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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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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 \ \ ` OCR for page 17
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

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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/ ~ ~ ~ \ OCR for page 17
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

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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-

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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

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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

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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

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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

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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

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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-

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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

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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.

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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

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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-

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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.

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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

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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.