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1
Introduction
The United States attempts to recluce the rate of extinction within its
cTiverse ancT valuable biota primarily through the EnciangerecT Species Act
(ESA) of 1973. The ESA prohibits or severely limits the intentional or
inciclental taking of species that are listecT as enciangerecT or threatened. The
ESA is ecologically practical in requiring that habitat necessary for each
life-history stage (critical habitat) of a species be preserved ancT, if possible,
expanclecT or enhanced. Among the requirements of the ESA, the prohibi-
tion of intentional taking is relatively easy to implement, the prohibition of
inciclental taking raises many practical cTifficulties because of its conflict
with ordinary human activities, ancT the requirement for protection of criti-
cal habitat can be troublesome in the extreme because it often is in cTirect
conflict with customary ancT valuecT uses of natural resources.
The ESA has been appliecT to the upper I(lamath River basin of Oregon
ancT California (Figure 1-1 ) for protection of the Lost River sucker (Deltistes
i?vxat?vsJ ancT shortnose sucker (Chasmistes brevirostrisJ ancT for the I(la-
math basin component of a genetically distinct population of coho salmon
(Oncorhynch?vs kis?vtchJ that is clesignatecT the southern Oregon/northern
California coasts (SONCC) revolutionarily significant unit" (ESU). The
listing of these three fish species has, as requirecT by the ESA, lecT to an
intensive effort on the part of fecleral agencies ancT others to identify critical
habitat ancT to propose fecleral actions that wouicT promote recovery of the
species. Analysis of the necks of the species has extenclecT necessarily to
private lancTs ancT to privately helcT water rights, given that the fishes range
well beyond the boundaries of fecleral lancT ancT water management.
17
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8
OREGON
,..
~( ~ `,;
~-~
:~\ ~ ~ ~CO' :~
of <~ Dwinnell
Etna . Lake Dam i
,.,~.
::~
FISHES IN THE KLAMATH RIVER BASIN
i;
::Crater /~e.
/ ~~q ~< ~
· Medford ~ ~) ~ ~ r
Lowe , :~Lake ~ '; ~
Klamath \; i)
Lake Clear
Lake ~;
N am. ~
'.) I,
CALIFORNIA
FIGURE 1-1 Map of the upper Klamath River basin showing surface waters and
landmarks mentioned in this report. Source: Modified from USFWS.
Requirements of the enciangerecT ancT threatened fishes (see Chapter 9
for the difference between these two clesignations) came into especially
sharp focus cluring 2001, a year of drought, when fecleral agencies, in an
effort to protect these fishes, all but eliminatecT the distribution of water
from Upper Klamath Lake for irrigation. The severe economic consequences
of that decision for some segments of the Klamath basin community brought
a sense of crisis to a controversy that hacT aireacly clevelopecT around envi-
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INTROD UCTION
19
ronmental, cultural, ancI commercial interests in fish as opposed to agricul-
tural ancI economic interests in the uses of lancI ancI water.
This report presents the results of a stucly concluctecI by the National
Research Council's (NRC) Committee on EnciangerecI ancI Threatened
Fishes in the I(lamath River Basin. The committee was formecI at the re-
quest of the Department of the Interior ancI the Department of Commerce,
whose agencies are responsible for implementing requirements of the ESA
in the I(lamath River basin. The committee's tasks were to evaluate the
scientific merit of fecleral agencies' proposals or requirements for protection
of the enciangerecI ancI threatened fishes ancI to analyze the long-term re-
quirements for recovery of these fishes. The committee's final report, which
is given here, presents conclusions ancI recommendations that bear on the
requirements of the enciangerecI ancI threatened fishes. The committee hopes
that its report will assist the fecleral government both in implementing the
requirements of the ESA ancI in minimizing adverse effects of ESA actions
on residents of the I(lamath River basin.
OVERVIEW OF THE ENVIRONMENT
For purposes of environmental analysis, it is convenient to clivicle the
I(lamath River basin into an upper basin, which extends north ancI east
from the Iron Gate Dam on the main stem of the I(lamath River, ancI a
lower basin, which extends south ancI west to the Pacific Ocean (Figure 1-
11. The upper basin is clominatecI by the activity of large volcanoes ancI
active faulting, which controls the location ancI shape of broacI valleys.
These fault-bounclecI valleys contain all of the large natural lakes ancI large
wetiancis of the I(lamath basin. Crater Lake, the second deepest lake in
North America ancI one of the most transparent of all lakes, is a notable
geographic feature of the upper basin, but is irrelevant to the welfare of the
enciangerecI ancI threatened fishes because of its hycirologic isolation. The
upper basin has a relatively ciry, high clesert climate typical of areas that lie
east of the Cascade Range. The wiclespreacI volcanic rocks of the upper
basin produce numerous springs that are important local sources of water.
Within the lower basin, below Iron Gate Dam, the I(lamath River is
incised cleeply into bedrock, forming a narrow canyon. The mountains that
surround the lower I(lamath, inclucling the Trinity Alps ancI Coast Ranges,
are rugged, with clense conifer ancI fir forests ancI steep tributary streams.
The climate is quite variable in the lower basin, but is clistinguishecI by its
very high annual rainfall ancI relatively milcI temperatures. Some fertile
valleys, inclucling those of the Shasta ancI Scott rivers, are founcI in the
lower basin.
Because the I(lamath River flows clirectly to the Pacific, it is isolatecI
from other iniancI waters. This isolation, which was compounclecI in the
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20
FISHES IN THE KLAMATH RIVER BASIN
past by separation of the upper anti lower parts of the I(lamath basin,
explains the high clegree of endemism in the fish fauna of the basin (Chap-
ter 51. Isolation also accounts for the spectacular ecological success, before
human intervention, of the endemic fishes of the upper basin, as shown by
formerly great abundances of the shortnose anti Lost River suckers, which
are aciaptecI for living in a naturally variable high clesert environment
(Chapter 51. Although isolation has been less absolute for anaciromous
fishes, which occupy the lower basin anti mix with other populations in the
Pacific Ocean, the homing characteristics of salmonicis in combination
with regional selective forces have lecI to the presence of genetically distinct
populations of anaciromous fishes, inclucling the SONCC population of
coho salmon, in the lower I(lamath basin anti several adjacent drainages
(Chapter 71.
With respect to water management, the upper basin has two parts: (1)
waters draining to Upper I(lamath Lake anti (2) I(lamath Lake plus all
lancis lying between it anti Iron Gate Dam, inclucling the Lost River basin.
There are no lakes of significance to the enciangerecI suckers above Upper
I(lamath Lake, but the streams anti rivers above Upper I(lamath Lake,
especially the Williamson anti WoocI rivers anti their tributaries, historically
were anti still are important for spawning of the enciangerecI suckers (Chap-
ter 61. The Lost River historically was isolatecI from the rest of the upper
basin in all but wet years anti has lakes that are or were important to
endemic fishes. It is now hycirologically connected to the I(lamath River
through water management.
The issues of importance above Upper I(lamath Lake inclucle physical
clegraciation anti blockage of tributaries by clams or water-management
structures anti misdirection of fish through entrainment. Correction of these
problems will involve private parties because most water management in
this portion of the basin is not uncler fecleral control. As explainecI more
fully in Chapter 2, cattle anti irrigated crops are important.
Below the Upper I(lamath Lake watershed, Upper I(lamath Lake, Ger-
ber Reservoir, Clear Lake, anti the now small remnants of Lower I(lamath
Lake anti Tule Lake all are affected by water management through the U.S.
Bureau of Reclamation's (USBR) I(lamath Project, as are the flows of all
tributary waters (most notably the Lost River) that lie below all of these
water bodies. Water management in this region is largely fecleral in that
USER clelivers water from Upper I(lamath Lake to the I(lamath Project anti
also stores anti routes water by using the other lakes anti waterways. Thus,
any loss of fish caused by hyciraulic manipulation or water-management
structures of the I(lamath Project is the responsibility of USER as it fulfills
its contracts for clelivery of water. Private water users, however, determine
lancI use anti application methods for water cleliverecI by USER anti use
privately managed diversion structures anti small clams to regulate the rout-
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Representative terms from entire chapter:
ilamath river
INTROD UCTION
21
ing of water. Thus, both USER anti private water users may affect the
suitability of environmental conditions for enciangerecI suckers. Although
the cletails are complex, the general pattern is that water stored in Upper
Klamath Lake, Clear Lake, anti Gerber Reservoir is clivertecI for agricul-
tural use, anti the unused portion of this clivertecI water is returned via Tule
Lake, Lower Klamath Lake, or the Lost River to the main stem of the
Klamath River (Figure 1-21. Approximate quantities of water flow are as
shown in Table 1-1.
| A CANAL
LINK RIVER
I DAM
~ i_ LOS~IVERSION \ , ~ ATION 4B
1
44~
| MATH STRAITS I
I DRAIN I
I ADY CANAL t \\
I ~ \'
~ w1~\1 \
\ `
22
FISHES IN THE KLAMATH RIVER BASIN
TABLE 1-1 Flows Uncler Conditions of Average Water Availability in
the Upper I(lamath Basina
Location
Amount
(acre-ft per yr)
Upper Klamath Lake outflowb
Outflow April-September
Directed to Klamath Project
Directed downstream
Clear Lake inflowb
Directed to Klamath Projects
Gerber Reservoir inflowb
Directed to Klamath Project
Total Klamath Project consumptive use, including refugesb
Total Klamath Project returns to Klamath Riverb
Nonproject irrigation diversions, upper basind
Total flow at Orleanse
Trinity River flow
Total flow at mouth
1,300,000
500,000
400,000
900,000
117,000
36,000
55,000
40,000
350,000
100,000
420,000
6,000,000
3,800,000
13,400,000
Approximate only actual values differ from year to year.
bUS13R 2000a.
Evaporative losses are especially high in Clear Lake (long retention time and evaporation at
about 3.8 ft/yr).
dNMFS 2001 (estimated from percentages).
eNear the mouth of the Klamath River, but above the Trinity River.
The upper basin contains seven national wilcIlife refuges anti several
other public anti private preserves, as shown in Figure 1-3. The abundance
of refuges anti preserves in the upper basin is an indication of its excep-
tional value for waterfowl anti other forms of life that clepencI on great
expanses of shallow water anti wetiancis. Refuges anti preserves around the
lakes can be consiclerecI a means of conserving or enhancing wetiancis that
may be relevant to the welfare of enciangerecI suckers.
Near Lower I(lamath Lake anti Tule Lake, water management is espe-
cially complicatecI in that the refuge lancis within the original inundation
zones of these two lakes now are used extensively for agricultural purposes
according to agreements that were reachecI cluring the early history of the
refuges (Chapter 21. The two lakes function hycirologically primarily as
drainage conduits; they are not allowecI to accumulate water because of
governmental commitments to continuing agricultural use of the former
lake becis. Thus, both lakes now lack the large populations of shortnose anti
Lost River suckers that once occupied them, although Tule Lake cloes still
support a small population of enciangerecI suckers (Chapter 61.
Also in the upper basin are six main-stem clams (Figure 1-41. The Link
River Dam (completecI in 1921), which is near the outlet of Upper I(lamath
INTROD UCTION
'boat
Cams (.
Sprague River
Klamath Marsh
Crater National Wildlife ;:
Lake Refuge ~ ~ Dim
~ 7~ ~ ~ ~
Wood River .,- ~ ~
Ranch (BLM) us ') r
Agency Lake \ 0 Ad 5~
Ranch (USER ~~~ a, \_
Upper Klamath 1 ~ ~ ~ ~] ) l
National Wildlife I ~ . ~\ . . . Cal
amson River
Refuge i/ ~ ~ ~ \
24
FISHES IN THE KLAMATH RIVER BASIN
Rivet
ello Dam
ant
~ 0 1 2 3 4 5
/ Iron Gate Dam
in,/ Miles
FIGURE 1-4 Main-stem dams on the I(lamath River.
main stem. The six clams block access of both enciangerecI suckers anti coho
salmon to large portions of their historical ranges anti can be clirect or
indirect agents of fish mortality. Through the operation of Link River Dam,
enciangerecI suckers have been historically entrained into the A Canal anti
thus killecI (Chapter 61. In aciclition, the suckers enter the unscreened in-
takes of the power-procluction facilities anti thus may pass through tur-
bines. Dams also are the means by which ramping of flow (change in
discharge over short periocis), which is consistent with optimal operation of
hydropower production facilities, is achieved; ramping of flow can be clet-
rimental to coho fry, which can become stranclecI at the river margin when
flow decreases rapicIly.
In the lower part of the basin (below Iron Gate Dam), the main stem of
the I(lamath River is the pathway of migration for numerous anaciromous
fishes anti is important for spawning anti rearing of some of them (Chapter
71. Flow to the main stem at Iron Gate Dam is reclucecI anti alterecI season-
ally through the operation of the I(lamath Project anti private water man-
agement above Iron Gate Dam anti is regulatecI hourly by PacifiCorp (Chap-
ter 41. Releases can be regulatecI to some clegree by control of storage in
Upper I(lamath Lake, but irrigation commitments constrain this manage-
ment flexibility, especially in ciry years. Although grounc~water flow is sub-
stantial in some parts of the I(lamath River basin, there appears to be little
accrual of grounc~water to the I(lamath main stem below Iron Gate Dam.
Increase in discharge downstream occurs through four large tributaries-
the Shasta, Scott, Salmon, anti Trinity rivers (Figure 1-1) anti through
numerous small tributaries. The large tributaries all are physically alterecI,
anti some show severe clepletion of flow anti are excessively warm because
of loss of riparian vegetation anti high relative contribution of irrigation
INTROD UCTION
25
return flows to total stream discharge (Chapter 41. As explained in Chap-
ters 7 and 8, the small tributaries now provide some of the best habitat for
coho salmon. Land and water relevant to the welfare of the coho and other
fishes in the lower basin are primarily under private control. Water-man-
agement structures interfere with the movement of fish in this part of the
watershed' as they do elsewhere.
The Trinity River, which is the largest tributary of the I(lamath River,
reaches the I(lamath about 43 mi from the estuary. In 1964, the Trinity
River Diversion began delivering up to 90°/O of the upper Trinity's flow out
of the basin to the Central Valley Project. This diversion and other changes
in the watershed were followed by a severe decline in the anadromous fish
populations of the Trinity River. Studies of coho salmon and other fishes of
the Trinity River have been conducted separately from those of the I(la-
math River basin through processes prescribed by the National Environ-
mental Policy Act, which involves an environmental impact statement (EIS)
rather than ESA procedures. In December 2000, the EIS resulted in a record
of decision (ROD) for the Trinity River (USFWS 20001. The ROD called
for increased minimum flows, habitat restoration for the benefit of anadro-
mous salmonid populations, and use of an adaptive management approach
involving further study and evaluation of the outcomes of flow and habitat
manipulations. As a result of judicial decisions, however, a supplementary
EIS is still in progress. Recovery of the Trinity River coho populations is
important for recovery of the coho in the I(lamath basin as a whole; hydro-
logic linkages between the two rivers are especially important for the migra-
tion of coho (Chapters 4, 7, and 81.
The hydrologic characteristics of the l~lamath diver main stem and its
major tributaries are dominated by seasonal melt of snowpack. Summer
storms and release of groundwater from springs also make contributions,
in. . . . . . . . ~ . . . .
but they are smaller in aggregate than the snowmelt effect. The schedule of
melting differs from year to year, reflecting climatic variability, but a uni-
versal feature of hydrographs is a spring pulse in flow followed by recession
to a baseflow condition by late summer. These main features of the hydro-
graph undoubtedly have influenced the adaptations of native organisms,
as reflected in the timing of their key life-history features (see Chapters 5
and 71.
Even though water is now managed (Table 1-1), hydrographs of the
I(lamath River basin still show the dominant influence of snowmelt and
spring precipitation on water flow. For example, Figure 1-5 compares the
flow near the mouth of the Williamson River, above which there are no
major impoundments, with the flow at Iron Gate Dam, above which a great
deal of water management occurs. Flows at the mouth of the Williamson
River are affected by privately managed irrigation diversions but, given the
large total flow in the Williamson, the hydrograph has predominantly natu-
26
12,000
10,000
8,000
6,000
a'
:~ 4,000
2,000
FISHES IN THE KLAMATH RIVER BASIN
+ Iron Gate Dam, 1993
Williamson River near
Chiloquin, OR, 1993
o
~3 ~
I at
it=,
-I ~
by
Ton Fob Mar Apr May Jun Jul Aug Sep Oct Nov Dec
FIGURE 1-5 Flow of the Williamson River, the largest water source for Upper
I(lamath Lake, and of the I(lamath River main stem (at Iron Gate Dam) in a year of
near-average water availability. Source: USGS gage records.
rat features. At Iron Gate Dam, the retention of water in reservoirs of the
Lost River anti in Upper I(lamath Lake has the potential to alter the
hycirograph more extensively. Alteration is, as expected, more severe clur-
ing years of drought than years of average flow.
The management of hycirographs, in combination with natural climatic
variation, now is a major focus of attention in the analyses of environmen-
tal factors that may affect the welfare of the two enciangerecI sucker species
anti the coho salmon (Chapter 41. Hycirology has environmental effects not
only through its clirect control of physical attributes of stancling anti flow-
ing water (mean depth, water velocity), but also because of its indirect
control of other aspects of the physical, chemical, anti biological environ-
ment such as temperature of flowing water, nutrient concentrations in
lakes, anti extent anti type of aquatic vegetation. Even so, numerous influ-
ences on the enciangerecI fishes, such as the introduction of nonnative fishes,
loss of riparian vegetation, anti anthropogenic mobilization of nutrients,
involve factors other than hycirology.
THE FISHES
The shortnose anti Lost River suckers are large, long-livecI fishes of
high fecundity. Although they spencI most of their lives in lakes, flowing
waters are important to them for spawning. Some subpopulations spawn
around the perimeter of Upper I(lamath Lake, particularly near springs, but
INTROD UCTION
27
fish of both species migrate or attempt to migrate into tributaries for spawn-
ing. Shortly after hatching, fry return to the lake, where they occupy very
shallow water at first ancI move to progressively greater depths as they
mature. The enciangerecI suckers clo not spawn until they are several years
oicI (Chapter 51.
The two enciangerecI sucker species were so abundant before coloniza-
tion that they servecI as a major foocI source for Indian tribes (Chapter 21.
After the I(lamath basin was colonizecI, the fish were harvested in large
numbers commercially. Because they are large ancI tencI to migrate cluring
spawning, they were highly vulnerable, ancI their numbers were cirastically
reclucecI through harvest. Records of the size of spawning runs ancI sport
fishing inclicatecI cluring the 1980s that both species hacI cleclinecI to such a
point that without special protection they might be extirpated. Fishing for
the species was eliminatecI except for very small numbers of fish allocatecI
for ceremonial purposes to Indian tribes. In 1988, both species were listecI
as enciangerecI uncler the ESA (53 FecI. Reg. 27130, 18 luly 19881.
It was clear in the 1980s ancI even earlier that prohibition of fishing,
although essential, might not be sufficient to produce recovery of the en-
ciangerecI suckers. Factors that probably have contributed to the suppressed
abundances of these species inclucle blockage of migration pathways to
spawning areas; entrainment of large numbers of fish by water-manage-
ment structures; poor water quality, especially in Upper I(lamath Lake;
physical clegraciation of habitat; ancI adverse genetic consequences of scar-
city ancI fragmentation (Chapter 61. Mass mortality of large fish in Upper
I(lamath Lake, although recorclecI for over 100 yr, caused particular alarm
cluring the 1990s because of its sequential occurrence in 3 yr (1995-19971.
The abundance of large aclults appears to have been strongly suppressed by
fishing, which was banned after 1987, ancI by mass mortality caused by
poor water quality. Although recruitment of young fish has been clocu-
mentecI since the listing of the suckers in 1988, there is no indication of
recovery in overall abundances (Chapter 61.
Populations of coho salmon in the I(lamath River were substantial
when commercial salmon fisheries first clevelopecI (Chapter 71. Abundances
of most anaciromous fishes in the I(lamath River basin ancI other Pacific
coast basins have cleclinecI cirastically since then. Decline of the coho salmon
in the I(lamath River basin lecI to fecleral listing of the SONCC ESU as
threatened in 1997 (62 FecI. Reg. 24588, 6 May 19971; California listecI the
ESU as enciangerecI in 2003.
The coho salmon, except in the case of some early-spawning males, has
a 3-yr life history that is cliviclecI almost equally between marine ancI fresh-
water environments. A fall-winter migration brings the fish up the main
stem of the I(lamath River. Although some spawning may occur in the main
stem, the primary spawning occurs in tributaries (Chapter 71. Young fish
INTROD UCTION
35
scientific justification for the proposals of USER, which would have al-
lowed the river to be operated at lower mean flows than had been the case
for specific categories of water availability applicable during the 1990s.
The committee, in drawing conclusions for its interim report, was
bound by its charge to evaluate and comment on the scientific strength of
evidence underlying various proposals. Its charge kept it from weighing
economic concerns or weighing the advisability of minimizing risk by using
professional judgment in place of scientific evidence to support particular
recommendations. As explained more fully in Chapter 9, agencies charged
with ESA responsibilities can be expected to use professional judgment
when no scientifically supportable basis is available for a decision, or where
they judge the scientific support to be inadequate. Thus, the agencies may
recommend practices for which the committee would find virtually no di-
rect scientific support. The committee acknowledges the necessity of this
practice in many situations where information is inadequate for develop-
ment of scientifically rigorous decisions (Chapter 91.
For its final report, the committee adopted some specific conventions
for judging the degree of scientific support for a specific proposal or hy-
pothesis; Table 1-2 gives a summary. Any proposal for specific actions of a
remedial or protective nature has an implicit or explicit underlying hypoth-
esis that connects the proposed action with a beneficial effect on a threat-
ened or endangered species. The scientific value of such a hypothesis ranges
from negligible to very high, depending on the amount of testing to which
it has been subjected. At the low end of the scale of scientific strength is an
assertion or proposal that is entirely intuitive and thus without scientific
support. For example, the catch phrase "fish need water" has been used as
an assertion supporting increased water levels in Upper I(lamath Lake and
TABLE 1-2 Categories Used by the Committee for fudging the Degree of
Scientific Support for Proposed Actions Pursuant to the Goals of the ESA
Scientific Possibly Potential to
Basis of Proposed Action Support Correct? be Incorrect
Intuition, unsupported assertion None Yes High
Professional judgment inconsistent with
evidence None Unlikely High
Professional judgment with evidence absent Weak Yes Moderately
high
Professional judgment with some supporting
evidence Moderate Yes Moderate
Hypothesis tested by one line of evidence Moderately Yes Moderately
strong low
Hypothesis tested by more than one line of
evidence Strong Yes Low
36
FISHES IN THE KLAMATH RIVER BASIN
increased flows in the main stem of the upper I(lamath River. The state-
ment is true, but it cloes not constitute a scientifically valicI argument for
specific flows or specific water levels.
Professional judgment has more value than unsupported intuition. It
typically is basecI on knowlecige of the importance of various environmental
factors or the requirements of various species in other locations or on
general experience with or knowlecige of the response of a particular cat-
egory of organism to specific kincis of environmental challenges.
Professional judgment can be used in three ways, ancI the distinctions
among them are quite important in the case of the I(lamath River basin.
First, for an issue about which there is no information whatsoever, an
agency that is charged with protecting a threatened or enciangerecI species
can justify the use of professional judgment. Such agencies are charged
with reduction of risk to the species; lacking site-specific information on a
particular type of risk, they wouicI logically ciraw analogies with the same
or similar risks in other settings or for other species, or they wouicI use
general principles relatecI to the known tolerance of particular species or
groups of species. Although such an approach is weak in that the transfer-
ability of ecological knowlecige from one set of circumstances to another
is problematic, there is some scientific basis for it, ancI barring the feasibil-
ity of other approaches, it can be saicI to have weak but not negligible
scientific strength.
Second, a resource agency might use professional judgment to endorse
various proposals for action when valicI scientific information contradicts
it. This use of professional judgment is clifficult to justify. The agency may
hoicI to its clesire to use professional judgment in preference to empirical
information of clirect significance to a particular issue on the grouncis that
something is wrong with the empirical information. Scientifically, however,
sound ancI relevant empirical information always trumps speculation or
generalization; an agency couicI argue the reverse only on the basis of a very
conservative approach to risk.
Third, an agency might choose to use professional judgment that is
consistent with a small amount of clirect evidence. In this case, the use of
professional judgment is reinforced rather than contraclictecI, ancI scientific
support for it can be cleemecI moderate rather than negligible.
A step beyond professional judgment is the empirical testing of scien-
tific hypotheses involving cause ancI effect. If a properly clesignecI single line
of evidence is clevelopecI as a means of testing such a hypothesis, ancI the
hypothesis is not invaliciatecI, scientific support for the hypothesis can be
consiclerecI moclerately strong. Icleally, this approach wouicI be extenclecI by
the collection of aciclitional, inclepenclent evidence through which the hy-
pothesis couicI be tested in a different way; barring contradiction between
the evidence ancI the hypothesis, the hypothesis couicI be consiclerecI a theory
INTROD UCTION
37
of consiclerable strength to be reliecI on in proposing anti pursuing vigor-
ously the action upon which the hypothesis is basecI.
The committee has used the six-tierecI system summarized in Table 1-2
anti clescribecI above in assessing the scientific basis of actions that have
been recommenclecI in the I(lamath basin for protection of the enciangerecI
suckers anti threatened coho salmon. It founcI its greatest differences with
the resource agencies in the second category: instances in which the agen-
cies have used professional judgment that is contraclictecI by scientifically
valicI, relevant evidence. In carrying out its task to categorize the scientific
support for specific proposals, the committee wouicI characterize any pro-
posal justified by such means as having negligible scientific support. This
cloes not preclucle the resource agency from using such an approach, but the
justification for it wouicI involve extreme sensitivity to risk, anti in this way
might be jucigecI not reasonable.
The committee's charge requires that it estimate the costs associated
with its recommendations. For the recommendations involving aciclitional
research or monitoring, the committee was able to approximate costs basecI
on the experience of the committee members with similar types of research.
Even so, the mocle of implementation of a particular research program
couicI cause costs to deviate markecIly from the committee's estimates. For
example, implementation couicI involve a much broacler or narrower geo-
graphic scope than suggested by the committee, or it couicI involve multiple
organizations in a way that wouicI increase costs. The committee also was
able to estimate, on the basis of general experience, the costs of selectecI
minor restoration activities. The committee clicI not attempt, however, to
estimate costs for major restoration activities. In most instances these ac-
tivities must be stucliecI for feasibility prior to the time any commitment is
macle to them, anti their final approval anti execution may be complicatecI
to an extent that cannot be meaningfully jucigecI by the committee in terms
of cost.
SUMMARY OF THE BIOLOGICAL ASSESSMENTS AND
BIOLOGICAL OPINIONS OF 2002
The biological assessments issued by USER in 2001 anti the biological
opinions issued by USFWS anti NMFS in 2001 all expired after 1 yr, so new
assessments anti opinions were issued in 2002. The assessments anti opin-
ions of 2002 cliffer from those of 2001 in several respects. First, they cover
a 10-yr interval rather than a 1-yr interval. In working with 10 yr rather
than 1 yr, the agencies are cooperatively attempting to stabilize anti acicI
flexibility to management in such a way as to benefit both water use anti
environmental remecliation. At the same time, consultation between the
agencies probably will continue, anti requirements of USFWS anti NMFS
38
FISHES IN THE KLAMATH RIVER BASIN
probably will be moclifiecI within the 10-yr interval as new information
becomes available. Reinitiation of consultation is required by ESA Section 7
uncler some circumstances, ancI both USBR ancI NMFS must issue a new
biological assessment ancI opinion in any case because of the ruling of a U.S.
District Court (see below). The texts of assessments ancI opinions of 2002
show that they were influencecI to some extent by the committee's interim
report. The interim report was not bincling on the agencies but proviclecI a
basis for aciclitional consultation ancI appears to have stimulatecI some new
kincis of discussions among the agencies.
Enciangerec! Suckers
The USBR Biological Assessment
The USBR, which in 2001 hacI prepared two assessments (one for the
threatened coho ancI one for the two enciangerecI sucker species), clealt with
all three species in a single document cluring 2002. This makes sense be-
cause water resources at times of scarcity must be shared not only among
consumptive uses ancI listecI species but also among the listecI species them-
selves, given that the coho ancI the suckers occupy different parts of the
basin. USBR proposed maintenance of specific water levels in lakes ancI
some other actions previously suggested by USFWS or others, reflecting the
consultation process through which gaps between the viewpoints of the
agencies are intenclecI to be minimized.
Table 1-3 lists in abbreviated form the commitments that USBR macle
in its 2002 assessment to accommodate the neecis of the enciangerecI suck-
ers. It proposed to manage water levels in Upper I(lamath Lake, Clear Lake,
ancI Gerber Reservoir so as to stay within the operating ranges of the l990s.
Specifically, it proposed not to allow water levels to fall below the 1990-
1999 minimums for specific water-year categories ancI not to allow the
mean water level for any water-year category to decrease through increased
average cirawclown. Thus, the water-level proposals in the assessment were
responsive to the criticism macle by the committee in its interim report
(2002) that the USBR proposal of 2001 wouicI have allowecI, without any
ecological rationale relevant to the suckers, greater mean cirawclown within
any given water-year category.
A second element of the assessment is a water bank, which USBR proposed
to be as large as 100,000 acre-ft. The water bank wouicI provide operational
flexibility in meeting multiple neecis for water cluring years of water scarcity
anti wouicI help USBR to ensure that water-level targets in lakes (or flow
requirements at Iron Gate Dam, for coho salmon) wouicI be met.
USBR also proposed a procedure for cleveloping project operations in a
particular water year. The procedure wouicI begin in April with classifica-
INTROD UCTION
TABLE 1-3 Summary of Commitments of the USBR Biological
Assessments of 2002 that are Relevant to the Two EnciangerecI Sucker
Species
39
Assessment Commitments
Water levels in Upper Klamath Lake, Clear Lake, and Gerber Reservoir:
Maintain water levels at or above 1990-1999 minimums for specific water-year typesa
Maintain mean water levels at or above 1990-1999 means for specific water-year types
Establish water bank of about 100,000 acre-ft
Use specific procedure for determining annual operations, including 70% exceedance
principle for water availability
Coordinate externally and produce annual report on operations
Reduce entrainment and enhance passage in Link River and at other locations
Enhance water supply
Cooperate with USFWS in operation of refuges
aSpecial concerns and procedures are clarified by subsequent memoranda on Clear Lake and
Gerber Reservoir (USER, unpublished memo, February 21, 2003; USFWS, unpublished memo,
March 4, 2003).
tion of the year by water-year type above average, below average, ciry, or
critical ciry (see Chapter 3 for cletails) through the use of forecasts from
the National Resource Conservation Service (NRCS). A 70°/O exceeciance
factor wouicI be used in applying the forecast; that is, forecasts of the
availability of water for the I(lamath Project wouicI be conservative in that
there wouicI be a 70°/O chance that the forecast wouicI be equalecI or ex-
ceeclecI by actual water availability. Having thus classifiecI a cleveloping
water year as belonging to one of the four categories, USBR wouicI follow
specifications on minimum water levels for the appropriate water-year cat-
egory. A second, later calculation wouicI facilitate maintenance of water
levels in lakes no lower than the average (rather than the minimum) encI-of-
month elevations for specific water-year types over the interval 1990-1999.
Another component of the assessment was a commitment to an annual
report on operations, which wouicI be useful because of the general interest
in operations anti the clifficulty of discovering the cletails of operations
without an interpretive document. Coordination not only with USFWS, as
required through ESA, but also with other groups is a component of this
portion of the assessment proposal.
The USBR proposed to recluce entrainment of fish by diversions anti to
increase fish passage in the Link River. Specifically, entrainment of fish at
the A Canal is known to be large. Entrainment of fish above a size of about
30 mm wouicI be reclucecI by installation of a permanent fish screen by a
specified ciate (April 1, 20041. Salvage operations are incluclecI, as are mea-
sures to promote fish passage at the Link River Dam to be completecI in
January 2006. Increase in water supply through increased storage capacity
40
FISHES IN THE KLAMATH RIVER BASIN
ancI leasing also is a component of the proposals from USBR for 2002, but
cletails are not yet available. Because these measures wouicI require congres-
sional approval ancI funding, they were not attached to a specific scheclule
in USBR's assessment.
The USFWS Biological Opinion
In responding to the portion of the USBR assessment clearing with
enciangerecI suckers, USFWS, through its biological opinion of 2002, re-
actecI favorably to a number of the USBR proposals, inclucling the water
bank ancI specifically scheclulecI actions intenclecI to recluce entrainment ancI
improve fish passage. In the text of its opinion, however, USFWS expressed
its position that water levels higher than those proposed by USBR wouicI be
favorable to the suckers through improvement in water quality ancI mainte-
nance of habitat (see Chapters 3 ancI 61. Overall, USFWS founcI that the
operations proposed by USBR wouicI leave the two enciangerecI sucker
species in jeopardy anti therefore formulatecI an RPA uncler which USBR
must operate (Table 1-41.
The USFWS concluclecI that low water levels in the lakes are less favor-
able than high water levels to the welfare of the suckers. It requirecI that
water levels in the lakes not deviate from minimums (for single years) or
averages (for groups of years) of the 1990s for specific categories of water
years, as proposed by USBR. In aciclition, USFWS requirecI through its RPA
that USBR use a 50°/O exceeciance probability rather than a 70°/O probabil-
ity in forecasting water availability. As shown in the USFWS biological
opinion, use of a 70°/O forecast, although favorably conservative for water-
management purposes in tending to underestimate water availability, couicI
be unfavorable from the environmental point of view if it were allowecI to
justify water-level cirawclown in lakes more extreme than wouicI be consis-
TABLE 1-4 Summary of Components of USFWS Biological Opinions of
2002 that are Relevant to the Two EnciangerecI Sucker Species of the
I(lamath River Basin
.
Component of Biological Opiniona
Use 50% rather than 70% exceedance probability for planning water levels in Upper
Klamath Lake
Screen power-plant intakes at Link River Dam
Study cause of death and habitat needs of endangered suckers in Upper Klamath Lake
Take actions leading to more favorable water quality and expansion of habitat
Monitor populations of endangered suckers
Produce annual assessment report on suckers
Follow specific implementation schedule
Components shown here are in addition to proposals of the USER in its biological assessment.
INTROD UCTION
41
tent with the actual availability of water. Thus, USFWS justified the 50°/O
exceeciance requirement for estimates as a means of ensuring that estimates
of water availability wouicI not be biased. Currently, it appears that USBR
ancI USFWS are in agreement that April projections can be corrected as
appropriate whenever they later appear to have been in error (USFWS 2002;
p. 1181.
A second element of the RPA was to recluce entrainment of fish at Link
River Dam ancI hydropower intake facilities. USBR hacI committed to
screening the A Canal, but it clicI not make the same commitment for the
power-procluction facilities at Link River Dam. Thus, the USFWS RPA
appears to extend USBR's commitment to screening. This requirement of
the RPA raises questions about the feasibility of requiring USBR to manage
entrainment for facilities that are operated by PacifiCorp, a power procluc-
tion company. The application of this feature of the RPA to the Link River
Dam will clepencI on the nature of the fecleral action that USBR takes with
respect to PacifiCorp's operation of the facilities. If USBR has sufficient
discretionary authority over PacifiCorp's operation within the meaning of
ESA Section 7 (carry out, funcI, or authorize operations) for the facilities
to be properly within the scope of the interagency consultation, the RPA
wouicI be an appropriate component of the USFWS biological opinion. If
not, USFWS wouicI neecI to explore application of ESA Section 9 to Pacifi-
Corp anti determine whether PacifiCorp wouicI be in violation of the ESA in
the absence of screening ancI other measures that may be clevelopecI be-
tween USFWS anti PacifiCorp (see Chapter 91. Thus, USFWS anti USBR
still must clarify the status of the Link River Dam operations uncler Section
7 of the ESA.
Other requirements of the biological opinion are that USBR stucly the
causes of mass mortality of fish ancI access of enciangerecI suckers to habitat
in Upper I(lamath Lake, take actions clesignecI to recluce unfavorable as-
pects of water quality or limitations in sucker habitat, monitor populations
of enciangerecI suckers, ancI produce an annual assessment report. A cle-
tailecI implementation scheclule anti requirements for collaborative work of
USBR with other parties accompany this element of the RPA.
Threatener! Coho Salmon
The USBR Biological Assessment
In its biological assessment of 2002, the USBR macle a number of
proposals relevant to coho salmon, as shown in Table 1-5. First, USBR
committed itself to maintain river discharges no lower than those observed
cluring 1990-1999 for the categories of water years that it uses in water
management. It also committed itself to maintain interannual averages no
42
FISHES IN THE KLAMATH RIVER BASIN
TABLE 1-5 Summary of Components of USBR Biological Assessments of
2002 that are Relevant to Threatened Coho Salmon of the I(lamath River
Basin
Assessment Component
Discharge of water from Iron Gate Dam
Above-average and below-average years: monthly flow will be no lower than 1990-
1999 year minimums or FERC minimums, whichever is greater
Dry and critical-dry years: monthly flow will be no lower than actual 10-yr
averages plus pulse of 10,000 acre-ft in April
Establish water bank of about 100,000 acre-ft
Use specific procedure for determining annual operations, including 70% exceedance
. .
prlnclp e
Coordinate externally and produce annual report on operations
Enhance water supply
lower anti sometimes higher than interannual averages of 1990-1999 for
specific categories of years, thus answering the concern expressed in the
committee's interim report that a commitment to maintain minimums with-
out a commitment to maintain averages wouicI in fact allow future opera-
tions to produce lower averages.
As was the case for water levels of Upper I(lamath Lake, Clear Lake,
ancI Gerber Reservoir, USBR proposed to use a 70th percentile exceeciance
factor appliecI to the April 1 forecast of NRCS for planning annual opera-
tions. For above-average anti below-average years, USBR proposed to pro-
vicle flows no lower than the minimums observed cluring the l990s ancI also
no lower than the Fecleral Energy Regulatory Commission (FERC) mini-
mums if the FERC minimums happen to be higher. For the two cirier
categories of years (city ancI critical ciry), USBR proposed to provide flows
no lower than the observed averages for the l990s ancI also to provide
10,000 acre-ft of aciclitional flow cluring April to facilitate smolt migration.
The use of averages rather than minimums from the 10-yr observation
period is a commitment of aciclitional water above what hacI been commit-
tecI by USBR in its 2001 assessment, as is the 10,000 aciclitional acre-ft for
April.
An aciclitional component of the proposed operating plan for any given
year is the establishment ancI operation of a water bank, which also serves
the neecis of enciangerecI suckers, ultimately to be as large as 100,000 acre-
ft. Mechanisms for water banking couicI involve offstream storage but also
couicI inclucle reduction in irrigation clemancI with compensation to irriga-
tors ancI conjunctive use of grounc~water ancI surface water to provide a
buffer that wouicI be especially useful in ciry years (Chapter 101.
The USBR proposal also macle a commitment to coordination extencI-
ing beyond the ESA implementation agencies to inclucle the tribes, Pacifi-
INTROD UCTION
43
Corp, ancI private water users. Coordination wouicI be supplementecI with
an annual report documenting the preceding year's activities. Enhancement
of water supply, not necessarily limitecI to the water-banking concept, was
also an element of the USBR proposal.
The NMFSBiologicalOpinion
After consultation with USBR cluring 2002,NMFS concluclecI that pro-
posecI actions of USBR as presented in its 2002 biological assessment,
although containing several constructive components, wouicI leave the
threatened coho in jeopardy. Thus, according to the requirements of the
ESA, NMF S prepare cI a bio logical op inion containing an RPA summarize cI
in Table 1-6. In revising its biological opinion of 2001,NMFS recognized
that the I(lamath Project accounts for about 57°/O of the total irrigation-
relatecI clepletions of flow at Iron Gate Dam. Thus, according to the opinion
of 2002, it wouicI not be reasonable to require USBR to provide clirectly ancI
immecliately all increments of flow jucigecI by NMFS to be necessary for
improvement of habitat in the main stem of the I(lamath River below Iron
Gate Dam. Accorclingly, NMFS assigned USBR a 57°/O share in the respon-
sibility for providing flows in the main stem to meet the requirements of the
threatened coho as jucigecI by NMFS. In cloing so, however, NMFSclicI not
absolve USBR entirely of responsibility for making up the other 43°/O of
flows. The biological opinion requires USBR to facilitate ancI coordinate a
phasecI effort to provide capacity for the aciclitional flows.
NMFS, as part of the RPA, requires USBR to builcI a water bank, which
USBR has agreed to be its preferred method for meeting its obligation to
provide the 57°/O of flow shortfalls that NMFS will require it to provide for
support of the threatened coho salmon (specific flows are shown in Table 9
TABLET-6 Summary of Components of NMFS Biological Opinions of
2002 that are Relevant to Threatened Coho Salmon in the I(lamath River
Basin
Component of Biological Opiniona
Apply 57% rule for proportionate USER direct responsibility for flow at Iron Gate
Dam
Use task force to develop the 43% additional flow from nonproject sources
Use phased approach to raising flows and lowering temperatures
Develop water bank (100,000 acre feet) on specific schedule
Adopt water-year types as identified in draft phase II flow study report (Hardy and
Addley 2001)
Limit ramping rates below Iron Gate Dam
Conduct designated scientific studies with advice from external experts
Components shown here are in addition to proposals of the USER in its biological assessment.
44
FISHES IN THE KLAMATH RIVER BASIN
of NMFS2002 ancI in Chapter 4 of this report). USBR must create a water
bank to 100,000 acre-ft capacity by 2006 according to the RPA. A U.S.
District Court jucige founcI cluring luly 2003, however, that reliance on the
water bank is unjustifiably speculative until more particulars are given.
Thus, USBR soon must issue a new biological assessment in consultation
with NMFS, which must issue a new biological opinion.
In its recommendation for flows, NMFS gave greatest emphasis to im-
provement of the conditions for smolt migration, probably because tribu-
tary conditions are most important for spawning ancI rearing, while the
main stem performs a critical anti irreplaceable function in smolt migration
(Chapter 71.
In prescribing flows, NMFS did not follow the method of USBR in as-
signing specific water years to categories. NMFS used estimates of unim-
pairecI flows from the Harcly Phase II ciraft report (Harcly anti AcicIley 2001)
anti the idea that the shape of the natural hycirograph anti a natural range
of interannual variabilities shouicI be represented as completely as possi-
ble in the flows of the main stem. The five categories anti their percentiles
used by NMFS in its flow prescriptions for the I(lamath main stem are as
follows: wet years, 10%; above-average years, 30%; average years, 50°/O;
below-average years, 70°/O; anti ciry years, 90°/O. The percentile in each case
indicates the proportion of years that wouicI exceed the unimpaired monthly
flows. The RPA provides specific ciates by which USBR must meet the flow
requirements.
NMFS specified upper limits on ramping rates below Iron Gate Dam.
The specifications are more stringent anti more cletailecI than those govern-
ing previous operations. As in the case of screening plant intakes, however,
the direct responsibility for meeting this requirement may lie with PacifiCorp
rather than USBR.
According to the RPA of 2002, USBR is required to convene a pane! of
experts capable of identifying studies that improve the current unclerstancI-
ing of relationships between river discharge anti welfare of coho salmon.
One specific element of the studies is a test of the effect of various flows on
thermal refugia in the main stem of the I(lamath River.
Overview of the 2002 Biological Assessments ant! Opinions
The USBR assessment anti the accompanying biological opinions of
USFWS anti NMFS for 2002 reflect consiclerable constructive interaction
among the agencies between 2001 anti 2002. There is still a gap between
the assessments anti the opinions, but the gap has narrowed from 2001
through some carefully consiclerecI movement toward consensus among the
three agencies. USFWS anti NMFS are requiring some substantial actions
beyond those proposed by USBR. In general, however, the actions adhere
INTROD UCTION
45
more closely than those given by the listing agencies in 2001 to the relevant
available scientific evidence or to professional judgment reinforced by at
least some scientific evidence. As explainecI in this report, USFWS ancI
NMFS in a few instances have macle requirements basecI almost entirely on
professional judgment, without clirect scientific support, as is their preroga-
tive. In cloing so, however, they appear to have macle a special effort to
frame their requirements in such a way as to cause minimal impairment of
I(lamath Project operations anti, in contrast with 2001, have recognized the
inevitable neecI to inclucle parties other than USER in modification of envi-
ronmental conditions for the benefit of the enciangerecI ancI threatened
fishes.
CONTEXT FOR THE COMMITTEE'S REPORT
The NRC committee has evaluatecI a very extensive accumulation of
ciata collectecI both in the fielcI ancI laboratory, historical records of various
kincis, opinions anti interpretations by inclivicluals intimately familiar with
the environmental conditions in the I(lamath, ancI numerical analyses of
many kincis. Though the documentation for questions relatecI to encian-
gerecI ancI threatened fishes in the I(lamath basin is impressive in scope ancI
volume, it must be viewed as a preliminary step toward what eventually can
ancI must be known about the I(lamath River basin in support not only of
the recovery of enciangerecI fishes but also of the more general restoration
of aquatic environments in the I(lamath basin. As will be shown by this
report, the number of firm conclusions that can be reachecI about cause-
ancI-effect relationships still is modest, yet these types of conclusions are
essential for planning, managing, anti predicting the outcomes of actions in
the I(lamath River basin. The NRC committee sees its own work only as a
best effort given the information available; the committee fully expects to
see new kincis of ciata ancI new tests of ideas yielcI insights that the commit-
tee couicI not have anticipated basecI on current information. Effective ef-
forts to cause recovery of the enciangerecI anti threatened fishes rest on
information, anti the committee urges the creation of new information that
will place management decisions on increasingly firm grouncI.
