A citizen's guide to fish kills and habitat degradation at the state and

A citizen’s guide to sh kills and habitat degradation at

the state and federal water project pumps in the Delta

| MARCH 2012

COLLATERAL

DAMAGE

The Bay Institute is a 501(c)(3) nonprot research, education and advocacy organization dedicated

to protecting, restoring and inspiring conservation of San Francisco Bay and its watershed, from the

Sierra to the sea.

Since 1981, The Bay Institute’s policy and scientic experts have worked to secure stronger

protections for endangered species and habitats; improve water quality; reform how California

manages its water resources; and promote comprehensive ecological restoration of the Bay-Delta

estuary and watershed. Since 2009, The Bay Institute has partnered with Aquarium of the Bay to

educate Californians about this unique ecosystem. An electronic version of Collateral Damage can be

downloaded at www.bay.org/publications.

The report was made possible by the support of the Dean Witter Foundation, the Keith Campbell

Foundation for the Environment, the Resources Legacy Fund, the Richard and Rhoda Goldman Fund,

and the Rose Foundation for Community and the Environment.

www.bay.org | 415.878.2929 | bayinfo@bay.orgwww.bay.org | 415.262.4735 | bayinfo@bay.org

First published March 2012

Executive Summary

Entrainment: Killing Machines in the Delta?

TABLE OF

CONTENTS

End of the Line: A Giant Sucking Sound

Understanding the Problem, Part 1: Direct and Indirect Mortality

Understanding the Problem, Part 2: The Other Victims

A Time for Action

Claims vs. Facts

Solving the Problem

To Learn More

REPORT

SUMMARY

arge-scale fish kills and habitat destruction aren’t an unusual occurrence at the giant federal

and state pumps that export water from the Sacramento-San Joaquin Delta to agribusinesses

and cities in the southern half of the state. These events are business as usual.

• Every day, between 870 and 61,000 fish – including from 200 to 42,000 native and endangered fishes –

are “salvaged” at the pumps. Most die in the process.

• On average, over 9 million fish – representing the twenty fish species considered in this report – are

“salvaged” each year at the pumps. As many as 15 million fish of all species encountered are “salvaged”

each year.

• Up to 40% of the total population of the endangered delta smelt and 15% of the endangered winter-run

population of Chinook salmon are killed at the pumps in some years. In the first half of 2011, over 8.6

million splittail were salvaged.

• Salvage estimates drastically underestimate the problem. The numbers do not factor in the results of

“indirect” mortality, as high levels of export pumping disrupt fish migration, shrink the amount of non-

lethal habitat available to fish species, and remove vast amounts of biomass, including fish eggs and

larvae too small to be screened at the pumps.

• Export pumping causes the lower San Joaquin River to flow backwards most of the year and removes

the equivalent of 170 railroad boxcars of water – and the accompanying fish, other organisms, and

nutrients – from the Delta ecosystem every minute.

• Large numbers of fish being entrained is a problem even for species that are not currently listed as

“endangered.” Killing large numbers of fish year after year cuts off population growth in response

to favorable conditions and can start the species on a downward path to extinction. As the species

declines, the population impacts of entrainment become proportionately larger.

• Entrainment is a real problem. But the same interests in the Delta export community who claim that it

isn’t also back constructing expensive new conveyance facilities such as a peripheral canal or tunnel to

solve the problem that they say doesn’t exist.

The problem of “collateral damage” can be solved using a combination of approaches:

• Reduce water exporter reliance on the Delta. Current federal and state commitments to deliver water

from the Delta are unrealistic and unsustainable. Fortunately, the potential for using existing water

supplies more efficiently and developing alternative sources from recycling, reuse, groundwater storage,

and land use changes is equal to about half the state’s total water demand today.

• Require more ﬁsh-friendly pumping levels. There is overwhelming scientific evidence that changing

pumping regimes to provide more flow into, through, and out of the Delta during much of the year will

help rebuild devastated fish populations and restore a functioning, healthy ecosystem.

• Create alternative ﬁsh migration pathways that permit migrating juvenile fish to avoid areas in the

high-impact pumping zone and access to critically imporant rearing habitat using restored floodplains,

flood bypasses and other corridors.

• Improve the water conveyance system. Proposed physical fixes to the system, such as pumping water

from a new facility in the North Delta and conveying it around the Delta, could help reduce some of

the worst impacts of the current export scheme and insulate the water supply system from catastrophic

failure or sea level rise impacts. But none of these proposed fixes will solve the problem if the state and

federal projects continue to withdraw unsustainable amounts of water from the Delta ecosystem.

Federal sh salvage facilities in the south Delta - and a “salvaged” sh. Photo: CA DWR and USBR

very so often, you may hear on the news

that some endangered fish were sucked

into or “salvaged” at the giant federal

and state pumps that export water from the southern

end of the Sacramento-San Joaquin Delta to the San

Joaquin Valley and southern California, and that

government officials, environmentalists and water

users are battling over what to do about it.

What’s not often discussed is that this is

business as usual at the pumps.

Of 20 fish species selected to encompass

the wide range of species and life history types that

are affected by the export pumps, between 870 and

61,000 fish, including between 200 and 42,000 native

and endangered fishes, are intercepted every day just

before entering the eleven pumps at the State Water

Project’s Banks facility and the six pumps at the federal

Central Valley Project’s Tracy plant in the southern

Delta. Most of these intercepted fish die during the

transport and release (“salvage”) process; but countless

others perish in the Delta on their way to the pumps

as a result of altered water flows or slip though the

antiquated fish screens and are killed in the pumps.

The exact number of fish that die before or

after the salvage process or that are not counted in the

salvage process at all remains unknown, and is not

factored into the “salvage” count. The actual numbers

of fish “entrained” (impacted by the water pumps)

may be an order of magnitude greater than the losses

that are counted in salvage.

Between January and July 2011, over 8.6

million Sacramento splittail (a fish found nowhere else

in the world) and over 35 thousand Chinook salmon

were ”salvaged” at the pumps. In some years, up to

Killing Machines in the Delta?

State Water Project pumps inside the Banks Pumping Plant.

Each machine is capable of extracting nearly one thousand cubic

feet of water from the Delta every second – that is nearly one-half

million gallons per minute! (Photo: California Water Atlas).

ENTRAINMENT:

“ENTRAINMENT” and “SALVAGE”

“Entrainment,” in this publication, refers to the lethal

entrapment of fish and other aquatic animals in the

water being pulled towards the pumps, either through

direct losses at the pumping facilities or through adverse

modification of fish habitat in areas affected by pump-

ing operations.

“Salvage” refers to the interception and capture of fish

in the fish screens and facilities in front of the pumps.

Not all entrained fish are intercepted, and thus the

salvage numbers are always smaller (sometimes much

much smaller) than the magnitude of entrainment. Even

worse, only a few species survive the salvage process;

to many other fish species the salvage itself is, unfortu-

nately, often deadly.

DECLINE OF THE DELTA SMELT (HYPOMESUS TRANSPACIFICUS) 1967 - 2009

Delta smelt, a native sh that

was abundant in the Delta as

recently as thirty years ago,

has experienced a dramatic

population decline - fewer

than 10% of the population

has survived in recent years.

In some years, up to 40%

of all smelt are killed at the

pumps.

40% of the entire population of the endangered delta

smelt may be killed at the pumps.

And this is only a glimpse of the losses

occurring daily at the Delta’s lethal pumps.

• How many fish are actually lost or affected by the

pumps in the South Delta?

• What’s the impact to the sustainability of our

commercial and sport fisheries and the survival of a

number of endangered species?

• What can be done to stop massive fish kills? Will

building a peripheral canal to carry water around

or under the Delta solve the problem?

Collateral Damage tells the story of how

massive water exports from the Delta kill tens of

millions of native fish every year, drastically reduce

the Delta’s natural productivity, and are an important

factor in the decline of endangered species. This guide

also describes some potential solutions, both at the

pumps and through changes in how we use water in

California.

In some years, up to 40% of the entire population of the

endangered delta smelt may be killed at the pumps.

DELTA PUMPING IS NOT THE

ONLY IMPORTANT PROBLEM*

Several other factors are also involved in the decline

of fish populations in the Delta, including:

• Severely reduced inflows to the Delta from the

Central Valley watershed

• Loss and modification of instream, channel,

floodplain, and wetland habitats

• Invasive species and related changes to the food

web

• Pollutants and toxic substances

All these factors may play an important role in the

decline of some fish species (although the evidence for

some, like flow reductions or floodplain loss, is much

better than for others). To recover fish populations, it

will be necessary to substantively address all credible

stressors. However, the lethal effects of high water

exports so profoundly damage ecosystem health that

addressing these other stressors without reducing or

eliminating the large-scale collateral damage at the

pumps will be unsuccessful in restoring the fish.

*(but it is one of the most serious)

he Sacramento and San Joaquin Rivers

and all of their tributaries drain water

from the Central Valley – over a third

of California’s land area. These rivers pour into the

Sacramento-San Joaquin Delta and, under natural

conditions, out to San Francisco Bay and the Pacific

Ocean. Dozens of native fish species (including

steelhead, Chinook salmon, delta smelt, longfin,

and two species of sturgeon) spawn, rear, or migrate

through the Delta during their life-cycle. The Delta is,

in many ways, the linchpin for much of California’s

aquatic biodiversity.

The Delta is also home to the largest water

diversion facilities in California and some of the largest

in the US. The enormous state-owned Harvey O.

Banks pumping plant can remove 10,600 cubic feet

of water from the Delta every second (cfs) and the

federally-owned C.W. Jones pumping plant is able to

divert an additional 4,500 cfs. Combined, these two

export pumping plants can suck out of the Delta nearly

113 thousand gallons per second, or enough to fill

over 170 railroad boxcars each minute! The federal

project delivers water mostly to agricultural users in

the San Joaquin Valley, while the state project delivers

water to both agricultural and urban users in Central

and Southern California, including the San Francisco

Bay Area. These diversions often cause the water in

the lower San Joaquin River to move towards the

pumps instead of the ocean – the river actually runs

backwards most of the year! The pumps also draw

water from the Sacramento River in the north across

the Delta to the south, rather than allow water to

follow its natural course to the ocean.

As these pumps draw water across the Delta

END OF THE LINE:

THE DELTA KILLING FIELDS

California Delta. Historical water ow is shown in dashed

green outline; current water ow in red (schematic – arrows

are not to scale). Lightning bolts mark the pumping facilities;

crossbones indicate the “reverse ow” in Old and Middle

rivers that bring the sh into the deadly vicinity of the pumps.

The concept of a “peripheral canal” or “peripheral tunnel” is

shown by the black pipes.

A Giant Sucking Sound

and out of the lower San Joaquin River, fish and

other aquatic organisms (including shrimp, plankton,

and other fish prey) are drawn towards the pumps

as well – they are “entrained”. In part, this is just

simple physics – suck out the water and what’s in the

water comes along for the ride. But the continued,

day-in/day-out pumping of water may also establish a

chemical pathway towards the pumps that misinforms

migrating fish about which way to swim. Thus, small

migrating fish trying to find the ocean may simply be

following the river “downstream” only to find that

the ocean has been replaced by the sucking maw of the

giant diversion machinery.

The pumping facilities are equipped with

rudimentary fish screens that rely on fish swimming

behavior to prevent entry into the pumps. This

technology may work well at times for juveniles of

some fish species (those that respond to the screens

by swimming away towards a “salvage” facility);

but it does not work for fish that are too small to

swim away successfully, for fish eggs, or for most of

the zooplankton on which fish feed. Furthermore,

before the fish reach these screens, they must survive a

RIVERS FLOWING BACKWARD

A badly injured Sacramento splittail, captured at the Tracy Fish

Facility. Note: these injuries were likely caused by predators at-

tracted to the screens and water diversion structures, not by the

pumps themselves (as this sh was intercepted before reaching the

pumps). Photo: USBR

...the water in the lower San

Joaquin River [moves]

towards the pumps instead

of the ocean - the river

actually runs backwards

most of the year.

“

journey through the canals that lead to the pumps and

Clifton Court Forebay, an artificial lake that regulates

water level at the state pumps.

Both the canals and the Forebay are densely

packed with predators. Studies indicate that less than

one in four individuals of some fish species, to as few

as one in one hundred individuals of other species

survive the journey from the canals through the

Forebay to the “salvage facility.” Finally, fish that are

successfully screened are processed and then shipped to

release locations away from the pumps. Unfortunately,

many fish species cannot tolerate such handling and

die in the process. And the salvaged fish that do

survive are released on a predictable schedule at only

a few locations in the Delta. There, predators await a

regular feeding of “salvaged” fish. In all, a tremendous

screening, counting, and release effort produces little

in the way of real protection for our fish. In the end,

“salvage,” although reassuring-sounding, is largely

ineffective in actually saving fish.

Between 2001 and 2005, high Delta export pumping rates

by the State Water Project and federal Central Valley Project

caused reverse ows in Delta and lower San Joaquin River

channels averaging more than minus 8,000 cubic feet per

second for about three-quarters of the year

UNDERSTANDING

THE PROBLEM PART 1:

nderstanding the scale of the entrainment

problem is challenging. First, let’s distinguish

between “direct” and “indirect” mortality.

Many fish die as a result of “direct” mortality

at the pumps; that is, only a fraction of the fish drawn

into the export facilities are screened out of the man-

made river running uphill to export pumps and many

of those that are “salvaged” die during the process

or soon after they are released back into the Delta.

Estimates indicate that up to 40% of the Delta smelt

population and 15% of the winter run Chinook

salmon may be killed at the export pumps in some

years.

However these numbers do not factor in

“indirect” mortality, the additional deaths of fish

that are displaced from productive to lethal habitats

by the altered water currents that result from export

pumping. Indirect mortality takes many forms:

• Successful juvenile outmigration to the ocean is

reduced, as young salmon, steelhead, sturgeon and

other migratory fish are diverted from their natural

migration pathway into less suitable habitats,

delaying migration and exposing them to a host of

new threats, including predators.

• Successful upstream migration of spawning-age

adult fish also declines because the chemical

signatures of their home streams are muddled when

high levels of pumping change patterns of water

circulation in the Delta.

• The amount of habitat available for spawning and

rearing of Delta-dependent species shrinks as the

area affected by export pumping loses its habitat

value and becomes a death zone.

The relative importance of direct vs. indirect

mortality is a subject of vigorous debate. But one thing

is certain: continued loss, year-in and year-out, of

millions of fish, eggs and larvae at and on the way to

the south Delta pumps makes recovery of endangered

species, conservation of other species, and maintenance

of a viable food chain much less likely.

Tracy sh facility schematic. The export pumps (not shown) are

located beyond the bottom of the picture. Note that the “primary

louvers” are the critical part of the system, designed to “guide”

the sh into the bypasses (from which they then reach the sh

facility – secondary louvers, tanks, etc.). However, the “primary

louvers” are wide enough for the sh to slip through: they rely

solely on sh behavior to function eectively, rather than posi-

tively excluding the sh from the exported water. Modied from

the USBR TFCF Reports, Volume 4.

TRACY FACILITY SCHEMATIC

..most organisms...pass

right through the screens

and are thus removed from

the Delta’s food web.

Direct & Indirect Mortality

SALVAGE TABLE

SPECIES OF FISH COMMONLY COLLECTED AT THE STATE FISH SALVAGE FACILITY

Endangered - Federal

Endangered - California

Threatened - Federal

Threatened - California

STATUS KEY:

LEGEND:

Fish were selected to encompass the

wide range of species and life history

types that are aected by water pumps.

“Average annual salvage” is mean yearly

salvage from 1/1993 through 12/2011;

“Maximum salvage” is the value for the

calendar year with the highest salvage

numbers (years dier among species).

These numbers underestimate the actual

sh kills by not counting the sh that

slipped through the bypass system and

were killed by the pumps, and by not

including indirect mortality. “Yearly Total”

refers only to the 20 species listed.

Native to CA

Recent decline

Important Fishery

Commercial/Sport

Fisheries Destroyed

Protection Removed

(for political reasons; species

has not recovered)

Selected Fish Species

1993-2011 Annual Salvage

Status

Average Maximum

American shad 1,022,700 2,510,184

Bluegill 127,133 394,952

Channel catsh 45,799 131,484

Chinook salmon (winter run)

51,955 183,890

Chinook salmon (spring run)

Chinook salmon (fall run)

Chinook salmon (late-fall run)

Delta smelt 29,918 154,820

Green sturgeon 58 363

Inland silverside 62,838 142,652

Largemouth bass 54,180 234,198

Longn 6,228 97,686

Prickly sculpin 76,403 274,691

Steelhead (Rainbow trout) 5,278 18,580

Redear sunsh 1,609 5,611

Rie sculpin 155 798

Sacramento sucker 3,443 27,362

Sacramento splittail 1,201,585 8,989,639

Striped bass 1,773,079 13,451,203

Threadn shad 3,823,099 9,046,050

White catsh 296,543 941,972

White sturgeon 151 873

Yellown goby 193,399 1,189,962

Average yearly salvage total: 9,237,444

Photo: CA DWR

he impact of increasing water

withdrawals from the south Delta

extends beyond the vast numbers of fish

killed directly at the pumps. Massive water exports

remove much of the food upon which all species –

endangered and non-endangered alike – depend. The

millions of fish that are “salvaged” at the pumps

represent a loss of potential food for other fish, bird,

and mammal species, not to mention the loss of fishing

opportunities for anglers and commercial fishermen.

The fact is that most organisms are not

screened at all: fish eggs and larvae, as well as

zooplankton and algae, pass right through the screens

and are thus removed from the Delta’s food web. The

pumping plants remove billions of gallons of water

from the ecosystem every day between January and

June (usually a bit less during the summer and fall),

and with the water go the tons of fish food, nutrients,

and sediments that once made this among the most

productive coastal ecosystems in America. The location

of the pumps in the once-productive south Delta means

that spawning and migratory corridors are lost or

blocked. For example, use of the San Joaquin River

as spawning habitat by longfin has declined, likely

because fish that attempt to spawn in the vicinity of

the pumps (and their offspring) are entrained and die.

Water exports not only entrain the many unlucky fish,

they make it difficult for survivors to migrate towards

the habitats that lie beyond the pumps.

WATER EXPORTS FROM THE

DELTA HAVE INCREASED

Increasing water withdrawals from the Delta and its water-

shed have cut outow in half. The exports from the south Delta

pumps, shown here, are especially problematic because they kill

large numbers of sh directly, remove vast amounts of biomass

from the aquatic ecosystem, and disrupt natural ow patterns in

the Delta and downstream habitats.

IMPACTS TO FISH HABITAT

A generalized representation of the interaction of sh habitat

(which includes ow) with the water export pumps in the south

Delta. The double-headed arrows symbolize natural ows in

the Delta, a combination of tidal and river ows; this natural

ow pattern is increasingly disrupted in the vicinity of the

pumps (the “impact zone”), resulting in both direct mortality

and in the degradation of sh habitat.

UNDERSTANDING THE

PROBLEM PART 2:

The Other Victims

Sacramento splittail (Pogonichthys macrolepidotus) is a fish

in the minnow family that is endemic to California (found

nowhere else in the world). Once numerous throughout

the watersheds of central California, these long-lived (5-7

years), low-oxygen-tolerant, and fertile fish (> 100,000 eggs/

female) have been confined to the Delta as a result of habitat

alteration and dams. Incredibly, in the first nine months of

2011, nearly nine million splittail were “salvaged” at the

pumps. This level of loss is devastating in multiple ways:

• The direct impact on the splittail population

• The removal of a large amount of biomass–food for

other fish and birds–from the estuary’s food web; and

• Loss of the opportunity to recover the population –

while the splittail populations are naturally depressed in

low-flow years, during years with better flow conditions

(like 2011) the Sacramento splittail population is

nevertheless not given a chance to recover (because of

the immense mortality at the pumps).

AN IMPERILED NATIVE:

SACRAMENTO SPLITTAIL

A TIME FOR

ACTION

he loss of millions of fish, removal of

nutrients from the ecosystem, and the

degradation of habitats represent huge

impacts to the Delta and its public trust resources

(i.e., the fish and wildlife resources and habitat

values of navigable waterways that the public has

a vested right in protecting). At worst, these losses

may drive our native species to extinction; at “best,”

this daily destruction prevents the ecosystem from

recovering when conditions improve and denies us

all access to our valuable natural resources. Reeling

from one crisis to another is neither a responsible

nor an effective way to manage natural resources.

Our society has greater expectations for managing

the Delta ecosystem than this, as expressed in a

variety of ways:

• California’s Constitution prohibits wasteful

and unreasonable use of water, and California

case law mandates the protection of public trust

resources.

• The state and federal Clean Water Acts require

actions to protect the biological, chemical and

physical integrity of fishable waters.

• California’s taxpayers have spent hundreds of

millions of dollars to try to restore the habitats

and fish populations that we all value.

• The state and federal Endangered Species Acts

promote the recovery of species and ecosystems,

not simply actions to avoid extinction.

• State and federal laws mandate doubling of

migratory fish populations from late-20th

century levels (which were still better than some

of today’s catastrophic numbers).

None of these mandates can be satisfied –

and our investment in recovering natural resources is

being wasted – as long as fish continue to die in large

numbers at the pumps.

Chinook salmon once represented a major commercial resource for

Californians. A number of factors - including the impact of the Delta

pumps - have devastated the shing industry, putting many sher-

men out of work. Photo: Barbara Emley, courtesy of Barbara Stickel

Photo: Professor P. Moyle, UC Davis

...if entrainment is “not a

big problem,” how can re-

ducing entrainment be used

to justify a multi-billion dollar

new... canal?

“The salvage numbers aren’t as bad as they

look.” Water users who receive water exported

from the pumps claim that entrainment-related

mortality is not as big a problem as the vast

numbers of salvaged ﬁsh would suggest. After

all, they claim, the salvaged ﬁsh are only a small

portion of the total population.

Salvage numbers drastically underestimate the

actual impact. Although the exact numbers are

uncertain, it is clear that tens of millions of sh are

killed each year, and only a small fraction of this is

reected in the salvage numbers that are reported.

A conservative estimate (Kimmerer, 2008) is that,

for juvenile salmon that have been pulled towards

the pumps, only 1 in 5 will survive long enough to

be counted in salvage (the rest are lost to predators

or other factors). For Delta smelt, which used to live

close to the pumps, the impacts are even worse.

An experimental study of “pre-screen loss and

sh facility efciency at the State Water Project”

found that that for every adult delta smelt counted

in salvage at least 37 individuals perished before

reaching the sh salvage facility; for delta smelt

juveniles the ratio of salvage to “pre-screen loss”

was even higher than that found for adults (Castillo,

2010). Overall (Kimmerer, 2008), 15% of adult smelt

population is estimated to be killed near the pumps

(salvaged or eaten on the way to sh screens) while

losses of larval smelt are unknown (because they

are too small to be screened and counted). In some

years, as much as half the Delta smelt population

may be killed at the pumps! The fact is, the salvage

numbers look really bad but the real impact of

export-related mortality is probably far worse.”

“Entrainment is not a problem... But a new

peripheral canal should be built because it will

reduce entrainment...”

Water exporters also claim that a new diversion

facility is necessary because it will reduce harm to

endangered species. But if entrainment is “not a big

problem,” how can reducing entrainment be used to

justify a multi-billion dollar new diversion and canal (or

tunnel)? Either entrainment-related sh mortality is a

big problem, meriting major changes in how we move

water through the Delta (as well as major changes in

where water exporters get their water and how much

water is needed for the Delta ecosystem), or it is

not a big problem, and changing the Delta pumping

infrastructure will not solve anything. In reality, of

course, mortality is a big problem, and improving

or changing the Delta pumping infrastructure could

be part of a solution (along with other elements

discussed below). But it is dishonest to argue in one

context (proposed controls on export pumping) that

entrainment mortality is not a signicant issue and to

argue in another context (proposed permitting of a new

diversion facility) that moving the pumps is necessary

to solve the entrainment mortality problem.

CLAIM #1

Fish intercepted at the pumps being transported to the release point

in the lower Delta, often only to be eaten by predators that have

learned to expect a “delivery” of dazed and stressed sh. This is

the last stage of the salvage process, often referred to as “cheater”

(from CHTR - collection, handling, trucking, release), a tting refer-

ence, as, despite all the eorts and expense, this process results in

death of many “salvaged” sh.

Photo: Michael Macor / The Chronicle

CLAIM #1.5

FACT

Large-scale entrainment-related mortality means, at

best that population growth is being negated, and

at worst that a large part of the population is being

eliminated. The sh species of the Bay-Delta evolved

in the highly variable environment characteristic of

estuaries in general and California in particular. This

means that these sh are adapted to take advantage

of those years with favorable conditions, during which

they experience high population growth. But the

pumps act as a large-scale stressor in good years

and bad, driving populations down when conditions

are moderate or poor, and preventing population

recovery when good conditions return. For instance,

Sacramento splittail are entrained in the largest

numbers following wetter years when the oodplains

where they spawn are inundated for a longer time;

the entrainment losses in effect offset the positive

gains from wet year conditions. A population can

begin to decline if a large part of its growth potential is

consistently eliminated in this way in good years.

In contrast, Delta smelt and longn are entrained

in the largest numbers in drier years when Delta

outows are low because they spawn and rear closer

to the pumps. Unfortunately, the dry conditions that

produce higher entrainment among these species

also mean poorer survival and growth of juvenile

sh. Thus entrainment often increases just when the

natural conditions result in a population decline – a

double-whammy! For these reasons, even a few dry

years in a row can produce extreme declines in certain

sensitive species; entrainment makes a bad situation

much worse.

“Large salvage numbers mean that the ﬁsh

populations are doing well” (and - you guessed

it - low salvage numbers mean that “entrainment

is not a big problem"). When millions of ﬁsh are

caught at the pumps in a single week, some

people say this indicates that populations are

doing well – more ﬁsh means more entrainment

of ﬁsh. Yet, when entrainment and salvage at

the pumps is low, these same people say that

entrainment is not a problem.

Hmm…we don’t know of any cases where entrainment

of sh has occurred in the absence of pumping. But

some claim that there is no correlation between the

level of pumping and the number of sh salvaged. Of

course, the logical outcome of this argument is that

there is no safe level of export pumping (since all levels

are claimed to produce the same impact).

Several interacting factors affect entrainment,

complicating a simplistic cause-effect analysis of the

relationship between export pumping and entrainment-

related mortality at the export pumps. A signicant

relationship between export rates and entrainment

rates exists for some species, such as longn. The

relationship is not a simple correlation (a straight line)

between exports and entrainment for all species,

however. One important reason is that entrainment

rates are related to where the sh are distributed – the

closer they are to the pumps, the more likely they are

to be entrained (see above). Another important reason

is that export rates must be considered in relation to

overall ow conditions. Pumping rates in drier years

may be lower in absolute terms than in wetter years,

but the relative entrainment effects may be equal or

greater. When spring ow conditions are poor, even

relatively modest increases in pumping can entrain

signicant numbers of pelagic species like Delta smelt

and longn that spawn closer to the south Delta pumps

in drier years. Pumping rates matter – how much they

matter depends on how the sh are responding to that

particular year’s conditions.

“Pumping rates are not related to entrainment.”

SALVAGE OF SPAWNING-AGE LONGFIN

SMELT VS. CVP/SWP

COMBINED EXPORT RATES, 1993-2007

A clear pumping-entrainment relationship. As the water export rates

increase (from left to right), so does the number of longn intercepted at the

pumps (moving up on the vertical axis).

CLAIM #2

FACT

CLAIM #3

FACT

SOLVING THE PROBLEM

At least four major approaches have been identified as

ways to end the massive collateral damage at the pumps:

MOVE THE PUMPS

The current system, designed to move water

from the Sacramento River across the Delta and up San

Joaquin River channels to the pumps, maximizes the

negative ecosystem impacts of water export and creates

the risk that our water supply will be interrupted in

the future. The south Delta export pumps operate in

close proximity to important spawning and migration

habitats and they are highly vulnerable to salt water

intrusion into the Delta; the risk of saltwater reaching

the pumps in the future is high because of projected sea

level rise and in the event of catastrophic levee failures

following an earthquake.

The current design also lacks effective fish

screens. Many scientists believe that constructing a

new diversion facility directly on the Sacramento River

in the north Delta – the latest version of the famous

‘Peripheral Canal’ – to move water around the Delta

instead of through it, and equipped with “positive

screens” that reliably exclude fish, could avoid some of

the worst impacts of water exports. Others advocate for

different physical fixes, such as upgrading the existing

screens at the south Delta pumps or relying more on

expanded south of Delta storage. But none of these fixes

are silver bullets: new pumping and conveyance facilities

or improved screening could make a difference, but

other factors are even more important than how water

is pumped and conveyed from the Delta.

PROVIDE MORE FRESHWATER

FLOW FOR FISH

Even more critical than the location of the

pumps is how much water is exported and when.

The scientific evidence for the primary importance of

more natural flow conditions for the health of aquatic

species and habitats is overwhelming. An export

schedule that more closely resembles natural amounts

and patterns of runoff (i.e., provides for increased

flows into, through, and out of the Delta during the

seasons when freshwater flows would increase under

more natural conditions) will benefit imperiled fish and

support natural ecosystem functions. Implementing

more environmentally friendly pumping regimes is a

necessary step in order to comply with laws mandating

protection of the Delta ecosystem, its species, and water

quality. Doing so becomes easier if at the same time

water exporters start shifting to alternative sources of

supply (see below).

CREATE NEW FISH MIGRATION PATHWAYS

When water floods the Yolo Bypass (south

and west of Sacramento), a portion of the migrating

juvenile fish are carried onto the floodplain and move

through the western Delta to the ocean. As a result, they

avoid much of the area where currents are impacted

by pumping in the south Delta. Of course, this only

benefits migratory species such as salmon and sturgeon

and only in years when the Yolo Bypass floods. There

are opportunities to modify the Yolo bypass (and

enhance other floodways) in order to maximize the

number of years when access to these areas benefits the

fish.

FIND WATER SUPPLY ALTERNATIVES TO

DELTA EXPORT

Current state and federal commitments to

deliver water from the Delta are unrealistic and

unsustainable. In most years, limited precipitation

prevents delivery of anything near the full amounts of

A oodplain in the Delta. Photo: CA DWR

Getting the most out of each drop of water: additional water (in million

acre-feet, MAF) that could be made available every year. A suite of water

conservation and use-eciency measures, together with some innovative

new supplies, holds great potential to increase reliability of California’s water

supply while decreasing the reliance on the Delta water exports. The sum

of these water eciency measures is equal to about half of the total water

demand in the State today.

IMPORTANCE OF EFFICIENT WATER USE

water in the federal and state water project contracts.

Less often, and to a much lesser extent, legal,

operational, and physical constraints on managing

the Central Valley water supply system (e.g. to protect

drinking water quality, avoid flood damage) affect

availability of supply.

Until these unrealistic water export contracts

are changed to match the amount of water that nature

actually provides—and are also adjusted to ensure

society’s minimum requirements for protecting water

quality and the environment are met—a completely

unnecessary conflict will be perpetuated.

Fortunately, the State has recognized

this problem with its policy (adopted in 2009)

of reducing human reliance on the Delta’s water

supplies. There are two main ways to achieve this

state policy. First, areas that currently import water

from the Delta must become more self-reliant

through water conservation, water recycling,

groundwater banking, water transfers, and other

proven mechanisms. Second, federal and state

contracts should be amended to reflect the amount

of water that can be sustainably delivered from

the Delta without destroying our fisheries and

ecosystems, forcing those who use exported water

to adopt more sustainable approaches to planning

for future water supplies. Making these changes

means that any new canal or tunnel can be sized at a

capacity and cost that reflect the real export supply

needs of water-importing areas and the real flow

needs of the Delta ecosystem.

A long-term, durable solution to the

problem of collateral damage at the pumps will

probably require some mixture of all four of these

approaches. Building a peripheral canal (or tunnel)

that maintains or even increases export pumping

will continue to degrade habitat conditions and

drive species declines – just in a different way from

the current system. But as long as a significant

amount of water continues to be exported from

Northern California to other parts of the state, there

will continue to be a need to improve the physical

infrastructure for doing so in order to minimize

its impacts. Together, moving the pumps (and

appropriately sizing the new canal or tunnel that

moves the water from these pumps), restoring more

natural timing and volumes of freshwater flows,

requiring more freshwater at the appropriate time

for the ecosystem, providing alternative pathways

for fish migration, and developing alternative water

supply sources, could result in a water transfer

system in the Delta that supports a healthier

ecosystem and provides more reliable water supplies

for all Californians.

Making each drop of water do more means a healthy

Delta and a healthy economy can coexist

Getting the most out of each drop of water: additional water (in million

acre-feet, MAF) that could be made available every year. A suite of water

conservation and use-eciency measures, together with some innovative

new supplies, holds great potential to increase reliability of California’s water

supply while decreasing the reliance on the Delta water exports. The sum

of these water eciency measures is equal to about half of the total water

demand in the State today.

IMPORTANCE OF EFFICIENT WATER USE

water in the federal and state water project contracts.

Less often, and to a much lesser extent, legal,

operational, and physical constraints on managing

the Central Valley water supply system (e.g. to protect

drinking water quality, avoid flood damage) affect

availability of supply.

Until these unrealistic water export contracts

are changed to match the amount of water that nature

actually provides—and are also adjusted to ensure

society’s minimum requirements for protecting water

quality and the environment are met—a completely

unnecessary conflict will be perpetuated.

Fortunately, the State has recognized

this problem with its policy (adopted in 2009)

of reducing human reliance on the Delta’s water

supplies. There are two main ways to achieve this

state policy. First, areas that currently import water

from the Delta must become more self-reliant

through water conservation, water recycling,

groundwater banking, water transfers, and other

proven mechanisms. Second, federal and state

contracts should be amended to reflect the amount

of water that can be sustainably delivered from

the Delta without destroying our fisheries and

ecosystems, forcing those who use exported water

to adopt more sustainable approaches to planning

for future water supplies. Making these changes

means that any new canal or tunnel can be sized at a

capacity and cost that reflect the real export supply

needs of water-importing areas and the real flow

needs of the Delta ecosystem.

A long-term, durable solution to the

problem of collateral damage at the pumps will

probably require some mixture of all four of these

approaches. Building a peripheral canal (or tunnel)

that maintains or even increases export pumping

will continue to degrade habitat conditions and

drive species declines – just in a different way from

the current system. But as long as a significant

amount of water continues to be exported from

Northern California to other parts of the state, there

will continue to be a need to improve the physical

infrastructure for doing so in order to minimize

its impacts. Together, moving the pumps (and

appropriately sizing the new canal or tunnel that

moves the water from these pumps), restoring more

natural timing and volumes of freshwater flows,

requiring more freshwater at the appropriate time

for the ecosystem, providing alternative pathways

for fish migration, and developing alternative water

supply sources, could result in a water transfer

system in the Delta that supports a healthier

ecosystem and provides more reliable water supplies

for all Californians.

Making each drop of water do more means a healthy

Delta and a healthy economy can coexist

FRESHWATER FLOWS:

For an introduction to the importance of freshwater

ows for sh and aquatic ecosystems in the San

Francisco Bay-Delta estuary and its watershed, see

The Bay Institute’s 2010 report “Gone With The Flow:

How the alteration of freshwater ows is killing the

Bay-Delta ecosystem” (www.bay.org/publications/

gone-with-the-ow).

More detailed technical discussions of the Delta’s

freshwater ow requirements in the Delta are

available in a series of expert reports written by

The Bay Institute for the 2010 proceedings by the

State Water Resources Control Board to develop

public trust ow criteria for the Delta (www.bay.org/

publications/ow-criteria-for-the-delta-ecosystem);

another critical document is the State Water

Board’s “Final Report” on ow criteria from those

proceedings (www.waterboards.ca.gov/waterrights/

water_issues/programs/bay_delta/deltaow/index.

shtml).

ALTERED FLOWS AND THEIR

IMPORTANCE TO FISH ENTRAINMENT:

For a detailed modeling account of what happens

to small particles (e.g., plankton or even some larval

sh) as they pass through the Delta, see Kimmerer,

W.J., and Nobriga, M.L. (2008). Investigating Particle

Transport and Fate in the Sacramento-San Joaquin

Delta Using a Particle Tracking Model. San Francisco

Estuary and Watershed Science, 6(1). Available at

http://escholarship.org/uc/item/547917gn.

FISH “SALVAGE”:

User-friendly salvage information can be found

at Department of Fish and Game’s Delta Oce

website www.dfg.ca.gov/delta/apps/salvage Choose

“Salvage/Export Data”, and then select a calendar

date (prior to the current date) to see a count of

“salvaged” sh and export ow information (for SWP,

CVP); a longer date range can be set as well, and

data can be exported.

TO LEARN MORE:

FISH MORTALITY:

For a discussion of the levels of mortality at the

pumps as a proportion of sh populations, see

Kimmerer, W.J. (2008). Losses of Sacramento River

Chinook Salmon and Delta Smelt to Entrainment in

Water Diversions in the Sacramento-San Joaquin

Delta. San Francisco Estuary and Watershed

Science, 6(2). Available at http://escholarship.org/uc/

item/7v92h6fs

PRE-SCREEN MORTALITY:

For another estimate for mortality caused by the

altered ow patterns, see Castillo, G. (2010) Initial

Evaluation of Entrainment Losses for Delta Smelt

in the State Water Project. Available at www.fws.

gov/stockton/jfmp/docs/Castillo_2010%20IEP_

WORKSHOP%20Initial%20Evaluation%20of%20

Entrainment.pdf

HABITAT:

For a discussion of the components of “habitat” in

estuaries, see Peterson, M. S. (2003). A Conceptual

View of Environment-Habitat-Production Linkages in

Tidal River Estuaries. Reviews in Fisheries Science,

11(4). www.usm.edu/gcrl/cv/peterson.mark/docs/

Peterson%202003%20Review.pdf

FISH SPECIES:

For a brief, clear overview of California sh, including

descriptions and habitat requirements of each

species, see the California Fish Website at UC Davis:

http://calsh.ucdavis.edu

DELTA BACKGROUND:

For a comprehensive discussion of key Sacramento-

San Joaquin Delta issues, with an emphasis on water,

see the Delta Vision documents http://deltavision.

ca.gov/index.shtml), especially the Final Report:

http://deltavision.ca.gov/BlueRibbonTaskForce/

FinalVision/Delta_Vision_Final.pdf.

A series of more recent white papers (http://

deltacouncil.ca.gov/white-papers) prepared for the

Delta Stewardship Council are also informative.

Graph showing the decline of Delta smelt: Figure

1 from The Bay Institute’s Exhibit 1 to the SWRCB

Flow Criteria Proceedings. Available at: www.bay.

org/assets/Bay-Delta%20Flow%20Criteria%20

Exhibit%201.pdf

SPECIES OF FISH COMMONLY

COLLECTED AT THE SALVAGE FACILITIES

From the California Department of Water Resources

brochure “John E. Skinner Delta Fish Protective

Facility” decribing the operation of the State sh

screens. Available at: www.water.ca.gov/recreation/

brochures/pdf/SkinnerFishFacility.pdf

Injured sh: Figure 12, from C. Karp, and J. Lyons.

2008, “Evaluation of Fish Holding at the Tracy Fish

Collection Facility, Tracy, California.” (TFCF Studies.

Volume 39). U.S. Bureau of Reclamation, Mid-Pacic

Region and Denver Technical Service Center. 26 pp.

Available at www.usbr.gov/pmts/tech_services/tracy_

research/tracyreports/TracyReportsVolume39.pdf

California’s sh – like this Chinook salmon – were once a great

commercial, recreational, and natural resource. With careful water

management, including a reduction in collateral damage, they

can once again thrive, to the delight of the present and future

generations of Californians. Photo: Courtesy of F. Gonzalez

SOLVING THE PROBLEM

The Bay Institute uses its scientic and policy

expertise to solve the problem of massive sh kills

at the pumps by advocating for more stringent

regulatory controls on Delta export pumping; more

protective ow requirements and more ambitious

habitat restoration programs to recover Delta species

and habitats; and more aggressive actions to shift

Delta exporters to alternative water supply sources.

You can help us solve the problem by going to www.

bay.org and making a donation to support our work.