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3
Stressors:
Environmental Factors and Their
Effects on the Bay-Delta Ecosystem
THE CHALLENGE: IDENTIFYING, DISTINGUISHING,
AND RANKING INTERACTING ENVIRONMENTAL
FACTORS AFFECTING THE BAY-DELTA ECOSYSTEM
Many environmental factors, including water diversions, affect the
structure and functioning of biotic communities in the delta. Although it
would be convenient if one or only a few of these factors could be identi-
fied as the source of the "problem," or even ranked with some certainty, it
is not possible to do that, for at least three reasons: the "problem" is not
easily definable, the suite of stressors is complex and interactive, and the
ecosystem and its components do not react to any stressor as a single unit.
"The Problem" of the Delta Is Not a Single, Easily Definable Problem
Although the ecosystem has been radically altered over the past 150
years, it nonetheless remains a biologically diverse and productive eco-
system. Some species have thrived, but others, including some listed as
threatened or endangered under the federal Endangered Species Act and
California's Endangered Species Act, have declined dramatically. In addi-
tion, species composition and environmental conditions in the delta have
undergone large changes over the period. Therefore, while an immediate
difficulty for some is that concern over some listed species has affected
water diversions, "the problem" is harder to define biologically, and is
perceived differently by various stakeholder groups, institutions, and other
interests.
57
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58 SUSTAINABLE WATER MANAGEMENT IN THE DELTA
The Suite of Stressors Affecting Water Quality, Habitat, and
Sustainability of the San Francisco Bay Delta Is Complex and Interactive
Interactions among stressors and between stressors and ecosystem pro-
cesses are common. Nutrient enrichment, toxic chemicals, and temperature,
for example, are affected by hydrology and hydrodynamics, that is, the way
tides and freshwater flow interact to determine the temporal and spatial
variability of the physical environment of the estuary. This complicates the
interpretation and evaluation as to positive, negative, or neutral overall ef-
fects of any single stressor on the ecosystem and its attributes. Furthermore,
species differ in their individual responses to most types of stress. The result
is a complex biological, spatial, and temporal mosaic of impacts from this
combination of influences.
To some extent, the evaluation of the impacts of these effects also
depends on which ecosystem services and needs are of interest or concern,
for example, safe and usable water supplies, recreational and commercial
fisheries, habitat condition, or public use of the delta. Thus, while it is
politically attractive to attempt to rank stressors so as to prioritize societal
investments in their amelioration, that task is much more complex than it
might at first seem. To some degree, priorities can be defined if the stress,
species, place, and time are first prioritized or defined. The stressors dis-
cussed below and shown in Figure 3-1 are highly dynamic; that is, they can
quantitatively change in time and space depending on changes in human
activities (including future management actions), climate, and combinations
thereof.
The Ecosystem and Its Components Do Not Necessarily
Respond as a Single Unit to Most Environmental Factors
For example, Chinook salmon (Oncorhynchus tshawytscha) spend
several years at sea and then return to pass through the delta as adults to
spawn; their eggs and young spend time in delta tributaries before passing
through the delta on their way to the ocean to mature. Returning adult
Chinook salmon always die after spawning, and so they are not susceptible
to chronic environmental factors, because they die before such factors can
affect them. They also are strong swimmers and therefore most changes in
flow patterns in the delta are reasonably small challenges for them. The eggs
and young are susceptible to conditions in the tributaries and are exposed
to them for considerable periods, and the outmigrating smolts are not as
strong swimmers as are the returning adults, and so probably are more sus-
ceptible to changes in flow patterns. By contrast, delta smelt (Hypomesus
transpacificus) spend their entire (short) lives in the delta and so they can
be chronically exposed to contaminants in the water; being smaller and
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STRESSORS 59
FIGURE 3-1Conceptual diagram showing the interactive stressors affecting San
Francisco Bay Delta water quality, habitat condition, and overall ecosystem struc-
ture and functioning. While this figure is focused on key fish species (e.g., salmo-
nids), these are intimately linked to other biotic components of the ecosystem,
including planktonic and benthic primary producers, grazers, larval, and juvenile
and mature invertebrate and fish species.
SOURCE: Courtesy of A. Joyner, University of North Carolina.
R02208
Figure 3-1
bitmapped
weaker swimmers than even salmonraster image
smolts, they likely are more suscep-
tible to changes in flow than salmon are. In addition, the behaviors, food,
distribution in the water column, and physiologies of salmon and smelt are
different, so even if they are exposed for a time to the same adverse envi-
ronmental conditions, their responses to them almost certainly are different.
The above discussion compared only two species, but other species
are important as well, including those that are not listed. Other biotic
components, ranging from phytoplankton to fish, are part of the ecological
community and yet they, too, differ in behavior, distribution, physiology,
and susceptibility to a wide variety of environmental conditions, including
contaminants. Thus most attempts to identify and rank single environ-
mental factors as stressors are very likely to fail, unless the factors can be
specifically related to a particular aspect of a species' life history. Even such
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60 SUSTAINABLE WATER MANAGEMENT IN THE DELTA
factors as dams, which would appear at first glance to adversely affect only
or mainly migratory species like salmon, steelhead (Oncorhynchus mykiss),
and green sturgeon (Acipenser medirostris), also affect flow patterns, water
temperature and quality, food availability, and so on, and they differentially
affect many species, even those that do not migrate. There is a complex in-
terplay between key water quality, habitat, and sustainability issues and the
drivers affecting them. Furthermore, uncertainties and scientific gaps exist
that further compound the problem (Table 3-1). Indeed, the delta prob-
lem is a "wicked" problem in the sense of Rittel and Webber (1973) and
Conklin (2005): the problem is hard to define objectively and the nature of
the problem depends on the values of those who define it.
For all the above reasons, the committee concludes that only a syn-
thetic, integrated, analytical approach to understanding the effects of suites
of environmental factors on the ecosystem and its components is likely to
provide important and useful insights that can lead to enhancement of the
delta ecosystem and its species.
ECOSYSTEM STRESSORS
Although the committee recommends a synthetic, integrated approach
to assessing environmental factors, such an approach first requires a de-
scription of the individual factors separately. Therefore, we provide such
descriptions, covering a variety of environmental factors that are important
or potentially important in the following sections. The current set of stress-
ors discussed is not an exhaustive list; rather, they are the most prominent
stressors in the delta system in the committee's judgment. Following this,
the committee provides its assessment of each stressor individually.
Physical Environment: Geomorphology and Delta Geometry
Changes in geomorphology of the delta in the last 150 years have been
dramatic. Alteration of tidal channels and drainage of wetlands within the
delta began for agricultural purposes, but eventually, as new centers of com-
merce and shipping developed, the drained lands supported urban develop-
ment. Levees surrounding delta islands isolate most land in the delta from
tidal or riverine flooding. Historically, periodic flooding of floodplains and
wetlands provided habitat for many species and reduced the risk of down-
stream flooding. The delta absorbed flood flows to become a vast shallow
lake. At its greatest extent prior to the transition to agriculture, the delta
covered 1,931 square miles of tidally influenced open water, intertidal flat,
and marsh. By 1930, however, 35 percent of the delta had been converted
(Thompson 1957), leading a trend of land conversion that established the
channel geometry and variability that is present today.
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STRESSORS 61
TABLE 3-1 Examples of the Interplay Among Ecosystem Processes
(Drivers), Stressors, Science Needs, and Policy
Uncertainties and Science
Driversa Stressors Water Policy Issues Needs
Anthropogenic Canals. Effects: benefits vs. Predicting influences of new
infrastructure Removing more adverse implications water routing? Implications
changes water from the for ecosystems of population growth,
resulting in system. water use or conservation?
changes in Reservoirs. Impediments and benefits
freshwater flow to fish passage.
and turbidity
Climate Temperature: Will future habitats Can we manage habitats to
change Changing ocean be suitable for create refuges and sustain
conditions. Changing species of concern? optimal carbon, nutrient,
hydrology. Can we save and and oxygen cycling?
manage sensitive
species?
Exports Entrainment. How to balance Effects on fish populations
Indirect effects on supply reliability vs. individuals? Quantifying
hydrodynamics. with ecosystem indirect effects?
Nutrient and carbon requirements. Quantifying effects of
loadings. upstream diversions?
Upstream diversions.
Food quality Nutrients: N,P,C. Declining quality Relative importance of
Flow. of food for grazers bottom-up vs. top-down
Grazing. and higher trophic controls on food web.
levels. Influence of habitat
changes. Feasibility of
management?
Habitat loss Nutrients. Can restoration of Restoration uncertainties:
Freshwater flows. habitat facilitate What is manageable against
Light, turbidity. recovery of key a changing baseline [climate
Physical disturbance processes and native change, invasive species,
and elimination. species? declining sediment inputs]?
Harvest and Top-down Implications for How to manage harvest for
fishing fisheries. sustainable populations and
to avoid top-down effects
on ecosystems [sustainable
production, desirable water
quality, and habitat].
Introduced Alteration of food Survival and Predicting success of
species webs and nutrient management of invaders and their
cycling. native species. ecological implications?
Alteration of food Fate of restoration Life cycle of invasive
availability. actions. species: can vulnerabilities
Changes in be found?
predation. Controlling inputs and
Change in physical managing habitat for
habitat from optimal production of
macroflora. native species.
continued
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62 SUSTAINABLE WATER MANAGEMENT IN THE DELTA
TABLE 3-1 Continued
Uncertainties and Science
Driversa Stressors Water Policy Issues Needs
Nutrients Nitrogen/phosphorus Nutrient input Determine nutrient input
(nitrogen and loads. reductions. and flow thresholds for
phosphorus) Flows. eutrophication and algal
Temperature. bloom formation and
macroflora. Roles of ratios
and forms of nutrients in
determining community
composition.
Passage Dams. Inability of species What species most affected
impediments Migration barriers. to utilize former by diversions?
Water diversions. habitats. Feasibililty of management?
Toxic chemicals Inputs of selenium, Concentrations not Selenium: San Joaquin
mercury, pesticides. declining and could River inputs to the Bay?
increase. Mercury: methylation
increase from wetland
restoration?
Pesticides: How many areas
of high concentration and
where?
Improved management.
aDrivers
listed in alphabetical order.
SOURCE: Modified from Healey et al. (2008a).
The Bay Delta Conservation Plan (BDCP) Independent Science Advi-
sors (BDCP 2007) identified two fundamental environmental gradients that
control physical characteristics of habitat for various species (Figure 3-2).
While the salinity gradient has always been oriented along the axes of the
major rivers flowing through the delta, elevation gradients existed at a
number of spatial scales. At the largest scale, there is a decrease in elevation
and slope along the river channels and banks from upstream as they enter
the delta, toward the bay. At the reach scale, the high natural river levees
resulted in a decrease in elevation away from the channel into floodplain
(upstream) and tidal marsh (downstream), and these "cross-channel" gra-
dients were multiplied by the complex system of river and tidal drainage
channels that previously occupied the delta.
Today, the network of delta levees has substantially reduced the area
exposed to the tides to about 618 square miles (Culberson et al. 2008).
The drainage density within the delta has been reduced and is restricted
to deep subtidal channels, resulting in a limited array of environmental
gradients within the delta. Natural high land (e.g., river levees) has been
essentially eliminated, as have shallow channels. Tidal and riverine flow,
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STRESSORS 63
FIGURE 3-2 Horizontal and vertical gradients that control environmental condi-
tions in the delta.
SOURCE: BDCP (2007).
across the salinity gradient, is confined to channels that do not drain at low
tide. Flooded delta islands (e.g., Franks Tract, Mildred Island, and Liberty
Island) are now lower than the marshes R02208
and channels in those areas would
have been prior to drainage. Figure 3-2
bitmapped
Isolated areas of naturally raster
inundated image
wetland still exist in the delta
(most of the wetlands in Suisun marsh are actually semi-impounded and
their inundation regime does not therefore reflect the environmental condi-
tions of naturally inundated wetlands). Forested floodplain with natural
inundation regime is now limited to the Cosumnes River, and Rush Ranch
in Suisun Bay is remnant salt marsh at the lower end of the system. Because
tules (Schaoenoplectus spp.) do not require substrate drainage and can
grow at elevations as low as ~0.5 m mean lower low water, tule patches ex-
ist in remnant midchannels islands and around the margins of some flooded
islands. Tules have a low salt tolerance, but current water management that
keeps the delta fresh for conveyance purposes allows tule wetlands to ex-
tend to the margins of Suisun Bay. Their ability to colonize into the subtidal
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64 SUSTAINABLE WATER MANAGEMENT IN THE DELTA
zone means that bare intertidal flats, which may have historically existed
throughout the delta in areas periodically influenced by salinity incursion,
have essentially been eliminated except in Suisun Bay. Tules can effectively
dampen wave action (e.g., Augustin et al. 2009) and thus limit resuspension
of sediment in shallow subtidal areas within the delta. Accordingly, the only
areas where wind waves routinely resuspend sediments and provide high
turbidity levels are in Suisun Bay. Ruhl and Schoelhammer (2004) found
that this effect was accentuated by the storage of highly erodible sediments
on mudflats in Honker Bay. If such sediments are deposited in areas colo-
nized by tules, resuspension would be limited. Thus, the changes in eleva-
tion gradients within the delta have limited the occurrence of wetlands of
various types and shallow turbid subtidal environments.
Physical Environment: Flows and Salinity
The committee's first report, A Scientific Assessment of Alternatives for
Reducing Water Management Effects on Threatened and Endangered Fishes
in California's Bay Delta (NRC 2010), dealt with aspects of flows, notably
Old and Middle River (OMR) flows and X21 positioning that are specific to
two biological opinions issued by the Fish and Wildlife Service (FWS) and
the National Marine Fisheries Service (NMFS) to protect listed fish species,
the delta smelt, and Chinook salmon. In what follows, we discuss flow ef-
fects on the aquatic resources of the bay delta more generally, aiming to
set existing knowledge about these flow effects in the same framework as
other stressors such as contaminants, nutrient inputs, and invasive species.
To do so requires that one consider first how flow affects organisms and
processes, in which cases it is anthropogenic changes to flows, volumes,
timing, and paths that are the stressor(s). As discussed below, flow volumes
and timing (i.e., the hydrograph) affect the temporal and spatial variability
of the physical environment, a term we use to mean environmental variables
like salinity, turbidity, turbulence level, as well as elements of habitat con-
nectivity associated with horizontal transport (Cloern 2007, Cowen et al.
2006) and vertical turbulent mixing (Lucas et al. 1998). By flow paths we
mean transport of organisms and materials through various regions of the
bay delta, including the entrainment of listed species by the water project
pumps. The issue of entrainment is dealt with below.
The distinction between these two types of flow effects on organisms,
the food web, and thus on the ecosystem more generally is important in
that sustainable approaches to reducing the effects of flow stressors may
be quite different. In particular, the issue of flow paths appears amenable
to engineering solutions: With the correct water engineering, entrainment
1 See page 20 for a definition of X2.
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STRESSORS 65
effects might be eliminated, allowing the maintenance of current diversion
volumes, or possibly even permitting increased diversions. In a similar fash-
ion, the problem some fish species have because of altered flow paths might
be solved via strategies such as using information about when specific fish
species (at various life stages) are at risk of entrainment and, with the aid
of modeling, modify pump operations to reduce entrainment.
In contrast, the effects of flow on the physical-chemical environment,
most notably the salinity field and its concomitant influences on circulation
and transport (Monismith et al. 2002, MacCready and Geyer 2010), do not
appear amenable to engineering solutions other than to use specific flow
standards tied to water year type and variability, that is, standards like the
X2 standard developed by the Environmental Protection Agency in 1995,2
which has subsequently been used as a basis for developing a variety of
standards, including the recently proposed and litigated Fall X2 standard
as well as X2 rules as described in State Water Resources Control Board
(SWRCB) decision 1641.3 In this case, the development of regulations to
maintain salinity gradients relies on the central hypothesis that the environ-
mentally optimum approach is to try and mimic the shape of the natural
hydrograph albeit at a lower level--in other words, to make the system
slightly drier than it would be naturally, but maintain the overall pattern
of flow. The key conceptual model on which this hypothesis is based is that
the current ecosystem is adapted to the presence of a particular seasonal
variability in flow, which certainly has varied on evolutionary time scales
(Ingram et al. 1996), as discussed by Moyle et al. (2010). As a consequence,
many species have life strategies that depend on particular features of flow
variability, such as the transport of eggs into suitable habitat at the correct
time or the aggregation of ichthyoplankton into regions of higher food
availability by gravitational circulation (Arthur and Ball 1979, Kimmerer
et al. 1998).
Also, the California SWRCB has recently been actively engaged in de-
veloping regulations for various aspects of flows and diversions,4 an effort
that has been backed up by a detailed examination of the manifold ways
in which flows affect bay-delta biota discussed in the technical report pre-
sented by Fleenor et al. (2010) to the SWRCB.
2 Federal Register, Volume 60, Number 244.
3 D1641 was finalized in March 2001.
4 Development of Flow Criteria for the Sacramento-San Joaquin Delta Ecosystem, August
3, 2010.
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66 SUSTAINABLE WATER MANAGEMENT IN THE DELTA
Hydrologic Factors
The term "flow" encompasses a broad range of effects in the bay-delta
estuary. We define flow here as freshwater flow, something that has multiple
components and in the context of the delta can best be thought of in terms
of four major components:5 Sacramento River inflow; San Joaquin River
inflow; net delta outflow, the total time averaged flow past Chipps Island
at the western edge of the delta; and in-delta diversions, most notably the
state and federal water projects. These four are not independent and are
represented in an average sense (to a good degree of approximation):6
et delta outflow = Sacramento River inflow
N
+ San Joaquin River inflow In-delta diversions
Both of the river flows include the effects of reservoir operations (storage
and releases) and diversions in and upstream of the delta, for example, the
Hetch Hetchy Aqueduct, which transports Tuolumne River water to the
San Francisco Bay Area. Because tidal flows at the eastern end of Suisun
Bay are generally an order of magnitude larger than are mean flows (e.g.,
Walters et al. 1985, Monsen 2000), net delta outflow is a calculated rather
than measured quantity.
One can look at anthropogenic changes in the hydrology of the bay
delta by comparing measured hydrographs with the "unimpaired" hy-
drograph, that is, the hydrograph that would have been observed in the
absence of the water projects, but including the present delta configura-
tion. For example, in their presentation to the SWRCB, Chung and Ejeta
(2011) more generally note that, as currently calculated, unimpaired flow
is based on the hydrologic behavior of the system at present, rather than
the system as it existed before dams, flood control levees, and so on were
built. For this reason, the calculated unimpaired flow might actually be
significantly different from what actually took place prior to development.
Consequently, unimpaired flow should be treated as an approximate upper
bound on the natural flow. To our knowledge, an appropriate lower bound
has yet to be defined.
Finally, besides a reduction in the overall volume of freshwater enter-
ing the bay, the timing of flows has also been altered, with peak flows now
occurring earlier in the year (February and March) than they would in
the absence of water resources development. Here too, the change is not
unequivocally due to water resources development: rather, it also appears
5 Besides these flows there are also the East Side streams; see http://www.water.ca.gov/
dayflow/.
6 A full water balance for the delta includes groundwatersurface water exchanges as well
as evapotranspiration by delta vegetation (see, e.g., Fox 1987).
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STRESSORS 67
that precipitation in the Central Valley watersheds is increasingly taking the
form of rain rather than snow (Dettinger and Cayan 1995, Cloern et al.
2011), a pattern that also tends to shift the hydrograph peak earlier in the
year. Thus, to a first approximation, the flow stressor is defined by changes
in hydrology, both in volumes and timing.
Flow Effects on the Physical Environment
In conjunction with mixing from the tides, freshwater flow determines
the spatial structure of the salinity field, via the relationship between flow
and the position of X2. (The position of X2 is a distance scale--kilometers
upstream, or east of the Golden Gate Bridge--for salinity intrusion. Thus,
if X2 is at 70 km, it is 70 km east of the Golden Gate Bridge.) The reason
is that at steady state the tendency for freshwater flow to carry salt out of
the estuary is balanced by the tendency for gravitational circulation and
tidal dispersion to carry salt upstream toward the delta. As a result of this
balance, the mean position of X2 is proportional to the net delta outflow
raised to the minus one-seventh power (Monismith et al. 2002), meaning
that it takes much higher flows to move X2 when X2 is farther to the west,
or nearer the Golden Gate Bridge, than when it is farther to the east (Figure
3-3). For example, to position X2 at 72 km (opposite Honker Bay), a flow
FIGURE 3-3 The position of X2 in kilometers east of the Golden Gate Bridge as a
function of flow.
SOURCE: Monismith et al. (2002).
R02208
Figure 3-3
bitmapped raster image
scaled for portait above, landscape below
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