**Fish and large-scale change in the San Francisco Estuary,
California:**

**towards a more sustainable future**

Peter B Moyle

Professor of Fish Biology

Center for Watershed Sciences and Department of Wildlife, Fish, and
Conservation Biology, University of California, 1 Shields Avenue, Davis,
California 95616-8751 USA

*Testimony for the hearing held by The Subcommittee on Water and Power,
Committee on Natural Resources, "Extinction if not sustainable water
policy: the Bay-Delta crisis and the implications for California water
management." Vallejo, CA. July 2, 2007*

***Summary.*** The San Francisco Estuary supports a diverse fish fauna
in which key species are in severe decline. The estuary is faced with
catastrophic structural and ecological changes, especially in the Delta
and Suisun Marsh, as the result of anticipated levee failure caused by
the combination of earthquakes, land subsidence, sea level rise, and
increased high outflows events (from climate change). The resulting
flooding of Delta islands and Suisun Marsh is predicted to disrupt
California's water supply system and, consequently, the state's economy.
From a fish perspective, the changes are likely to create conditions in
which desirable species can persist at least at present low levels,
after a period of possible high mortality created by the initial
flooding events. Taking actions to regulate ecological changes in the
estuary *before* the disaster could actually improve conditions for
desirable fishes while being highly compatible with delivering services
the Delta provides, especially water supply. Specific actions include
improving habitat for fish in Suisun Marsh, Cache Slough, the Yolo
Bypass, and the San Joaquin River, while creating islands in which
flooding can be managed. The key is increasing habitat heterogeneity
over present and now-likely future conditions. No matter what actions
are taken there will be a high degree of uncertainty as to their
ecological benefits but the present situation in estuary represents an
unprecedented opportunity to reverse the impacts of over 150 years of
negative ecological change.

**Introduction**

The San Francisco Estuary (SFE) is the largest estuary on the west coast
of North America and one of the most altered (Nichols et al. 1986). It
is highly urbanized but contains extensively diked agricultural lands
and marsh habitats. It is also highly invaded by alien species,
especially the aquatic habitats. Not surprisingly, the native species of
plants and animals have declined in abundance; several are extinct and
others are listed as threatened or endangered under state and federal
laws (Herbold et al. 1992). Human caused changes to the SFE are still
taking place at an accelerated rate and there are strong indications
that major, catastrophic changes to the SFE are imminent (Mount and
Twiss 2005; Lund et al. 2007). The changes are likely to be most
dramatic in the upper part of the estuary, the Sacramento-San Joaquin
Delta (the Delta), where large-scale levee failure can seriously disrupt
local, regional, and state economies. A principal concern is disruption
of California's water distribution system. Much of the fresh water used
by San Joaquin Valley farms and the vast urban areas of southern
California originates (directly or indirectly) from the estuary's
inflowing rivers. This water is pumped from the Delta by the State Water
Project and the federal Central Valley Project. Additional water is
removed to supply aqueducts to cities around San Francisco Bay and to
water farms in the Delta. Large scale flooding could also eliminate
farming in thousands of acres of island land, threaten urban areas, and
disrupt railroads, pipelines, and other infrastructure (Lund et al.
2007, available on line at ***PPIC.org***). Likewise, a sudden
catastrophic change to the Delta and SFE will affect already declining
native species and encourage the further spread of alien species.

A major question being asked by management agencies and regional
stakeholders is "how can we prevent large-scale change from taking place
in the SFE, especially the Delta?" Answering precursors to this question
(mainly, how do we protect endangered fish and fisheries?) was one of
the reasons for the establishment of CALFED in 1996, a massive joint
state-federal management and research effort (http://calwater.ca.gov/)
which has been criticized for not quickly solving the problems of the
SFE (Little Hoover Commission 2006). A report produced by the University
of California, Davis and the Public Policy Institute of California (Lund
et al. 2007) turned the original question on its head, asking instead
"How can the Delta be managed to accommodate large-scale change before
undesirable changes are forced by catastrophic events?" In this essay,
key findings of Lund et al. (2007) are summarized in relation to aquatic
organisms, especially fish. I first describe the SFE, provide a brief
introduction to the fish fauna, and then discuss the major drivers of
change. I then describe what is likely to happen to key fish species if
present management trends continue, followed by suggestions for major
actions that could be taken to improve the SFE for fishes even in the
face of large-scale change.

**The San Francisco Estuary**

The SFE is the outlet of the Sacramento and San Joaquin Rivers, which in
turn drain much of central California. A primary source of the water for
the rivers is the Sierra Nevada, which intercept moisture-laden clouds
coming off the Pacific Ocean. The estuary has three distinct segments,
San Francisco Bay (including San Pablo Bay), Suisun Bay and Marsh, and
the Sacramento-San Joaquin Delta (Figure 1). Each segment has a confined
outlet through which the tides surge back and forth, creating complex
hydrodynamics: the Golden Gate (San Francisco Bay), the Carquinez
Straits (Suisun Bay), and the river confluence at Sherman Island
(Delta), respectively. These narrows have allowed the three regions to
have distinct identities, emphasized by human modifications to them. The
Delta is perceived as region where fresh water from the rivers tidally
sloshes back and forth in leveed channels, flowing between islands of
agricultural fields. The islands are highly subsided (many are 5+ m
below sea level), surrounded by 1800 km of fragile levees made of local
materials, often peat. Historically, the Delta was a vast marshland that
was flooded annually by undammed rivers (Lund et al. 2007).

Suisun Bay, in contrast was, and still is, a large area of open water
that is transitional between the fresh waters of the Delta and the salt
waters of San Francisco Bay; it is a shallow region of wind-stirred,
brackish water, lined with tidal marshes. The largest of these marshes,
in fact nearly as large as Suisun Bay itself, is Suisun Marsh. This
30,000+ ha marsh is largely managed today as freshwater marsh, mostly
for duck hunting in both private duck clubs and public wildlife areas.
The key for maintaining its freshwater character is inflow from the
Sacramento River via Montezuma Slough. Montezuma Slough has large tidal
gates on its upper end which control salinity in the marsh by allowing
fresh water to flow in but prevent the tides from pushing it back out
again. Over 360 km of levees separate the marsh islands from the tidal
channels, in which water is still seasonally brackish. The channels are
highly productive of fish, however, which are a mixture of freshwater
and marine species (Matern et al. 2002).

![](media/image1.jpeg){width="5.235416666666667in"
height="6.120833333333334in"}

> Figure 1. The San Francisco Estuary, showing the extent of the legal
> Delta and other key features. From Moyle (2002).

The marine species in Suisun Marsh come from San Francisco Bay, which is
largely a saltwater system, with variable but high salinities; the
actual salinity value depends on location and season. San Francisco Bay
is ringed by cities and its fringe marshes are fragments of its original
tidal marsh system.

All three parts of the SFE were once more variable in their salinities
and river-driven hydrodynamics than they have been for the past 50-60
years (Bay Institute 1998). During wet years, the spring snow-melt from
the Sierra Nevada could temporarily make fresh the surface waters of San
Francisco Bay, while during late summer of drought years ocean salt
could be detected at the upper ends of the Delta (DWR 1993), especially
once agriculture diverted large amounts of water. The advent of the
federal Central Valley Project and the State Water Project, however,
allowed the system to stabilize, so that, for the purposes of policy and
public perception, the Delta and Suisun Marsh became permanent
freshwater systems, Suisun Bay became a brackish water system, and San
Francisco Bay became an exclusively marine system. The two water
projects (and other related projects) constructed huge dams on the
Sacramento and San Joaquin rivers and all their major tributaries in the
1930s-1960s, with such perverse consequences as increasing the summer
flows of the Sacramento River and drying up the San Joaquin River. The
dams allowed for the regulation of salinity in the upper SFE. By
releasing large quantities of water, especially in the summer, the dam
operators could both keep salt water out of the Delta and Suisun Marsh
and permit the pumping of the water, from the southern edge of the
Delta, for agricultural and urban use.

For further information on the environmental and ecological history of
the SFE see Herbold et al. (1992), Hollibaugh (1996), Bay Institute
(1998), and Lund et al.. (2007) or see http://www.deltavision.ca.gov.
The rest of this essay will focus primarily on the Delta and Suisun Bay
and Marsh, because the lowermost part of the SF Estuary, San Francisco
Bay, has a whole additional set of problems related to its intense
urbanization.

**The Fishes**

SFE has a high diversity of fishes, representing marine, freshwater,
anadromous, and estuarine species, as well as native and alien species
(Matern et al. 2002, Moyle 2002). About 75 species, largely marine, are
known from SF Bay in recent years, of which only 5 are alien species. In
Suisun Marsh and Bay, 53 species are known, a mixture of marine,
freshwater, and anadromous (sea-run) species. They represent 28 native
species and 25 aliens (Matern et al. 2002). In the Delta, there are
about 46 regularly occurring species, a mixture of freshwater and
anadromous fishes, of which 27 are aliens. The total fish fauna consists
of about 120 species that can be found in one environment or another on
a fairly regular basis, of which about 30 (25%) are aliens, mostly in
fresh and brackish water. The invasion of alien species has accompanied
past large-scale environmental change and has been a driver of declines
of native species, including extinctions of native species such as
thicktail chub and Sacramento perch (Moyle 2002, Marchetti and Light
2007). Changes over the past 50 years, since the advent of the major
water projects, have led to severe declines of most native species,
including four runs of Chinook salmon and the delta smelt. This result
has been that five fishes, including delta smelt and two runs of Chinook
salmon, are currently listed as threatened or endangered by state and
federal governments (Moyle 2002). In more recent years, declines in
fisheries have also been of major concern, especially of fall-run
Chinook salmon, white sturgeon, and alien striped bass. Some of the
fishes most likely to affected by future large scale changes to the SFE
and also likely to drive policy decisions are listed in Table 1.

+----------------+------+---------------------+-----------------------+
| Species        | Nat  | Why important       | comments              |
|                | ive? | (status)            |                       |
+----------------+------+---------------------+-----------------------+
| Delta smelt    | yes  | T&E species,        | Open water pelagic,   |
|                |      |                     | near extinction       |
| *Hypomesus     |      | endemic             |                       |
| t              |      |                     |                       |
| ranspacificus* |      |                     |                       |
+----------------+------+---------------------+-----------------------+
| Longfin smelt  | yes  | Special concern     | Open water pelagic,   |
|                |      | species             | in severe decline     |
| *Spirinchus    |      |                     |                       |
| thaleichthys*  |      |                     |                       |
+----------------+------+---------------------+-----------------------+
| Splittail      | yes  | Special concern     | Spawns on             |
|                |      | species, endemic    | floodplains, rears in |
| *Pogonichthys  |      |                     | brackish water        |
| m              |      |                     |                       |
| icrolepidotus* |      |                     |                       |
+----------------+------+---------------------+-----------------------+
| Tule perch     | yes  | Native, declining   | Represents complex of |
|                |      |                     | native fishes         |
| *Hysterocarpus |      |                     |                       |
| traski*        |      |                     |                       |
+----------------+------+---------------------+-----------------------+
| Sacramento     | yes  | Extirpated          | Reintroduction        |
| perch          |      |                     | program proposed      |
|                |      |                     |                       |
| *Archoplites   |      |                     |                       |
| interruptus*   |      |                     |                       |
+----------------+------+---------------------+-----------------------+
| Striped bass   | no   | Estuarine sport     | Pelagic, uses entire  |
|                |      | fish.               | estuary               |
| *Morone        |      |                     |                       |
| saxatilis*     |      | declining           |                       |
+----------------+------+---------------------+-----------------------+
| White sturgeon | yes  | Sport fish,         | Anadromous, rears in  |
|                |      | declining           | estuary               |
| *Acipenser     |      |                     |                       |
| transmontanus* |      |                     |                       |
+----------------+------+---------------------+-----------------------+
| Southern Green | yes  | Endemic, threatened | Anadromous, rears in  |
| sturgeon       |      |                     | ocean                 |
|                |      |                     |                       |
| *A.            |      |                     |                       |
| medirostris*   |      |                     |                       |
+----------------+------+---------------------+-----------------------+
| Chinook salmon | yes  | Four runs, all in   | Anadromous            |
|                |      | decline             |                       |
| *Oncorhynchus  |      |                     |                       |
| tshawytscha*   |      |                     |                       |
+----------------+------+---------------------+-----------------------+
| Chinook        | yes  | threatened          | Appears in estuary    |
| salmon,        |      |                     | mainly as smolts      |
|                |      |                     |                       |
| spring run     |      |                     |                       |
+----------------+------+---------------------+-----------------------+
| Chinook salmon | yes  | endangered          | Appears in estuary    |
|                |      |                     | mainly as smolts      |
| winter run     |      |                     |                       |
+----------------+------+---------------------+-----------------------+
| Chinook salmon | yes  | Sport and           | Large numbers of fry  |
|                |      | commercial          | in estuary but        |
| fall run       |      | fisheries, hatchery | survival low          |
|                |      | driven              |                       |
+----------------+------+---------------------+-----------------------+
| Largemouth     | no   | Alien predator,     | Represents complex of |
| bass           |      | game fish,          | alien pond fishes in  |
|                |      |                     | Delta                 |
| *Micropterus   |      | Increasing in       |                       |
| salmoides*     |      | abundance           |                       |
+----------------+------+---------------------+-----------------------+
| Threadfin shad | no   | Locally abundanct   | Regarded as part of   |
|                |      | but in decline      | Pelagic Organism      |
| *Dorosoma      |      |                     | Decline               |
| petenense*     |      |                     |                       |
+----------------+------+---------------------+-----------------------+

**Table 1. Fish species that of major importance for management in the
San Francisco Estuary. Information from Moyle (2002).**

**Drivers of Change**

The major drivers of change in the SFE that are together or individually
likely to result in major shifts in environmental conditions, including
catastrophic shifts are: earthquakes, island subsidence, sea level rise,
climate change, and invasions of new alien species (Lund et al. 2007).
Human land and water use could arguably be listed as another driver of
change but these uses are strongly affected by the first five drivers
(i.e., are the reason the first five are of concern) so will not be
treated further as drivers here. The major catastrophic consequence of
the five major drivers is extensive levee failure in the Delta and
Suisun Marsh. From an ecological perspective, the consequence is sudden
change of in the hydrodynamics of the two regions as the islands fill
with water, creating new habitat conditions, followed by invasions of
undesirable species into the new habitat space.

*Earthquakes.* There are at least five faults in the Delta region but
there have been no major earthquakes in the region since the great 1906
San Francisco Earthquake. This means that pressure is building up on the
faults, steadily increasing the probability that one will move as time
goes by (Mount and Twiss 2005). The major impact likely from earthquakes
is collapse of levees in the Delta and Suisun Marsh because of their
poor foundation soils and weak construction.

*Island subsidence.* The islands of the Delta were originally marshlands
on a thick base of peaty soils. Over 182,000 ha of islands were diked
and drained for farming in the 19^th^ century and soils were typically
burned annually to release nutrients from the peat, causing the
interiors of the islands to subside rapidly. Even after burning stopped
subsidence continued through oxidation of plowed soils and dust carried
off by the frequent winds. As a result, all islands with peat soils used
for farming have subsided, with subsidence greatest (3-7 m below sea
level) in west and central Delta (Figure 2). Subsidence continues as
long as farming continues. The effect of subsidence is to create a
series of depressions surrounded by water, which will pour in if given
the chance to break through the levees.

*Sea level rise*. Sea level is rising in the SFE and has been for at
least thousands of years. Because of global warming, the rate of rise is
accelerating. There is scientific debate about how rapidly and how much
sea level will continue to rise, but a 30-50 cm rise in the next 50
years is plausible. The higher mean sea levels result in much higher
high tide levels, increasing the probability that levees in the Delta
and Suisun Marsh will overtop and then collapse, especially if combined
with flood flows coming down the rivers.

*Climate change.* The climate of California is becoming significantly
warmer, a trend that is likely to continue for some time (Dettinger
2005). While average precipitation is not expected to change much, more
will fall as rain and less as snow in the high mountains. Year to year
variability in rainfall is also expected to increase, as will the
frequency of extended droughts and big floods. Once result of this
change is increased hydrostatic pressure on levees during storms and
floods and increased likelihood of failure.

*Invasive species*. The SFE has the reputation of being the most invaded
estuary in the world and new invasions continue at a high rate of
frequency (Cohen and Carlton 1998). Recent invaders (e.g.,overbite clam,
Brazilian waterweed) have already had major impacts on ecosystem
structure and function. New invaders or expanding populations of
existing invaders are likely to take advantage of the new habitats
created by large-scale levee failure (Marchetti and Light 2007), further
exacerbating the effects of levee failure and increasing the difficulty
of protecting native species.

![](media/image2.png){width="4.946527777777778in"
height="7.292361111111111in"}

**Figure 2. Map of the Sacramento-San Joaquin Delta showing land
subsidence. From DWR (1993). Recent surveys indicate that subsidence in
most areas is 1-5 ft greater than shown (DWR, unpublished data).**

**Ecological effects of large-scale change**

The likelihood is high that two or more of the above drivers of change
will act together to create catastrophic levee failure and other changes
within the next 50 years (Mount and Twiss 2005; Lund et al. 2007),
assuming the SFE continues to be managed as it is today. The probability
of such an event is high enough so that it is presumably more a matter
of "when" and "how much" rather than "if." In recognition of this, the
Delta Risk Management Strategy (DRMS) team of the California Department
of Water Resources has modeled the effects of up to 50 simultaneous
levee breaches on Delta islands (http://www.drms.water.ca.gov). Other
signs of high levels of interest include (1) the appointment by Governor
Arnold Schwarznegger in February 2007 of the Delta Vision Committee with
a Blue Ribbon Task Force to find ways to prevent or reduce the impacts
of the impending disaster, (2) the recent passage of bond issues to fix
levees and other infrastructure affecting urban areas,(3) the
establishment of a Bay-Delta Conservation Plan process and (4) numerous
other actions and processes by agencies at all levels of government. The
scenario of most concern is simultaneous and cascading failures of
levees throughout the Delta because of the impact of such failures on
southern California's water supply, on agriculture and other uses of
Delta islands, and on urban areas in and around the Delta (Lund et al.
2007). Here, however, we discuss mainly the impacts on the ecosystems of
the Delta and Suisun Marsh, especially with respect to fish.

***Delta.*** For the central and western Delta, the basic 'disaster'
scenario is that following multiple levee failures, water would rush in,
filling as much as 2.5 *billion* cubic meters of space in the island
basins. If the levee collapses occurred as the result of the combination
of high outflows and high tides, the islands would likely fill mostly
with fresh water. If the levee collapses occurred as the result of an
earthquake during a low-flow period, much of the water filling the
islands would be drawn up from Suisun Bay and even San Francisco Bay
creating lagoons with varying degrees of salinity

The open-water habitat thus created would be up to 10 m deep and subject
to strong tidal currents, as well as mixing from frequent winds. The
hydrodynamic and salinity regimes of each flooded island would depend on
the number and location of levee breaches, closeness of the area to
Suisun Bay (source of salt water) and to inflowing rivers, and
relationship to infrastructure such as the ship canal that goes through
the system. As levees continued to erode, many of the flooded islands
would presumably come to resemble Frank's Tract, a large island in the
central Delta that flooded in the 1930s and was left that way. It is
currently freshwater lagoon with complex hydrodynamics that is dominated
in summer by dense growths of Brazilian waterweed, *Egeria densa.*

Presumably, the flood water would initially be highly turbid from the
disturbance of peat and sediment on the islands (DWR 2007) but once the
suspended material had settled there would be massive blooms of algae
because of the release of nutrients from the soils and the increased
water transparency. Depending on the species making up the algal blooms
(diatoms vs green algae vs cyanobacteria), a bloom of zooplankton should
quickly follow. Within a year, island lagoons with brackish water
lagoons would be heavily colonized by the overbite clam, an alien
species which currently dominates the benthos of Suisun Bay. Presumably,
the clams would then consume much of primary production and carbon of
the new lagoons, as they do in Suisun Bay, reducing zooplankton
populations. Island lagoons that contain fresh or low salinity water,
would likely be colonized in 1-2 years with the species that dominate
similar areas in the Delta: Brazilian waterweed and, in areas with
sufficient flow, Asian clams. The combination would result in lagoons
choked with weeds, with low zooplankton populations (like Frank's Tract
today). It is possible that flooded islands located close to both
sources of freshwater inflow (Sacramento River) and tidal sources of
salt water could maintain a pool of water that would fluctuate enough in
salinity on either an annual or interannual basis to keep either the
overbite clam or Brazilian waterweed-Asian clam from becoming dominant.
Biomass production in such lagoons would be concentrated in a pelagic
system of phytoplankton, zooplankton, shrimp, and fish, such as was the
case of Suisun Bay before the invasion of overbite clam in the 1980s.
Obviously, these scenarios can all be strongly affected by local
conditions of wind, tide, and river, as well as the diverse
configurations of the lagoons (which will change constantly as levees
deteriorate after the initial breeches).

***Suisun Marsh***. Suisun Marsh, for the most part, is not subsided as
much as the Delta, although much of it is 0-2.3 m below sea level (which
is rising) and some (ca. 16%) is more than 2.3 m below sea level (C.
Enright, DWR, pers. comm.). Before European settlement it was high
marsh, mostly flooding on high tides and high river flows. A scenario of
wide-scale levee failure in the Delta is likely to include Van Sickle
Island, located at the entrance to Montezuma Slough, the main artery of
the Marsh. Van Sickle Island is already subject to frequent levee
failures, although failures are quickly repaired. The rapid repair
response (by public agencies) occurs in good part because if the island
floods, the entire freshwater distribution system of the central Marsh
(Roaring River Slough) ceases to work efficiently and the southern third
of the Marsh (between Montezuma Slough and Suisun Bay) becomes tidal and
brackish. Future failure will likely make much of the central Marsh
tidally brackish. Less dramatically, increasingly high tides (from sea
level rise) and increasingly large flood events (from climate change)
are likely to cause levee over-topping and failures within the Marsh at
increasing rates. Thus the ultimate fate of much of Suisun Marsh is to
be inundated with tidal waters and to become a tidal brackish-water
marsh, with seasonally higher salinities in many areas than were
historically present. Much of it is likely to be permanently inundated.
How the future marsh will actually look will depend on the interactions
of a number of factors: (1) the rapidity and extent of sea level rise,
(2) the depth of tidal and other flooding, (3) the residence time of the
water in different areas i.e. the relationship between the flooded areas
and the deeper channels/sloughs that drain them, (4) response of the
natural vegetation to the inundation and salinity gradients, and (5) the
influence of existing artificial dikes and channels, including railroad
and road beds. This future Marsh, however, will certainly have a mosaic
of habitats including, most importantly, extensive tidal brackish water
marsh areas. These areas will be drained by channels that should
gradually recover their historic dendritic nature and be kept open by
strong tidal action.

**Effects on fishes of large-scale change**

In the broadest sense, the creation of more aquatic habitat in the Delta
and Suisun Marsh will be good for fish, resulting in a net increase in
numbers and biomass, once the initial flooding period is past. The
important question is what will happen to the species that people care
most about (Table 1). These are native species that are listed as
threatened or endangered or are in severe decline or fishes that support
fisheries. The effects suggested in the following accounts are highly
speculative, but based on extensive knowledge of the fishes, which are
well studied (Moyle 2002, see also recent review papers by various
authors in the on-line journal *San Francisco Estuary and Watershed
Science*).

*Delta smelt**. ***The single most important species from the viewpoint
of affecting management of water in the Delta is the delta smelt, which
is listed as threatened by both state and federal governments and is on
the verge of extinction (Bennett 2005). It has a one-year life cycle, is
a pelagic planktivore, and is endemic to the SFE, spawning in the Delta
and rearing in Suisun Bay and Marsh (Moyle 2002, Bennett 2005). It is
highly likely that most delta smelt will be sucked into the rapidly
filling islands under multiple levee breach scenarios, whether they were
upstream spawning in the upper Delta, downstream rearing in Suisun Bay,
or moving between the habitats. A few smelt might be able to avoid the
displacement if they were located in the distant peripheral habitats
such as the mouth of the Napa River, Montezuma Slough, or Cache Slough
in the north Delta. The DRMS study (DWR 2007) predicts that many, if not
most, fish sucked into the flooding islands will die of stress,
especially that created by particulate matter in the water abrading
gills and creating high turbidity. The delta smelt, as a small (\< 9 cm
TL) delicate, mid-water, visual feeder, would seem especially vulnerable
to these conditions. Unfortunately, data is lacking to support the high
turbidity mortality hypothesis. Previous levee breaches on single
islands have not been accompanied by reports of fish kills, but no one
was looking in the haste to repair the levees and pump out the islands.
It seems unlikely, however, that a complete fish kill would result from
filling process, given the volumes of water involved and the nature of
the matter (organic matter, mainly peat particles) most likely to be
suspended. The filling would be most disastrous for Delta smelt if they
were spawning because it would suck them away from suitable spawning
areas and would likely create hydrodynamic conditions (diminished tidal
range in channels) that would make return difficult. Likewise, surviving
larval smelt would likely find unfavorable conditions for feeding in the
newly filled islands and could starve before large populations of
microzooplankton (especially rotifers) developed.

Assuming massive blooms of toxic algae (e.g., *Microcystis*) do not
occur, a month or so after island filling and hydrodynamic
stabilization, conditions for plankton feeding fish such as smelt should
start becoming favorable with the development of blooms of one or more
species of small food organisms. Delta smelt that survived up to this
period in the islands should then find conditions extremely favorable
for growth and survival, especially in islands that maintained
salinities of \< 2 mg/l and temperatures of \<20°C. Thus impact of a
large-scale levee breach event on delta smelt depends in good part on
the timing of the event. Presumably, a higher proportion of the
population would be able to survive an event in July- November, than in
December-June.

In the long run, however, permanently flooded islands in the right place
could *increase* the amount of favorable habitat for delta smelt. If a
flooded island had conditions (mainly fluctuating salinity) that
excluded dominant invasive benthic species, it would likely become
highly productive pelagic habitat, habitat which is apparently in short
supply for smelt at times today (Bennett 2005, Hobbs et al. 2006, 2007).
Delta smelt would presumably also benefit from a flooded Suisun Marsh as
rearing habitat, if flooding increased productivity of intersecting
channels, especially Montezuma and Suisun sloughs, and salinity
fluctuations reduced the impacts of invasive species.

One indirect positive effect for smelt of large-scale island flooding
would be that the large pumps of the State Water Project and the federal
Central Valley Project in the South Delta would be shut down for long
periods of time because of salty water at their intakes. Because in some
years pumping from the two plants can negatively affect delta smelt
populations through entrainment and other effects (Bennett 2005),
shutting down the pumps will remove one potential major source of
mortality, perhaps compensating for some of the flooding mortality.

*Longfin smelt*. Longfin smelt have a 2-3 year life cycle, much of which
is spent in San Francisco Bay and/or the Gulf of the Farallons, outside
the Golden Gate (Moyle 2002, J. Rosenfield, unpublished analysis). They
spawn in the western Delta in winter and often spend the first year of
their life in Suisun Bay and Marsh. Being anadromous and iteroparous
with multiple age classes, they are less vulnerable to extirpation by a
large-scale event than are delta smelt. Like delta smelt and other
planktivores, however, longfin smelt have suffered a large decline in
their population in recent years. Thus large scale levee collapse in the
Delta could initially harm longfin smelt, as indicated above for delta
smelt, although a least a portion of the longfin smelt population would
have reduced vulnerability because of distance from the flooded islands.
For over half the year (May- November), most of adult smelt would be
beyond the likely reach of a flooding event.

Permanently flooded islands in the western Delta could ultimately become
important rearing habitat for larval and juvenile longfin smelt,
depending on whether or not large zooplankton populations developed.
Increased productivity of sloughs/channels in Suisun Marsh would
presumably also benefit these smelt.

*Striped bass*. With high fecundity, interoparity, large size, and a
life span of 40+ years, non-native striped bass have a high capacity to
survive environmental disasters. Nevertheless, they have suffered a
long-term decline in the SFE, although they still support a valuable
fishery (Moyle 2002). In the SFE, striped bass migrate 125-200 km
upstream to spawn in the Sacramento River in late April- early June. The
embryos drift downstream and hatch about the time they reach Suisun Bay,
where the larvae rear at low salinities. Juveniles rear throughout the
estuary but seem to be most abundant in Suisun Marsh and Bay, where they
feed on zooplankton. By the time they are 10 cm TL, they have largely
switched to feeding on small fish. Adult striped bass are largely
piscivorous and a major prey in the SFE is small striped bass. Adults
will spend their entire life in the SFE, especially in San Francisco
Bay, but when ocean conditions are right, some will go out into the
ocean as well (Moyle 2002).

Overall, striped bass seem relatively immune to long-term effects of
large-scale levee breaching. If the breaching occurred in early summer,
then large numbers of larvae and juveniles could die, but in following
years they could benefit from increased pelagic habitat, especially if
portions of it were highly productive of zooplankton and small fish.
Larger juveniles and adults are strong swimmers and could presumably
quickly leave a submerged island after the initial event, assuming they
survived the flooding event itself.

*Sacramento splittail*. Splittail are largely confined today to the SFE,
where they rear in Suisun Marsh and other places with fresh to brackish
water sloughs (Moyle et al. 2004). A separate population lives in the
Petaluma River estuary, tributary to San Pablo Bay. Adults, which live
up to 9 years, migrate up river to spawn (mostly) on floodplains in or
just above the Delta (Moyle et al. 2004). Timing of spawning depends on
timing of natural flooding, sometime between January and May. Juvenile
splittail rear on the floodplain for a month or so and then migrate
rapidly downstream to rearing areas, where they feed on benthos.

During a major island flooding event, many splittail are likely to be
drawn in, although it is also likely that many others would remain in
place because of living in small sloughs distant from the event and also
being strong swimmers. If the levee breaching occurs in conjunction with
natural high flows in January-May, large number of migrating adult or
juvenile splittail could be captured. Although sudden entrainment on the
flooded islands could result in high mortality, the high tolerance of
splittail for poor quality (low dissolved oxygen, high turbidity,
variable salinities, etc.) suggest adults and large juveniles are likely
to survive the experience. The flooded islands are not likely to be
great habitat for splittail until significant benthic fauna develops,
especially amphipods and mysid shrimp. However, permanently flooded
islands that remain brackish enough to exclude Brazilian waterweed
should ultimately become suitable habitat for splittail, especially
shallower areas.

*Chinook salmon***.** Four runs of Chinook salmon pass through the SFE
on their way upstream to spawn in the Sacramento River: fall run,
late-fall run, winter run, and spring run (Moyle 2002). All runs are
depleted from historic numbers and the winter and spring runs are listed
as endangered and threatened species, respectively. The fall run is
supported in good part by hatchery production and occurs in tributaries
to the lower San Joaquin River, as well as the Sacramento River. Fry and
smolts of the salmon are found seasonally in the estuary, on their way
downstream to the ocean. When the Delta was a giant tidal marsh, it was
likely a major rearing area for fry before they moved out to sea as
smolts. At the present time, rearing habitat for fry in the SFE is
minimal and fry survival is low; higher returns of adults from hatchery
fry generally occurs when the fry are planted in the SFE below the Delta
(Brandes and McClain 2001, Williams 2006). Highest survival of fry and
smolts in the SFE occurs in years of high outflow in both the Sacramento
and San Joaquin rivers, suggesting that it pays the fish to move through
the Delta rapidly. Survival of fry and smolts is also highest when the
fish are largely confined to the main river channels and do not get
moved into the Central Delta (Brandes and McClain 2001). Although
juvenile salmon can be captured in SFE at almost any time of year, most
movement is in December through April.

As with other fish, the immediate effect of a major levee failure in the
Delta depends on the time of year in which it occurs, with the greatest
impact likely to be in February --April, assuming migrating juvenile
salmon, especially fry, sucked into the flooded islands would mostly
die. The effect would be greater for San Joaquin River salmon than for
Sacramento River fish because there would more likely be a continuous
river channel for the fish to follow on the Sacramento side, due to
location and greater flows. Once the island lagoons had become
established, they would generally be unfavorable habitat for juvenile
salmonids because they would contain little of the shallow water edge
habitat preferred by juvenile salmon. Instead, they would be open water
or weed-choked and contain fairly high densities of predators such as
striped bass or largemouth bass. The effect would be determined in large
part by how easily it would be for juvenile salmon to be carried into
the lagoons from the rivers and how easy it would be escape from them.
High outflows down both rivers should minimize the effects of the
lagoons, while low outflows should increase the likelihood that juvenile
salmon would wind up in them, especially on the San Joaquin side of the
Delta. It is possible that Suisun Marsh will be heavily used by juvenile
salmon once it floods, because much of it will be productive shallow
water habitat, if saline.

Effects on adult salmon would presumably be small because of their focus
on swimming upstream through the Delta, although there would no doubt be
some mortality if the breaches occurred during a period of significant
migration.

*Largemouth bass*. Largemouth bass are introduced piscivores that have
greatly expanded their populations in the Delta following the invasion
of Brazilian waterweed. The waterweed provides habitat for the bass by
creating cover for juvenile and adult bass, reducing flow rates through
channels, and causing sediment to settle from the water, resulting in
clearer water. It is only the most visible species of a complex of alien
'pond' species that thrive in waterweed dominated freshwater sloughs,
including redear sunfish, bluegill, white catfish, black bullhead, and
common carp. By and large these are the same species that are dominant
in upstream reservoirs (Moyle 2002).

Largemouth bass and associated species would expand their populations
further in flooded freshwater islands, once the Brazilian waterweed
became established. While these species can survive in brackish water
habitat, most of them avoid it and will probably be present in only low
numbers in brackish lagoons without dense beds of waterweed.

*Marine fish***.** San Francisco Bay supports a diverse fauna of marine
fishes that includes most of the common species found along the central
California coast. The abundances of different species fluctuate both in
response to ocean conditions and to freshwater flows into the Bay. Not
surprisingly, some of the most abundant species are species that can
tolerate moderately low salinities (euryhaline), such as Pacific
herring, northern anchovy, staghorn sculpin, yellowfin goby, and starry
flounder. Juvenile of these forms frequently appear in the upper
estuary, especially in Suisun Bay and Marsh, usually during periods of
low river flows. Thus, the expanded brackish water habitat in the upper
estuary is likely to increase habitat space for euryhaline marine
species, especially during dry years.

*Overall fish responses***.** It should be evident from the above
descriptions that responses of fish species to large-scale island
flooding will be highly variable, a reflection of the complex habitat
and the complex fish fauna. Unanticipated responses are also likely to
the changed conditions. For example, inland silverside are now abundant
in the shallow flooded areas of Sherman Island in the western Delta (W.
A. Bennett, pers. comm.) and it is possible that it could colonize some
of the newly flooded areas, depressing other fishes through predation
and competition (Bennett and Moyle 1996). In addition, new alien
invaders could cause major shifts in abundance of established species.
For example, two piscivores are poised to invade the SFE: northern pike
and white bass (Moyle 2002, Lund et al. 2007). However, the general
patterns of fish response to sudden large scale flooding would roughly
be the following:

1\. Fishes within the suction zone of Delta levee breaks (which could be
a large area, given the capacity of the islands to accept large volumes
of water) would be sucked into the island with some mortality from
sediment in the water column, sudden changes in water quality (salinity,
temperature, etc.), and other factors associated with the sudden
movement of large volumes of water. The species affected would depend on
time of year of flooding and the location of the flooded islands.

2\. Once the waters had settled down, there would be an initial period
of low plankton densities, followed by blooms first of phytoplankton,
then zooplankton, perhaps within a period of 1-3 months.

3\. In the longer term (1-5 years), the new lagoons would assume the
character of areas in the SFE with similar depths, flows, and
salinities. Thus, those in the more eastern and central parts of the
Delta would likely become dominated by Brazilian waterweed and a
variable assemblage of alien freshwater fishes. Lagoons in the western
Delta that maintained low (2-10 mg/l) salinities most of the time would
have conditions similar to those in Suisun Bay. Planktonic productivity
is greatly reduced in Suisun Bay by the filter-feeding overbite clam,
but it still serves as an important rearing area for pelagic fishes, at
least in some areas (Hobbs et al. 2006). These areas would provide
expanded habitat for species such as striped bass, longfin smelt, and
delta smelt, as well as additional feeding areas for sturgeon*,*
splittail, and other benthic feeders that can consume clams and their
associated faunas. A few lagoons that were created in intermediate
locations, where salinities and other conditions would become highly
variable among years and seasons because of the combination of river
inflow and tidal exchange, could be highly productive systems that would
support dense populations of plankton and planktivores, including delta
smelt and striped bass. Such areas could become a source for enhanced
populations of euryhaline fishes.

4\. Over a longer term (5+ years), conditions in the lagoons would
change further as levees continued wash away, parts of the lagoons
filled in with sediment, and islands not flooded previously gave way to
new hydraulic forces created by the lagoons (waves, changed current
patterns, etc.), assuming most levees were not repaired. Essentially,
much of the Central and South Delta could become one large embayment,
similar to Suisun Bay, but fresher on its upper end. By size alone, this
area would increase the amount of habitat for fishes. Presumably, the
increased habitat would increase populations of some of the desirable
open-water species although much of it would be dominated by waterweed
and alien pond fishes or by relatively low productivity habitat
dominated by overbite clam. In this period, Suisun Marsh would also have
become at least partially flooded, with the potential for large
increases in tidal brackish water habitat, favorable (depending on
salinity regime) to desirable species such as longfin smelt, delta
smelt, spittail, striped bass, and possibly juvenile Chinook salmon.

Thus the overall effect of massive flooding would likely to be to
increase the populations of at least some desirable species while
greatly increasing the abundances of less desirable aliens, such as
largemouth bass and common carp. While there are fisheries for such
species, they are deemed less desirable because the fish are non-native
and have large populations outside the SFE, unlike the species deemed
desirable.

**Improving the estuary for fish**

The above speculative discussion is based on the scenario that
California will continue on its present track of managing the Delta
environment through a combination of applying band-aid levee repairs,
poorly regulating invasive species, removing large quantities of fresh
water, managing Suisun Marsh as freshwater marsh, and monitoring
desirable species as they decline. In short, the status quo consists of
continuing business as usual until large-scale levee collapse forces
large-scale action, much of it likely to be poorly planned and futile in
the long run (Lund et al. 2007). As indicated above, the massive
collapse of levees in the Delta and Suisun Marsh would not be a
long-term disaster for fish and fisheries and could even be a slight
benefit. The collapse could be a disaster for the California economy,
however, mainly because it would disrupt the state's water supply system
and other infrastructure (Lund et al. 2007). Thus a movement to actually
'fix' the Delta and Suisun Marsh before the inevitable disaster is
highly desirable and several processes are underway at the state level
to determine options. Lund et al. (2007) present nine scenarios for a
future Delta and Suisun Marsh, five of which they regard as feasible.
The four of the five protect water supply while allowing some portion of
the Delta to remain as habitat for native fish and other desirable
organisms. The five options provide suggestions for significantly
improving the habitat in the Delta and Suisun Marsh for desirable
species, provided action is taken before large-scale levee collapse
occurs. The options of Lund et al. (2007) are only a tiny fraction of
the hundreds of permutations and combinations of actions that could be
taken; they are designed to represent examples of the reasonable
alternatives possible to provide a visualization of management options.

Here I will not go through the alternatives but instead discuss actions
that will allow fish-friendly habitat to develop while not necessarily
reducing most of the services to humans that the SFE provides. These
actions could be part of any scheme that seeks to modify the Delta to
improve or protect its water supply functions as well its ecological
functions. The general approach towards creating an environment in the
SFE that is more friendly to desirable fish species (and other biota)
presented here is to increase habitat heterogeneity. The basic concept
is as follows: as much area as possible should support conditions
resembling those of the historic SFE, especially in the Delta and Suisun
Marsh, because these are the conditions to which the native fishes are
adapted. However, the improved habitats are likely to be in different
locations than they were historically because of changed elevations due
to subsidence and sea level rise. Thus habitats once present in the
deeply subsided center Delta will have to be located in the
less-subsided peripheries.

A key part of a habitat creation program will be to have as much area as
possible that fluctuates in salinity enough so freshwater and brackish
water benthic invaders are discouraged while desirable (mainly native)
pelagic species are favored. The exact extent, frequency, and range of
salinity fluctuation needs to be determined by further studies of key
organisms (both desirable and undesirable species), but present
distributional limits of the organisms suggest that fluctuations
required are likely to be in the range of 0 to 12 mg/l over 1-2 years,
with high and low values sustained for 4-5 months at a time.

The following are some general, large-scale actions that could improve
habitat heterogeneity and create areas with desirable conditions of
water quality, including fluctuating salinity. This list is neither
complete nor inclusive (Lund et al. 2007).

1\. *Suisun Marsh.* This region of the SFE is headed inexorably to
becoming brackish tidal marsh, unless huge amounts of money are spent on
raising levees; such action may not even be possible as a permanent
solution, given the compressibility of the marsh soils underlying the
levees. Most of Suisun Marsh is currently intensely managed in diked
sections, principally as freshwater habitat for waterfowl. Even under
these conditions the intervening sloughs, especially in the few undiked
areas, provide good, often brackish, habitat for desirable fish (Matern
et al. 2002, R. E. Schroeter, unpublished data). Improving the Marsh for
fish will require systematically breaching or removing levees, initially
in the areas most vulnerable to flooding and preferably after
reconstruction of the original marsh drainage system and removal of
infrastructure. Models for the creation of the new tidal (and subtidal)
marsh areas can be found in the currently undiked section of marsh (Rush
Ranch) that is part of the San Francisco Bay National Estuarine Research
Reserve (http://rtc.sfsu.edu/nerr/sf_bay_reserve) and by an on-going
experimental levee breach at Blacklock
(http://www.iep.water.ca.gov/suisun/restoration). Even after radical
restructuring of the Marsh, it may be desirable to continue to operate
the large salinity control gates at the upstream end of the Montezuma
Slough. This slough and Suisun Slough are the deep (2-6 m) main arteries
of the Marsh and are the principal habitats of pelagic fishes such as
delta smelt and longfin smelt, so it may be possible to operate the
gates to increase the ranges of salinity that favor these species and
discourage undesirable alien species.

2\. *Cache Slough*. Cache Slough and adjoining areas make up essentially
the northwest corner of the Delta. The region is of high restoration
potential as tidal freshwater marsh and slough because (1) island
subsidence is low compare to other parts of the Delta, (2) it maintains
much of its original drainage pattern, even though most of the channels
are leveed and artificial cross channels exist, (3) it is a major
spawning and rearing region for delta smelt, (4) it has strong tidal
currents that move water from the Sacramento River in and out of its
channels, (5) it drains the lower end of the Yolo Bypass (next section),
and (6) it contains the large recently (1998) flooded Liberty Island
that is being used as an example of a "passive" restoration project
(<http://www.delta.dfg.ca.gov/jfmp/libertyisland.asp>). The region can
be relatively easily converted into an expanded version of the favorable
tidal habitat for desirable fishes (as well as waterfowl and other
biota) through levee breaches, elimination of cross channels, and other
projects that improve circulation. It is also a region where it should
be possible to create favorable habitats for delta smelt, mainly
spawning beaches and productive rearing areas for larvae, that also
discourage their egg and larval predators, especially inland silverside.

3\. *Yolo Bypass*. To keep Sacramento from flooding, an artificial
floodplain, the Yolo Bypass, was constructed in the 1930s. Essentially,
when the Sacramento River reaches a certain stage of flow, it spills
over two low barriers (Fremont Weir, Sacramento Weir) and into the
24,000 ha, 64 km long bypass (Sommer at al.2001a, b). The flood waters
flow down the bypass and re-enter the Sacramento River via Cache Slough.
The principal permanent water in the Yolo Bypass is the Toe Drain, which
runs along the levee on eastern edge. About half the bypass is in the
Delta; the Toe Drain in this region is essentially a leveed tidal
slough, a branch of Cache Slough. The land in the bypass is a mixture of
farmland and wildlife areas but when it floods it is high quality
rearing habitat for Chinook salmon fry and splittail, as well as other
fishes. The flood waters may also mobilize nutrients from the bypass,
helping to support Delta food webs. From an ecological perspective, a
problem with the Yolo Bypass is that is does not flood, even partially,
every year. Construction of a gate on the Freemont Weir would permit
limited controlled flooding from the Toe Drain every year, improving
growth and survival of salmon and splittail and improving flows through
Cache Slough to benefit delta smelt.

4\. *San Joaquin floodplain.* The channel of the San Joaquin River above
and through the Delta is highly channelized, and provides little
favorable habitat for desirable fishes: the water tends to be deep and
polluted in places (e.g., Stockton Ship Channel) and dominated by
invasive aquatic plants and invertebrates in others. One way to improve
the habitat for fish is to create one or more bypasses like the Yolo
Bypass. This would involve removing or breaching levees from islands
(e.g., Stewart Tract) that border the river to promote annual flooding.
Such floodplain habitat is likely to be especially beneficial as rearing
habitat for juvenile salmon coming from the San Joaquin River basin. An
example of the benefits of restored floodplain in the Delta is provided
by the small restored floodplain along the lower Cosumnes River, on the
eastern fringe of the Delta, which has proved to be beneficial to
several native fishes and provides experience in methods of modifying
agricultural lands into fish-friendly floodplains (Moyle et al. 2007).

5\. *Managed Delta islands.* The previous four actions have focused on
areas at the edges of the upper estuary because of assumption that the
subsided islands of the Delta will fill with water and together will
become a large open-water system over which little control can be
exerted, aside from regulating freshwater inflow under some conditions
(Lund et al. 2007). However, with some foresight, it may be possible to
retain the levee integrity of some islands, by making them into islands
of regulated aquatic habitat. Essentially this concept follows the lead
of Delta Wetlands, a private group that has sought to use Delta islands
for water storage and wildlife habitat
(<http://www.deltawetlands.com/>). The levees of habitat islands would
be reinforced on the inside by having gradual slopes towards the
interior, which would be planted with native vegetation to stabilize the
soils. Gates on the upper and lower ends of the islands would be used to
regulate water quality on the islands, including salinity. This concept
would be especially useful for islands (e.g., Twitchell Island) in the
western Delta located close the Sacramento River so that salinity could
be manipulated by trapping either river or tidal water in the island as
needed (as is currently done with tidal gates in Suisun Marsh). The
islands of water could then be managed as nursery areas for desirable
fishes. Ideally, the gates would also allow an island to be dried out
completely on occasion to control undesirable alien species.

**Invasive species**

A major uncontrolled (for now) factor that can negatively affect efforts
to create a more desirable, diverse (heterogeneous) ecosystem in the
Delta is the invasion of new alien species that become agents of
ecosystem change, such as the overbite clam or Brazilian waterweed have
in the past. There is an identified queue of harmful invaders that are
likely to arrive in the near future (Lund et al. 2007). Thus part of any
program of ecosystem creation must include vigorous efforts to exclude
new invaders from all sources, including the shipping, horticultural,
pet, and aquaculture industries. There should also be in place a
mechanism that allows quick action to eradicate a new invader before it
spreads from the site of an invasion.

**Conclusions**

The San Francisco Estuary, especially the Delta and Suisun Marsh, is
predicted to undergo drastic change in the next 50 years, with the
probability of a major 'disaster' increasing through time, just on the
basis of earthquakes and land subsidence alone (Mount and and Twiss
2005). When sea level rise and increased frequency of flooding due to
climate change are factored in, major change in this period seems
inevitable. The disaster scenario, however, is mainly for human goods
and services, especially water supply to urban and agricultural areas.
From a fish perspective, the ecological changes resulting from flooding
of numerous Delta islands and Suisun Marsh are likely to create
conditions that should be at least as favorable for desirable species as
present conditions, after a period of possible high mortality created by
the initial flooding events. Potentially *more* favorable habitat will
result from a disaster scenario simply because there will be increased
area of open water and tidal marsh, some of it with enough fluctuation
in salinity to be especially favorable to delta smelt, striped bass, and
other pelagic species now in decline. There is much uncertainty,
however, about how much favorable habitat will be created under disaster
scenarios because of the tendency of alien invaders to quickly dominate
so many habitats. Thus, making efforts to control the way the habitat
changes, as suggested above and in Lund et al. (2007), could have major
benefits while being highly compatible with changing the ways in which
services the Delta provides are delivered, especially water supply. The
principal basis for action is to increase habitat heterogeneity over
present and likely future conditions, as well as to increase the total
amount of aquatic habitat. No matter what actions are taken there will
be a high degree of uncertainty in the ecological benefits but the
present situation in the estuary represents an unprecedented opportunity
to reverse the impacts of over 150 years of negative ecological change.

**Acknowledgements**

The ideas expressed in the essay come from discussions with my
co-authors on the UCD-PPIC report: Jay Lund, Ellen Hanak, William
Fleenor, Richard Howitt, and Jeff Mount, as well as with the many
friends and colleagues who work in the San Francisco Estuary, but
especially William Bennett, John Burau, Christopher Enright, and Robert
Schroeter. This essay has not been peer-reviewed. Any mistakes and
misconceptions are entirely my own.

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