1
Introduction

The Klamath River basin of northern California and southern Oregon has been the scene of controversies over water allocations in recent years. The basin has been extensively modified by levees, dikes, dams, diversion of tributary waters, and the draining of natural water bodies since the Klamath Project was begun in 1905 to improve the region’s ability to support agriculture; other changes have occurred as well (NRC 2004a).

The changes made to the system have been accompanied by changes in the biota of the basin as well. This report particularly focuses changes in the distribution and abundance of several species of fishes of concern in the Klamath River, Upper Klamath Lake, and their tributaries. Those fishes were the subject of earlier reviews by the National Research Council (NRC 2002, 2004a), the first of which focused on specific documents related to water management in the basin and its effect on the fishes and the second of which focused on broad aspects of the basin’s management and options for arresting and perhaps reversing the declines of the basin’s fishes. The evaluations were prompted by conflicts that arose following actions taken to protect the basin’s fishes during the very dry year of 2001. One result of those actions was a severe reduction in the water available for agriculture.

THE KLAMATH RIVER BASIN

The Klamath River basin in southern Oregon and northern California covers 40,632 km2 (15,688 mi2) or slightly more than 4 million hectares (10 million acres). In Oregon the basin occupies portions of Jackson, Lake, and Klamath counties; in California, it includes parts of Siskiyou, Modoc,



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1 Introduction The Klamath River basin of northern California and southern Oregon has been the scene of controversies over water allocations in recent years. The basin has been extensively modified by levees, dikes, dams, diversion of tributary waters, and the draining of natural water bodies since the Klam- ath Project was begun in 1905 to improve the region’s ability to support agriculture; other changes have occurred as well (NRC 2004a). The changes made to the system have been accompanied by changes in the biota of the basin as well. This report particularly focuses changes in the distribution and abundance of several species of fishes of concern in the Klamath River, Upper Klamath Lake, and their tributaries. Those fishes were the subject of earlier reviews by the National Research Council (NRC 2002, 2004a), the first of which focused on specific documents related to water management in the basin and its effect on the fishes and the second of which focused on broad aspects of the basin’s management and options for arresting and perhaps reversing the declines of the basin’s fishes. The evalu- ations were prompted by conflicts that arose following actions taken to pro- tect the basin’s fishes during the very dry year of 2001. One result of those actions was a severe reduction in the water available for agriculture. THE KLAMATH RIVER bASIN The Klamath River basin in southern Oregon and northern California covers 40,632 km2 (15,688 mi2) or slightly more than 4 million hectares (10 million acres). In Oregon the basin occupies portions of Jackson, Lake, and Klamath counties; in California, it includes parts of Siskiyou, Modoc, 16

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1 INTRODUCTION Trinity, Humboldt, and Del Norte counties (NRCS 2006) (Figure 1-1). Annual precipitation in the upper basin, that is, above Iron Gate Dam, averages from 68 to 69 cm (about 27 in.) (Risley and Laenen 1999) but is only about 30.5 cm (12 in.) at Klamath Falls (from Weather Underground 2007). In the lower basin, annual precipitation can exceed 255 cm (100 Crater Lake OREGON Chiloquin Upper Gerber Medford Klamath Reservoir Klamath Lake Falls Keno Tule Iron Lower Lake Gate Klamath Lake Dam Clear Lake Dwinnell Dam Lake Etna Shastina Orleans Trinity Lake CALIFORNIA Weaverville FIGURE 1-1 Map of the upper Klamath River basin showing surface waters and landmarks mentioned in this report. 1-1.eps SOURCES: Reproduced from NRC 2004a, modified from U.S. Fish and Wildlife Service.

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18 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN in.). Above about 1,600 m (5,000 feet), large snowpacks accumulate in wet years, and runoff is high. Land elevations exceed 2,000 m to the west, east, and south of Upper Klamath Lake. The Klamath River and its tributaries flow through mountainous regions from Iron Gate Dam (Figures 1-2 and 1-3) downstream almost to the coast. Most of the activities of the Klamath Project occurred in the relatively flat region around Upper Klamath Lake, mainly to the south and east. Much of the region’s agriculture occurs in this area, and most of it is below 1,600 m in elevation and depends on irrigation. The upper Klamath River basin, which includes Upper Klamath Lake is home to 18 species of native fishes, two of which, the shortnose sucker (Chasmistes brevirostris) and the Lost River sucker (Deltistes luxatus), inhabit the lake and are listed as endangered under the U.S. Endangered Species Act (ESA); one widespread species, the bull trout (Salvelinus con- fluentus), is listed as threatened. The upper basin also is home to 18 species of nonnative fishes, some of which are strains or subspecies of the native species (NRC 2004a). FIGURE 1-2 Iron Gate Dam on the Klamath River is the dividing point between 1-2.eps the upper and lower Klamath River basins. The penstock for the power generators is on the right, and the spillway is on the left in this view looking upstream. SOURCE: Photograph by W.L. Graf, University of South Carolina, July 2006.

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1 INTRODUCTION FIGURE 1-3 A short reach of the lower Klamath River near Gottsville, California, 1-3.eps shows the complexity of the channel and the variety of aquatic habitats in the stream. A shallow bar in the foreground separates a swift-water riffle from a quiet backwater pool on the left. SOURCE: Photograph by W.L. Graf, University of South Carolina, July 2006. The lower Klamath River and its tributaries support 20 native fish species, one of which, the coho salmon (Oncorhynchus kisutch), is listed as threatened in the basin (and elsewhere in Oregon and California, but not throughout its range). Other anadromous salmonids of interest include Chinook salmon (O. tshawytscha) and steelhead, the anadromous form of rainbow trout (O. mykiss). All three of the anadromous salmonid species were much more abundant previously than they are today, as described in Chapter 2. Sixteen nonnative species have been reported from the lower Klamath River. The management and uses of the natural resources of the basin, includ- ing water and the fishes, are complex. Many federal, state, county, and other agencies and organizations are involved, and the basin’s resources are managed to achieve a variety of divergent purposes. More information on the region, its biota, human history and hu- man activities there, and management issues are in an earlier NRC report (2004a) and in Chapter 2 of this report.

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20 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN RECENT HISTORY We begin our discussion of the recent history of the region, including the events leading to the NRC’s involvement, with the very dry year of 2001. The description of the period up to 2002 is adapted from the NRC (2004a) report. The ESA, which pertains in this region to the two endan- gered suckers of the upper basin and the threatened coho salmon of the lower basin, requires that the U.S. Bureau of Reclamation (USBR) assess the effects of the Klamath Project operations on those species and consult with the U.S. Fish and Wildlife Service (USFWS) about the assessments on suckers and with the National Marine Fisheries Service (NMFS) on coho (USBR 2001a,b). These biological assessments and the USBR’s revised as- sessments in 2002 proposed operations that the USBR judged would offset some of the project’s adverse effects on the species (USBR 2002). The USFWS (2001, 2002) endorsed some of the USBR proposals, but concluded that more water was needed to maintain Upper Klamath Lake at levels that would protect the suckers. The NMFS also agreed with some of the URBS proposals, but concluded that more water was needed to maintain higher minimum flows in the Klamath River below Iron Gate Dam than proposed by the USBR (NMFS 2001, 2002). The “biological opinions” of the USFWS and the NMFS indicated that some of the USBR’s proposals would jeopar- dize the continued existence of the listed species, and therefore the USBR was required to allot more water to the lake and to the river than had been planned, leaving less than had previously been allocated for agriculture. Those restrictive allocations, coupled with a very dry year, resulted in hardships for many of the basin’s water users, and the controversy sur- rounding the allocations became intense. As a result of the controversy, the U.S. Department of the Interior asked the NRC to review the scientific bases of the USBR biological assessments and the USFWS and NMFS biological opinions. In response, the NRC established the Committee on Endangered and Threatened Fishes in the Klamath River Basin, which issued an interim report focused on the biological assessments and biological opinions (NRC 2002), and a final report that took a broader look at strategies for recovery of the endangered and threatened fishes of the basin (NRC 2004a). The interim report concluded that most of the recommendations of the bio- logical opinions had scientific support but that available scientific data did not support the higher minimum lake levels or the higher minimum river flows recommended in the biological opinions to benefit the species listed under the ESA. The later report confirmed those conclusions and included many recommendations for actions to benefit the listed fish species and to improve scientific understanding of the basin. In addition, a group known as the OSU-UC Davis group (Braunworth et al. 2002) and an independent group of scientists, mainly from the Pacific

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21 INTRODUCTION Northwest (IMST 2003), also reviewed biological opinions, management, and science in the Klamath basin. The IMST report has a useful chart com- paring its conclusions with those of the biological opinions, Braunworth et al. (2002), and the NRC interim report (2002). Since the publication of the NRC reports in 2002 and 2004, two new documents became available: an estimate of natural or unimpaired flows in the basin as they were before the project was begun (Natural Flow Study or NFS; USBR 2005), and a model of the relationship between flows in the Klamath River and the habitat there for anadromous fishes, especially sal- monids and including the threatened coho salmon (Oncorhynchus kisutch) (the study often is referred to as Hardy Phase II; here referred to as Instream Flow Study Phase II or IFS) (Hardy et al. 2006a). A more detailed history of these two documents and related ones is in Figure 1-4. Because the new documents have the potential to change scientific conclusions and manage- ment options based on earlier information, the Department of the Interior asked the NRC to evaluate them and their implications for the biota of the basin. In response, the NRC established the Committee on Hydrology, Ecol- ogy, and Fishes of the Klamath River Basin, which prepared this report. In addition to the history summarized above, several other develop- ments have occurred in the Klamath basin since the NRC report published in 2004. These developments include the full implementation of the Trinity River restoration program (Schleusner 2006). Scientific advances have oc- curred since the NRC (2004) report, largely stimulated by the mass mortal- ity of fish in the lower Klamath River of September 2002, when more than 33,0001 mostly adult fish died in the lower Klamath river, about 95% of which were Chinook salmon, the remainder being mostly steelhead; less than 1% of the deaths were coho salmon. The precise cause or causes of the event cannot be determined (NRC 2004a, CDFG 2004), although the proximate cause was infection with two ubiquitous pathogens, the proto- zoan Ichthyopthirius multifilis and the bacterium Flavobacter columnare. The flow and water volume in the river were atypically but not unprec- edentedly low, and the water temperatures were high but not exceptionally so. The salmon run was somewhat larger and earlier than average. The CDFG (2004) hypothesized that recent changes in the river channel made upstream migration more difficult during low flows, and thus the fish were concentrated in poor conditions, leading to critically high infections of the pathogens. As the NRC (2004a) recommended, these factors need further investigation. The advances, described in CDFG (2004) and Hardy et al. (2006a), 1 The California Department of Fish and Game, which made this estimate, described it as “conservative.”

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22 FIGURE 1-4 Chart of recent history of events in the Klamath basin related to threatened and endangered fishes. 1-4.eps SOURCE: Data from published rules are light, type Hardy, USU, and J. Hicks, USBR fixed image—gray information and from T. at broadside view is about 5.5 pts (but extended)

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23 INTRODUCTION include an improved understanding of diseases of Klamath River salmon and the factors that cause the diseases to become problematic, new informa- tion on thermal refugia and temperatures in the main stem of the Klamath River and its tributaries, and new observations of coho salmon using the main stem as habitat. THE pRESENT STuDY Statement of Task A multidisciplinary committee will be established to evaluate new sci- entific information that has become available since the National Research Council issued its 2004 report Endangered and Threatened Fishes in the Klamath River Basin. The new information to be evaluated by the commit- tee will include two new reports on (1) the hydrology of the Klamath basin and (2) habitat needs for anadromous fish in the Klamath River, includ- ing coho salmon. The committee will also identify additional information needed to better understand the basin ecosystem. To complete its charge, the committee will 1. Review and evaluate the methods and approach used in the Natu- ral Flow Study to create a representative estimate of historical flows and the Hardy Phase II studies, to predict flow needs for coho and other anad- romous fishes. 2. Review and evaluate the implications of those studies’ conclusions within the historical and current hydrology of the upper basin; for the biol- ogy of the listed species; and separately for other anadromous fishes. 3. Identify gaps in the knowledge and in the available scientific information. The Committee’s Process To execute its charge, the committee met four times: in Sacramento, CA. February 13-14, 2006; in Yreka, CA. October 2-4, 2006; in Klamath Falls, OR. January 29-31, 2007; and in Irvine, CA. April 11-13, 2007. At the first three meetings, the committee heard presentations from scientists and others, including agency officials, familiar with various aspects of the region and the operation of the Klamath Project; the committee also received presentations from the public (see list of presenters in Appendix B). At its second meeting, the committee visited a restoration and research project on the upper Shasta River, the Iron Gate Dam and hatchery on the Klamath River, and the monitoring station near the mouth of the Shasta River. Individual members of the committee and staff also visited

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24 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN other parts of the basin, including Upper Klamath Lake; the Williamson, Sprague, and Wood rivers; the Link River and Link River Dam; and Keno Dam. Groups of committee and staff members visited Dr. Thomas Hardy in Logan, Utah, on October 1, 2006 and the USBR office in Denver, Colo- rado, on November 20, 2006, to discuss the respective reports with their authors in detail. Relationship of This Report to Previous NRC Reports This is the third NRC report on the Klamath River basin and its fishes. The first (NRC 2002) focused narrowly on the scientific bases for the biological opinions of the USFWS and the NMFS and the biological assessments of the USBR. The second (NRC 2004a) took a broad look at the Klamath basin and considered options for reversing the declines of the listed species of fishes. The present report was requested after two significant documents were made public (USBR 2005, Hardy et al. 2006a), and it addresses the documents in some detail. However, this report also addresses the implications of the two reports for the anadromous fishes in the Klamath River and the broader context in which science is conducted in the basin. New developments have occurred since the previous reports were published, and this report is not a revisiting of the issues covered by the earlier NRC reports. Indeed, this committee endorses the recommenda- tions of the earlier reports for reversing the declines of the listed species, and this report should be considered as building on the previous ones and continuing where they left off. REpORT ORGANIzATION Chapter 2 provides a description of the Klamath basin, along with descriptions of its hydrology and biota. There is a description of the life histories of three anadromous species of greatest interest: coho salmon, Chi- nook salmon, and steelhead. Chapter 3 provides an analysis of the use and development of models, as well as their capabilities and shortcomings. The considerable detail of this chapter is important because models are central to the two documents this committee reviewed; therefore, the appropriate context is required for evaluating them. Chapters 4 and 5 provide descrip- tions, analyses, and evaluations of the Natural Flow Study and the Instream Flow Study Phases I and II, respectively. Chapter 6 presents a discussion of systematic approaches to the use of science in decision making and their relevance to the scientific activities that have been and are being conducted in the Klamath River basin. Chapter 7 presents the committee’s conclusions and recommendations.