTY future generations. 80 Courtland 5 The Act further states that the ba- to Vallejo sic goals of the state for the Delta are 160 to protect, maintain, and where pos- to Fairfield Locke 220 Walnut Grove sible, enhance and restore the overall 113 quality of the Delta environment, in- 12 R RIVE cluding, but not limited to, agriculture, Isleton Rio Vista wildlife habitat, and recreational activi- 12 Lodi GRIZZLY ties; assure orderly, balanced conser- BAY 12 vation and development of Delta land Collinsville SAN JOAQUIN 160 BAY HONKER COUNTY J resources; and improve flood protec- BAY N OA SA QUI tion by structural and nonstructural N Pittsburg Antioch means to ensure an increased level of 4 Oakley public health and safety. Knightsen P R I M A R Y Stockton The 23-member Delta Protection Brentwood ZONE 4 Commission (Commission) was cre- Discovery Bay 99 CONTRA COSTA ated under the Act to complete and RIVE implement a Land Use and Resource COUNTY R CLIFTON 5 COURT Management Plan for the Primary FOREBAY

Zone of the Delta (Management Lathrop 120 Plan). The Management Plan, com- Tracy

205 pleted and adopted in 1995, contains 580 S E C O N D A R Y to Fresno findings, policies, and recommenda- ALAMEDA COUNTY ZONE tions in the areas of environment, 580 This map and/or data has been prepared for general information purposes only. utilities and infrastructure, land use, The map and/or data has not been approved by the Delta Protection Commission and does not constitute an official map or dataset of the Commission, nor does it establish the boundary lines or land uses of any lands depicted on the map or described in the data. The map and/or data is preliminary, is based upon available information, and is subject to revision as the need arises. Any agriculture, water, levees, recreation republication or other distribution of this map and/or data, by any means whatsoever, must include this disclaimer. and access, and boating. The Manage- ment Plan has been adopted in Delta local government general plans, and 78 State Of The Estuary 2008 D N A L

impedes children’s lung growth. Air The Bay Area has made great E S U Linking Air Quality, pollution can also negatively affect water progress in improving air quality over Water Quality, quality and plant growth via acid rain the past 50 years—but we still face and deposition of pollutants. Other major challenges. These include reduc- Land Use, and impacts from poor air quality include ing traditional air pollutants such as reduced visibility, wear and tear on build- particulate matter, , and toxic air Transportation ings, odors, and economic damages. emissions, as well as greatly reduc- DAVE BURCH Motor vehicles are the major source ing emissions of carbon dioxide and Bay Area Air Quality of air pollution in the Bay Area. Vehicles other greenhouse gases that con- Management District also contribute to water pollution tribute to global warming. Improved through deposition of tailpipe emis- emission control systems, more fuel Problem air pollutants in the sions; road runoff from tire and brake efficient vehicles, and alternative fuels Estuary watershed include: particles (polyaromatic hydrocarbons will all play key roles in confronting • ozone or smog, formed via pho- from tires and copper from brake pads these challenges. However, it will also tochemical interaction of volatile are a major concern); fuel and oil spills be important to constrain the rapid organic compounds and nitrous and improper disposal of oil, brake growth in motor vehicle use (VMT). oxide compounds. fluid, antifreeze, and transmission fluid; Reducing VMT will require changes in • particulate matter, composed of as well as nutrients and pollutants from land use patterns, which dictate travel ultrafine, fine, and coarse particles on-street car washing. Tailpipe emis- choices. We need to better integrate from wood smoke, fossil fuel com- sions have been greatly reduced on a land use and transportation plan- bustion, and geologic dust per-mile basis in recent decades, due ning, to rely more on “smart growth” • air toxics, including diesel particu- to cleaner fuels and stringent vehicle principles such as infill and transit- late matter, benzene, 1,3 butadiene, emission standards. However, a rapid oriented development, to encourage and increase in total vehicle miles of travel more walking, biking, and public transit • greenhouse gases such as carbon has eroded progress from technological use. Fewer vehicle miles traveled per dioxide and methane. improvements. Vehicle miles traveled household will reduce emissions of (VMT) are projected to continue serious air pollutants and greenhouse Air pollution contributes to asthma, increasing twice as fast as population gases, and can help us to improve air lung disease such as emphysema, and growth in the Bay Area. quality and water quality, protect our risk of cancer. Poor air quality also climate, preserve open space, and create and maintain healthy com- PM10 Emissions Inventory Trend 2000-2020 munities, all of which contribute to our high quality of life in the Bay Area. The Association of Bay Area Govern- ments, the Metropolitan Transporta- tion Commission, the Bay Area Air Quality Management District, and the Bay Conservation and Development Commission are partnering with cit- ies to try to strengthen existing city centers, locate housing near transit, encourage more compact and walk- able suburbs, and protect regional open space. We need to continue to expand and strengthen our partner- ships, to encourage greener building, water conservation, and energy effi- ciency, and mitigate urban heat islands with activities like tree planting.

Petroleum refining is responsible for less than 0.5% of PM10 emissions in the Bay Area, MORE INFO? and therefore does not show up at the scale used. Refineries do produce ozone-pre- [email protected] cursor emissions but not a lot of PM10. A Greener Shade of Blue?

Pollutants 80 State Of The Estuary 2008 ANTS T N TA U L L O P

San Francisco Bay Harbor Seal Health

DENISE GREIG and FRANCES GULLAND The Marine Mammal Center MEG SEDLAK San Francisco Estuary Institute A.J. HALL University of St Andrews, Scotland Harbor seals have lived in the San Francisco Estuary for thousands of years. They rest, give birth, and feed within the Bay and consequently are exposed to a variety of anthro- pogenic and terrestrial sources of contamination. As long-lived Estuary residents feeding at the same trophic level as humans, they are ideal for monitoring the effects of emerging marine contaminants on mammalian physiology, and hence humans. Their use of an accessible subcutaneous blubber layer to store energy further enhances their utility for monitoring persistent lipophilic compounds in their environment. Previous studies of contaminants in harbor seal tissue have reported varying levels of PCBs, DDTs, and PBDEs, but few have been able to link their results to harbor seal health or mortality. We are investigat- ing the effects of these contaminants on harbor seal health by analyzing the blood and blubber of harbor seals for PCBs, DDTs, PBDEs, and perfluorinat- ed compounds, while simultaneously developing health profiles for these individuals using hematology, morpho- metrics, prevalence of fecal pathogens, and indicators of infectious disease exposure. In 2007, blood and blubber samples for contaminant analysis were greater than previously reported for contaminants, rather than levels collected from live and dead stranded marine mammals in other locations. alone, on the health of this sentinel harbor seals admitted to The Ma- We plan to further analyze blubber of estuarine health, the harbor seal. rine Mammal Center, as well as from samples for PCBs, DDTs, and PBDEs MORE INFO? seals from Castro Rocks under the and evaluate the levels in conjunc- [email protected] Richmond Bridge. Preliminary data on tion with measures of health, immu- levels of perfluorooctane sulfonate nity, and disease exposure. This will (PFOS) compounds in serum were provide data on the effects of the A Greener Shade of Blue? 81 ANTS T N TA U L L O P

Investigation of Non-PBDE Flame Retardants in San Francisco Bay

Polybrominated diphenyl ethers (PBDEs) are chemicals used as flame re- tardants that are incorporated into a variety of consumer products to comply with fire safety regulations. Restrictions on the use of PBDEs due to environ- mental and human health concerns has resulted in an increase in the use of other chemicals to meet the flammability standards still in effect. Compared to the PBDEs, however, much less is known regarding the toxicity and fate of these alternative flame retardant chemicals, and information on their use (e.g., volume and sources) is generally not available. Examples of chemicals that have report- edly been used to replace PBDEs include hexabromocyclododecane (HBCD), a ubiquitous contaminant that biomagnifies in food webs, and tris (1,3-dichloro-2- propyl) phosphate, a probable human carcinogen. A pilot study will be conducted in 2008 to assess the extent of contamination of several potential PBDE replace- ment chemicals in the San Francisco Estuary ecosystem. Sport fish, bird eggs, and harbor seal blubber, and surface water collected from the Bay will be analyzed for 15 flame retardant chemicals suspected to be in use in the U.S. Results from this study will allow us to determine the risk of exposure of these chemicals to the estuarine food web and to humans consuming sport fish.

Investigation of Perfluorinated Compounds in San Francisco Bay Harbor Seals In 2007, the Regional Monitoring Program began collaborating with the Ma- rine Mammal Center to monitor perfluorinated compounds in Pacific harbor seals. This study is part of a larger three-year study of the health and well being of harbor seals. Harbor seals are an ideal indicator species for persistent bioac- cumulative contaminants in the Estuary because they are apex predators, eating a diet consisting primarily of fish. Perfluorinated compounds are of particular concern because they are very stable compounds that have been identified in foodwebs throughout the world and have been associated with deleterious health effects. Preliminary data from the first year of the study of seals suggests that the concentrations of perfluorinated compounds, particularly PFOS, are elevated in seals relative to concentrations observed in pristine environments. —Meg Sedlak, SFEI 82 State Of The Estuary 2008 ANTS T N TA U L L O P

in both eggs and chicks. Mercury Mercury Risk to concentrations in failed-to-hatch and TAKE HOME POINTS Birds in the San abandoned Forster’s tern eggs were significantly higher than mercury · Mercury bioaccumulates to Francisco Estuary concentrations in randomly collected, levels of concern in several COLLIN EAGLES-SMITH, ET AL. apparently healthy tern eggs. Further, waterbird species nesting in U.s. Geological Survey we found a 32% reduction in tern the San Francisco Bay Estuary, hatching success over the observed suggesting that populations SUSAN DE LA CRUZ and range of egg mercury concentrations. may be at risk. JOHN TAKEKAWA We also found that mercury con- · Mercury levels are not only U.s. Fish & Wildlife Service centrations in down feathers of stilt elevated in high trophic The San Francisco Estuary is a chicks found dead on colony were level, fish eating birds, (such site of hemispheric importance for significantly higher than in randomly- as Forster’s terns) but also waterbird populations. It is also a sampled, apparently healthy chicks of in some birds that eat invertebrates (such as black- site of high mercury concentrations similar age. These results indicate that necked stilts) in marsh and salt in sediments and biota. The risks of mercury may be impairing repro- pond habitats. methyl mercury bioaccumulation and duction in both Forster’s terns and its toxic effects on avian reproduction black-necked stilts, and potentially · Both hatching success and may be greater in waterbirds than other breeding waterbirds, in San chick mortality may be currently being impaired by other wildlife in San Francisco Bay. We Francisco Bay. We recommend that mercury exposure, suggesting examined mercury concentrations in an expanded waterbird monitoring program be established in the Estuary that a more thorough five species of waterbirds common in assessment of mercury effects to more thoroughly assess mercury San Francisco Bay: American avocets, on waterbird reproduction is risk, and suggest using eggs as an ideal black-necked stilts, Forster’s terns, warranted. Caspian terns, and surf scoters. Using bio-indicator of risk to multiple avian · Waterbird eggs have been telemetry, diet, and stable isotope lifestages. developed as a sensitive analyses, we quantified key habitats, MORE INFO? bio-indicator of mercury risk, locations, and prey items utilized by [email protected] and we suggest that a region- pre-breeding and breeding waterbirds. wide monitoring program be We examined mercury concentra- established. tions in adults, chicks, and eggs, and concentrations in their prey. We also monitored nest success and chick survival of Mercury in bay birds three of the locally breeding species (avocets, stilts, and Forster’s terns) at several colonies throughout the Estu- ary. We found that in general, mercury concentrations were highest in Forster’s terns, followed by stilts, Cas- pian terns, avocets, and surf scoters. Using a risk factor analysis, we estimated that 58% of breeding Forster’s tern adults and 46% of eggs exceeded toxicity thresholds established for other avian taxa. We also found evidence of mercury-related effects A Greener Shade of Blue? 83 ANTS T N TA U L L O P

nants affect different endocrine axes Environmental via distinct mechanisms, the kinds of TAKE HOME POINTS Endocrine Disruption endocrine disturbances observed are typically highly reflective of the kind of · Endocrine responses/endocrine in Bay Shiner Perch pollutant present. We have targeted disruption serve as sensitive two indigenous fish species, the shiner bio-markers of environmental and Pacific perch (Cymatogaster aggregata) and perturbations. the Pacific staghorn sculpin (Leptocot- Staghorn Sculpin · Endocrine systems: tus armatus), to assess the degree KEVIN KELLEY, ET AL. to which they are experiencing o are highly responsive to environmental stressors California State University, environmental endocrine disruption Long Beach, CA in association with different regional o respond proportionally Our studies have been aimed locations, including Regional Monitor- to the need to maintain at characterizing the incidence and ing Program study areas. homeostasis potential magnitude of environmental Data emerging from these studies o show alterations reflect- endocrine disruption occurring in na- indicate that both species are accumu- ing the kind of stressor(s) tive fishes resident in the San Fran- lating a variety of contaminants in their present (different cisco Bay Estuary. There is at present livers, including chlorinated pesticides, endocrine-disrupting ample evidence that many locations in PCBs, and PAHs. The same animals also compounds affect dif- ferent endocrine axes the Bay are significantly contaminated exhibit distinct types of endocrine- via distinct underlying with continuing and legacy pollutants disrupted states, with location-associ- mechanisms). of several kinds. Because endocrine ated differences in the functions of systems are highly sensitive and typi- endocrine systems regulating thyroid · Endocrine-disrupted condi- cally respond to presence of environ- hormones, somatic growth, stress tions are observed in SF Bay fish (particularly in urban, mental stressors to a degree com- responses, and . industrial, boat marina areas). mensurate with the need to maintain MORE INFO? homeostasis, they are increasingly [email protected] · Endocrine disruption is evi- being used as effective bio-indicators dent in different fish species. of the effects of pollution and other · Endocrine disruption is oc- anthropomorphic stressors. In addi- curring in different endocrine tion, since different types of contami- systems (stress, thyroid, re- production, growth and repair, defense, metabolism).

ThyRoxine (T4) Levels in SF Bay Fish · There may be interactions among endocrine systems (this means wider impacts on physiological performance).

Pacific Staghorn Sculpin

Shiner Surfperch 84 State Of The Estuary 2008 ANTS T N TA U L L O P

biota throughout the ecosystem, biota, integrated across ecologically Protecting Estuaries including humans, and not just the relevant habitats and food webs. from Toxic benthos. As a result, biologically-based These data provide environmen- monitoring is increasingly recognized tal indicators of trends in estuary Contaminants: The as an important component of efforts health, serve as performance mea- to protect estuaries from toxics. We sures for management actions, and give early warning of unanticipated Role of Biological recommend that biologically-based exposures or biological effects (e.g. monitoring be incorporated into a Observing Systems red flags). broader ecosystem context, which TRACY COLLIER we call a biological observing system 3. Funding for ancillary studies that Noaa Fisheries (BiOS). A BiOS for toxic contaminants piggyback on the monitoring framework to follow up on “red should enhance our ability to protect SANDIE O’NEILL flags.” Such investigations should estuarine ecosystems, and would Washington Department of Fish and provide causality links on which to include: Wildlife base further actions. Our nation’s estuaries are re- 1. A conceptual (or numerical) MORE INFO? cipients of a wide range of toxic model detailing the understanding [email protected] of current loadings and the fate chemical contaminants resulting from and transport of toxics within the human activities, which has led to estuary. Understanding the rela- the implementation of monitoring tive importance of contaminant TAKE HOME POINT programs in most major estuaries. reservoirs in water, sediments, and Much of this monitoring is focused on biota, and the fluxes among these · Compared to monitoring abiotic matrices, primarily water and compartments, will allow manag- sediment and water, monitor- sediments, with sediments viewed as ers to focus on appropriate toxics ing animals can tell you more. repositories for many toxics enter- management actions that maximize ing aquatic ecosystems. However, we benefit to biota. are increasingly aware that we have 2 A biologically-based monitoring underestimated the ecological ramifi- program, assessing exposure and cations of toxic releases: toxics affect effects of chemical contaminants in

American avocet by Bob Lewis A Greener Shade of Blue? 85 ANTS T N TA U L L O P

of California estuaries and embay- Statewide Assess- ments, or 217 square kilometers, was TAKE HOME POINTS ment of Embayment found to be unimpacted, but this was unevenly distributed. More than 70% · A sediment quality objectives Sediment Quality of sediments outside of San Francisco assessment framework was Bay were found to be unimpacted, successfully applied through- Using Multiple Lines while only 4% of the area within the out the state, and data from 6 surveys and 381 stations Bay was unimpacted. The draft sedi- of Evidence integrated. ment quality objectives include three STEVE WEISBERG classifications for impacted sediments · Regional differences in sediment Southern California Coastal Water (possibly, likely, and clearly), and most condition were observed: there Research Project Authority Bay sediments were in the lowest of was a greater area of impacts in San Francisco Bay due to higher Numerous surveys have been those categories (possibly impacted). prevalence of both sediment The high level of mixing within the conducted to study sediment chem- toxicity and benthic community istry, but few link contaminants with Bay may be redistributing contami- disturbance. The cause of the biological effects. We used a multiple nants and producing a low level im- impacts is uncertain. lines of evidence approach to inte- pact to sediments over a wider area, · These results provide a focus grate chemistry, toxicity, and benthic in contrast to the more localized hot for research and management spots in smaller, hydrologically-isolated infauna data to provide an overall actions, including stressor assessment of sediment conditions in embayments of other regions. identification studies in San California. We used five probability- MORE INFO? Francisco Bay and other areas; based data sets collected over the last [email protected] increased monitoring in the seven years, and data were integrated San Francisco Bay with multiple using the state’s draft sediment qual- lines of evidence indicators; ity objectives. Seventeen percent and improved chemistry evalu- ation tools.

Most sites are “possibly impacted” although impacts are greater near ports and commercial areas. 86 State Of The Estuary 2008 ANTS T N TA U L L O P

Targeting Trash: Time for Action DAVID LEWIS Save The Bay Trash and plastic debris pollution is a serious water quality problem in the Bay and its creeks. The California Ocean Protection Council has made reducing and preventing marine debris a top state priority. A San Francisco Bay Regional Water Quality Control Board study found that on average there are three pieces of trash along every foot of streams Walnut Creek leading to the Bay. Save The Bay mem- bers and other citizens have collected extensive photo documentation of releasing phthalates and other toxins trash screening and capture devices in Bay shoreline trash, and last year vol- into the water; deterring recreation; place, and locally-generated funding to unteers removed 686,000 pieces of and reducing how much the public reduce runoff pollution. The new Bay trash from the Bay on just one day. values the Bay. Area Municipal Regional Permit for Like other TMDL pollutants, trash Stormwater runoff is a major stormwater could require significant and plastic debris is a with se- source of Bay trash that has received reductions in Bay trash over the rious impacts: harming fish and wildlife minimal attention until recently. The next several years—adoption and that ingest it or become entangled; Los Angeles region is far ahead of the enforcement of such reductions is a smothering wetland habitat and jeop- San Francisco region on this issue, top priority for improved Bay health. ardizing priority restoration projects; with a strong trash TMDL, extensive To implement a stronger regulatory regime, new infrastructure to remove trash from the storm- water system could prove a cost-effective strategy. Save The Bay has launched a major public education cam- paign on preventing trash pol- lution, and some Bay cities are pioneering source reduction of non-biodegradable trash com- ponents. These efforts must be accelerated throughout the region to achieve significant reductions in trash and marine debris. MORE INFO? [email protected]

Guadalupe River in the South Bay A Greener Shade of Blue? 87 ANTS T N TA U L L O P

lower watershed sites where trash ac- Sources, Amounts, cumulates in the wet season is dispos- TAKE HOME POINTS and Patterns of able plastic. This suggests that urban runoff is a major source of floatable · All watersheds are trashed, Trash in Bay Area plastic found in the Estuary, the ocean. regardless of socioeconomic Streams and on beaches as marine debris. status or population density. Parks with management of trash by · Lower watersheds are more STEVE MOORE city staffs and local volunteers, includ- heavily trashed, due to their Nute Engineering ing cleanup within the creek channels, position in the landscape. had measurably less trash pieces and In 2002, the Surface Water Ambi- · Streams are likely the main deposition rates. ent Monitoring Program (SWAMP) of pathway of floatable plastic to the Regional Water Board developed MORE INFO? marine waters. a rapid trash assessment methodol- [email protected] · Trash levels are not improving ogy. The study report was scientifi- and may be getting worse. cally peer reviewed, and finalized by SWAMP in 2007, and documents sources, amounts, and patterns of Trash Rapid Assessment Results trash in creeks from five Bay Area counties that drain to the Estuary. At selected sites trash was removed, counted, and categorized along a land-marked 100-foot section of stream. These sites were re-visited two or three times in the following months to document trash deposition rates in pieces per 100-ft per day in both dry and wet seasons. Twenty- four regional sites were visited at least three times between spring 2003 and summer 2005. By documenting return rates of trash, the method helps to evaluate the effectiveness of trash cleanup and current management ap- proaches at a specific site. All watersheds studied had high levels of trash, regardless of demo- graphics. Lower watershed sites had higher densities of trash due to their position in the landscape. Most of the trash items are not deposited locally but are conveyed from various storm drains and roads throughout the watershed. Trash source hotspots, usually associated with parks, schools, roads, or poorly kept commercial fa- cilities near creek channels appear to contribute a significant portion of the trash at lower watershed sites. There Coyote Creek, San Jose is significant dry season deposition of trash associated with wind and dry season runoff. The majority of trash at Laurel Creek, San Mateo 88 State Of The Estuary 2008 ANTS T N TA U L L O P

in it, and by contaminating bottom and trash pickup program. Though Oakland’s Programs sediments. Along with the impacts there are many technical and societal to Reduce Trash in of altered hydrology from urbaniza- challenges that face an urbanized lake tion, an abundance of trash degrades like Lake Merritt, the city of Oakland Bay Waters wildlife habitat and water quality in is committed to the challenge and LESLEY ESTES Lake Merritt. Beyond habitat degrada- will continue to experiment with City of Oakland tion, trash accumulation in the lake is and implement new strategies and unsightly to visitors and residents and technologies. Lake Merritt is one of the city impacts the recreational and aesthetic MORE INFO? of Oakland’s finest attractions and experience of Lake Merritt. In 1999, [email protected] is home to boaters, rowing clubs, the U.S. EPA included Lake Merritt on pedestrians, runners, Children’s its 303(d) list for water quality impair- Fairyland, garden clubs, outdoor ment due to trash. In 2001 the City of nature programs, and an array of Oakland established the Lake Merritt wildlife. In fact, Lake Merritt is the first Water Quality Committee consisting TAKE HOME POINTS wildlife refuge established under the of city engineers, naturalists, parks and California Wildlife Act of 1870, and is recreation and watershed program · Structural trash removal de- home to thousands of migratory and staff, Alameda County Flood Control vices (stormwater separators) resident birds. However, the lake sits and city of Piedmont staff, community have been very successful in a in the middle of a highly urbanized, experts, and the Lake Merritt Institute. select few locations; however, mostly paved 4,000-acre watershed The committee developed an evolv- they require significant capital and is beleaguered by trash. Between ing, multifaceted approach to improv- expenditure. 1998 and 2006 an average of 45,000 ing the Lake Merritt environment. The · Stormwater separators pounds (or 22.6 tons) of trash per approach has included piloting and require regular maintenance year has been removed from the constructing new structural stormwa- several times a year, especially lake. Trash degrades water quality by ter trash technologies, adopting new during the storm season. interfering with growth of aquatic anti-trash regulations, including bans · In an older, built-out city like vegetation, decreasing spawning and on Styrofoam take-out containers and Oakland there are significant foraging habitat for fish and other liv- plastic bags, altering street sweeping infrastructure challenges and ing organisms, harming wildlife when and maintenance schedules, and fund- barriers to installing stormwa- they ingest it or become entangled ing a large volunteer-based outreach ter separators. · Trash solutions need to be multi-pronged: In addition to structural solutions, Oakland uses bans on Stryofoam take- out containers and plastic bags, anti-littering programs in schools, “adopt a spot” cleanup programs with citi- zens, clean creeks campaigns, and targeted street sweeping, and employs youth to pick up trash. The city also enforces penalties for illegal dumping.

Damon Slough, Oakland, with trash boom A Greener Shade of Blue? 89 ANTS T N TA U L L O P

Structural Storm Drain End-of-pipe trash removal Retrofits Trash Removal In Southern California MARK CUNEO City of Santa Monica The city of Santa Monica is a vibrant beach community adjacent to Santa Monica Bay in the Los Angeles Basin, where Ballona Creek and the Los Angeles River have been put on the 303(d) list of impaired water- ways due to trash, and a trash TMDL has been put in place. The Santa Monica community has a reputation as a leader in the implementation of sustainable practices; it has a goal of protecting and enhancing environ- mental health, and improving water quality for residents and visitors. The local economy depends on tourism that may be negatively affected by fail- ure to make the beaches and ocean cleaner and safer. Santa Monica oper- ates and maintains 20 miles of storm drains, 650 catch basins, and various other storm drain facilities. Over the past 10 years, the city has spent $120 million implementing many structural best-management practices to reduce Santa Monica the discharge of trash and debris from the municipal storm drain system. The city uses a combination of structural controls in catch basins and at the end of pipes to reduce discharge of trash to local receiving waters. In dry years, it “boards over” storm drain inlets to keep trash out. MORE INFO? [email protected]

TAKE HOME POINTS

· Try to avoid litigation over TMDLs and regulations. · Trash doesn’t magically disap- pear out of structural controls; maintenance is needed. 90 State Of The Estuary 2008 ANTS T N TA U L L O P

and erosion of legacy contaminated atmospheric transport and more Sources of Bay sediments. Of these pathways, ubiquitous historic and ongoing uses. Pollutant Loads to the mass load in stormwater has the Remaining challenges for Hg and greatest uncertainty and is the most PCBs include improving knowledge San Francisco Bay: difficult to quantify. Stormwater mass on sources, determining PCBs and loading studies began in 2002 on the Hg source-release processes, the Knowledge and Sacramento River. Since then, studies character of released material, and Challenges Ahead have been carried out on Guadalupe the significance of dry-weather flows. River, Coyote Creek, and in a storm PBDE challenges include improving LESTER MCKEE ET AL. drain in Hayward. knowledge of source areas and the San Francisco Estuary Institute These studies demonstrate that mechanisms of release, and deter- Fish and biota in San Francisco Bay stormwater mass loads have the mining if mass loads from each main are contaminated with mercury (Hg) potential to significantly decrease pathway stabilize or begin to decrease and polychlorinated biphenyls (PCBs), the rate of recovery of the Bay to in response to bans. and public health advisories recom- desirable standards. The recently MORE INFO? mend limited consumption of fish released total maximum daily load [email protected] caught from the Bay. In addition, poly- (TMDL) reports call for 50 and 90% brominated diphenyl ether (PBDE) stormwater load reductions for Hg concentrations in the Bay Area are and PCB respectively, but there is little amongst the highest reported in the information on where highest con- SUGGESTED world. Hg, PCBs, and PBDEs may be centrations occur and how PCBs and SOLUTIONS considered priority contaminants. Hg cycle through the urban environ- Contaminants enter the Bay via river ment. First-of-their-kind studies in the • Develop side-by-side special flow from the Central Valley, local Bay Area indicate that much of the studies that link hypoth- tributaries and storm drains, mu- PCB mass occurs in older industrial esized stressors with the Bay nicipal and industrial stormwater and areas. In contrast, Hg is more evenly food-web. wastewater, atmospheric deposition, distributed given its propensity for • Employ source tracking tools (more of the same). • Choose a series of “ob- servation watersheds” for How the mercury Pie is Cut long-term monitoring. • Employ watershed models: o To help determine priority watersheds to manage. o To focus data collection. o To improve loads estimates on a regional scale. • Add analytes to the loading studies as new information emerges on impairment. • Encourage more integrated water management (drinking water/flood management/ water quality). A Greener Shade of Blue? 91 ANTS T N TA U L L O P

New P2 initiatives and new chal- Successes and lenges include diverting unused phar- CHALLENGES AHEAD maceuticals from the sewer. EBMUD Opportunities in • Pharmaceuticals—countering is establishing a user-friendly pilot the “sewer it” or “flush it” mes- Pollution Prevention pharmaceutical diversion program sage and dealing with take-back Gayle Tupper that meets stringent Drug Enforce- hurdles ment Agency requirements. EBMUD East Bay Municipal Utility District • Emerging contaminants has also discovered the benefits of Pollution prevention is a proven ef- partnering with environmental non- • Personal care products fective and efficient means for utilities governmental organizations through • Antibacterial products to achieve compliance and protect joint efforts with Save The Bay, Bay- • Flame retardants San Francisco Bay. East Bay Municipal keeper, and Environmental Working Utility District has an innovative and Group. These activities provide an • Nanoparticles successful pollution prevention (P2) effective synergy between EBMUD’s • Fats, oil, and grease (“FOG”); program, focusing on pollutants of technical resources and the grassroots metals concern for EBMUD and the Bay. P2 outreach capabilities of the NGOs at EBMUD has grown from control- to communicate the importance of UPCOMING PRIORITIES ling discharges at large industries to P2 to a wider audience. Opportuni- providing education and best manage- ties in P2 abound in partnering with • Continue to build upon mer- cury program ment practices to smaller commercial additional agencies, institutions, and businesses, and to residential outreach organizations. Each partnership can • Sanitary sewer overflow reduc- and collaboration with a range of enhance the effectiveness of pollution tion through regional fats, oils, partner organizations. prevention efforts for the partners, and grease control program Successful approaches to P2 for the target audience, and for the • Emerging pollutants—residen- include the zero discharge program environment. tial focus for industries that are able to elimi- MORE INFO? • Continued development of nate their discharge for all regulated [email protected] partnerships wastewater. Cost-saving incentives encourage businesses to implement zero discharge and thereby remove potentially significant amounts of pol- lutants from EBMUD’s influent. Wastewater Treatment Plant San Francisco Bay TMDLs are a Mercury Mass Loading 2001-06 driver for P2 efforts, with mercury 12 Month Rolling Average as a primary example. EBMUD’s multifaceted mercury program includes requirements for dentists to install amalgam separators, working with schools and colleges to remove all non-essential mercury from their campuses, and an ongoing residential thermometer exchange program. EBMUD has detected measurable re- ductions in mercury loading since the mercury program’s implementation.

The result of our concerted mercury reduction efforts over the past five years. 92 State Of The Estuary 2008 ANTS T N TA U L L O P

Stormwater or remove it from drainage systems through activities such as street TAKE HOME POINTS Drainage System sweeping, drop-inlet cleaning, and dredging flood control channels. By • We have a good understand- Maintenance removing sediments, these practices ing of the sources and distri- also remove sediment-associated pol- bution of mercury and PCBs. Practices to Reduce lutants such as PCBs and mercury. • There is no “silver bullet” con- Pcb and Mercury Several recent studies have at- trol measure; we need to use tempted to characterize the mass a combination of measures, Discharges to the of sediment, PCBs, and/or mercury including reducing local air removed through these practices. Re- sources, and to work with the Bay sults indicate that standard sediment state on remediation. Jim Scanlin Et Al. removal practices conducted by mu- Alameda Countywide Clean Water nicipalities and flood control districts Program remove a significant mass of these pollutants from stormwater drain- The San Francisco Bay is listed as age systems that may have otherwise impaired due to elevated concentra- reached the Bay. In Alameda County, tions of polychlorinated biphenyls street sweeping removes 100,000 (PCBs) and mercury in Bay fish and cubic yards of material per year, potential adverse effects to wildlife. including 3 kilograms of PCBs and 8 Elevated concentrations of these kilograms of mercury. Ninety percent pollutants have also been found in of PCBs and mercury are removed by sediments within stormwater drain- street sweeping in the northern part age systems throughout the Bay Area. of the county. High-efficiency sweep- Sediments within these drainage ers show a 70% increase in removal systems are carried by stormwater efficiency, but cost two to three times directly to the Bay. Municipalities and as much as current sweepers. flood control districts throughout the Region prevent sediment from MORE INFO? entering stormwater drainage systems [email protected] A Greener Shade of Blue? 93 ANTS T N TA U L L O P

ers are faced with the difficult task of shed. The results show the deficiency Structural Control choosing best management practices of monitoring data for verification, the Solutions: Options, (BMPs) with very little guidance or need for additional BMP performance assurances that they will work, or that criteria, and the near absence of crite- Information Gaps, the selection is anywhere near an ria to insure that BMP selections can optimal selection. Los Angeles’ Propo- comply with institutional and regula- and Challenges sition O, which allocated $500 million, tory constraints. A particular prob- Mike Stenstrom is a good example of the difficulty. The lem is locating BMPs in a developed University of California, Los Angeles full expenditure will reduce emis- urban area, where virtually no land is sions, in the best example, for a single available. In such cases, it is difficult to After the construction of second- pollutant by only 13%, far short of the avoid selecting BMPs simply on the ary treatment plants, urban runoff has TMDL requirements. Many tools are basis of “what can fit.” The exercise become the major source of many available for ranking BMPs but few also shows that BMPs may help meet pollutants, especially of heavy metals can be applied to understand how to several different TMDLs but are only and trace organics associated with meet a TMDL within existing con- being selected on the basis of a single pesticide application and vehicular straints. We used modeling tools and TMDL. activities, and legacy pollutants such existing monitoring data to evaluate as mercury, chlorinated pesticides and MORE INFO? alternatives for meeting the TMDLs polychlorinated biphenyls (PCBs). Fur- [email protected] for the upper Ballona Creek water- ther reductions of emissions of these pollutants must be obtained through urban runoff management. The recent implementations of total daily maxi- mum loads (TMDLs) sets goals for these reduced emissions but provides little or no guidance about how to achieve the reductions. Decision mak-

TAKE HOME POINTS

· We have a way to predict run- off and pollutant loads. · We can identify the spatial origins of the loads. · We can work with existing data although there is room for improvement. · We can prioritize and locate BMPs. · Our analysis suggests that we Example of an infiltration trench that can be used in an urban parking strip. need small BMPS, applicable to road shoulders, small parking lots, medians, etc. An oyster shell beach and backbarrier marsh, covered with gulls, Forster’s terns, and willets, from Fos- ter City. Photo and caption courtesy of Peter Baye. A Greener Shade of Blue?

Restoration Restoration with levee in place

96 State Of The Estuary 2008 TION O I AT R O T S E R

Managing Wetland Habitats as Sea Level Rises JEREMY LOWE,Restoration PWA, Ltd. and withPHYLLIS levee FABER, Faber in place& Associates

Restoration with Levee in Place In the last century sea level rise has accelerated and the land- ward movement of the marshes has been restricted by bayfront levees. The marshes have been “squeezed” between the rising water and the levees, resulting in erosion of the mudflats and loss SOE 2007 of marsh. In turn, the loss of marsh in front of the levees has allowed larger waves to reach and erode the levees. Most restoration projects in San Francisco Bay are subsided sites separated from the Bay or Levee failure after restoration slough by levees. The levees front- ing marshes and mudflats play Levee Failure After Restoration SOE 2007 important, but poorly understood, roles in the evolution of restored sites and in flood management. The bayfront levee blocks tidal flows across the marsh but also blocks the movement of sediment, organic plant material, and detritus Levee failure after restoration that would otherwise move between the outboard mudflat and the marsh on spring tides or during storm surges. The bayfront levee and outboard marsh may provide protection to the evolving site from the erosive effects of waves, allowing sedimentation to occur within the site and protect-

At the same time that sea level rise is creating a demand for more sediment, the construction of bayfront levees has restricted the transgression of the system, potentially reducing the availability of sediment to the marshes. SOE 2007 Top: This diagram shows a levee dividing the baylands from the Bay. Inboard of the levee is a subsided site which, through some combination of filling and natural processes, will sediment up to colonization elevation. The levee protects the site during its early evolution allowing sediment to build up and vegetation to establish. However, outboard of the levee the natural forces of the Bay are still at work. The sweep zone continues to erode, the sweep zone profile lowers, and the edge of any outboard marsh is eroded. The levee prevents the landward transgression of the profile. The mudflats and marsh are “squeezed” between the rising Bay water and the levees, resulting in erosion of the mudflats and loss of marsh. In turn, the loss of marsh and mudflat in front of the levees allows larger waves to reach the levees and causes the toes of the levees to be undermined. 4 Bottom: If the erosion of the levee continues, and the levee eventually fails, the sweep zone-marsh system is reconnected. The sweep zone profile is now much lower and the marsh edge too far seaward, and exposed to greater wave action. The consequence of this is rapid erosion of the marsh edge to reestablish the equilibrium profile. SOE 2007

4 A Greener Shade of Blue? 97 TION O I AT R O T S E R

Dredged Sediments, Cleaned Contaminated Sediments, and Creative Wetland Restoration Solutions NAOMIE FEGER, San Francisco Bay Regional Water Quality Control Board ing the inboard levee until marsh Roger Leventhal, FarWest Restoration Engineering vegetation can colonize. Therefore, The San Francisco Bay Regional Water Quality Control Board has made signifi- there is a tradeoff between leaving cant progress during the last decade on two fronts: addressing “toxic hot spots” the levee in place to provide suf- remediation along the margins of San Francisco Bay and promoting the beneficial ficient protection from waves and reuse of dredged sediment. Remediation of contaminated sediment hot spots pres- reconnecting the geomorphic unit ents significant challenges from multiple perspectives. Many of the Bay “toxic hot and ecological processes so that the spot” cleanups are associated with existing wetlands or planned wetland restoration restored marsh, outboard marsh, and projects and thus must meet stringent cleanup standards to protect endangered mudflat are sustainable. species. Cleanup actions can be constrained by potential impacts to existing endan- San Francisco Bay marshes have gered species, complicating the execution of any remedial action. Restoration proj- handled historic sea level rises well. ect designs that include the beneficial reuse of dredged sediments are not always But sea level rise will accelerate. Will popular, yet they can present advantages where cleanup is necessary and may lead the marshes keep up? As the waters to the inadvertent creation of endangered species habitat. rise, mudflat and marsh systems tend Recent projects using dredged sediments for tidal marsh and seasonal wetland to move landward—if enough sedi- restoration include the Montezuma and Hamilton restoration projects, and the ment is available. In the long-term, we Bair Island restoration projects, which used a combination of dredged sediments may need to recharge mudflats with and upland soils for creating tidal marsh habitats. dredge soil. MORE INFO? MORE INFO? [email protected] [email protected]

Schematic Cross-Section of Non-Cover Sediment Isolation

TIDAL CHANNELS COMPACTED CLAY LEVEES TIDAL CHANNELS 98 State Of The Estuary 2008 TION O I AT R O T S E R

Effects of Inundation TAKE HOME POINTS and Salinity on Tidal • Reducing the rate of change Marsh Vegetation in wetlands depends on maintaining or enhancing TOM PARKER ET AL. freshwater flows into the San Francisco State University Delta in the summer/fall Climate change models for the San periods (levee protection, Francisco Bay-Delta Estuary predict in- less diversion). creased salinity and inundation due to • Restoring new marshes reduced freshwater inflows from the sooner might increase their Bay-Delta watershed and increased likelihood of long-term suc- rates of sea level rise, both likely to cess and persistence. cause a considerably negative impact on wetland biodiversity and pro- ductivity. Our recent research at six sites across the North Bay and Delta indicate that inundation is a much better predictor of tidal marsh plant distributions than elevation alone. Plant species richness increased from 10 to 20 species in Bay salt marshes to over 100 species in freshwater tidal systems. Similarly, end-of-year biomass increased from 600-800 to 2,500 g C/m2/yr from salt marshes to Delta freshwater tidal marshes. As a way of Sarcocornia pacifica investigating more specific impacts from climate change, we evaluated changes in pickleweed (Sarcocornia pa- Global Warming Impact on SF Bay-Delta cifica) productivity along a salinity gra- dient in the Bay. Within three marshes, plots were established near channels with good drainage and in poorly Increasing Ppt drained sites away from channels. We Temperatures Smaller Shifts from found that increases in soil pore salin- Snowpack ity had no measurable effect on plants Snow to rain near channels but had a strongly nega- tive impact on productivity in poorly Lower drained plots. Taken together, these Earlier melt Summer results suggest that, for the most salt Spring floods flows tolerant plant species in San Francisco Bay, increases in inundation greatly Increased Reduced increase sensitivity to salinity, implying Increased inundation Peat that primary productivity will diminish Estuarine formation at faster rates than expected. These salinity changes could cascade into terrestrial and pelagic animal communities linked to wetlands. Sea level MORE INFO? Rise [email protected] A Greener Shade of Blue? 99 TION O I AT R O T S E R

Spartina, by moving the tidal breach Invasive Spartina away from hybrid Spartina patches or TAKE HOME POINTS Control: Clearing by steepening the channel banks to reduce “optimal” seedling habitat, have • New tidal restoration projects in The Way For Tidal proven futile—nearly all sites were the vicinity of seed-producing hybrid quickly invaded, and most became Spartina have an extremely high Marsh Restoration dominated by hybrid Spartina. likelihood of becoming invaded by PEGGY OLOFSON Recognizing the unacceptable the hybrids and then becoming mass San Francisco Estuary Invasive effect of hybrid Spartina on tidal exporters of seed and propagules to other locations, including other Spartina Project marsh habitat, and the looming threat restoration projects. to planned major restoration in the A historical review of tidal marsh South Bay, the State Coastal Con- • Restoration proponents can reduce restoration in southern and central servancy initiated a regional plan of the risk of project invasion by fol- San Francisco Bay shows that where control and eradication in 2000. The lowing “best practices” developed by tidal flows are restored, invasive the ISP, in collaboration with USFWS, San Francisco Estuary Invasive Spar- hybrid Spartina soon follows. The DFG and others. tina Project systematically mapped data suggest that tidal marsh restora- and developed control strategies for These practices include tion has even accelerated the spread every non-native Spartina population of invasive Spartina. The soft, open 1. not opening new projects too in the Bay (now more than 140 sites), sediment and quiescent hydrology near hybrid Spartina acquired environmental authoriza- of newly opened diked ponds are 2. not planting non-native Spartina tions, developed extensive partner- ideal nurseries for hybrid Spartina, species ships, and began implementing ag- which can become established and gressive control in 2005. In 2006 and 3. verifying the genetics of native start spreading seed long before any 2007, the control program treated Spartina and not planting native other type of vegetation appears. more than 1,600 net acres of Spartina Spartina if it could be pollinated Efforts to “design around” invasive (more than 98% of the Bay-wide by hybrid pollen population), and showed 4. rigorously monitoring new proj- remarkable efficacy (60-90% ects and removing any non-na- killed). Unfortunately, in the tive Spartina last two years, the plant has 5. making sure equipment and also spread into two newly dredged materials are free from opened restoration sites in Spartina seed and fragments. the East Bay, and into a small Complete practices can be portion of the Petaluma found at www.Spartina.org. River. Nevertheless, barring • The ISP staff is available to advise and additional ex- assist project planners in assessing pansion into invasion risk and developing site-spe- new areas, cific procedures. Call 510-548-2461 the Invasive or email project specifics to info@ Spartina Proj- Spartina.org. ect expects • With the work of Spartina Project to achieve partners and the cooperation and eradication assistance of the restoration commu- of all visible populations of nity, we can clear the way for a future non-native Spartina by 2011. of successful, large-scale restoration, MORE INFO? unimpeded by invasive Spartina! [email protected] 100 State Of The Estuary 2008 TION O I AT R O T S E R

that most of the Delta is not feasible templates. Other ecosystem types Determinism, Chaos, for restoration; we can restore tidal are also necessary to restore Delta and Randomness: wetlands in certain perimeter areas ecosystem function: floodplains, ripar- only, even considering rapid peat ac- ian, and “green” levees. Water supply, Restoring Delta cumulation of emergent vegetation. entrainment, and food resources all Sea level rise dictates the need for must be addressed for effective eco- Ecosystems landscapes that can shift inland over system restoration. STUART SIEGEL ET AL. time. The near total loss of historic MORE INFO? Wetlands and Water Resources, Inc. Delta wetlands equates to no design [email protected] Possibilities? Needs? Wants? Re- storing Delta ecosystem functions is • Determinism = some aspects of the system will go in a well-understood complex and uncertain yet possible. direction UNLESS perturbed. Restoring habitats and key processes • Chaos = some aspects of the system could go in unpredictable directions IF and reducing stressors comprise the perturbed. triad necessary to “fix” the Delta. • Randomness = drivers of change can be unpredictable in space, time, intensity. Because the Delta of the past cannot be restored and it is not possible for Estuarine and floodplain restoration the Delta to become all things to all opportunity areas people and all organisms, we must consider the probabilities and bound- ing conditions to frame our visions. Drivers of ecosystem restoration complexity and uncertainty fall into three categories. Delta services— water supply, agriculture, recreation, flood management, transportation, utilities, and typically last, ecosystem— create competing demands and major constraints that require give-and-take and money to restore ecosystem functions. The intersection of natural processes and human-based stressors within and outside the Delta—water quality, subsidence, channel geometry, levee failures, invasive species, sea level rise, climate change, urbanization, seismicity, upstream water diversions, etc.—present major boundaries on restoration opportunities. Current planning efforts—Delta Vision, Bay Delta Conservation Plan, Ecosystem Restoration Program Conservation Strategy and the Delta Restoration Plan, Delta Risk Management Strategy, Pelagic Organism Decline Action Plan, and Recovery Plans—provide vital planning vehicles and raise the key question about establishing priorities. Tidal restoration remains a clear priority though it will take decades to achieve its goals. The Delta’s subsid- ence and low sediment supply means A Greener Shade of Blue? 101 TION O I AT R O T S E R

maps of historical landscapes can help associated native species assemblages. Planning Ecosystems elucidate the relationship between Some riparian habitats, such as the Based on Historical native habitats and physical processes now-rare sycamore alluvial woodland, such as local topography, soils, and cli- have experienced disproportionate Landscapes mate. Historical data can thus help us decline and may be more appropri- ROBIN GROSSINGER design new ecosystems based on an ate restoration targets in some places San Francisco Estuary Institute understanding of the natural controls given likely future climate scenarios. on habitat form and function. Similarly, floodplain sloughs are a Historical data are essential for Through historical ecology significant missing element on some both understanding how ecosystems research in the San Francisco Bay streams but not others. Information have changed through human land area, scientists are recognizing that a from historical landscapes can help use and for identifying the full range diverse range of natural stream, ripar- explain the limitations of current con- of potential future scenarios. Using ian, and wetland functions have been ditions and provide new management diverse historical records, a wide tended to be overlooked because options for contemporary watershed range of information about historical of their early modification. Many management. landscapes can be confidently re- watersheds had large, mid-elevation MORE INFO? constructed. These data often reveal wetlands that trapped fine sediment, [email protected] that our current assumptions about maintained base flow, and provided the “appropriate” or “target” habitats calories for juvenile salmonids. Some for restoration are based more on streams that are currently being relatively recent, disturbed conditions managed for perennial flow using than actual pre-modification condi- imported water were largely intermit- tions. In contrast, spatially accurate tent under natural conditions, with

A rare sycamore alluvial woodland 102 State Of The Estuary 2008 TION O I AT R O T S E R

management has been replaced with Restoration in South true adaptive management. The South TAKE HOME POINTS San Francisco Bay Bay Salt Pond Restoration Project led by the California Coastal Conser- • Restoration has evolved from CLYDE MORRIS vancy, California Department of Fish simply fulfilling compensa- U.s. Fish & Wildlife Service and Game, and the Refuge is planning tory mitigation requirements to meeting society’s goals for The South San Francisco Bay has the restoration of 15,100 acres of salt improving water quality, flood ponds over the next 50 years, with a long history of restoration that protection, wildlife conserva- includes some fairly old but significant 2,940 acres of tidal marsh and 710 tion, and wildlife viewing. projects such as the creation of Coy- acres of managed ponds to be estab- • We have a long (20 plus ote Creek Lagoon in south Fremont, lished in the near future. The project’s years) history of a variety of Coyote Creek salt marsh restored by science team has developed specific wetland restoration projects, studies to be conducted as a part of the Santa Clara Valley Water District, from tidal marsh to vernal the Don Edwards San Francisco Bay the Phase 1 projects to address key pools to salt pans for snowy National Wildlife Refuge’s (Refuge) uncertainties such as bird use in re- plovers. restoration of La Riviere Marsh in configured ponds, wildlife response to • Many of these projects have Fremont, and Cargill’s restoration public access, and legacy mercury in been monitored, some for Bay muds. Results of these studies will of the Whale’s Tail in Hayward. The decades, and the results made Coyote Creek Lagoon project is one help us to better plan future projects. available for us to learn from. of the longest continuously monitored Bair Island restoration of 1,400 Our monitoring techniques restoration projects in the Bay Area. acres by the Department of Fish and have evolved from a focus on More recent restoration projects Game and the Refuge has finally be- meeting permit requirements include the Mid-Peninsula Open gun, thanks to a long list of partners. to studies designed to learn Space District’s tidal restoration of Although this project has confirmed how to do it better. the Cooley Landing pond and the the long held theory of the strength • We are moving from mitiga- Refuge’s 2005 restoration of the for- of partnership, it has some new tion projects consisting of mer Cargill Island Ponds in coopera- twists too. Beneficial reuse of dredge small patches to large scale tion with the Santa Clara Valley Water material to restore Inner Bair Island restoration opportunities. District. Catellus’s creation of vernal is on schedule. Charging construction • We are now using true adap- pools for three endangered species in companies for the discharge of clean tive management instead the Warm Springs area of the Refuge fill for restoration of tidal marsh may of just talking about it. We has greatly expanded this resource, be just the ticket for funding future identify key uncertainties that which is rare in the South Bay. restoration of subsided ponds. may impede us from meet- More recent projects have dem- MORE INFO? ing our restoration goals and onstrated changing approaches to [email protected] are designing studies into the restoration in the Bay Area. We are restoration projects to address no longer just these uncertainties. South Bay Salt Pond Restoration Project focused on • Funding for adaptive manage- projects as ment is more challenging to compensatory obtain then other types of mitigation but restoration funding. We need have turned to- to commit to not allowing future large scale restoration ward restora- such as is proposed with the tion to achieve South Bay Salt Pond Restora- all the intrinsic tion Project without assuring values wetlands funding for studies to address offer society. key uncertainties, which will al- We have also low for true adaptive manage- moved beyond ment. just trial-and- error efforts, as knee-jerk A Greener Shade of Blue? 103 TION O I AT R O T S E R

Tidal Restoration and Enhancement on San Pablo Bay National Wildlife Refuge CHRISTY SMITH LESSONS LEARNED U.S. Fish & Wildlife Service • Use adaptive management. The San Pablo Bay National • Keep partners involved. Wildlife Refuge encompasses 13,190 acres of open bay, slough, • Seek additional information: tidal marsh, and seasonal wetlands Throughout the planning in the northern portion of the process, scoping process, and San Francisco Bay Estuary. Restora- all processes, remain open and ready to receive new infor- tion and enhancement activities of mation and/or ideas and be these areas range from treatment prepared to modify, adapt, or of invasive non-native plants, limited change things within the project mosquito control, improvement of as needed. The entire process tidal exchange, and complete tidal should be about learning, adapt- restoration planning. Our work ing, and bringing the best avail- involves partners including other able and most current knowl- landowners or agencies. Lower edge, science, and experience Tubbs Island and Lower Tubbs to the table. In cases where Setback taught the Refuge many the project cannot be changed, lessons that are being used to plan adapted, or modified, communi- the Cullinan Ranch tidal restoration. cations and messages should be continually fine-tuned to better MORE INFO? articulate the project and its [email protected] issues.

Tubbs Island Setback: Tidal Restoration

[BOBBI, WILL SLIDE 5 WORK?] THIS ONE might need TO SHARE A PAGE WITH ANOTH- ER since it is so short 104 State Of The Estuary 2008 TION O I AT R O T S E R

Small Mammals and the Success of Salt Marsh Restoration Projects HOWARD SHELLHAMMER H.t. Harvey and Associates Small mammals (salt marsh harvest mice and various species of shrews) depend on higher marsh zones and adequate escape cover, both of which are reduced or lacking in much of San Francisco Bay, especially in the South Bay. Salt marsh harvest mice need large, deep, mature, salt marshes with internal escape cover and high marsh zones that provide escape cover at the upper edge. Salt marsh wandering shrews need the high and higher half of the middle (pickleweed) marsh, as well as debris and wrack. Restoration projects that produce more pickleweed zones and escape cover will serve these species best. Sea level rise will greatly impact both of these marsh components and potentially compromise the suc- cess of marsh restoration projects. The sustainability of mid- and high-marshes during the rise of sea level needs to be studied. Additional research that needs to be done includes evaluating the success of marsh restoration projects, particularly in the South Bay, to find out the degree to which salt marsh harvest mice use brackish marshes; and understanding the role of the higher marsh zone in brackish marshes, population size (presence) of shrews, both pre- and post-restoration, and effects of pure stands of pepper- grass on salt marsh harvest mice. MORE INFO? [email protected]

A draft recovery plan with good mouse architecture would include: • Marsh complexes of at least 1,000 acres in size. • Broad connections between viable habitat areas within marsh com- plexes allowing for movement of mice. • Mid-marsh or pickleweed zone 200 meters deep or more, ma- turing over time to support internal escape cover along smaller internal channels. • Outboard dikes with 10 to 1 slope on outboard sides to provide escape cover at the upper edges of the marshes. A Greener Shade of Blue? 105 TION O I AT R O T S E R

trends and the proximate and ultimate metrics may be more appropriate for Avian Demographic factors that influence and collectively monitoring clapper rails and other tidal Parameters and determine trends in abundance and marsh-dependent species. in presence of species. Reproduc- MORE INFO? Tidal Marsh Restora- tive success serves as an important [email protected] component of population change, tion Success one that reflects local (site-specific) NADAV NUR and conditions, as well as broadscale influ- MARK HERZOG ences (e.g., due to climate variability). TAKE HOME POINTS Prbo Conservation Science In addition, one can determine critical ANITRA PAWLEY baseline values of reproductive success · It’s important to determine Stillwater Sciences that are required to maintain target whether restoration sites are populations. Data on tidal marsh population sources or sinks. Restoration of tidal marsh habitat song sparrows at newly restored and One of two restoration sites is a high priority for government agen- studied appears to function as mature sites provide an example of cies, non-governmental organizations, a population source. our demographic-based monitoring and multi-partner collaborative efforts, approach, which is applicable at the · Sites differ in bird population such as the San Francisco Bay Joint regional scale as well. Among our find- response: not all mature sites Venture. Many restoration projects are ings, song sparrow nest survival rates are alike; neither are all resto- underway or planned throughout the ration sites. at restoration sites were as high or San Francisco Estuary, and some have higher than those observed at mature · Different metrics work best already been completed. There is a sites. At some marshes (including for different species: pres- critical need for metrics of restoration restoration sites), nest survival met ence/absence for clapper success that can be applied to these the minimum requirement necessary rail; abundance for common projects, both at the single-site level, yellowthroat; nest success for to maintain population stability. Using and at a broader, programmatic level. song sparrow. information collected at an earlier Developing informative and effective stage to refine the sampling design · Monitoring an important pa- metrics will be of great value in design- and/or effort and fine-tune benchmark rameter such as nest success ing restoration projects at both local values of parameters, we can build an can be more cost-effective and Bay-wide scales, and in evaluating than complete demographic adaptive approach into the monitor- projects while they are underway so as studies. ing process. Less-intensive population to contribute to adaptive management of these projects. In addition, these metrics can inform decisions regarding the role of restoration in the context Clapper Rail Comparisons: 1992/1993 vs. 2005/2006 of larger programs that may incorpo- rate mixed land uses (e.g., the decision between restoration and enhancement). We have developed a framework for the collection and evaluation of monitoring data of birds that incor- porates different spatial and temporal scales, using current projects through- out the San Francisco Bay/Delta region. Our approach is both hierarchical and integrated, in which some metrics are collected with broad spatial coverage (e.g., species presence or absence), while other metrics pertain to esti- mates of demographic parameters, requiring more intensive fieldwork at fewer sites. We focus on population 106 State Of The Estuary 2008 TION O I AT R O T S E R

San Francisco Bay Area Upland Where Do We Go Habitat Goals with the Baylands NANCY SCHAEFER Ecosystem Habitat Land Conservation Services STUART WEISS Goals? Creekside Center For Earth Observation CARL WILCOX RYAN BRANCIFORTE California Department of Greeninfo Network Fish and Game The San Francisco Bay Area Upland Habitat Goals Project, modeled after The completion of the Baylands the successful San Francisco Baylands Ecosystem Goals Project, is determining Ecosystem Habitat Goals Project in how many acres of what types of habitats—and in what configuration—are 1999 was a milestone for the Bay. necessary to preserve biodiversity in the nine-county Bay Area. Initiated by It was an articulation of a blueprint the Bay Area Open Space Council to address the lack of a scientific vision for restoration of the Bay shoreline, for biodiversity preservation, the Upland Goals Project will recommend a reconnecting uplands with the Bay. network of conservation lands that will include existing protected lands (lands The Goals strove to provide a bio- permanently protected by fee or conservation easement ownership by public logically based vision for ecosystem agencies or conservation nonprofits for natural resource protection) as well restoration to address the compet- as additional lands proposed for conservation. The project applies the coarse ing needs of tidal marsh dependent filter/fine filter approach to conservation planning. The coarse filter analy- species and those species that had sis sets protection goals for all vegetation types while the fine filter analysis come to use the habitats provided selects specific conservation targets to refine the coarse filter recommen- by diked baylands. Since that time, dations. The project is using conservation-planning software supplemented habitat acquisition and restoration ef- with expert opinion to arrive at conservation land network options. The final forts have accelerated, with the Napa report will not only make recommendations for habitat protection goals but Salt Ponds, Eden Landing Ecological will also address stewardship, implementation strategy, research needs, and Reserve Restoration, Bair Island, evaluation criteria. The planning process will create a framework to allow for South Bay Salt Pond Restoration, and the goals to be updated as new data become available and progress is made other projects all helping to complete in accomplishing the goals or finer-scale planning is desired. The GIS database the mosaic anticipated in the Goals compiled for the Upland Goals Project is available via the Internet at http:// Project. As the Goals Project nears its openspacecouncil.org/projects/upland/download. 10th anniversary, we should review MORE INFO? it in light of new knowledge acquired [email protected] since it was initially written, perhaps in a workshop venue. It should also be linked with other regional efforts such as subtidal, upland, and riparian goals, as well as CALFED’s Ecosystem Restoration Program. MORE INFO? [email protected]

Coastal scrub A Greener Shade of Blue? 107 TION O I AT R O T S E R

bathymetric changes, water control ment in San Francisco Bay. Resource Hidden Bay Habitats: in the Delta, and both point and managers will be able to use the The Subtidal Habitat nonpoint source pollution. As a result resulting document to make informed of these and other impacts, habitats decisions; restoration advocates will Goals Project have been degraded or lost and be able to prioritize restoration activi- KORIE SCHAEFFER native species are in decline. These ties and pursue funding for subtidal NOAA Fisheries pressures are creating an increased restoration projects; and researchers CAITLIN SWEENEY need to develop a plan to protect will be able to prioritize research and Bay Conservation and and enhance subtidal resources within monitoring needs and pursue funding Development Commission San Francisco Bay. for subtidal projects. The San Francisco Bay Subtidal The San Francisco Bay Subtidal The subtidal habitats of San Habitat Goals Project will establish a Habitat Goals Project is a collab- Francisco Bay face numerous pres- comprehensive and long-term vision orative interagency effort between sures. Human uses such as fishing, for research, restoration, and man- BCDC, the California Coastal marinas, shipping and ports, dredging, agement of the subtidal habitats of Conservancy, National Oceanic and sand mining, transportation projects, the San Francisco Bay. The primary Atmospheric Administration (NOAA), recreational use, and industrial uses product of the Subtidal Habitat Goals and the San Francisco Estuary Project. have direct impacts on Bay subtidal Project will be a document that pro- MORE INFO? habitats. Subtidal habitats are also vides recommendations and goals for [email protected] threatened by non-native species and protection, restoration, and research other systemic alterations such as to improve subtidal habitat manage-

Process for Developing subtidal habitat Goals

Habitat Report July 2007

Develop Research Strategy Identify habitat types Identify research needs - Prioritize by management based on uncertainty, and restoration questions Science Goals data gaps, assumptions - Interdisciplinary studies Identify species - Evaluate feasibility associated with habitats

Develop Restoration Strategy Evaluate distribution of Identify habitats and/or - Objectives for habitat types habitats locations for restoration - Regional/subregional objectives Restoration Goals based on - Restoration design distribution and condition - Evaluate feasibility Evaluate condition of habitats

Identify needs for Develop Management Strategy Evaluate impacts to resource management - Protection by habitat type Resource Management habitats from human based on - Protection of locations Goals activities distribution, condition, - Address specific impacts and impacts - Evaluate feasibility

Review existing Determine relevance management documents for to subtidal habitats large-scale concerns Policy-level and need for policy regarding health of San level goal Goals Data gaps, assumptions, Francisco Bay and uncertainty

Stressor Discussion Review (10 year) Goals Document Papers 108 State Of The Estuary 2008 TION O I AT R O T S E R

tiger salamander, Alameda Turning Conflict whipsnake, and 25 other into Cooperation: species. Similar plans are currently underway in Solano Bay Area Habitat and Santa Clara Counties. These multi-species landscape scale plans Conservation California Department are sponsored by local governments of Fish and Game Planning and are community based planning processes involving a broad array of ERIC TATTERSALL ET AL. development, environmental group, U.s. Fish and Wildlife Service landowner, and other interested Multi-species Habitat Conservation stakeholders in the affected area. Plans (HCP) and their state counter- Successful development requires part Natural Community Conserva- commitment by local governmental tion Plans (NCCP) are tools for creat- leaders and strong public involvement ing community based conservation along with state and federal resource plans that contribute to the recovery agencies. More recently significant of state and federally listed plant and progress has been made toward animal species while providing for melding wetland permitting into the orderly and streamlined development plans to provide enhanced wetland within the planning area. They are de- conservation and added permit signed to provide for landscape scale streamlining. conservation instead of mitigation on While development of HCP/NC- a project-by-project basis. The first CPs can often be a time consuming HCP in the nation was completed in process, issuance of permits is not the the Bay Area for San Bruno Mountain end: it is only the beginning, as these in the mid 1980s. Currently there are plans have 30-50 year life spans. They three HCP/NCCPs in preparation or take ongoing active involvement of completed in the Bay Area. all of the interested parties to ensure On July 25, 2007, permits under successful implementation through the state and federal endangered adaptive management. species acts were issued to the cities MORE INFO? of Pittsburg, Clayton, Brentwood, and [email protected] Oakley, and Contra Costa County for the East Contra Costa County HCP/NCCP with broad landowner, environmental group, and developer Conservation Biology 101 support. The plan covers 225,000 acres and au- thorizes up to 15,000 acres of development while protecting and managing 30,000 acres of habitat and open space for the San Joaquin kit fox, Cali- The science of conservation biology has important principles that were used to design fornia red-legged frog, California the proposed HCP/NCCP preserve system. Examples of these principles are repre- sented in the box. A Greener Shade of Blue?

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Quality, and Flux Using a Combination Conditions Affecting Entrainment of Prey Selection of Larval and Juvenile of Optical and Acoustic Measurements Delta Smelt Planktivorous Fish in the San Fran- cisco Estuary A Greener Shade of Blue? 119 I b b Y H P A R G O I L Sung, J., C. Enright, K. Minn, V. Pacheco, Topping, B.R., C.L. Brown, J.L. Dyke, of Wisconsin; B.A. Mohammad, C.J. DWR. Levee Conceptual Model USGS. Correlation of Metal Concen- Zabin, Smithsonian Environmental trations between Clams and Overly- Research Center. A New Invasion of Sustaita, D., S. Estrella, L. Thompson, ing Water in Suisun Bay an Old Invader: Batillaria attramentaria DFG; L. Patterson, P. Quickert, DWR. in San Francisco Bay Seasonal Demographic Patterns and Tucci, L.E., D. Le Fer, R. Churchwell, Habitat Associations of the Salt Marsh SFBBO. Salt Pond Use by Northern Werner, I., R.E. Connon, L.A. Deanovic, Harvest Mouse in Suisun Marsh Harriers J.P. Geist, T. Ha, UC Davis. 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Takata, L.T., N. Dobroski, M.Falkner, Vines, C.A., W.A. Bennett, G.N. Cherr, Whitcraft, C.R., D.M. Talley, SFSU. The California State Lands Commission. N. Ikemiyagi, UC Davis; J.A. Hobbs, Impacts of Perennial Pepperweed Protecting California’s Coasts from UC Berkeley. Population Status and Invasion in Wetlands Along an Inunda- Ship-Borne Invaders: Recent Major Endocrine Disruption in Longjaw tion Gradient Initiatives of the California Marine Mudsucker (Gillichthys mirabilis) in San Invasive Species Program Francisco Bay Wintzer, A.P., P.B. Moyle, UC Davis. Interactions Between Fishes and Talley, D.M., C.R. Whitcraft, SFSU. Walther, D.A., USFWS; S. Bynum, Invasive Jellyfish in the Upper San Closing the Gap: Rapidly Integrating Scientific Principle, Inc. Understanding Francisco Estuary, CA Science and Management to Address Boater Activity as a Potential Pathway Urgent Ecological Issues for the Spread of Quagga and Zebra Woodleys, C.M., J.J. Cech Jr., P.B. Moyle, Mussels in California UC Davis; L.R. Brown, USGS. The Tashjian, D.H., S.S. Hung, UC Davis. Se- Contribution of Physiological Energet- lenium Toxicokinetics, Chronic Toxicity, Wardani, J., J. Cain, W. Eisenstein, B. ics to Conservation: A Case Study and Interaction with Salinity Stress in Smith, A.R. Westhoff, UC Berkeley. The Sacramento Perch White Sturgeon Great Delta Charrette *Titles within Presentations and Post- Tejeda, C.L., S.M. Schultz, USACOE. Warner, C.H., SFBJV. Mission 37: ers are based on abstracts and posters US Army Corps of Engineers Delta A Comprehensive Outreach Cam- submitted prior to the conference. Initiatives paign for Wetland Projects Along Some details may have changed since Highway 37 then: see abstracts for updates. Thompson, J.L., USFWS. HACCP: A Tool for Preventing the Spread of Webb, H., R. Wilder, USFWS. Compar- Invasive Species in Natural Resource ison of Growth Rates of Native and Management Activities Non-native Juvenile Fishes between the Yolo Bypass and the Sacramento Thompson, B., B. Greenfield, S. Lowe, River A. Melwani, A. Robinson, SFEI. Indica- tors of Anthropogenic Contamination Weiskel, H.W., E.D. Grosholz, UC in the Estuary Davis; J.E. Byers, University of New Hampshire; T.C. Huspeni, University 120 State Of The Estuary 2008

Acronym Key PBDE: Polybrominated Diphenyl Ether PUBLISHED BY The San Francisco Estuary Project and ABAG: Association of Bay Area PEEIR: Pacific Estuarine Ecosystem CALFED, July, 2008. This report can be Governments Indicator Research downloaded at www.sfestuary.org

BCDC: (San Francisco) Bay Conser- PRBO: PRBO Conservation Sci- SFEP DIRECTOR vation and Development Commis- ence, formerly Point Reyes Bird Judy Kelly sion Observatory CALFED: CALFED Bay-Delta Pro- PWA: Philip Williams & Associates SFEP PROJECT MANAGER Marcia Brockbank, retired gram RCD: Resource Conservation CCC: California Coastal Conser- District CONFERENCE DIRECTOR vancy Karen McDowell SJSU: San Jose State University CEMAR: Center for Ecosystem Man- REPORT EDITOR agement and Restoration SBSP: South Bay Salt Pond Restora- Lisa Owens Viani tion Project CEQA: California Environmental SFBBO: San Francisco Bay Bird Ob- VITAL STATISTICS Quality Act Joe Eaton servatory CSU: California State University SFBCDC: San Francisco Bay Conser- CONTRIBUTING WRITERS, CVP: Central Valley Project vation and Development Commission EXECUTIVE SUMMARY Joe Eaton and Kristi Coale CVRWQCB: Central Valley Regional SFBJV: San Francisco Bay Joint Venture Water Quality Control Board RESEARCH AND EDITING SFBRWQCB: San Francisco Bay Re- ASSISTANCE DFG or Cal Fish & Game: California gional Water Quality Control Board Joe Eaton and Ron Sullivan Department of Fish and Game SFEI: San Francisco Estuary Institute ILLUSTRATIONS DHS: California Department of Lisa Krieshok Health Services SFEP: San Francisco Estuary Project DWR: California Department of SFSU: San Francisco State University PHOTOGRAPHS Peter Baye, Robert Lewis, Jean Matuska, Water Resources STRAW: Students and Teachers Wendy Murphy, Heidi Perryman, Cheryl Restoring a Watershed EBMUD: East Bay Municipal Utility Reynolds, others as noted, and courtesy District SUNY: State University of New York of authors. Front cover Jean Matuska, back cover Wendy Murphy GGNRA: Golden Gate National SWP: State Water Project Recreation Area DESIGN SWRQB: State Water Resources Bobbi Sloan HSU: Humboldt State University Control Board PRINTING IEP: Interagency Ecological Program TBI: The Bay Institute Alonzo Printing IRWM: Integrated Regional Wetland TMDL: Total Maximum Daily Load Monitoring Program questions, comments, UC: University of California concerns? ISP: Invasive Spartina Project [email protected] USF: University of San Francisco MLML: Moss Landing Marine Lab USACOE: United States Army Corps Thank you to the CALFED Science Program MTC: Metropolitan Transportation of Engineers for reviewing a draft of this report and pro- Commission viding financial assistance for publication. USBR: United States Bureau of MWD: Metropolitan Water District Reclamation A Note to State of the Estuary of Southern California Conference Participants USDA: United States Department of This report includes a mixture of original NEPA: National Environmental Policy Agriculture unpublished and published research presented Act at the October 2007 State of the Estuary USEPA: United States Environmental (SOE) conference. NMFS: National Marine Fisheries Protection Agency Service Thank you to all those who responded to our USFWS and/or U.S. Fish and Wildlife: call for updated abstracts after the confer- NOAA: National Oceanic and Atmo- ence. The Estuary Project appreciates your United States Fish and Wildlife extra work in helping us put together this spheric Administration Service report. Due to budget and space constraints, information from some posters and presenta- NOS: National Ocean Service USGS: United States Geological tions could not be included, especially if not OEHHA: California Office of Environ- Survey submitted in digital form as requested soon after the conference. Apologies to any of those mental Health Hazard Assessment we were not able to include. Information from all posters and presentations can still be found in the original conference abstract book.