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					      The STaTe of The BirdS
       San franciSco Bay
PRBO Conservation Science and the San Francisco Bay Joint Venture
Purpose                                                Produced by PRBO Conservation Science and the San Francisco Bay Joint Venture.

  This report summarizes the current state                                     PRBO Conservation                                  The San Francisco Bay
of knowledge on the bird populations of San                                    Science (PRBO) is                                Joint Venture is one of
Francisco Bay, while also recommending                                         dedicated to conserving                          eighteen Joint Ventures
science-based actions needed to conserve them                                  birds, other wildlife,                           established under The
and the habitats they depend upon.                                             and ecosystems through                           Migratory Bird Treaty Act
  Within this report are population trends,                                    innovative scientific                            and funded under the annual
threats, and recommended actions for land and                                  research and outreach. Our                       Interior Appropriations Act.
water managers, policy-makers, non-profit              120 staff and seasonal biologists use the studies    It brings together public and private agencies,
conservation groups, and researchers.                  of birds and their habitats to guide biodiversity    conservation groups, development interests, and
                                                       conservation from Alaska to Antarctica. PRBO is      others to restore wetlands and wildlife habitat
  The messages delivered through the report
                                                       especially active in San Francisco Bay wetlands,     in San Francisco Bay watersheds and along the
aim to enhance bird conservation in San
                                                       where we currently play a lead role guiding the      Pacific coasts of San Mateo, Marin and Sonoma
Francisco Bay by (1) guiding habitat restoration,
                                                       restoration and management of thousands of           counties. The goal of the San Francisco Bay
management, and acquisition; (2) increasing
                                                       acres of tidal habitats. PRBO also studies the       Joint Venture is to protect, restore, increase, and
knowledge of the population status of San
                                                       ecosystem effects of climate change and uses         enhance all types of wetlands, riparian habitat,
Francisco Bay’s birds and the threats to their
                                                       scientific analyses to inform land managers          and associated uplands throughout the San
habitats; and (3) influencing public policy
                                                       and decision-makers about priority actions for       Francisco Bay region to benefit birds, fish, and
and public awareness of bird and ecosystem
                                                       conserving ecosystems and wildlife.                  other wildlife.
conservation needs.

Please cite as: Pitkin, M. and Wood, J. (Editors). 2011. The State of the Birds, San Francisco Bay.
                PRBO Conservation Science and the San Francisco Bay Joint Venture.

Foreword ......................................2     Human-created Habitats ................18

Overview .....................................4      Upland Habitats ...........................20

Tidal Flats .....................................6   Endangered Species .....................22

Managed Ponds ............................8          Policy .........................................30

Tidal Marsh .................................12      Success Stories ............................34

Tidal Marsh Herons and Egrets .......14              Contributors.................................38

Subtidal Habitat ...........................16       Photographers .............................40

                                                     Funders ......................................41

                                                                South San Francisco Bay salt pond restoration area

    Foreword                                             about bird populations and their recent
                                                         trends in the Bay Area.
       San Francisco Bay and its surroundings have         San Francisco Bay is an area of
    always been in a state of change, but the rate       hemispheric importance to migratory
    and magnitude of changes have accelerated            waterbirds. It harbors populations of
    dramatically ever since gold mining in the           species that have undergone evolution-
    mid-1800s deluged the Bay with sediments and         ary diversification in different parts of
    contaminants. More recently, burgeoning urban        the Bay. Several of these populations
    development and the alteration of freshwater         are officially recognized as Threatened
    flows into the Bay – resulting from massive          or Endangered, and others are of
    re-engineering of water distribution in the          special conservation concern. In a
    Sacramento-San Joaquin Delta – have increased        broader sense, birds are indicators of
    pressures on natural ecosystems. And while           the overall condition of habitats and
                                                                                                       Shorebirds in San Francisco Bay
    the future is always uncertain, there is little      ecosystems in the Bay – the proverbial
    question that sea level rise and storm surges will   “canaries in the coal mine.” Tidal-                          The State of the Birds report details the many
    fundamentally alter both urban and natural areas     marsh species can tell us not only about the con-          factors that threaten bird populations in the Bay
    around the periphery of the Bay.                     dition of the marshes, but about the capacity of           Area. Some of these – predators ranging from
      In order to manage and conserve ecological         those marshes to provide huge benefits to people           house cats to Peregrine Falcons; competition
    systems in the context of past changes, and          – ecosystem services – through flood protection            with invasive species such as Barred Owls;
    adaptively respond to ongoing and future             and enhancement of water quality. And, at the              or continuing loss of habitat in the face of
    changes, it is essential to understand where we      end of the day, birds are an essential part of what        development – are clear and present dangers.
    are now. The State of the Birds: San Francisco       makes San Francisco Bay a truly special place.             Others, such as the drowning of marsh habitats
    Bay 2011 summarizes what we currently know                                                                      due to sea level rise, are lurking in the future.

2                                                                                                                             John A. Wiens (PRBO Conservation Science)
  Yet others may be consequences of our own           Dealing with the conservation
conservation work. A major effort is now            challenges is not simple. But
underway to restore a network of artificial         neither is it impossible. At a
ponds once used for salt production to tidal        time when news reports seem
marshes. This restoration will create new habitat   to contain only discouraging
for marsh-dwelling species such as Common           messages about the state of
Yellowthroats and Clapper Rails. At the same        nature, The State of the Birds
time, it will reduce the amount of shallow open-    indicates that populations of
water ponds that some nesting birds, ducks, and     many species in the Bay Area
wintering shorebirds currently use.                 are stable or increasing, and it
   How these ripple effects play out may depend     highlights several examples of
on whether other processes (such as sea level       conservation success. These,
rise) create suitable habitat elsewhere and         together with the many specific
if habitat created specifically for ducks and       recommendations for actions
shorebirds within the restoration project proves    by managers, scientists, or the
successful. This largest restoration project on     public that may help to counter
the West Coast is something to be proud of,         downward trends for other          Arrowhead Marsh, Oakland shoreline
especially as it moves forward with ongoing         species, give hope.
monitoring helping to quantify the impact to          Above all, the report emphasizes the           for more than a decade. Continued monitoring
birds, making course corrections as needed          importance of monitoring. We know what           will enable us to spot troubling trends and take
to ensure the most benefit for birds in the San     we know now because populations of several       actions to address the root causes before they
Francisco Bay Estuary.                              species in the Bay Area have been monitored      become emergency-room cases.

    Overview                                             low levels, and the Least Tern may be starting to
                                                         stabilize after years of population growth.
      In this first ever State of the Birds report for
    San Francisco Bay, we learn that most bird           Grassland and coastal scrub-chaparral
    populations are stable. Some species are clearly     birds are losing habitat.
    benefiting from conservation action while others       Species in these habitat types continue to be
    are struggling. In the following pages, the report   impacted by loss and degradation of habitat
    highlights these trends, challenges, and the         from development, invasive species, and lack of
    actions people can take to make a difference.        natural disturbances such as fire. These trends
                                                         are consistent with the declining trend found in
    Most bird populations are stable.                    the National State of the Birds Report, 2009.
      When we evaluated groups of birds for each
    habitat, we found that most are now stabilizing.     California Clapper Rail still struggles.              Over one million shorebirds use the tidal flats and
                                                                                                               shallow ponds of the San Francisco Bay each year.
    This includes birds dependent upon subtidal            Perhaps one of the Bay’s most iconic birds,
    (submerged) habitats, tidal flats, marshes, and      this rail still struggles because of habitat loss,    All habitat types harbor species at risk.
    oak woodlands and the endangered Spotted Owl.        predator pressure, and invasive species. Sea
                                                                                                                 Declines can be early warnings of a decline
                                                         level rise will make it even harder for rails to
    Riparian birds and two endangered                    persist as they are pushed into marginal habitat
                                                                                                               in ecosystem function. Causes of declines need
    species have increased.                              with rising seas and strong storms. Tidal marsh
                                                                                                               to be investigated and actions should be taken
      Riparian birds – species that require stream-                                                            to stabilize bird populations. Species to watch
                                                         restoration efforts and scientific monitoring must
    side habitat – and two of our threatened and                                                               include: California Clapper Rail, Western
                                                         continue to ensure that this endangered bird can
    endangered species, the Snowy Plover and Least                                                             Sandpiper, Forster’s Tern, Caspian Tern,
                                                         persist into the future, especially as the location
    Tern, have shown some increases. Recently, the                                                             Black-crowned Night Heron, Snowy Egret,
                                                         and extent of marsh habitat change.
    Snowy Plover has been increasing from very                                                                 Canvasback, Northern Pintail, scaup and scoters.

4                                                                                                                             Melissa Pitkin (PRBO Conservation Science)
Sea level rise is a critical threat.                   Predator and invasive species control
Habitat restoration needs to take advantage of         must continue.
the best scientific modeling to predict the best       Both animal and plant, and native and non-
places to restore marshes and guide restoration        native predators and invasive species, remain an
design to ensure that marshes, and the benefits        ongoing threat. Funding is needed for predator
they provide wildlife and people, are maintained.      control, invasive removal, and outreach to the
                                                       public on their role in reducing predators (such
Extreme weather events are predicted.
                                                       as feral cats) and invasive species.
Climate models predict more frequent extreme
weather events, such as strong storms and heat         Human activities can be designed to
waves, as the climate changes. These unusually         reduce impacts to birds.
strong events can cause nest failure, facilitate       Disturbance from human recreation, mainte-          Critical long-term monitoring research for
predation, and cause individual bird death.            nance, and transportation activities is something   Clapper Rails and Black Rails.
                                                       we can control and reduce to lessen pressures to
The amount of tidal flat habitat needed
                                                       birds during their sensitive nesting period.        Science must continue.
requires more study.
                                                                                                           Continued monitoring of the Bay’s bird
Keeping one million shorebirds in San Francisco
                                                                                                           populations is necessary, to evaluate our success
Bay requires better understanding of how many
                                                                                                           at maintaining healthy ecosystems. Birds are the
acres of tidal flats are needed to maintain the
                                                                                                           proverbial “canary in the coal mine.” Tracking
Bay’s high shorebird numbers. Understanding
                                                                                                           their populations will help us solve problems
how sea level rise will change the amount and
                                                                                                           before they become “emergency-room cases.”
location of tidal flats is a high research priority.
                                                                                                           A mix of public and private funding is
Restorationists can learn from one
                                                                                                           To ensure our ability to protect existing habitats,
The South Bay Salt Pond Restoration Project
                                                                                                           respond to new threats, and maintain and
will provide valuable lessons for future marsh
                                                                                                           enhance the quality of Bay waters upon which
restorations within the Bay.
                                                                                                           birds and people depend, a mix of funding
                                                       Restored wetlands in Sonoma Baylands.               sources is necessary.

Tidal Flats

                                                                                                                                      Status — Overall stable, with a geographic
                                                                                          South          Central    North
                                                                                                                                      shift from south to north.

                                                                                300,000                                               Trends — Overall, the shorebird population

                                                   Total Number of Shorebirds
                                                                                                                                      in San Francisco Bay has remained stable
                                                                                                                                      since the 1990s, but an increase in the
                                                                                                                                      North Bay and apparent decrease in the
                                                                                                                                      Central and South Bays indicate a shift of
                                                                                100,000                                               shorebirds from south to north.
                                                                                 50,000                                               One of the more common species, the
Dunlin feeding
                                                                                     0                                                Western Sandpiper, appears to have
                                                                                             1990-1992             2006-2008
                                                                                                                                      declined Bay-wide.
Exposed twice a day by the Bay’s low tides,
                                                  November high tide roost counts of shorebirds                                       Two other common species — Least
tidal flats are teeming with life. Small clams,
                                                  throughout San Francisco and San Pablo Bays.                                        Sandpiper and Willet — have increased
marine worms, and crustaceans feed more                                                                                               greatly.
than one million shorebirds each year. Today,                                                                                         Keeping one million shorebirds in San
42% of the Bay’s tidal flats have been lost                                                                                           Francisco Bay will require maintaining
compared to historic levels.                                                                                                          sufficient tidal flat habitat as well as other
                                                                                                                                      shallow water habitats, especially as sea
In addition, shorebirds in San Francisco Bay
                                                                                                                                      level rises. The amount of tidal flat and other
are also dependent on salt ponds, many of                                                                                             habitats needed by shorebirds should be
which are now managed to maximize their                                                                                               determined.
value as shorebird breeding and foraging
habitat. (See Managed Ponds, pages 8–11,
for more information.)
San Francisco Bay is so critical to the health
of shorebird populations that it has been
designated a Site of Hemispheric Importance       Willet
for Shorebirds (

 6                                                                                                                             Julian Wood and Gary Page (PRBO Conservation Science)
Threats                          Actions
 Primary threat: Loss of        Planning, Management, and Restoration
tidal flat feeding habitat        Plan for mudflat creation and          Minimize pollution
due to sea level rise, erosion   sustainability by conducting            from runoff on paved
from storm surges, and           physical modeling exercises and         surfaces, allowing
invasive plants (e.g., hybrid    assessing those results over time       rainfall to soak into the
Spartina).                       to ensure that current and future       ground; convey and
 Loss of shallow water          coastal defense (e.g., levees,          treat storm water runoff
feeding habitat, as former       rip-rap, and seawalls), salt pond       using landscape features      Western Sandpipers
salt ponds transition to         restoration, and development            such as rain gardens and
tidal marsh through active       does not reduce mudflats. Future        other water conservation
restoration or through levee     restoration should focus on             systems.
failure due to impacts of sea    increasing both tidal flat and tidal                                            Determine the amount of ponds,
                                                                          Manage for a mix of pond
level rise.                      marsh habitats.                                                                other shallow water habitat,
                                                                         conditions with depths ranging
                                                                                                                and tidal flats needed to support
 Reduction of food               Maintain shallow pond feeding         from 2 to 5 cm and salinities
                                                                                                                the Bay’s breeding and migratory
(invertebrates) caused by        and roosting habitat, especially        from 120 to 200 ppt for optimum
invasions of non-native          when tidal flats are inaccessible       shorebird use.
invertebrates, pollution, and    during high tides.                                                              Conduct early winter Bay-wide
                                                                          Provide and protect roosting
climate change impacts.                                                                                         shorebird surveys annually to spot
                                  Control non-native plants that        habitat away from areas of
                                                                                                                potential declines quickly. Participate
 Human-caused                   colonize mudflats (e.g., hybrid         frequent human use.
                                                                                                                as a citizen scientist in the Pacific
disturbance to feeding and       Spartina).
                                                                          Reduce human-caused                  Flyway Shorebird Survey (www.
resting shorebirds, resulting     Remove non-essential barriers         disturbance (e.g., hiking, dog
in birds having less energy      such as dams, culverts, levees, and     walking, boating) in areas where
for migration and survival.                                                                                      Monitor site-specific shorebird
                                 other structures that inhibit natural   shorebirds feed in high densities
                                                                                                                response to restoration, and study
 Loss of high tide              flow and settling of sediment.          (e.g., Napa River tidal flats,
                                                                                                                how mudflat characteristics influence
roosting habitat such as                                                 San Leandro Bay, and Hayward
                                  Restore watersheds to facilitate                                             habitat quality for shorebirds.
levees, islands, structures,                                             southward to southern San
                                 movement of tidal flats to higher
and high ground as sea level                                             Francisco Bay). Collaborative           Conduct research to better
                                 areas as sea level rises and to
rises, levees are removed                                                planning between the San               understand and predict changes
                                 promote movement of sediment
or deteriorate, and islands                                              Francisco Bay Water Trail and the      in tidal flat habitat in the context
                                 downstream to feed tidal flats.
within restored ponds are                                                Bay Trail can consider actions to      of sea level rise and potentially
submerged.                                                               minimize disturbance.                  decreasing sediment supply.

Managed Ponds

                                                                                   Northern Shoveler                                                             Status: Mixed.
                                                                                   female                                                                        As restoration progresses, the bird community
                                                                                                                                                                 may change: tidal marsh species (pages
                                                                                                                                                                 12–13) will colonize newly created salt
                                                                                                                                                                 marsh habitat; some waterbirds, such as
                                                                                                                                                                 shorebird and duck species that use open
                                                                                                                                                                 water or tidal flats, may move out. Ongoing
                                                                                                                                                                 monitoring will track how bird species and
Commercial salt ponds were constructed                                                                                                                           numbers change over time.
around the edge of San Francisco Bay begin-
ning in the mid 1800s. Many former salt
production ponds in San Francisco Bay have                                                                                                                                                             Caspian Terns       Forster’s Terns

                                                                                                        Number of Breeding Terns in San Francisco Bay
recently transitioned to public ownership and                                                                                                           4,000

are being restored and managed for wildlife.                                                                                                            3,500

These shallow ponds now provide habitat for

hundreds of nesting terns, gulls, and shorebirds,                                                                                                       2,000

and roosting and feeding habitat for hundreds                                                                                                           1,500

of thousands of migrating and wintering shore-                                                                                                           500

birds and ducks.                                                                                                                                           0
                                                                                                                                                                1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010

The South Bay Salt Pond Restoration Project
                                                                                                       Forster’s and Caspian Tern use of salt ponds –
(15,100 acres) plans to restore 50–90% of the                                                          Declining; the Forster’s Tern breeding population varies
South Bay ponds to a mix of tidal marsh and                                                            annually but is declining Bay-wide. Caspian Terns show a
shallow managed ponds. The Napa-Sonoma                                                                 decrease, especially in recent years.
                                                    Forster’s Terns at nest site
Marshes Wildlife Area in the North Bay is
restoring 4,200 acres of salt ponds to tidal
marsh. Cargill Salt still manages about 11,000
acres for salt production, all in the South Bay.

 8                                                                                                                                         Josh Ackerman and Arriana Brand (U.S. Geological Survey);
                                                                                       Jill Demers and Catilin Robinson-Nilsen (San Francisco Bay Bird Observatory)
                                                                                                                                                                                                      Nesting Shorebirds (South Bay
                                       50,000                                                                                      70,000
                                                                                                                                                                                                      ponds) – Population trends unknown,
 Number of Breeding California Gulls


                                                                                                                                                                                                      underscoring the need for ongoing
                                       35,000                                                                                      50,000                                                             monitoring of breeding shorebirds.
                                                                                                                                   40,000                                                             American Avocets and Black-necked

                                       20,000                                                                                      30,000                                                             Stilts are the most abundant nesting
                                       15,000                                                                                      20,000
                                                                                                                                                                                                      shorebirds; breeding American Avocets
                                       10,000                                                                                                                                                         are estimated at 1,380 pairs, and
                                                                                                                                                                                                      Black-necked Stilts are estimated at
                                           0                                                                                            0
                                                1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010               2003   2004   2005   2006   2007   2008   2009   2010   590 pairs, as of 2003.

California Gulls (South Bay ponds) – Increasing rapidly; the                                                                      Wintering Dabbling Ducks (South Bay ponds) –
population is now at 46,000 gulls.                                                                                                Have increased in the last seven years: see the Success
                                                                                                                                  Stories section, page 34.

  250,000                                                                                                                          45,000

                                                                                                                                                                                                      Black-necked Stilt
  100,000                                                                                                                                                                                             Note: The Western Snowy Plover
                                                                                                                                                                                                      also nests in the salt ponds; see the
                   50,000                                                                                                                                                                             Endangered Species section, page 24.
                                          0                                                                                         5000
                                                      2003     2004      2005     2006      2007      2008     2009      2010                2003    2004   2005   2006   2007   2008   2009   2010

Spring-Migrating Small Shorebirds (North and                                                                                      Spring-Migrating Medium-sized Shorebirds (North
South Bay ponds) – Have remained relatively stable.                                                                               and South Bay ponds) – Have increased slightly, according
                                                                                                                                  to eight years of monitoring by USGS.*

                                                                                                                                                                                                        Threats, Actions
*Data for medium-sized and small shorebirds and dabbling ducks come from peak counts for shorebirds (spring) and
                                                                                                                                                                                                        Please turn to page 10.
ducks (winter) in North and South Bay ponds.

Managed Ponds
(continued from page 9)

 Primary threat: Loss of shallow pond               Contaminants impairing bird reproduction.
habitat for roosting, foraging, and nesting         Mercury, a legacy of years of mercury mining
waterbirds. Wintering and migratory shorebirds      and use of mercury in gold mining, is a prevalent
roost and feed in salt ponds at high tide. Ducks    contaminant throughout San Francisco Bay.
utilize shallow, low salinity ponds to forage and   Mercury is especially high in the South Bay,
roost. Terns and shorebirds nest on islands and     where runoff from a large mercury mine in the
levees in pond habitat.                             upper watershed has released, and continues
                                                    to release, mercury-laden sediments. Mercury
 Rising sea levels from global climate change
                                                    impacts waterbird reproduction, specifically for
may increase water depths or erode levees and
                                                    the Forster’s Tern, in which 48% of breeding
nesting islands, impacting habitat for wintering,
                                                    adults are at or above high risk of impaired
migrating, and nesting birds.
                                                    reproduction due to their present methylmercury
 Nest predation and competition from a             concentrations.
growing population of California Gulls,
which prey upon eggs and chicks or displace
nesting waterbirds. Forster’s and Caspian Terns
have already been displaced from some of their
historic nesting colonies by gulls.

                                                                                                        Shorebirds in managed pond habitat
             American Avocets in breeding plumage

Planning, Management, and Restoration                     Scientists
 Convert a large proportion of salt ponds to              Monitor changes in abundance of breeding,
managed ponds. Maintain ponds with appropriate            migrating, and wintering waterbirds over time to
depths – and habitat of varying salinities – to benefit   evaluate the overall effects of restoration.
nesting, migrating, and wintering shorebirds and                                                                     Northern Shoveler male
                                                           Determine current breeding population size of
                                                          nesting American Avocets and Black-necked Stilts.
 Practice adaptive management by monitoring              Monitor their use, density, and reproductive success at
waterbird responses to restoration and modifying          created islands.
restoration as needed (as in the South Bay Salt Pond
                                                           Assess habitat characteristics that enhance
Restoration Project).
                                                          waterbird densities, (e.g. water quality, water depth,
 Continue to create islands within managed ponds         salinity, invertebrate biomass, island characteristics),
for breeding and roosting birds. Experiment with          and provide restoration project managers with habitat
adding vegetation to some islands to create cover for     characteristics that could maximize densities of
chicks.                                                   waterbirds in the remaining ponded habitat as tidal
                                                          marsh restoration proceeds.
 Improve dissolved oxygen within managed ponds
by optimizing water flow between pond and Bay              Suggest ways to reduce the population growth of
waters and reducing nutrient inputs from adjacent         California Gulls and their impact on other breeding
uplands.                                                  waterbirds by identifying the causes of population
                                                          growth and evaluating methods to control it.
 Conduct an education campaign to highlight the
connection between urban waters and the Bay.               Assess and track the changes in methylmercury
                                                          concentration in nesting Forster’s Terns, American
 Slow the growth of the California Gull population
                                                          Avocets, and Black-necked Stilts as tidal restoration
by reducing gull access to trash at local landfills
                                                          proceeds. Determine reproductive threshold
and other areas. Evaluate whether removal of target
                                                          concentrations of methylmercury in waterbirds to
gulls helps reduce predation pressures on nesting
                                                          assess changes in risk of contaminant exposure as a
                                                          result of tidal restoration efforts.
 Identify, protect, or manage key existing
waterbird nesting areas Bay-wide, given that
waterbird populations may be affected by a reduction
of pond habitat.

Success Story • South Bay Salt Pond Restoration Project – See page 34



Tidal Marsh                                                       4



                                                                                                                                                 Status: Stable to increasing
                                                                       1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008          The three species chosen to indicate the
                                                                                                                                                 state of the tidal marsh are Song Sparrow,
                                                   Song Sparrow – The most common tidal marsh bird is                                            Common Yellowthroat, and Black Rail. Data
                                                   overall stable, but the last 10 years show declines.                                          were collected from over 200 locations
                                                                                                                                                 throughout San Francisco Bay Estuary using
                                                                0.5                                                                              5-minute point count surveys during April–
                                                                                                                                                 May to assess breeding season density (birds
                                                                                                                                                 per hectare).
Tidal marshes are the vegetated, tidally             Density
                                                                                                                                                 Song Sparrow – Stable overall (decreasing
influenced wetlands found along the edges of                    0.2                                                                              North Bay and Suisun Bay; increasing South
San Francisco Bay and associated channels.                                                                                                       Bay)

Pacific cordgrass, pickleweed, and other                                                                                                         Salt Marsh Common Yellowthroat – Slightly
specialized plants adapted to salty water                              1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008          increasing.
provide important habitat for many animal                                                                                                        California Black Rail – Recently increasing.
                                                   Saltmarsh Common Yellowthroat – Prefers channels
species, such as young salmon and other
                                                   and brackish marshes and has increased since the 1990s.                                       Note: For California Clapper Rail, see
fishes, rails, songbirds, shorebirds, egrets,                                                                                                    Endangered Species section, page 22.
ducks, and the endangered salt marsh harvest                    0.25

mouse. Some animals, like the indicator                         0.20

species here and the salt marsh harvest
mouse, are endemic to the tidal marshes of                      0.15

San Francisco Bay – meaning they do not                         0.10

occur anywhere else in the world. While                         0.05

80% of historic tidal marsh habitat has been
lost since the mid-1800s, growing marsh                                1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

restoration efforts are reversing this trend and                                                                                                 California Black Rail
                                                   California Black Rail – Recent increases give hope for
causing the acreage to increase again.             this State-listed species.

 12                                                                                                                                       Julian Wood and Nadav Nur (PRBO Conservation Science)
                                                                                                                      Common Yellowthroat
Threats                                                       Actions
 Primary threat: Rising        Invasive plants,             Planning, Management, and                          Halt development on
sea level resulting in some    particularly invasive          Restoration                                       existing or potential
marshes “drowning” or          Spartina hybrids (crosses       Support and use sea level rise modeling         future baylands
disappearing and other         between native cordgrass       tools to better understand impacts on tidal       including salt ponds,
marshes transitioning from     and introduced cordgrasses),   marsh habitat due to climate change, and          diked baylands, and uplands with future
fresh water to brackish        cover mudflat areas and        to prioritize areas for preservation and          marsh potential.
marsh or from high marsh       channels, eliminating          restoration of marsh habitat. For an example       Control introduced predators such as
to low marsh. Limited space    important feeding sites        of a model focused on predicting Bay-wide         red foxes and feral house cats, especially
remains along the Bay’s        for shorebirds and marsh       changes to the tidal marsh ecosystem, visit       in areas with high concentrations of marsh
shoreline for marshes to       birds. Pepperweed invades                            birds. Educate the public about the impact
expand or regenerate.          marshes and channel edges,                                                       of cats on bird populations, and remove
                                                               Identify and protect upland areas for
 Loss and conversion of       outcompeting gumplant and                                                        feral cat feeding stations.
                                                              marshes to move to as sea level rises.
restorable marsh due to        other native marsh plants
                                                               Promote restoration in high-priority             Reduce native predator populations
urbanization (especially       required by Song Sparrows
                                                              areas like the Petaluma and Napa River            (raccoon, skunk, crow, and raven) by
in south and central Bay)      and Common Yellowthroats
                                                              systems and South San Francisco Bay that          eliminating or securing food waste in parks,
threaten potential future      for nesting and cover.
                                                              are better able to cope with rising sea levels.   residential areas, businesses, and other
marsh locations.                Introduced and                                                                 sources near the Bay.
                               increased predators such        Promote re-use of clean sediment from
 Extreme storm events                                                                                           Monitor and control introduced invasive
                               as non-native red foxes,       dredged navigation channels to jump-start
push water beyond typical                                                                                       plants early, when costs are lower, or when
                               Norway rats,and house          marsh restoration in subsided areas or to
high tide levels, eroding                                                                                       a direct threat to marsh birds is likely.
                               cats, and native raccoons,     help marshes keep pace with sea level rise
marsh habitat and flooding
                               corvids, and gulls prey        in the future.
high marsh – critical as                                                                                        Scientists
refugia for marsh birds.       upon birds nesting in           Restore high-ground refugia, such as
                                                                                                                 Monitor marsh bird population sizes
High water can flood           marshes surrounding the        broad levee slopes and gradual upland
                                                                                                                and reproduction annually to determine
nests and push rails and       Bay. Predator numbers are      transitions, with native vegetation to offer
                                                                                                                Bay-wide trends and to evaluate the success
other marsh animals to         usually inflated near urban    birds and small mammals refuge from high
                                                                                                                of conservation efforts. Make results known
higher ground and adjacent     areas.                         tide events.
                                                                                                                to conservation practitioners and the public.
urbanized areas, where they     Pollution, contaminants,      Support the South Bay Salt Pond
                                                                                                                 Advance predictive modeling of future
are vulnerable to predators.   and toxic events such          Restoration Project, and promote it as
                                                                                                                habitat conditions and bird response, to
High water events are          as oil spills directly kill    a model for future restoration efforts.
                                                                                                                guide habitat acquisition and restoration.
predicted to become more       birds as well as vegetation,   This large restoration project can serve
severe and more frequent       fish, and invertebrates.       as a demonstration project, as it is being         Assess contaminant thresholds in birds,
with climate change.           Mercury, PCBs, and             adaptively managed to ensure the most             to evaluate impacts of mercury and other
                               other contaminants affect      benefit to the San Francisco Bay ecosystem.       toxins to marsh birds.

Success Stories South Bay Salt Pond Restoration Project – See page 34 Carl’s Marsh restoration – See page 34

Tidal Marsh
Habitat Type                                                                                                                                                          Status: Overall stable with large
                                                                                                                                                                      variation between years
Herons and Egrets
                                                                                                                                                                    Status: Stable to decreasing.
                                                                              Great Blue Heron          Great Egret
                                                                                                                                                                    The number of nests of herons and egrets
                                                                                                                                                                    throughout San Francisco Bay shows
                                                                     800                                                                                            dramatic variation from year to year with an
                                                                     700                                                                                            apparent decrease in the last 5–10 years.

                                                  Number of Nests
                                                                                                                                                                    Large between-year declines are related to
                                                                                                                                                                    heavy rainfall, which can reduce the survival
                                                                     300                                                                                            of young birds before they are old enough to
                                                                     200                                                                                            breed.
                                                                           1991   1993   1995    1997      1999     2001     2003   2005   2007   2009

                                                 Great Blue Herons (blue) and Great Egrets (red) reveal
                                                 dynamic but generally stable populations.

Nest colony on Sherman Island in the
North Bay                                                                     Black-crowned Night Heron           Snowy Egret


San Francisco Bay’s herons and egrets                               700

depend on large trees, dense types of
                                                  Number of Nests

vegetation, and man-made structures                                 400
surrounded by tidal marsh, tidal mudflats, and                      300

non-tidal wetlands for nesting in spring and                        200

summer and for feeding year-round. Important                        100                                                                                             Great Egret feeding half-grown chicks
feeding sites also include creeks and ponds.                               1991   1993   1995    1997      1999       2001   2003   2005   2007   2009

View a map of the locations of all known egret
                                                 Black-crowned Night-Herons (blue) and Snowy Egrets
and heron colonies in the San Francisco Bay      (red) show dramatic variation in nesting abundances; however,
Area:        recent trends (since 2005) suggest regional declines.

 14                                                                                                                                                                              John Kelly (Audubon Canyon Ranch);
                                                                                                                                                                Contributors: John Kelly (Audubon Canyon Ranch) and
                                                                                                                                                         Caitlin Nilson-Robinson (San Francisco Bay Bird Observatory)
Great Blue
                Threats                                Actions
                 Primary threat: Loss or              Planning, Management, and Restoration
                disturbance of colony nesting
                sites from damage to nest trees or      Protect and restore tidal marsh and tidal flat habitat within
                construction activities (noise) that   1-6 miles of nesting sites. This is the most urgent action needed
                scare birds away from nesting sites.   to protect or sustain heron and egret nesting populations in San
                                                       Francisco Bay.
                 Loss of wetland feeding areas
Great Egret     close to the nesting colony (within     Provide year-round protection to colony nesting sites. They
                1–6 miles). Greater distance           are frequently destroyed when trees or other habitat features are
                between nest and feeding areas         removed or damaged during the non-breeding season (fall and
                reduces the chance of survival for     winter). Such protection depends on local action, recognizing that
                their young.                           heron and egret use of surrounding areas depends on the year-round
                                                       protection of colony sites.
                 Degradation of wetland feeding
                areas and associated declines           Create 200-meter buffer zones of no human activity around
                in prey (fish, small mammals,          nesting areas during the nesting season (January–August).
                invertebrates).                         Protect and restore wetland areas surrounding colony sites.
Snowy Egret
                 Nest predation by native or non-      Create and protect clumps of native trees at distances of 5
                native animals, such as raccoons,      miles or greater from existing colonies, preferably near open water.
                feral cats, raptors, or ravens.
                 More intense winter storms, as
                predicted with climate change, lower    Improve models of heron and egret habitat sensitivity as
                the survival of young egrets and       potential biological indicators of wetland condition, and identify
                herons.                                factors that can determine the linkage between colonies and
                                                       surrounding habitat.


                Success Story West Marin Island National Wildlife Refuge – See page 35


                                                                                                             Sea Ducks       Diving Ducks
                                                                                                                                                                       Status: Most diving and sea duck species
                                                                                                                                                                       are stable, but four species are declining.
                                                                              280,000                                                                                  The species of sea and diving ducks
                                                                                                                                                                       wintering in San Francisco Bay show stable

                                                    Number of birds counted
                                                                              200,000                                                                                  populations, with the following exceptions:
                                                                              160,000                                                                                  Canvasback (a diving duck): Nationally,
                                                                              120,000                                                                                  Canvasback numbers are highly variable
                                                                               80,000                                                                                  around a long-term average of about
                                                                               40,000                                                                                  600,000. Locally, their wintering numbers
                                                                                    0                                                                                  in the Bay have shown long-term decline,
                                                                                        1955 1959 1963 1967 1971 1975 1979 1983 1987 1991 1995 1999 2003 2007 2011
                                                                                                                                                                       perhaps due to habitat loss in the Bay or the
                                                                                                                                                                       creation of habitat in areas like the Central
                                                    Sea Ducks (blue) – Overall stable but may be declining in the                                                      Valley.
Subtidal habitat is the habitat below the surface   past two decades. Diving Ducks (red) – Populations are variable                                                    Scaup (a diving duck) and scoters (sea
                                                    with no clear trend.                                                                                               ducks) are declining throughout North
of San Francisco Bay, typically submerged.
Birds using the subtidal habitat in the Bay                                                                                                                            America as well as in the Bay. The San
                                                                                                                                                                       Francisco Bay populations of these two
feed on fish, shellfish (including mussels),
                                                                                                                                                                       groups of ducks represent, on average,
invertebrates, underwater plants, and algae.                                                                                                                           between 40% and 50% of all scaup and
                                                                                                                                                                       scoters counted in the Pacific Flyway. If
                                                                                                                                                                       conditions change in San Francisco Bay, a
                                                                                                                                                                       large percentage of the population may be

                                                    Greater Scaup                                                            Surf Scoter


 16                                                                                                                                          Mark Herzog, Josh Ackerman, Susan W. De La Cruz (U.S. Geological Survey);
                                                                                                                    Jill Demers (San Francisco Bay Bird Observatory); Cheryl Strong (U.S. Fish and Wildlife Service)
Threats                                       Actions
 Primary threat: Reduced quality             Planning, Management, and Restoration                  Scientists
and quantity of wintering habitat
                                               Ensure that wintering habitat remains available       Continue the USFWS mid-winter
from increasing contaminants (selenium,
                                              for sea ducks and diving ducks, by restoring and       waterfowl survey, which has provided
cadmium, and mercury); loss of deep
                                              preserving deeper and less saline water ponds within   a consistent record of winter waterfowl
pond habitat; and changes in prey
                                              restoration areas such as South San Francisco Bay      populations since 1955.
species composition.
                                              and Napa-Sonoma Marsh.
                                                                                                      Study prey density and waterfowl feeding
 Climate change and sea level rise,
                                               Minimize pollution from runoff by working            behavior to determine high-quality habitat that
resulting in changed salinities and water
                                              with local governments and communities to              should be protected or enhanced (e.g. eelgrass,
depth. This could alter prey composition
                                              create programs that reduce runoff (e.g. reducing      creek mouths, ponds, shoals).
and herring spawning.
                                              impervious surfaces) and upgrade storm water and
                                                                                                      Model carrying capacity of intertidal and
 Loss of herring stock in San                sewage treatment plant facilities.
                                                                                                     subtidal habitats to help set wintering population
Francisco Bay and along the Pacific
                                               Reduce contaminant release when conducting           goals. Current efforts have shown the value
Coast. Herring spawn is important in
                                              restoration activities by maintaining deeper water     of San Pablo Bay subtidal habitats, and they
diving duck diets, particularly for scoters
                                              depths. Special care should be taken to minimize       point to prey distribution and fish and shorebird
during spring migration, but also is used
                                              actions that increase contaminant release (mercury,    competitors as key elements in future modeling
heavily by scoters and scaup throughout
                                              selenium, and cadmium) or methylmercury                efforts that incorporate all sub-bays.
the winter.
                                              production in shallow water areas.
                                                                                                      Evaluate the effects of human disturbance on
 Disturbance from boat traffic flushes
                                               Minimize disturbance in key foraging areas           foraging and roosting birds.
resting or foraging ducks off the surface
                                              from recreational and ferry boats, especially in the
of the water.                                                                                         Model sea level rise, salinity, and sediment
                                              following areas: in northern San Pablo Bay; near
                                                                                                     to help predict how benthic prey availability in
 Winter oil spills have the potential for    eelgrass beds; and within the central part of San
                                                                                                     subtidal and intertidal habitats may change in
catastrophic impact to duck populations.      Francisco Bay from the Bay Bridge to the San Mateo
                                                                                                     the future.
 Declining availability of quality
                                                                                                      Determine habitat connectivity among
breeding habitat in Alaska, Canada,            Encourage restoration of eelgrass, which is a
                                                                                                     San Francisco Bay, migratory corridors, and
and the northern Intermountain West           substrate for herring spawn and prey species like
                                                                                                     breeding areas to help establish flyway-wide
Region.                                       crabs, mussels, and small fish.
                                                                                                     conservation efforts year-round.
                                               Implement the Subtidal Habitat Goals Report
                                              recommendations for the restoration, protection,
                                              and science needed to protect this habitat type –

                                                                                                                                                                              Status: Stable
                                                                                        Brandt’s Cormorant    Brandt’s Cormorant anomalies      Western Gull
                                                                                2000                                                                                          Seabirds are long-lived birds; thus their
                                                                                                                                                                              populations can withstand occasional years
                                                                                                                                                                              of poor reproduction or reduced reproductive

                                                     Number of Breeding Pairs
                                                                                                                                                                              effort. Because of this, evaluating the status
                                                                                1000                                                                                          of a nesting colony is done by looking at the
                                                                                                                                                                              reproductive success or breeding population
                                                                                                                                                                              size. The figures at left present over two
                                                                                                                                                               (208)          decades of data on reproductive effort for
Several human-created habitats are used by
                                                                                                                                                                              cormorants and gulls.
birds: levees, bridges, and buildings, to name                                    0
                                                                                       1990   1992   1994    1996   1998   2000   2002   2004   2006   2008    2010
                                                                                                                                                                              Western Gull and Brandt’s Cormorant:
a few. Data on the bird use of all these habitats
                                                                                                                                                                              Stable. In 20 years of monitoring the nesting
are not available. In this section we discuss       Brandt’s Cormorants (blue) and Western Gulls (red) –
                                                                                                                                                                              success of these long-lived seabirds, repro-
                                                    Alcatraz Island reproductive success.
two key places, Alcatraz Island and some of                                                                                                                                   ductive success has remained largely constant
the Bay’s bridges, where bird monitoring data                                                                                                                                 until 2009 and 2010. The complete nesting
exist.                                                                                        San Francisco–Oakland Bay Bridge        Richmond–San Rafael Bridge              failure in 2009 and 2010 was likely due
                                                                                 900                                                                                          to a low anchovy population throughout the
Alcatraz, once a barren sandstone rock                                           800                                                                                          Central California coast region.
originally inhabited by seabirds, faced a                                        700
                                                                                                                                                                              Double-crested Cormorant: Stable, though
                                                      Peak Nest Count

long period of human settlement. In the last                                                                                                                                  their reproductive success has varied over
20 years, the island has once again begun                                        400
                                                                                                                                                                              the last 26 years. In 2009 and 2010, these
to attract seabirds that use its human-created                                   300
                                                                                                                                                                              cormorants showed a sharp decline, but they
                                                                                                                                                                              appear to be recovering. The low number of
structures as home.                                                              200

                                                                                 100                                                                                          nesting pairs in 2009 was likely due to a low
Over100 feet above the water the I-beams and                                       0                                                                                          anchovy population throughout the Central
                                                                                       1984 1986 1988 1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010
other support structures under the roadways of                                                                                                                                California coast region.
the Richmond–San Rafael Bridge and the San          Double-crested Cormorants – Number of nesting pairs on Bay
Francisco–Oakland Bay Bridge serve as nest-         bridges.
ing platforms for Double-crested Cormorants.

 18                                                                                                                                                                Meredith Elliott and Sara Acosta (PRBO Conservation Science);
                                                                                                                                                                                                 Mark J. Rauzon (Laney College)
Threats                               Actions
 Primary threat: Human               Planning, Management, and Restoration
disturbance, including main-
                                       Adjust timing of maintenance and construction activities and
tenance activities, tourism, and
                                      manage tourism to reduce bird disturbance during the months of
boating, can cause seabirds to
                                      February–July. If not possible, maintenance and construction personnel
abandon the nesting colony.
                                      should work with biologists on ways to limit disturbance.
 Lack of food due to steep
                                       Create new habitat on bridges and piers when possible. Explore
declines in common prey
                                      using methods of social attraction to draw birds to newly built
species, as evidenced by the                                                                                      Double-crested
                                      ‘cormorant condos’ (artificial nesting structures on the new San
2009 region-wide anchovy crash,                                                                                   Cormorant
                                      Francisco–Oakland Bay Bridge).
can cause seabirds not to breed.
                                       Re-install historic buoys at Alcatraz and work with the Bay
 Losing nesting sites on
                                      Conservation Development Commission to implement seasonal closures            Success Story
human-created structures. On
                                      to create a boat-free buffer zone during the seabird nesting season.          Seabirds on Alcatraz
Alcatraz, if nesting areas are
opened for public tourism during       Educate tourists on Alcatraz about the sensitivity of nesting               Island – See page 35
the spring and summer, nesting        seabirds. National Park Service programs should continue to increase
habitat will be lost.                 tourist awareness of nesting seabirds on Alcatraz, especially with regard
                                      to closed areas during the nesting season.
 Contaminants accumulation
in adult birds, in high               Scientists
concentrations, can affect
                                       Assess contaminants through studies of nesting birds. Failed-
reproduction and chick survival.
                                      to-hatch eggs have been collected opportunistically from the bridge
Cormorants are fish-eating birds
                                      colonies, but eggs should be collected and analyzed for contaminants
and are at risk of accumulating
                                      on an annual basis. Relating cormorant contaminants with prey
contaminants (e.g., mercury,
                                      contaminants can help identify which fish species carry the most
lead) from San Francisco Bay.
                                      contaminants in San Francisco Bay. Further research on lethal levels of
 Climate change effects such         these contaminants in Double-crested Cormorants should be considered.
as extreme high temperatures
                                       Prey studies are needed. A better understanding of Double-crested
result in heat stress in nesting
                                      Cormorant diet is needed, since food affects the survival of this
birds (nausea, dizziness, seizures,
death) and nest abandonment, as
witnessed in 2008 on Alcatraz          Conduct complete annual monitoring of all known Double-crested
Island.                               Cormorant breeding sites, especially the South Bay power towers.

                                                                                                                  Western Gull at nest site, Alcatraz

Upland Habitats

                                                                                                                                                                                  Status: Mixed
                                                                           Riparian     Oak Woodland    Coniferous-Redwood Forest   Coastal Scrub/Chaparral    Grasslands

                                                                                                                                                                                  Each upland type was assigned a suite of
                                                                                                                                                                                  indicator species that best represent that
                                                                                                                                                                                  habitat in the Bay Area. Over the 42 years

                                                Estimated Percent Change
                                                                                                                                                                                  of study:

                                                                              -10                                                                                                 Indicators for riparian birds show an
                                                                              -20                                                                                                 increase of greater than 20%. Riparian
                                                                              -30                                                                                                 habitats are recognized as one of the most
                                                                              -40                                                                                                 important upland habitat types in the West for
                                                                              -50                                                                                                 birds and other wildlife. Streams were heavily
                                                                                      1970    1975     1980     1985       1990     1995     2000       2005    2010
                                                                                                                                                                                  impacted in the past. In response to the listing
                                                                                                                                                                                  of imperiled salmonids and concern for water
                                                Birds in Upland Habitats – Data are from the Breeding Bird                                                                        quality, stream restoration has increased
Surrounding the waters and wetlands of          Survey for 14 routes in eight Bay Area counties.                                                                                  dramatically over the past several decades,
San Francisco Bay are a variety of ‘upland’                                                                                                                                       benefiting birds as well.
habitats including the five most common                                                                                                                                           Indicators for oak woodland and coniferous-
types – coastal scrub-chaparral, coniferous-                                                                                                                                      redwood forest birds are stable.
redwood forests, grasslands, oak woodlands,
                                                                                                                                                                                  Coastal scrub-chaparral and grassland
and riparian (streamside) forests. These                                                                                                                                          birds are declining, coastal scrub by 27%
vegetation communities vary in their mix of                                                                                                                                       and grassland by over 45%. Species in these
native and non-native plant species and the                                                                                                                                       habitat types continue to be impacted by loss
composition of bird communities they support.                                                                                                                                     and degradation of habitat. These trends are
                                                                                                                                                                                  consistent with the declining trend found in
                                                                                                                                                                                  the National State of the Birds Report, 2009.

                                                Savannah Sparrow in                                                            Acorn Woodpecker in
                                                grassland                                                                      oak woodland

 20                                                                                                                                                                         Tom Gardali and Leo Salas (PRBO Conservation Science)
  Threats                                                 Actions
   Primary threat: Habitat loss and degradation          Planning, Management, and                       Scientists
  caused by land-use changes such as open space           Restoration:
                                                                                                           Determine which species are most
  conversion to housing or intensive agriculture,          Adopt and implement the Uplands               vulnerable to the effects of climate change.
  invasions of native and non-native species, and         Habitat Goals and Bay Area Critical Link-
  lack of ecological disturbances such as fire. For                                                        Map future distributions of species under
                                                          ages documents:
  example, the two habitat types with the greatest bird                                                   climate and land use change scenarios.
  declines, coastal scrub-chaparral and grasslands, are    Control the most destructive invasive
                                                                                                           Monitor upland birds to track distribution
  transitioning to other habitat types due to lack of     species, and support and participate in the
                                                                                                          and abundance changes and nest success and
  disturbance and the invasion of native species (such    Bay Area Early Detection Network
  as Douglas fir), non-native plant species (such as      (
  broom), and annual grasses that alter fire regimes.                                                      Identify Bay Area species population
                                                           Use disturbance (e.g., fire and grazing) to
                                                                                                          targets, working with the San Francisco Bay
   Lack of appreciation for the habitat value of         create and maintain diverse upland habitats.
                                                                                                          Joint Venture.
  scrub-chaparral and grasslands. Not typically            Promote conservation on private lands,
  thought of as beautiful or in need of protection,                                                        Study the use of grazing and other
                                                          including thorough use of economic incentive
  scrub-chaparral is seen as an eyesore or fire hazard,                                                   disturbances as vegetation management tools.
  and a “clear the brush” attitude reduces habitat.
                                                           Continue to restore riparian areas.
   Climate change affects vegetation type and water
  availability, thereby altering the amount, type, and     Promote wise water use in order to
  quality of habitats available to birds.                 maintain stream flows and groundwater
   Gaps in scientific knowledge that is needed to
  inform and evaluate land management decisions and        Educate the public on the value of
  policy actions.                                         habitats such as coastal scrub-chaparral and

                                                          Success Story Riparian restoration on Chileno Creek (Marin County) – See page 36
Wilson’s Warbler in       Wrentit in coastal scrub-
riparian habitat          chaparral

Endangered Species
Clapper Rail

                                                                                                                                         Status: Decreasing
                                                                                                                                         Clapper Rails in San Francisco Bay have

                                                 Minimum Population Estimate
                                                                               4000                                                      decreased dramatically from the tens of

                                                 Minimum Population Estimate
                                                                                                                                         thousands that roamed the undiked marshes
                                                                               3000                                                      before the California Gold Rush.
                                                                                                                                         Hunting, then development reduced popula-
                                                                                                                                         tions and pushed Clapper Rails into smaller
                                                                               1000                                                      marshes separated by urban landscapes.
                                                                                                                                         More recently, the rail population hit a low
                                                                                       1970s   1980s   1990s   2005-08                   point in the early 1990s, likely due to preda-
                                                                                                   Year                                  tion by non-native red foxes. The Clapper
                                                Clapper Rail populations have declined                                                   Rail’s rebound during the 1990s was possibly
                                                since the 1970s. Population estimates                                                    due to fox control but also coincided with
                                                using different methods from published                                                   the rapid invasion of a tall non-native plant
California Clapper Rails nest in the tidal      and unpublished sources should be                                                        (invasive Spartina). This invader benefited
marshes of San Francisco Bay, and recovery      interpreted with caution.                                                                rails because it provided nesting habitat and
of this species has been a major impetus                                                                                                 protection from predators and high tides.
for marsh restoration around the Bay.                                                                                                    Beginning in the mid-2000s, the rail popula-
Unfortunately, the Clapper Rail struggles to                                   1.25                                                      tion declined sharply, due in part to the
                                                 Expected Counts at a Point

                                                                                                                                         removal of invasive Spartina, which threatens
survive because of habitat loss, predator                                      1.00
                                                      Density Index

                                                                                                                                         tidal flat and marsh ecosystems as a whole.
pressure, and invasive species. The growing                                    0.75
                                                                                                                                         This recent decline may be leveling off, but
threat from sea level rise also threatens the                                  0.50                                                      the future of Clapper Rails in San Francisco
Clapper Rail.                                                                  0.25
                                                                                                                                         Bay remains tenuous. However, we can be
                                                                                                                                         hopeful that as thousands of acres are being
                                                                                       2005 2006 2007 2008 2009 2010
                                                                                                                                         restored to tidal marsh habitat, California
                                                                                                                                         Clapper Rails will be back on the road to
                                                Standardized Bay-wide point count                                                        recovery.
                                                surveys for Clapper Rails show a
                                                steep decline that may be leveling off.

 22                                                                                                                                                             Contributors: name, name
                                                                                                                         Julian Wood, Len Liu, and Nadav Nur (PRBO Conservation Science)
Threats                                                              Actions                                         Continue funding and support for
                                                                                                                    tidal marsh restoration such as the South
 Primary threat: Predators,       Pollution, contaminants,         Planning, Management, and                      Bay Salt Pond Restoration Project, which
including introduced species      and toxic spills (including        Restoration                                    aims to restore over 15,100 acres of former
such as Norway rats, house        oil spills) directly kill rails,                                                  salt ponds to a diversity of habitat types
cats, and red foxes prey on       vegetation, fish, and the           Prioritize sites: Use the most current       to benefit all birds, including tidal marsh-
Clapper Rails and their nests.    invertebrate community             and thorough scientific modeling of            dependent species.
Some native species of raptors,   that sustains marsh wildlife.      climate change scenarios to prioritize areas
snakes, and mammals also          Toxins (e.g., mercury, lead)       for acquisition and restoration (an example    Scientists
prey on Clapper Rails.            accumulate in rails, impairing     is PRBO’s sea level rise modeling tool:
                                                                                                                     Support research that seeks to under-
                                  their reproduction and survival.
 Invasive non-native plant                                                                                         stand marsh development processes in the
species can reduce nesting and     Rising sea levels from            Acquire and restore uplands and diked        face of sea level rise, as well as potential
foraging habitat for Clapper      global climate change              areas where current shoreline marsh may        management actions that can mitigate
Rails, even changing the          will drown some marshes            migrate as sea level rises.                    these impacts.
invertebrate community on         and increase nest flooding,
                                                                      Control predators by eliminating cat          Study the effect of trail use on
which they feed. Perennial        making the habitat unsuit-
                                                                     feeding stations, supporting predator          Clapper Rails – both direct impacts from
pepperweed reduces high-          able for Clapper Rails. See
                                                                     control programs, and keeping marshes,         disturbance as well as potential increased
tide refugia, and hybrid to
                                                                     public parks, and adjacent housing areas       predator access from trails.
Spartina may reduce channel       view maps of projected
                                                                     free of garbage.
and mudflat areas important       change in marsh habitat and                                                        Support research on Clapper Rail
for foraging rails. However,      changes in bird and plant           Enforce regulations on unlawful              population trends (including reproductive
invasive plant control/removal    species distribution.              recreation in sensitive marshes.               success, which has not been closely
decisions should always                                                                                             studied at a Bay-wide scale), habitat
                                                                      Conduct active marsh planting
consider short-term and long-                                                                                       use, and the impacts of invasive hybrid
                                                                     in restored areas where plants are not
term effects on birds (e.g.,                                                                                        Spartina and its removal.
                                                                     regenerating on their own, or in sites
invasive Spartina eradication                                                                                        Support research that can inform how
                                                                     where non-native plant removal has
may have contributed to                                                                                             to create upland transition zone habitat as
                                                                     reduced overall plant cover.
significant reductions in                                                                                           refugia for Clapper Rails.
Clapper Rail populations at                                           Restore high ground adjacent to
some sites and should proceed                                        marshes, such as levees and uplands with        Update habitat models as new data
with caution).                                                       dense vegetation, to offer birds refuge from   become available, to better predict areas
                                                                     high-tide events.                              where tidal marsh will persist given sea
                                                                                                                    level rise.
                                                                      Locate public access points and trails
                                                                     to the Bay shore away from Clapper Rail
Success Story Carl’s Marsh – See page 34

Endangered Species
Western Snowy Plover

                                                                                                                                                                         Status: Uncertain – appears to be recover-
                                                                                350                                                                                      ing in the South Bay.
                                                                                                                                                                         Snowy Plovers in San Francisco Bay have

                                               No. of Snowy Plovers in SF Bay

                                                                                250                                                                                      decreased from historic numbers but more
                                                                                                                                                                         recently show an increasing trend, possibly
                                                                                                                                                                         reflecting improved survey effort. Snowy
                                                                                                                                                                         Plover reproductive success is low in the Bay
                                                                                                                                                                         and has decreased over the past four years.

                                                                                      1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001 2004 2007 2010

                                              How long will it take Snowy Plovers to rebound to their
                                              1970s level?
The Western Snowy Plover is a federally
threatened species under the Endangered
Species Act. Primarily found nesting on
coastal beaches, a subset of the population
nests in San Francisco Bay. Plovers use dry
pond bottoms, isolated islands, and levees
in managed ponds as well as active salt
ponds for nesting.

                                              Snowy Plover chicks

 24                                                                                                                                                                                            Conservation Science);
                                                                                                                                                              Gary Page and Lynne Stenzel (PRBOContributors: name, name
 24                                                                                                                                                      Caitlin Robinson-Nilsen (San Francisco Bay Bird Observatory)
Threats                              Actions
 Predators impact Snowy             Planning, Management, and Restoration                     Prevent California Gulls from establishing colonies
Plovers by preying upon their                                                                 near plover nesting habitat.
                                      Continue to control predators in San Francisco
eggs and chicks. Nest cameras        Bay, to reduce depredation of plover eggs and chicks.     Practice adaptive management. Support ongoing
have documented a large suite of                                                              monitoring of managed ponds and nesting islands to
predators, including California       Remove feral cat feeding stations near plover          determine their effectiveness in supporting plovers.
Gulls, Common Ravens, Northern       nesting areas in the South Bay, and educate the public   Employ an adaptive management approach to pond
Harriers and the native gray fox.    about the need for this action.                          design, acreage, and public access if the current plan
Maintaining predator control          Continue to create and improve plover nesting          proves to be ineffective.
measures is costly, and funds are    within restoration projects. Specifically, continue to
scarce.                                                                                        Conduct public outreach to reduce disturbance
                                     create nesting islands, shallow ponds, and cover for     to nesting plovers from public access and use of
 Habitat loss from salt pond        plover nests and chicks.                                 recreation trails. Close trails seasonally around nesting
conversion projects is a threat to    Maintain 500 nesting plovers in San Francisco          habitat.
the Snowy Plover, as some of the     Bay, as set by the U.S. Fish and Wildlife Service
ponds it nests in are former salt    Western Snowy Plover Recovery Plan. The South            Scientists
ponds that are now being converted   Bay Salt Pond Restoration Project aims to support         Experiment with substrates that provide cover.
to marsh in the North and South      250 breeding Snowy Plovers. Other federal and state      Test the effectiveness of oyster shells on the pond
Bay.                                 agencies need to collaborate to develop a strategy       bottom to camouflage Snowy Plover nests and chicks,
 Rising sea level from global       to support at least 250 additional plovers within San    reduce predation, and increase nesting density.
climate change may submerge          Francisco Bay.
                                                                                               Assess the implications of public access on nesting
the shallow ponds where Snowy         Provide dry spring nesting habitat and late season     plovers to determine the level of disturbance likely
Plovers nest.                        nesting habitat. Initiate managed pond draw-down         from future public access and trail use. Determine
 Disturbance to nesting plovers     early enough in the spring to provide dry early season   consequence of disturbance on flushing rates, nest
by the public, from future public    nesting habitat, and continue to draw down ponds         temperatures, incubation duration, and nest success of
access and recreation trails.        throughout the season to create optimal late season      the plovers.
                                     nesting habitat.
                                      Prevent avian predators from nesting and
                                     perching near nesting plovers by modifying the design
                                     of power towers and by removing predator perches
                                     (e.g. sign posts, old duck hunting blinds).

Endangered Species
California Least Tern

                                                                                                                                                          San Francisco Bay Status: Stable

                                                                            400                                                                           Since 1984, the number of California
                                                                            350                                                                           Least Tern pairs in the Alameda colony has

                                                 Number of breeding pairs
                                                                            300                                                                           increased by 9.7% per year, but the colony
                                                                            250                                                                           size appears to have stabilized in the last

                                                                            100                                                                           Dropped prey items have revealed the diet
                                                                             50                                                                           and foraging habits of Least Terns at the
                                                                                  1984 1986 1988 1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010
                                                                                                                                                          Alameda Point colony from 1981 to present.
                                                                                                                                                          They show that small estuarine fishes are
                                                                                                                                                          the dominant prey item. Since the 1990s,
                                                 Breeding pairs of Least Terns in the Alameda Point colony.
                                                                                                                                                          northern anchovy and surfperches have
                                                 While the colony has grown over the last 26 years, it appears
                                                                                                                                                          declined in the tern’s diet, while Clupeids
                                                 to be stabilizing.
                                                                                                                                                          (e.g., herring, sardine) have increased.
The largest Least Tern colony in San Francisco
                                                                                                                                                          Understanding prey items is important,
Bay is located at Alameda Point on the
                                                                                                                                                          because diet is critical to tern reproductive
runway complex of the former Naval Air                                                                                                                    success.
Station, Alameda. The 3.9–hectare breeding                                   Atherinopsidae (silversides)

area is surrounded by a chain link fence.                                    Engraulidae (anchovies)

                                                                             Clupeidae (herrings)
Smaller colonies can be found at Napa–                                       Salmonidae (salmon)
Sonoma Marshes Wildlife Area, Montezuma                                      Embiotocidae (surfperches)
Wetlands, and Hayward Regional Shoreline.                                    Gobiidae (gobies)

                                                                             Osmeridae (smelts)


                                                 Average percent of each fish in the diet of Least Terns in the
                                                 Alameda Point colony. Small fishes are the dominant prey item.

 26                                                                                                                                                                              Contributors: name, name
                                                                                                                                                           Meredith Elliott (PRBO Conservation Science);
                                                                                                                                                             Susan Euing (U.S. Fish and Wildlife Service)
Threats                                                        Actions
 Primary threat: Avian predators including falcons,           Planning, Management, and Restoration
hawks, owls, crows, and ravens prey upon young and              Continue predator management, especially of
adult terns. Human activities, such as leaving food for        Peregrine Falcons. The increase in local Peregrine
predators and altering native habitat, result in higher than   Falcon attacks on the terns at Alameda Point is a
normal predator populations.                                   growing concern. Authorization to permanently remove
 Development of the Naval Air Station looms, as the           marauding Peregrine Falcons from Least Tern sites needs
base has been decommissioned.                                  to be given to predator management personnel by the
                                                               appropriate state agency.
 Encroaching vegetation is reducing the nesting area
available to the birds. The California Least Tern needs         Control vegetation by continuing to apply herbicide,
bare ground for nesting and roosting. Encroachment of          remove weeds, and add gravel to the nesting substrate.
vegetation reduces the amount of nesting habitat.               Reduce air traffic disturbance by expanding outreach
 Low flying aircraft over the nesting colony flush adult      to local airports and pilots regarding impacts to the
terns from their nests, leaving young and eggs vulnerable      endangered Least Tern.
to predators and unfavorable weather conditions.                Secure/identify adequate undeveloped space beyond
 Sea level rise from climate change threatens to              the existing colony to allow for colony movement or
submerge the colony site, as it is built on reclaimed land     persistence in the long term, given the uncertain future of
close to sea level.                                            the Navy’s presence.
 Loss of common prey species, such as the region-wide         Scientists
anchovy crash in 2009, can result in fewer feedings to          Study the diet and energy requirements of
chicks, nutritional deficiencies, and higher rates of chick    developing terns and evaluate the nutritional content of
death.                                                         common prey species.
 Contaminants can directly kill birds, but they also kill      Monitor contaminant impacts to terns. Failed-to-
the prey items that birds depend upon for food. California     hatch eggs should continue to be collected and analyzed
Least Terns feed on fish and are at risk of accumulating       for contaminants. Further research on lethal levels of
contaminants (e.g., mercury and lead) found in San             these contaminants in Least Terns is needed.
Francisco Bay. These contaminants, in great enough
concentrations, can affect survival and breeding success.

Success Story Monitoring Least Terns at Alameda Point – See page 37

Endangered Species
Northern Spotted Owl

                                                                                                                                                                                                    Status: Stable

                                                               % sites occupied by pair of Nthrn. Spotted Owls

                                                                                                                                                                                                    The Bay Area’s population of Northern
                                                                                                                  85                                                                                Spotted Owls is thought to be stable;
                                                                                                                                                                                                    however, thorough population monitoring is
                                                                                                                                                                                                    not available as all sites are not monitored
                                                                                                                                                                                                    every year.

                                                                                                                                                                                                    While fecundity (reproductive success) is
                                                                                                                  40                                                                                generally high, we lack survival data for
                                                                                                                       1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
                                                                                                                                                                                                    owls, which may be more important to the
                                                 Percent of Northern Spotted Owl sites surveyed that                                                                                                overall number of birds in the population.
                                                 were occupied by a pair. All sites are not surveyed every                                                                                          Current monitoring occurs on the following
                                                 year; however, sites surveyed likely reflect the overall                                                                                           public lands: Point Reyes National Seashore,
                                                 population of owls in Marin County. In general, the number                                                                                         Golden Gate National Recreation Area,
In the San Francisco Bay Area (primarily         of Northern Spotted Owls in Marin County appears stable.                                                                                           Marin Municipal Water District, Marin
Marin County), Northern Spotted Owls nest                                                                                                                                                           County Open Space District, and California
in both old-growth and mature second-growth                                                                                                                                                         State Parks (Tomales Bay, Mount Tamalpais,
                                                  Northern Spotted Owl Fucundity in Marin County


forests of Douglas-fir, coast redwood, bishop                                                                    0.7                                                                                and Samuel P. Taylor).
pine, mixed conifer–hardwood, and other
evergreen hardwood trees. This varies from
the rest of the population of Northern Spotted                                                                   0.3

Owls in the Pacific Northwest, where they are                                                                    0.2

commonly associated with mature coniferous                                                                       0.1

forests.                                                                                                         0.0
                                                                                                                       2000   2001   2002   2003   2004   2005   2006   2007   2008   2009   2010
                                                                                                                       n=26   n=41   n=43   n=48   n=38   n=42   n=18   n=35   n=32   n=47   n=44

In Marin County, unique forest types are
                                                 Except for 2007 when almost no young were produced,
bishop pine and evergreen forests.
                                                 Spotted owl fecundity (reproductive success) appears stable.

 28                                                                                                                                                                                                                      Contributors: name, name
                                                                                                                                                                                                       Renée Cormier (PRBO Conservation Science);
                                                                                                                                                                                                                 Dave Press (National Park Service).
Threats                                                        Actions
 Primary threat: Barred Owls pose a threat to Spotted         Planning, Management, and Restoration
Owls by competing for space and food and through direct         Follow U.S. Fish and Wildlife Service guidelines
aggressive interactions. Currently, the number of Barred       for protecting Spotted Owls. Restrictions for habitat
Owls in the Bay Area is relatively small but is predicted to   modifications around Spotted Owl territories are
increase.                                                      in effect year-round, and modifications to potential
 Rat poisons. Spotted Owls feed upon rats; when rats          Spotted Owl habitat may require consultation with
have been poisoned with rodenticides used by residents         USFWS personnel.                                         Spotted Owl fledgling
and businesses, the owls can become sick or die.                Limit loud noises, such as motorized gardening
 Sudden Oak Death changes the forest structure and            equipment, during the nesting season (February 1st to July 9th) near Spotted Owl habitat.
plant composition, and the loss of tanoaks in particular        Discontinue the use of rodenticides as a means to kill pests in areas with Spotted Owl
threaten the owl’s preferred food source, the dusky-footed     habitat. Residents and business owners should consider rodent prevention and trapping
woodrat, which depends on the tanoak for cover and food.       instead of poisons that harm more than the rodent.
 Loss of forests due to urban development along national       Communicate to the public the USFWS guidelines pertaining to activities such as
park and county open space boundaries and the threat of        noise disturbance and construction near Spotted Owl habitat during the nesting season
wildfires. Losing forests reduces feeding, roosting, and       (February 1st to July 9th).
nesting habitat for Northern Spotted Owls.
 Human activities, such as extended presence near             Scientists
Spotted Owl nest trees and noise disturbance from yard          Continue and expand monitoring of Spotted Owl and Barred Owl populations on
maintenance, tree trimming, and construction activities in     public lands. Current research is ongoing in Marin County but should be expanded to
the communities neighboring owl nesting sites, can disturb     include Sonoma and Napa counties, on both public and private lands.
nesting owls and may prevent them from feeding their
young. Community awareness of regulated protections for
Spotted Owls is lacking.                                        Leave owls alone. Spotted Owls reside near many busy trails in the Bay Area, and it
                                                               is not uncommon for fledgling owls to perch on the ground. If you see an owl, give it
 Genetic isolation. The Marin County population of
                                                               space and keep pets on leash. The parents will continue to care for a fledgling owl on the
Northern Spotted Owls is isolated from populations to the
north because of a break in forested habitat needed for
dispersal. Small populations, such as those found in Marin      Discontinue the use of rodenticides as a means to kill pests. Residents and business
County, are at a higher risk of local extinction.              owners should consider rodent prevention and trapping instead of poisons that harm more
                                                               than the rodent.

 Success Story Spotted Owl monitoring on public lands – See page 36


   The human population of the San Francisco           flood protection as sea levels rise; healthy streams
Bay Area has more than tripled since the 1950s,        improve our water quality; diverse and abundant
yet the ponds, open waters, mudflats, and              bird populations provide us with recreation,
marshes continue to support rich and abundant          inspiration, and enjoyment; and birds’ presence
birdlife. Protection of birds and their habitats has   in the Bay Area indicates the sustained quality of
resulted from decades of public involvement,           those habitats and the services they provide.
conservation investments, and a strong frame-            Today the most fundamental policy challenges
work of laws and regulations. However, we              to maintaining and enhancing conservation in the
cannot assume that all threats to birds and their      Bay Area, across a broad array of habitat types,
habitats have been averted and that all protection     can be grouped into four categories: 1) funding;
is permanent. We need an engaged public and            2) climate change including sea level rise; 3)
informed decision-makers to continue to protect        threats from development; and 4) balancing
                                                       public use with adequate protections for birds.
the hundreds of thousands of majestic and
                                                       The State of the Birds Report offers policy
ecologically important birds that depend on the                                                               Caitlin Robinson-Nilsen (left) and Cheryl Strong hold
                                                       recommendations for each.
San Francisco Bay Estuary region.                                                                             Black-necked Stilt chicks at Hayward Regional Shoreline.
  The future state of the birds in San Francisco
Bay region is at significant risk, resulting from        Our ability to protect existing habitats                To protect birds in San Francisco Bay region:
the urban use of the area, the looming threat of       and respond to new threats is compromised
                                                       without adequate funding to: 1) acquire,                Support the efforts of the San Francisco Bay
climate change and associated sea level rise,
                                                       restore, and manage important habitats in               Restoration Authority (California Government
and funding limitations during this period of
                                                       public spaces; 2) continue incentives for the           Code §66700 et seq.) to establish a regional
economic uncertainty. It is time to develop and
                                                       private protection of open spaces; and 3)               funding program in the Bay Area. Doing
support solutions that benefit our environment,
                                                       continue efforts to maintain and enhance the            so would support wetlands restoration,
economy, and community. A more resilient San
                                                       quality of Bay waters upon which birds and              enhancement, and management, and associated
Francisco Bay will be better for birds, people,
                                                       people depend.                                          public access and flood management.
and the economy: healthy tidal marshes provide

 30                                                                                                                                      Dan Taylor (Audubon California);
                                                                                                                            Beth Huning (San Francisco Bay Joint Venture).

    Support full funding for the Federal Land and     isms, and continue the systematic
    Water Conservation Act, the North American         removal and control of the species
    Wetlands Conservation Act, and other relevant      that pose a significant threat to
    federal authorities to increase and improve        birds’ habitats in the Bay region,
    wetland habitats and wetland-dependent bird        such as invasive Spartina hybrids.
                                                       Restore full funding for the
    Support federal appropriations to the U.S.        Williamson Act (California
    Army Corps of Engineers for wetland restora-       Government Code §51200 et seq.),
    tion projects authorized in the Water Resources    which has historically provided
    Development Act; appropriations for the            critically important property tax
    San Francisco Bay National Wildlife Refuge         incentives and prevents urban
    Complex; and appropriations for NOAA and           development for over 1.23 million
    USEPA for programs focused on wetlands res-        acres of upland bird habitat and
    toration and water quality improvements in San     open spaces in the nine-county Bay
    Francisco Bay.                                     Area region. State funding for this
                                                       program has been deeply cut and is      Alcatraz Island
    Ensure adequate funding for the San Francisco     threatened with elimination.
    Bay Regional Water Quality Board’s effective
    enforcement of the Federal Clean Water Act         Support continued state funding for the San
                                                                                                             nongovernmental organizations active in
    and the Porter-Cologne Water Quality Control       Francisco Bay Area Conservancy Program of the
                                                                                                             protecting habitats in the Bay Area.
    Act (California Water Code §13000 et seq.),        State Coastal Conservancy, which provides grants
    and to local jurisdictions for infrastructure      to multiple organizations for wetland restoration     Support science and monitoring associated with
    improvements to aid in keeping sewage and          and other projects that benefit birds, and support    restoration and management projects that answer
    animal waste out of the Bay and reducing           funding for the California Department of Fish and     key uncertainties and help guide priorities for
    storm-water pollution, to reduce the threat of     Game to manage their ecological reserves and          future bird habitat protection and enhancement.
    catastrophic spills and improve water quality      wildlife areas in the San Francisco Bay Area.
                                                                                                             Climate change and sea level rise
    and supply for wildlife and for people.
                                                       Increase local funding for habitat acquisition
                                                                                                               To ensure that critically important habitat areas
    Ensure adequate funding for the early detection   and management actions by entities such as
                                                                                                             for people and birds are preserved, we encourage:
    of non-native invasive plants and aquatic organ-   Open Space Districts, land trusts, and other

(continued from page 31)

Rapid reduction of greenhouse gases through             Support dredging policies and regulations that       Efforts to exempt projects, or to weaken
the full implementation of AB 32, the California         require beneficial re-use of material currently       existing development protection provisions
Global Warming Solutions Act of 2006                     being disposed offshore or in-Bay. Sediment that      of the California Environmental Quality Act
(California Health and Safety Code §38500 et             is in the system will enable marshes to better        (California Public Resources Code §21000
seq.), and support for national climate change           build and keep pace with sea level rise, protecting   et seq.) or the McAteer-Petris Act (California
legislation to help mitigate the most extreme            not only marsh and mudflat habitats but enabling      Government Code §66600 et seq.) establishing
levels of climate change.                                them to serve their natural functions as buffers      the Bay Conservation Development Commission
                                                         against sea level rise and storm events.              (BCDC), should be opposed.
Full implementation of the California Climate
Adaptation Strategy of 2009. On the issues of            Support science and monitoring to improve our        Implement the Climate Change amendments to
sea level rise, discourage urban development in          ability to predict the effects of climate change      BCDC’s Bay Plan.
areas containing habitat and habitat restoration         as a means to prioritize future land acquisition,
                                                                                                               The recommendations in the Subtidal Habitat
potential and that are vulnerable to sea level rise.     management, and restoration efforts and to
                                                                                                               Goals report should be implemented in order to
                                                         mitigate sea level rise impacts.
The acquisition and restoration of remaining                                                                  maintain and improve fish and wildlife habitat in
open space areas in proximity to existing                Threats from development                              the Bay.
wetlands to provide for future habitat refugia             With the population of the Bay Area estimated       Utilize decision-support tools, such as that
for tidal marsh and tidal flats, birds, and other        to grow to over eight million people by the end       developed by the Bay Area Open Space Council’s
wildlife in the face of rising sea level; and            of this decade, there will be additional pressures    Upland Habitat Goals project, and the San
to allow for tidal wetlands to migrate up the            to fill baylands and adjacent restorable uplands      Francisco Bay Sea Level Rise decision support
shoreline as the Bay rises.                              for urban development. To ensure that habitat         tool developed by PRBO Conservation Science
When practical, encourage the use of natural            protection and restoration objectives can be met,     and its partners, as resources for determining
shoreline protection and buffer lands such as tidal      we encourage that:                                    priority parcels for future protection and
marsh, eelgrass and oysters, and rocky subtidal          Further development should be prohibited on          restoration.
habitat, in contrast to sea walls and other artificial   Bay wetlands or lands adjacent to, and restorable     The San Francisco Bay Regional Water Quality
barriers that are prone to catastrophic failure and      to, wetland conditions.                               Control Board should complete and adopt its
provide little habitat value.

 32                                                                                                                     Contributors: John Kelly (Audubon Canyon Ranch) and
                                                                                                                 Caitlin Nilson-Robinson (San Francisco Bay Bird Observatory)
                                                                                                                Regulations regarding dogs and cats should be
                                                                                                                implemented to protect key shoreline areas used
                                                                                                                by endangered bird species.
                                                                                                                New boat launching and access points should be
                                                                                                                developed away from sensitive habitats. Boating
                                                                                                                activities should avoid those areas that provide
                                                                                                                important foraging and resting for diving ducks,
                                                                                                                grebes, and waterbirds during the migratory and
                                                                                                                wintering seasons when those species are present.
                                                                         Clapper Rail, dependent on tidal
                                                                                                                Study impacts of public access on wildlife as a
                                                                         marsh habitat in the Bay
                                                                                                                means to improve future planning for beneficial
                                                                                                                public access.
                                                                                                                Support educational programs and facilities to
                                                                                                                help the public to appreciate, understand, and
Tidal marshland is likely to be inundated by sea level rise. Here,                                              value birds and the ecology of San Francisco Bay.
winter rainwater and an extreme high tide flood the Bay shore.

Wetlands and Riparian Area Protection Program             Protect and enhance values of tidal marsh,
recommendations in order to provide protection            managed pond, open Bay, and other sensitive
for many bird species.                                    habitats, particularly those utilized by listed and
Public use and bird protection                            sensitive wildlife species. Where wildlife would
                                                          be negatively impacted by public use, public
  A balancing act exists in wildlife conservation:        access should be limited. As much as possible,
the needs of sensitive wildlife populations versus        access should be designed in ways and locations
the need to connect the public with the outdoors          that both provide public enjoyment and reduce
and provide opportunities to observe wildlife. We         impacts to sensitive habitats and species.
recommend the following policy considerations
to accommodate habitat protection and outdoor

                                                                                                                                Status: Overall stable with large
Success Stories                                                                                                                 variation between years

 Managed Ponds           South San Francisco Bay Salt Pond Restoration                                                  Tidal Marsh     Carl’s Marsh

  With the transfer of over 15,000 acres to          70,000
                                                                                                                          Carl’s Marsh is a great example of
public ownership in 2003, the South Bay Salt         60,000                                                            successful tidal marsh restoration.
Pond Restoration Project is the largest wetland      50,000                                                            After this 42-acre dry fallow field
restoration on the West Coast. An early goal in      40,000
                                                                                                                       was breached in 1994, sediment
the long-term restoration plan was to reduce                                                                           began accumulating with each tidal

salinity in open ponds from their inherited toxic    10,000
                                                                                                                       cycle, and the site is now a lush
production concentrations to those of ambient            0
                                                              2003    2004   2005   2006   2007   2008   2009   2010
                                                                                                                       tidal marsh supporting a diversity of
Bay waters. The U.S. Geological Survey began                                                                           birds including several endangered
                                                     Dabbling ducks have increased in South Bay ponds.
monitoring birds and water quality from the start                                                                      California Clapper Rails. This collab-
of the project and has documented increases          Western Sandpipers. Further north, in the Eden                    orative project between California
in shorebirds and ducks as the restoration has       Landing pond complex, small shorebirds during                     Department of Fish and Game (CDFG) Song Sparrow
proceeded. Examples include the 480-acre             spring have increased from 10,000 to over                         and Sonoma Land Trust was more
Island Ponds that were opened to tidal action        50,000 birds observed in monthly surveys, as                      successful than expected. The transition from
in 2006. As salinity declined from 160 to less       water depths declined in former commercial salt                   fallow agricultural land, to productive mudflat
than 20 ppt, average numbers of dabbling ducks       ponds now maintained as seasonal wetlands.                        habitat for shorebirds, to a fully vegetated
increased from zero in 2003 to over 4,000 birds      Numerous ponds are planned for enhancements                       marsh was rapid, occurring within the first
at high tide on a given winter day in 2009. In the   or restoration to tidal marsh within a 50-year time               five years. Carl’s Marsh now supports over 60
larger Alviso system and across the South Bay’s      horizon, and continued monitoring is critical to                  pairs of breeding Samuel’s Song Sparrows.
managed ponds, dabbling ducks such as Northern       learn from successes or unexpected changes that                   This subspecies of Song Sparrow is found
Shoveler increased substantially through winter      can feed back into adaptive management in this                    only in the tidal marshes of San Pablo Bay and
2010. The restoration project occurs within a        extremely important area for birds within San                     is recognized by CDFG as a Bird Species of
designated area of Hemispheric Importance            Francisco Bay.                                                    Special Concern.
for migratory and wintering shorebirds such as                       —L. Arriana Brand and Cheryl Strong                            —Julian Wood and Nadav Nur

 Tidal Marsh Herons and Egrets                                                           Human-created Habitats

West Marin Island                                                                       Seabirds on Alcatraz Island
  The West Marin Island National                                                         Prior to human settlement, Alcatraz Island
Wildlife Refuge is a protected home                                                    was home to thousands of nesting seabirds,
to one of the largest nesting colonies                                                 as indicated by the guano-covered sandstone.
of herons and egrets in San Francisco                                                  As early human settlement took place, birds
Bay, and is a true bird conservation                                                   left the island and did not return throughout
success story. During the 1980s                                                        the military and prison history. Over a century
the Marin Islands were slated for                                                      later, Alcatraz became part of the Golden
development. Over the next 12 years,                                                   Gate National Recreation Area (GGNRA),
local citizens, the Friends of the                                                     a unit of the National Park Service (NPS),          Brandt’s Cormorant
Marin Islands, the California Coastal                                                  and birds slowly began to return to reclaim
                                          Snowy Egret with nest material
Conservancy, the Trust for Public                                                      the island. The Brandt’s Cormorant colony on Alcatraz is one of
Land, and at least 14 other agencies                                                   the few known estuarine breeding sites for this species. Pigeon
and organizations participated in the establishment of the Marin Islands               Guillemots are not known to breed elsewhere in San Francisco Bay.
National Wildlife Refuge and State Ecological Reserve. Senator                         The Western Gull and Black-crowned Night Heron colonies are
Barbara Boxer designated September 19th as Marin Islands National                      the largest in the Bay. Currently, this diversity of species exists in a
Wildlife Refuge Day in 1992.                                                           delicate balance with the considerable human presence both on and
   The establishment of West Marin Island Wildlife Refuge was largely                  around Alcatraz Island. Over the last 10 years, PRBO Conservation
due to data provided by ongoing monitoring, which began in 1979 and                    Science and the NPS have been monitoring the return of the
documented the importance of the island to nesting herons and egrets.                  nesting birds and especially the growth of the cormorant colony.
Region-wide monitoring of heronries throughout the San Francisco                                            With cooperative efforts between biologists and
Bay Area by Audubon Canyon Ranch substantiated the importance                                               NPS staff, improved public outreach (signage,
of this nesting colony and now guides the management of the Marin                                           bird interpretive displays, tours), and island
Islands National Wildlife Refuge. Today the Refuge is home to over                                          management (altered tourism, maintenance, and
500 nesting pairs of herons and egrets each year.                                                           construction activities to protect nesting birds)
                                                     —John Kelly                                            human-caused disturbance to the cormorants has
                                                                                                            been reduced and the colony has grown.
                                                                                                                                              —Sara Acosta
                                                                           Pigeon Guillemots

Habitat Type
Success Stories
                                                                                                                            Status: Overall stable with large
                                                                                                                            variation between years

  Upland Habitats          Chileno Creek, Marin County
                                                                                                                 Over the years, neighboring ranches joined in
                                                                                                               and the cumulative effect in Marin and southern
  Sally and Mike Gale live and                                                groundwater, and provide
                                                                                                               Sonoma counties has greatly increased the
work on a 600-acre ranch first                                                better wildlife habitat.
                                                                                                               number and diversity of birds.
purchased by Sally’s great-                                                   Working with the Marin
grandfather in 1856. The Gale                                                 Resource Conservation                                                   —Tom Gardali
Ranch is located in Marin                                                     District, the Natural
County’s picturesque Chileno                                                  Resource Conservation              Endangered Species            Spotted Owls
Valley, where agriculture has been                                            Service, and the Students
a way of life for 150 years. Mike                                             and Teachers Restoring             For over 10 years, the
and Sally took over operation of                                              a Watershed Program              National Park Service, Marin
the ranch in 1993 and currently                                               (STRAW), the Gales               Municipal Water District, and
tend a humanely raised grass-fed                                              undertook a seven-acre           Marin County Open Space
beef herd of about 100 cows as                                                riparian restoration project.    have been conducting surveys
well as other farm enterprises such                                               The restoration has          on their lands to ensure that
as u-pick apples.                                                              successfully increased          Northern Spotted Owls are
  Mike and Sally are stewards of                                               native vegetation (see          not disturbed by management
the land and quickly noticed that                                              photo), especially to benefit   activities. Their commitment to
the creek running through their       Riparian habitat on the Gale Ranch,      birds. The number of            the protection of Spotted Owls
property, Chileno Creek, was          before and after restoration began       bird species found on the       has resulted in better timing of    Adult Spotted Owl
completely lacking vegetation and                                              Gale Ranch has increased        management activities (e.g.,
drying out in the summer. The Gales recognized           significantly since the restoration project began.    trail work) to avoid disturbance to nesting owls
the need to revive Chileno Creek in order to             The growing populations of the 33 bird species        and increased knowledge about the status of
retain soil and prevent creek sedimentation, keep        inhabiting the ranch tell us the restoration is       Northern Spotted Owls in Marin County.
evaporation in check, retain water, replenish            really paying off.                                                     —Renée Cormier and Dave Press

 36                                                                                                                   Contributors: John Kelly (Audubon Canyon Ranch) and
                                                                                                               Caitlin Nilson-Robinson (San Francisco Bay Bird Observatory)
  Endangered Species—Least Tern Watch                                  Marshland on Reclaimed Shoreline

Monitoring and Protecting a California                                Sonoma Baylands
Least Tern Breeding Colony
                                                                         Much of the historic
   Tern Watch is a volunteer predator observation program at          marshland in the North Bay
Alameda Point. The intention of Tern Watch is to give a broader       was diked from the Bay
picture of predator presence during the least tern breeding season,   and drained in the late 19th
allowing USFWS to conduct proactive predator management.              century for farming oat hay
Annually, volunteers are recruited and trained to observe the tern    and other crops. From 1991
colony from a vehicle outside the colony fence line, for three        to 1996, the State Coastal
hours at a time. Volunteers record predator and Least Tern activi-    Conservancy and the Sonoma
ties during daytime hours, seven days a week.                         Land Trust conceived and
  Not only are the Tern Watch data useful for understanding           developed the Sonoma
the local predators at the Least Tern colony, but the volunteers      Baylands Project to restore
themselves act as predator deterrents. The physical presence of a     tidal marsh on 320 acres. This
human in their vehicle close to the Least Tern colony appears to      pioneering project of wetland creation used dredged materials from navigation
deter many avian predators from entering the nesting area, thus       channels to jump-start the restoration.
giving more protection to the terns. The Tern Watch volunteers          While it took many years to establish, the site now boasts large numbers of
also record least tern activities and their responses to predator     shorebirds (sometimes as many as 18,000 individuals), with at least 23 species
presence. While conducting a tern watch, each volunteer is able to    amassing on the mud before and after high tides. As rising water pushes the
enjoy the behaviors and nature of the Least Terns in their breeding   birds off these restored bay mudflats, they pause at the Baylands for a last frantic
habitat, a rare sight to see.                                         forage before moving to upland habitats where they rest and preen until the tide
  In 2010, the presence and vigilance                                 begins to drop again. During high tide in the winter, 18 species of ducks and
of volunteers at the Least Tern colony                                geese have been recorded in the aquatic habitats within the Sonoma Baylands.
helped thwart several hunting attempts                                With its ability to attract large populations of wading birds, the site is also
made by juvenile Peregrine Falcons. The                               attractive to diurnal raptors including Merlin, Prairie and Peregrine Falcons.
quick response time by volunteers alert-                              Surveys for endangered California Clapper Rails by PRBO biologists since 2008
ing the biologists of predators enabled                               have documented their presence, along with Black Rails, in the restored Sonoma
them to chase off marauding predators                                 Baylands.
in time.                                                                The restoration of Sonoma Baylands has enhanced opportunities for San Pablo
  —Meredith Elliot and Mark Rauzon Least Tern incubating              and San Francisco Bays’ wildlife, especially birds, in ways only dreamed of 30
                                            eggs                      years ago.
                                                                                                                   —Caroline Warner and Rich Stallcup

                                                                                                                                                  Status: Overall stable with large
Contributors                                                                                                                                      variation between years

Josh Ackerman, PhD;            Sara Acosta; Marine            L. Arriana Brand, PhD;     Renee Cormier; Avian      Susan W. De La Cruz;           Jill Demers; Executive      Meredith Elliott;
Research Wildlife              Ecologist, PRBO                Wildlife Biologist, U.S.   Ecologist, PRBO           Wildlife Biologist,            Director, San Francisco     Marine Ecologist,
Biologist, U.S.                Conservation Science           Geological Survey,         Conservation Science      U.S. Fish and Wildlife         Bay Bird Observatory        PRBO Conservation
Geological Survey                                             Western Ecological                                   Service                                                    Science
                                                              Research Center

Tom Gardali; Director,         Mark Herzog, PhD;              Beth Huning,               Amy Hutzel; Program       John P. Kelly, PhD;            Leonard Liu;                Nadav Nur, PhD;
Pacific Coast and              Wildlife Biologist, U.S.       Coordinator, San           Manager, San Francisco    Director, Conservation         Wetlands Ecologist;         Population Ecologist;
Central Valley, PRBO           Geological Survey              Francisco Bay Joint        Bay Area Program, State   Science and Habitat            PRBO Conservation           PRBO Conservation
Conservation Science                                          Venture                    Coastal Conservancy       Protection, Audubon            Science                     Science
                                                                                                                   Canyon Ranch
Not pictured: Susan Euing; Wildlife Biologist; U.S. Geological Survey

  38                                                                                                                                        Contributors: John Kelly (Audubon Canyon Ranch) and
                                                                                                                                  Caitlin Nilson-Robinson (San Francisco Bay Bird Observatory)
Gary Page; Wetlands    Claire Peaslee; Editor,   Melissa Pitkin;          Dave Press; Wildlife      Mark Rauzon;            Caitlin Robinson-       Leonardo Salas, PhD;
Ecologist; PRBO        PRBO Conservation         Director, Education      Ecologist, Point Reyes    Geography Department    Nilsen; Waterbird       Senior Scientist,
Conservation Science   Science                   and Outreach and San     National Seashore         Chair, Laney College    Program Director, San   Informatics and
                                                 Francisco Bay groups,                                                      Francisco Bay Bird      Climate Change, PRBO
                                                 PRBO Conservation                                                          Observatory             Conservation Science

Rich Stallcup;         Lynne Stenzel;            Cheryl Strong;           Dan Taylor; Director of   Caroline Warner;        John Wiens; PhD         Julian Wood; San
Naturalist, PRBO       Wetland Ecologist,        Wildlife Biologist,      Public Policy, Audubon    Outreach Coordinator,   Chief Scientist, PRBO   Francisco Bay Program
Conservation Science   PRBO Conservation         U.S. Fish and Wildlife   California                San Francisco Bay       Conservation Science    Manager, PRBO
                                                 Service                                            Joint Venture                                   Conservation Science

 Photo credits

 Sara Acosta—p19 gull; p31 Alcatraz                            Caroline Hardter (Creative Commons)—p24 landscape
 Audubon Canyon Ranch —p14 Sherman Island                      Beth Huning—front cover marsh landscape; p5 surveying;
 Brian Aydemir (Creative Commons)—p18 Alcatraz                  p8 salt ponds; p10 landscape, shorebirds; p12
 Mike Baird—p6 Willet; p16 row of scoters                       landscape; p22 marsh; p30 landscape; p32 landscape
 Peter Baye—p33 flood tide                                     Scott Jennings—p29 owl
 Len Blumin—p19 cormorant                                      Bruce Jensen—p20 large landscape
 Philip Bouchard (Creative Commons)—p6 tidal flat              Walter Kitundu—front cover and p22 clapper rail
 Cris Benton—p1 South Bay; p2 South Bay; p8 South              Peter LaTourrette—front cover, canvasback; p11 flying
  Bay; p40 tidal marsh; p41 aerial flock                        shoveler; p12 rail; p21 warbler
 Von Canon (Creative Commons)—p14 flying heron                 Lorenz-Avelar (wwwlorenz-avelarcom)—p16 underwater
 Renée Cormier—p28 owls; p36 owl                               Marin RCD—p36 two views Gale Ranch
 Corinne C DeBra—p12 marsh landscape; p20 trail                James Matuszak—p2 shorebirds
 Franco Folini (Creative Commons)—p2 SF Bay                    David Reinsche—p30 field biologists
 Wally Gobetz (Creative Commons)—p4 Bay bridge                 Caitlin Robinson-Nilson—p24 plover, chicks
 Tom Grey—front: terns, egret, sparrow, avocets; p8            San Francisco Bay Subtidal Goals Project—p12 tidal
   shoveler, terns; p9 stilt; p10 avocets; p13 yellowthroat;    marsh
   p14-15 herons & egrets; p16 three duck species; p20         Sonoma Land Trust— p5 wetlands, p37 wetlands
   sparrow, woodpecker; p21 wrentit; p26 tern; p33 rail;       Jack Snell (Creative Commons)—p18 Richmond Bridge
   p34 sparrow; p35 three bird species; p36 warbler;           Ingrid Taylar—p3 landscape; p4 shorebirds; p34 flying
   p37 tern                                                      willets; back cover flying avocets

 Anonymous photographers (Creative Commons)—cover aerial landscape; p6 dunlin; p18 Alcatraz; p28 forest

 Diana Howard—treatment of all graphs                                                                                   South San Francisco Bay tidal marsh

Reviewers (does not include contributors)

John Baker                 Ryan DiGaudio            Amy Hutzel                 Barbara Salzman
Grant Ballard              Wendy Eliot              Brooke Langston            Nat Seavy
Kathi Borgman              Arthur Feinstein         Jen McBroom                Christina Sloop
John Bourgeois             Michael Fitzgibbon       John Parodi                Laura Valoppi
Ellie Cohen                Geoff Geupel             Steve Rottenborn


The 2011 State of the Birds Report, San Francisco Bay was funded by the following:

The Joseph and Vera Long Foundation (formerly the J.M. Long Foundation)
Pacific Gas and Electric Foundation
PRBO Conservation Science
San Francisco Bay Joint Venture
San Francisco Estuary Partnership
U.S. Fish and Wildlife Service

American Avocets                                                                                 Aerial view of shorebird flock over saltworks

The State of the Birds San Francisco Bay 2011 is a collaborative
project of PRBO Conservation Science and the San Francisco Bay
    Joint Venture, with contributions from numerous partners.
     Found online at of the birds

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