2
The Klamath Basin

The Klamath basin has long been celebrated for its lakes, streams, forests, hunting, fishing, and agriculture. In particular, the Klamath River was once the third-largest salmon-producing stream on the West Coast behind the Sacramento and Columbia Rivers (EPA 2006). This chapter provides a brief summary of the social, economic, and biological resources of the basin. Further detail can be found in the NRC (2004a) report on the Klamath River. To set the following chapters in their physical and biological contexts, this chapter provides a broad regional introduction to the Klamath River basin by describing its physical geography, geology, and hydrology. The chapter continues with a description of the fish communities of the basin and a brief review of the human institutions that manage these physical and biological resources. Finally, the chapter summarizes the changes in physical and biological systems brought about by their human management.

DESCRIPTION OF THE BASIN

Physical Characteristics and Land Use

The Klamath basin is located in south-central Oregon and northwestern California (Figure 1-1). The basin drains approximately 16,000 mi2 with 35% of the watershed in Oregon and 65% in California. The uppermost reaches of the watershed originate in Oregon, and the main-stem river flows through the basin for about 250 miles and enters the Pacific Ocean about 20 miles south of Crescent City, CA, in Del Norte County. In Oregon, the



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2 The Klamath Basin The Klamath basin has long been celebrated for its lakes, streams, forests, hunting, fishing, and agriculture. In particular, the Klamath River was once the third-largest salmon-producing stream on the West Coast behind the Sacramento and Columbia Rivers (EPA 2006). This chapter provides a brief summary of the social, economic, and biological resources of the basin. Further detail can be found in the NRC (2004a) report on the Klamath River. To set the following chapters in their physical and biological contexts, this chapter provides a broad regional introduction to the Klamath River basin by describing its physical geography, geology, and hydrology. The chapter continues with a description of the fish communi- ties of the basin and a brief review of the human institutions that manage these physical and biological resources. Finally, the chapter summarizes the changes in physical and biological systems brought about by their human management. DESCRIpTION OF THE bASIN Physical Characteristics and Land Use The Klamath basin is located in south-central Oregon and northwestern California (Figure 1-1). The basin drains approximately 16,000 mi2 with 35% of the watershed in Oregon and 65% in California. The uppermost reaches of the watershed originate in Oregon, and the main-stem river flows through the basin for about 250 miles and enters the Pacific Ocean about 20 miles south of Crescent City, CA, in Del Norte County. In Oregon, the 2

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26 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN basin occupies portions of Jackson, Lake, and Klamath counties; in Califor- nia, it flows through the counties of Siskiyou, Modoc, Trinity, Humboldt, and Del Norte (NRCS 2006). For discussion and management, the Klamath basin is divided into the upper and lower Klamath basins. The generally accepted boundary between the two is Iron Gate Dam on the Klamath River. All lands upstream (that is, east and west) of the dam are within the upper Klamath basin (area: 8,060 mi2); and those below (that is, south and west of) the dam comprise the lower Klamath basin (area: 7,628 mi2). The lands within the upper basin fall within the U.S. Bureau of Reclamation (USBR) Klamath Project. A number of sub-basins are present throughout the watershed (Table 2-1). A large portion of the upper basin is in agriculture and rangeland use, whereas in the lower basin, forest land dominates the landscape with the exception of the Scott and Shasta basins which have large portions of area in agriculture and rangeland (Figure 2-1). The largest towns in the basin are Klamath Falls, Oregon, which has a total metropolitan population of about 42,000 (City of Klamath Falls 2007); Yreka, CA (7,300), (Yreka Chamber of Commerce 2007); and Weaverville, California (3,550) (City-Data.com 2007). The basin is home to six federally recognized American Indian tribes: Yurok, Hoopa Valley, Karuk, Quartz Valley, Resighini (all in California) and the Klamath in Oregon. TABLE 2-1 Klamath Basin Sub-basins Shown in Figure 2-1 USGS Identification Name Area in acres Upper Klamath Basin 18010201 Williamson River 934,490 18010202 Sprague River 1,029,824 18010203 Upper Klamath Lake 464,903 18010204 Lost River 1,926,303 18010205 Butte Creek 386,034 18010206E Upper Klamath, East Section 416,786 Upper Klamath Basin Total (acres; sq mi) 5,158,340; 8,060 Lower Klamath Basin 18010206W Upper Klamath, West Section 489,887 18010207 Shasta River 508,841 18010208 Scott River 520,612 18010209 Lower Klamath River 984,709 18010210 Salmon River 480,178 18010211 Trinity River 1,303,253 18010212 South Fork Trinity River 594,895 Lower Klamath Basin Total (acres; sq mi) 4,882,015; 7,628 SOURCE: Modified from NRCS 2006.

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2 THE KLAMATH BASIN FIGURE 2-1 Land use throughout the Klamath basin divided into sub-basins. SOURCE: NRCS, National Hydrography data set, December 4, 2002. The upper and lower basin economies are similar in size and output; however, the products are very different. The economy of the upper Klam- ath basin, which is home to approximately 120,000 people, is heavily de-

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28 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN pendent upon agriculture, the forest-products industry, tourism, and public employment. In 1998, the area had 60,000 jobs, produced about $4 billion in output, and added about $2.3 billion in value to purchased inputs (NRC 2004a). The lower Klamath basin, which is home to about 167,000 people, in 1998 produced $5.9 billion of output, added more than $3.3 billion in value to purchased inputs and had more than 84,000 jobs. The greatest numbers of jobs were represented by the retail trade, educational services, and health care and social assistance industries (NRC 2004a). The prominent water feature of the Klamath basin is Upper Klamath Lake, the largest lake in Oregon (Oregon Lakes Association 2005). Up- per Klamath Lake varies in width from about 6 to 14 miles and is about 25 miles long (USBR 2005). Upper Klamath Lake’s perimeter is about 88 miles, its surface area is about 61,520 acres (96 mi2), the mean surface elevation is about 4,140 feet above mean sea level, the mean depth about 13 feet, and the maximum depth about 49 feet (Oregon Lakes Association 2005). The USBR maintains the lake’s surface elevation at 4,136 to 4,146 feet above mean sea level by virtue of a dam constructed in 1917 (Oregon Lakes Association 2005). The USBR estimates the lake’s total capacity to be about 650,000 acre-ft with an operational capacity of about 486,800 acre- ft; its net mean annual inflow is 1,200,000 acre-ft, ranging from 576,000 to 2,400,000 acre-ft (USBR 2005). As an important component of water- resource utilization in the region, Klamath Lake provides water for irriga- tion and power generation. Other lakes in the upper Klamath basin include Lower Klamath Lake (4,700 acres; 7.3 mi2); Tule Lake (9,450-13,000 acres; 14.8-20.3 mi2); Clear Lake (highly variable area; average of 21,000 acres; 32.8 mi2); and Gerber Reservoir (highly variable area) (Figure 2-1). The upper basin has several tributaries. The Williamson and Wood rivers provide the major flow contribution to Upper Klamath Lake. The Sprague River is a tributary to the Williamson River, and Chiloquin Dam, which is slated for removal, is located just upstream of the confluence with the Williamson River. The Sycan River is a major tributary of the Sprague River. Link River flows from Klamath Lake into Lake Ewauna, from which the Klamath River emanates. There are six main-stem dams in the upper Klamath basin, listed in order downstream from Upper Klamath Lake: Link River, Keno, J.C. Boyle, Copco No. 1, Copco No. 2, and Iron Gate. Link River Dam is for ir- rigation purposes and for controlling lake levels in Upper Klamath Lake (Figure 2-2a-d). All other dams except for Keno generate power. Reaches of the Klamath River below J.C. Boyle Dam experience substantial daily fluctuations in response to operating rules for dams that generate electrical power to meet peak demand periods, while flows above this structure have flows that change more gradually. Relicensing hearings by the Federal Energy Regulatory Commission

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2 THE KLAMATH BASIN FIGURE 2-2a This reach of the Link River below Upper Klamath Lake, shown here 2-2a.eps in 1919, is the site of Link River Dam. Note the bedrock outcrops forming ledges and rapids in the channel that act as a sill for the level of the lake upstream. SOURCE: Boyle 1976. Reprinted with permission; copyright 1976, Klamath County Museum. FIGURE 2-2b The newly completed Link River Dam spans the channel and diverts 2-2b.eps much of the river’s discharge into the Keno Canal on the right bank in this 1922 image made from the same location as in Figure 2-2a. SOURCE: Boyle 1976. Reprinted with permission; copyright 1976, Klamath County Museum. (FERC) are under way at this writing. The six dams block access of migra- tory fish to their historical upstream spawning habitat, and their removal has been proposed as a potential option for fishery restoration. Current is-

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30 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN FIGURE 2-2c The Link River Dam,2-2c.eps the same location as in Figures 2-2 shown from a and b, diverts water into the Keno Canal and the Ankeny Canal in this view made about 1940. Riparian vegetation has colonized channel areas downstream from the dam. (Boyle indicated that the date of the image is 1924, but given the size of the trees in the image that were completely absent only 2 years previously, as shown in Figure 2-3b, 1924 is highly unlikely.) SOURCE: Boyle 1976. Reprinted with permission; copyright 1976, Klamath County Museum. FIGURE 2-2d The Link River Dam, shown in this 2006 view from the same loca- 2-2d.eps tion as the views in Figures 2-2 a, b, and c, now includes a fish ladder, recently installed near the right abutment (left side of the dam in this image). SOURCE: Photograph by W.L. Graf, University of South Carolina, July 2006.

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31 THE KLAMATH BASIN sues regarding hydropower include the fact that the Klamath dams produce less than 1% of the energy demanded by Pacificorp’s customers and that low electric rates for the Klamath Reclamation area have resulted in little incentive to conserve water by reducing pumping of irrigation water. The Klamath-Trinity river system is the largest between the Sacramento and Columbia rivers in terms of flow, salmon production, and economic importance, and one of the most highly modified. In the lower basin, there are four major tributaries: the Shasta River, Scott River, Salmon River, and the Trinity River. Many smaller tributaries enter the Klamath River between Iron Gate and Orleans. The Trinity River watershed, draining 2,966 mi2, is the largest tributary watershed to the Klamath River and comprises about 19% of the total basin area. With an average annual precipitation of about 57 in., the watershed produces more runoff and sediment than any other Klamath River tributary. The narrow alluvial corridors on the main-stem Trinity River and its largest tributary, the South Fork of the Trinity River, allow for a meandering stream with coarse-grained channels that provide excellent spawning and rearing grounds for coho salmon and other anad- romous fishes. The size of the watershed and its high-quality spawning and rearing grounds made the Trinity River extremely productive for anadromous fishes (USFWS/HVT 1999). The smaller Salmon River watershed encompasses about 750 mi2. Its lack of large alluvial valleys means that the land-use practices that can severely affect anadromous fishes are limited, thereby enhancing its fishery characteristics as opposed to the Scott and Shasta watersheds (NRC 2004a). Water runoff from precipitation events is buffered by the landscape in the upper watershed, and thus runoff production in the entire basin is heavily weighted toward the lower basin watersheds. Despite the fact that it comprises more than 50% of the entire basin, the upper Klamath basin produces only about 12% of the average annual runoff, which is approxi- mately 13 million acre-ft at the mouth of the Klamath River (NRC 2004a). The upper Klamath basin produces less runoff as a result of the generally low relief, presence of marshes and wetlands (which increase hydraulic residence times), and its location in the rain shadow of the Cascades (NRC 2004a). In contrast, the lower Klamath basin watersheds, near the coast, have portions with as much as 100 in. of annual precipitation. In addition, elevations above 5,000 feet often have winter and spring snowpacks in wet years, which produce much runoff during warm winter storms (NRC 2004a). The physiography of the Klamath basin is quite different from most watersheds in that the greatest relief and topographic complexity occur in the lower basin (Mount 1995). The Klamath basin occurs at or near the convergence of several tectonic plates: the Pacific, Juan de Fuca, and North

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32 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN American plates (see Figure 2-1 from NRC 2004a), the subducting Juan de Fuca plate off the northern California and Oregon coasts (and farther north, the Gorda plate), moving beneath the North American plate, has given rise to the Cascade Mountains, a volcanic arc. Two of the more prominent Cascade volcanoes, Shasta and Mazama (in whose caldera Crater Lake now sits), are in this volcanic arc. Most of the upper Klamath basin lies within the so-called back-arc area, whereas the lower Klamath basin lies within the dynamic fore-arc area. The volcanic arc essentially separates these two basins. The rapid tectonic uplift of portions of the lower Klamath basin is evidenced by the steep, rugged watersheds of the Salmon and Trinity rivers. The other major lower Klamath watersheds, the Scott and the Shasta, have broad, alluvial valleys in the central portions that support agriculture. Fish Communities in the Klamath River Basin Lower Basin Fishes. The Klamath basin below Iron Gate Dam supports a fish community mainly comprising anadromous fishes that spend a portion of their lives in fresh water and a portion in the ocean. There are 19 spe- cies of native fishes in the Klamath basin below Iron Gate (Table 2-2). Of the 19 species, 13 are anadromous and 2 are amphidromous (larval stages in saltwater). In addition to these 19 species, another 17 nonnative species are present in the lower basin, of which only two (American shad [Alosa sapidissima] and occasionally brown trout [Salmo trutta]) are anadromous. The nonnative species are mainly warm- and cool-water species that thrive in slow-current or reservoir environments (NRC 2004a). Anadromous Species. Species with a life history of anadromy reproduce or spawn in freshwater rivers or lakes; the young then migrate out to sea, or “smolt,” to grow to maturity and return to their natal streams. The strategy of anadromy is thought to have evolved as an approach to take advantage of the relatively protected environments found in rivers while exploiting the productive abundance of the ocean to grow to large sizes (Gross 1987). The process of smoltification in the emigrating juvenile fish is physiologi- cally complex; it prepares the young fish for life in saltwater conditions (McCormick and Saunders 1987). The process results in both internal and external physical changes as well as in behavioral changes. The young fish become more slender and elongated, their internal organs prepare for life in saltwater, and the fish school and move downstream together. This process is cued and supported by photoperiod and river temperatures and flows. A narrow window of water temperature, which is species specific, supports the smoltification process in early spring. Increases in stream temperature above the smolting thresholds will result in juvenile fish delaying emigra-

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33 THE KLAMATH BASIN TABLE 2-2 Native Fishes of the Lower Klamath River and Its Tributaries and Their Status Name Status Comments Anadromous Species Chinook salmon, Much reduced in numbers Oncorhynchus tshawytscha Southern Oregon-Northern 1. Much reduced California ESUa in numbers; Upper Klamath and Trinity focus of hatchery Rivers ESU supplementation 1. Fall run 2. Possibly extinct 2. Late fall run 3. Endangered but not 3. Spring run recognized as an ESU; distinct life history Chum salmon, O. keta Rare; state special Southernmost run of species; TTSb concern Coastal cutthroat trout, State, special concern Found only in lower main stem and tributaries; O. clarki clarki resident populations above barriers; TTS Coho salmon, O. kisutch; Federally threatened Being considered for state Southern Oregon–Northern listing; TTS California ESU Eulachon, Thaleichthys State, special concern TTS; huge runs were once present in lower 5-7 miles pacificus of Klamath River Green sturgeon, Acipenser State, special concern; TTS; important fishery; posed for listing infrequently observed as far medirostris upstream as Iron Gate Dam Longfin smelt, Spirinchus State, special concern Small population mainly in the estuary thaleichthys Pacific lamprey, Lampetra Declining TTS; probably multiple runs tridentate Pink salmon, Extirpated TTS; infrequent captures do occur (Hardy et al. 2006) O. gorbuscha River lamprey, L. ayersi Uncommon Little known Steelhead (rainbow trout), Common but declining, TTS; nonmigratory posed for listing populations present above O. mykiss Klamath Mountains Province Most abundant barriers ESU Endangered but not Winter run listed as a separate ESU Summer run continued

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34 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN TABLE 2-2 Continued Name Status Comments Threespine stickleback, Common Near the ocean exhibits anadromy; farther Gasterosteus aculeatus upstream present as nonmigratory White sturgeon, Uncommon May not spawn in the river; infrequently observed as far A. transmontanus upstream as Iron Gate Dam Amphidromousc Coastrange sculpin, Common Larvae wash into estuary C. aleuticus Prickly sculpin, Cottus asper Common Larvae wash into estuary Nonmigratory Klamath River lamprey, L. Common Little known simulis Klamath small-scale sucker, Common, widespread Catostomus rimiculus Klamath speckled dace, Common, widespread Rhinichthys osculus Lower Klamath marbled Common Endemic sculpin, C. klamathensis polyporus aEvolutionarily significant unit. bTribal trust species. cAmphidromous species, sometime called euryhaline species, can move back and forth between fresh, brackish, and salt water at various life stages, but they do not normally do so for breeding, as anadromous species do. SOURCE: Adapted from NRC 2004a. tion and possibly remaining in a stream environment unsuitable for their survival. The duration spent in either the ocean or river habitat is specific to each species and strains within species, as is the timing of emigration of juveniles and immigration of adults. The historical hydrologic conditions of the river shaped and defined the instream habitats that supported these various life history strategies. Examples include the development of clean gravels in riffles for invertebrate production and juvenile feeding habitat, as well as the high flow scouring action to maintain deeper pools for adults holding in the river before spawning. Natural variability of climatological

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3 THE KLAMATH BASIN conditions in the basin produced some years that were more favorable for one species than for others. Thus the development of these various life histories within species is an important strategy for ensuring reproductive success through a variety of habitat conditions. Physical instream habitat in many areas throughout the basin has been altered as a result of land-use ac- tivities that increased sedimentation, channelization, decreased streamside riparian vegetation, and physical blockage of fish from upstream habitat areas. Alteration of the flow regime in the basin as a result of hydropower, irrigation, and other off-channel uses has resulted in changes in the annual pattern of stream flow as well as altered the thermal properties of the river and its tributaries. In some areas, the combination of altered flow regime and land-use activities has resulted in water quality conditions that do not support all of the life history phases of the salmonids that use the area. Un- derstanding the complexity of the life history needs of the anadromous fish community, reflection on the current status of the stocks, and an overview of the instream habitat conditions are important for defining and evaluating the management directions and goals for the basin. Of the anadromous species complex, much of the fishery focus is on those species of high commercial and recreational value, such as Chinook salmon, coho salmon, and steelhead. Other anadromous fishes of general interest in the lower Klamath River include tribal trust species, such as the green sturgeon, white sturgeon, Pacific lamprey, eulachon, and some other species, but these fishes have had less economic importance than the three salmonids, and they are not federally listed. Most of them are more com- mon in the lowest part of the river than farther upstream, and they have not been the subject of as many studies or the focus of as many recent contro- versies as the salmonids. For these reasons, they receive less attention than the salmonids in this report. However, the relative scarcity of information on them, noted also by Hardy et al. (2006a), is an impediment to develop- ing management plans for all the anadromous species, rather than for coho, Chinook, and steelhead (see Table 2-3). Before development of the basin, anadromous species ranged widely through the tributaries and upstream of Upper Klamath Lake into the Sprague and Williamson basins and Spencer Creek (Coots 1962; Fortune et al. 1966; Hamilton et al. 2005, as cited in Hardy et al. 2006a). Access to the upper Klamath basin by anadromous species ended with completion of Copco Dam No. 1 in 1918, the reduction in access occurring during earlier construction of the Lost River diversion canal and Chiloquin Dam in 1912-1914 (Hardy et al. 2006a). Upper Basin Fishes. This report focuses more on the lower than the up- per basin fishes, but for completeness, Table 2-4 describes the native and nonnative fishes of the upper Klamath River basin.

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42 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN TABLE 2-6 A Sampling of the Many Government Agencies, Stakeholder Organizations, and Working Groups in the Klamath Basin Basin Groups Klamath Basin Coordinating Group Klamath Basin Compact Commission Klamath River Basin Fisheries Task Force Upper Klamath Basin Working Group Trinity River Restoration Task Force Sub-basin Groups Upper Basin Mid Basin Upper Klamath Watershed Council Mid-Klamath Watershed Council Klamath River Working Group Shasta River Coordinated Resources Sprague River Working Group Management & Planning West Klamath Lake Working Group Scott River Watershed Council Cloverleaf Stewardship Group Salmon River Restoration Council Upper Williamson Catchment Group Lower Williamson Working Group Lower Basin Klamath Project Area Working Group Klamath Fishery Management Council Urban Issues Working Group Trinity River Adaptive Management Work Group Trinity River Fisheries Task Force Trinity Management Council Stakeholder Groups California Trout Klamath Basin Coalition Friends of the Trinity River Klamath Basin Ecosystem Foundation Klamath Basin Crisis Klamath Basin Rangeland Trust Klamath Basin Haygrowers Association Klamath Forest Alliance Klamath Bucket Brigade Klamath Restoration Council Klamath Outdoor Science School Klamath Water Users Association Klamath Salmon Action Network Oregon Trout Nature Conservancy Oregon Wild Oregon Waterwatch RCAA Natural Resources Services Siskyou County Farm Bureau Water for Life Pacific Coast Federation of Fishermen’s Associations Government Agencies Federal State Bureau of Land Management Oregon Bureau of Reclamation Water Resources Department Fish and Wildlife Service Watershed Enhancement Board Forest Service Department of Fish and Wildlife National Marine Fisheries Service Department of Environmental Quality Natural Resources Conservation Service

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43 THE KLAMATH BASIN TABLE 2-6 Continued Government Agencies (continued) Tribal Counties Hoopa Tribe Del Norte Karuk Tribe of California Humboldt Klamath Tribes Klamath Lake Quartz Valley Indian Community Modoc Yurok Tribe of California Siskyou Trinity Intertribal Fish and Water Commission Cities Klamath Basin Tribal Water Quality Workgroup Bonanza Klamath Falls Chiloquin Malin Dorris Merrill Tulelake Weaverville Yreka California Biodiversity Council Department of Fish and Game Department of Water Resources Five Counties Salmonid Conservation Program Ocean Protection Council Water Resources Control Board National Coast Regional Water Quality Control Board SOURCE: Modified from information at www.onebasin.org. and placer mining, using the river to float logs downstream to sawmills and building splash dams to release large volumes of water abruptly to carry logs downstream in a wave, and blasting rock outcrops in the bed of the river to improve log passage. The timber harvest and transport in the upstream, volcanic part of the basin is well documented, including the log drives to the large mill at Klamathon, a now-abandoned site several miles upstream of Hornbrook (Shaw Historical Library 1999, 2002; Beckham and Canaday 2006). Those activities probably had the effect of simplifying channel form through the direct elimination of bedrock and other channel irregularities that interfered with the efficient flow of water and the physical effect of the logs themselves battering the banks. Mining occurred downstream of Hornbrook, along the axis of Cotton- wood Creek, where there is a sharp contact between the volcanic Cascades and the Klamath geologic provinces. The Klamath Province includes a wide range of rock types, including ores of gold and other precious metals. Nu- merous mining claims (that sought to follow mineralized veins) are visible

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44 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN on hillslopes, and accumulation of gold in alluvial deposits led to extensive placer mining along the river in the nineteenth and early twentieth centu- ries. Most of the alluvial bottoms of the river downstream of Hornbrook were reworked by placer mines, often from valley wall to valley wall (Ayres Associates 1999). Such reworking would include displacing the channel and in excavating down to bedrock, piling gravel into linear tailing deposits. It probably resulted in increased exposure of the bedrock area and in hypo- rheic exchange (exchange between shallow groundwater and surface water beneath and adjacent to the streambed). Hardrock mining in the uplands draining to the river would have increased delivery of fine (and some an- gular coarse) sediments to the channel. Dredging of gravels on the flood plain would have simplified the channel through direct modification and, in many cases, displacement to the other side of the valley so that gravels below the current channel could be mined. Dredging and processing of the placer deposits would have released fine sediments into the water column, potentially damaging aquatic habitat. Dams and diversions have had geomorphic effects, although the ef- fects are less striking than they are in rivers where the dams are larger and impound flows with greater sediment loads, and where the downstream channels are fully alluvial. The dams on the main-stem Klamath are located in the upper river, within the volcanic lithologies of the basin and Range Province (which includes the Cascade and Modoc geologic provinces), upstream of the Cottonwood Creek confluence near Hornbrook. This part of the basin has less rainfall, lower sediment yields, and more bedrock- controlled channel (and thus less alluvial channel) than the Klamath Prov- ince downstream. As described elsewhere, six dams are part of the Klamath River hydroelectric project owned by PacifiCorp (the “PacifiCorp Project”): Link River, Keno, J.C. Boyle, Copco 1 and 2, and Iron Gate (Boyle 1976, PacifiCorp 2004) (Figure 2-3). In considering how these dams might affect flow, channel form, sedi- ment, and ultimately habitat on the Klamath River, it may be helpful to review the effects observed generally in the literature. Recent NRC reports also have reviewed the effects of dams on salmon (for example, NRC 1996, 2004b). Much of the concern about dam effects on fish habitat has been about salmonid spawning gravels. Dams can affect spawning gravels in two principal ways. When reservoirs are large enough to reduce floods, fine sediment from tributaries (and from bank erosion and other sources) can accumulate on the bed downstream because it is no longer flushed away by high flows. This fine sediment can infiltrate spawning gravels and reduce incubation success (for sediments finer than about 1 mm) or affect the ability of fry to emerge from the gravel (for sediments of 1 to 10 mm in size) (Kondolf 2000). This effect has been documented in many rivers, including in the Trinity River below Lewiston Dam, a notable example for

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2-3.eps FIGURE 2-3 Conceptual model of thefixed image—typechannel geomorphology in the Klamath River in the reaches affected sediment transport and could be more legible by the PacifiCorp hydroelectric project dams. (made broadside to make type larger) 4 SOURCE: PacifiCorp 2004. Reprinted with permission; copyright 2004, PacifiCorp.

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46 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN the present study because it is one of the best-documented examples of this impact and because it is an important tributary to the Klamath (Milhous 1982). Reservoirs whose capacity is relatively small in relation to river flow typically allow high flows to pass while still trapping gravels supplied from upstream. Downstream of such reservoirs, the bed may progressively coarsen as the smaller gravels are transported downstream without being replaced (as they were before the dam was constructed) by gravels sup- plied from upstream. As a result, the bed may become dominated by larger gravels and cobbles that are unsuitable for use by spawning fish (Kondolf and Matthews 1993). Reservoirs also can cause downstream changes in the distribution of riparian vegetation resulting from changes in hydrology and the availability of sediments. Reduced flood flows can result in less active bed scour, ero- sion, deposition, and channel migration, thereby resulting in smaller areas of fresh sediment surfaces available for colonization by seedlings of woody riparian species, but also in less frequent scour and removal of seedlings from the active channel. Thus, riparian vegetation can invade formerly scoured areas of the channel bed, but over time the riparian community may tend toward older individuals and later successional-stage species with less diversity of species and structure (Johnson 1992). Even if reservoirs do not substantially affect the high flows that erode and deposit sediment, they may affect the shape of the hydrograph during the seasons that riparian seedlings would normally become established, resulting in changes in the extent of riparian vegetation. Moreover, changes in water quality (from upstream land uses or transformations within reservoirs) can affect the growth of riparian vegetation through supply of nutrients for plant growth. Riparian vegetation is important as a resource in its own right, especially as it can provide important habitat to terrestrial and aquatic species. It also can affect geomorphic channel processes by increasing hydraulic roughness, by inducing deposition on bars and along channel margins, and by changing the direction of flow. Changes Caused by Main-Stem Dams The probable effect of the Pacificorp hydroelectric project reservoirs on various reaches of river is summarized in Figure 2-3. To understand the effects of these dams, it helps to recognize that they are small compared with the river’s annual runoff. Upper Klamath Lake is large, but it is mostly natural, and its outflow is controlled not for hydroelectric production but for irrigation by the U.S. Bureau of Reclamation (USBR) in its operation of the Klamath Project. Keno Reservoir is an artificial structure at the site of a natural “reef” or bedrock sill that historically acted as a hydraulic control for Lake Ewauna, and the impoundment above J.C. Boyle Dam is

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4 THE KLAMATH BASIN essentially a forebay. By far the largest reservoirs are Iron Gate and Copco,1 but even they impound only 4% and 5% of annual runoff, respectively. These relatively small impoundment ratios probably would not affect high flows substantially, except in bypassed reaches (reaches in which flows are reduced by diversion through penstocks for hydroelectric generation, such as the J.C. Boyle bypass reach and the Copco No. 2 bypass reach). As a result, the effect of the hydroelectric dams would be more likely to cause bed coarsening than accumulation of fine sediment (PacifiCorp 2004). As discussed further in Chapter 3, there were important changes in how floods were routed between Upper and Lower Klamath lakes a cen- tury ago. Construction of the railroad embankment (and USBR control gates) blocked flood overflow into Lower Klamath Lake, as had occurred formerly. Current USBR irrigation facilities are managed so that in a flood situation Upper Klamath Lake water can be moved to the Lost River sys- tem. Water also can be evacuated from Keno Reservoir to the Klamath Irrigation Project via the Ady canal. Although data are not available, it is reasonable to conclude that elimination of flood overflow into Lower Klamath Lake would have increased the magnitude of flood flows in the Klamath River below Keno over that of conditions prevailing before the late nineteenth century. The increase in the magnitude of floods in the main stem also would tend to produce coarsening of the bed. In bypassed reaches, the net effects of the dams would depend on the degree to which floods of various magnitudes have been reduced and on the base-flow conditions in the reach. For example, the relatively low (10 cfs) base flow maintained in the Copco No. 2 bypass reach, combined with changes to relatively short return-interval flood flows, has resulted in significant riparian vegetation encroachment. However, any such effects in the J.C. Boyle bypass reach, where the base flow is higher (100 to 300 cfs) and flood flow conditions are similar, are much more subtle. Changes Caused by Tributary Dams Dams on tributaries also are important and should be analyzed more comprehensively in the search for solutions to threats to fish populations. Irrigation storage dams on the Shasta River system result in large increases in water temperature and nutrient loads and are being studied by the University of California, Davis. The largest Klamath River tributary is the Trinity River, which has been regulated since the early 1960s by Trinity and Lewiston dams for power production and transfer of water to the Sacramento River system for irrigation, as part of the Central Valley Project. Approximately 51% of the Trinity’s flow on average is transferred to the Sacramento River, 1 This refers to Copco 1; Copco 2 is a run-of-the-river dam without substantial storage.

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48 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN based on five water-year types as described in USFWS/HVT (1999) and cur- rently managed by the Trinity River Management Council. By the 1970s, an abrupt decline in wild anadromous fish populations led to the first studies and restoration efforts. Continued studies and management manipulations have led to increased releases and a hydrograph more similar to a natural hydrograph in attributes important for fish life histories and to other efforts to restore dynamic channel processes, such as addition of gravel in sediment- starved reaches below dams (USFWS/HVT 1999). Changes in Fish Populations Steelhead run size before the 1900s is thought to have been up to sev- eral million fish per year. In 1960, run size was estimated at 400,000 fish, and the numbers continued to decline through the 1970s, 1980s, and 1990s. Returns of hatchery fish to Iron Gate Dam reflect an index of abundance and survival. From 1963 to1990, the average number returning was 1935 fish per year. From 1991 to1995, the average was 166 fish per year and in 1996, only 11 steelhead returned to the hatchery (as summarized in Hardy et al. 2006a). The Klamath Mountain Province steelhead populations do not appear to be self-sustaining and if trends continue, endangerment is pos- sible. Steelhead have not been listed under the Endangered Species Act. Coho salmon annual spawning escapement to the Klamath River sys- tem was estimated to be 15,400 to 20,000 fish in 1983 (Leidy and Leidy 1984). That estimate is less than 6% of their estimated abundance in the 1940s, and a 70% decline has been observed since the 1960s (CDFG 1994, as cited by Weitkamp et al. 1995). Coho salmon returns to Iron Gate Hatchery ranged from 0 in 1964 to 2,893 fish in 1987, and they are highly variable. From 1915 to 1928, total annual harvest and escapement of Chinook salmon in the Klamath River was between 300,000 and 400,000 (Rankel 1982). In 1972, numbers were estimated to be 148,500 (Coots 1973). From 1978 to 1995, the average annual fall escapement, including hatchery fish, was 58,820 with a low of 18,133 (CDFG 1995). Spring Chinook salmon runs appear to be only remnants of the historical numbers. The numbers of Chinook spawning salmon, both wild and hatchery produced, from 1978 through 2006 are shown in Figure 2-4. The Iron Gate Hatchery was established in 1963 at river mile 190 to mitigate the effects of the dams on anadromous species. Production goals for the hatchery include 4,920,000 Chinook salmon smolts, 1,080,000 Chinook salmon yearlings, 75,000 coho salmon yearlings, and 200,000 steelhead yearlings (Richey 2006). The decline in numbers of anadromous fishes in the basin is commonly attributed to a list of anthropogenic factors, such as flow alterations due to

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4 THE KLAMATH BASIN 180000 Number of Wild Spawning Chinook Salmon in the 160000 140000 Trinity and Klamath Basins 120000 100000 80000 60000 40000 20000 0 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002 2004 2006 Year FIGURE 2-4 Spawning Chinook salmon, 1978-2006. 2-4.eps SOURCE: USFWS 2006, unpublished data. irrigation and hydropower; temperature alterations as a result of riparian shading decreases and flow alterations; and land-use practices that alter in- stream habitat and contribute to sedimentation, including logging, mining, and agriculture. Other landscape factors that contribute to reproductive success and survival include fires, climatic changes, floods, droughts, and El Niño (Table 2-7). Other biological factors include reduced genetic integrity from hatchery production, predation, disease, and competition or preda- tion by introduced species. No single factor is known to be responsible for the decline in populations. It probably is the combination of the impacts and the timing of the impacts that can influence the productivity of these anadromous species. Thus, the pathway to reversing the trend of declining numbers is to determine the magnitude of the influences of the various fac- tors and to set priories for restoration efforts accordingly. SuMMARY The Klamath River basin is a complex hydrologic, geomorphic, and biological system with two sharply different sub-regions. The upper Klam- ath basin, the portion of the system upstream from Iron Gate Dam, includes extensive source areas for surface runoff along with irrigated agricultural

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0 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN TABLE 2-7 Overview of the Habitat Factors Considered Important in the Decline in Anadromous Fish Populations and Their Potential Impacts Factor Impact to habitat Impact to fish Dam construction (a) Limits access to upstream (a) Reduction in available habitat (b) Alters habitat spawning and rearing habitat upstream and downstream thus a reduction in potential by the creation of reservoirs juveniles produced upstream and sediment deficit (b) Creation of habitat suitable downstream leading to a for nonnative species upstream channelized or armored zone and a decline in suitable instream habitat downstream through zone of influence Flow alteration Reduced channel-shaping flows; Reduced available habitat for in amount, reduced maintenance flows spawning due to decreased timing, duration, for instream habitat; increased water depths or changes in magnitude, and river temperatures; altered substrate conditions; stranding frequency (both annual seasonal pattern; of juvenile fishes when flow tributary and main reduced base flows; can changes are rapid; dewatering stem; resulting observe cumulative impacts of redds from water and to basin when multiple land management) tributaries are affected Timber harvest Increased delivery of sediment Effects on spawning and changes without proper to the channel, especially in channel habitat consideration tributaries for riparian or watershed dynamics Placer, gravel, suction Removes gravel from channel, Reductions in spawning gravel mining resulting in changed and homogenization of habitat geomorphology and instream types, leading to a reduction in habitat carrying capacity for juvenile fishes and/or a decline in invertebrate production Fires Increased sediment delivered to Effects on spawning and changes streams in channel habitat Predation by No habitat impacts Excessive predation may result in nonnative species higher mortality rates than are and mammals sustainable by the population Land use practices Changes in riparian zone Increased algal blooms can such as agriculture reduce shading especially result in dissolved-oxygen in tributaries resulting in deficits; decreased usable increased temperatures; habitat due to increased increased delivery of sediment; temperatures; sedimentation increased delivery of nutrients decreases spawning habitat, or chemicals to stream macroinvertebrate production, channels and changes in juvenile habitat

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1 THE KLAMATH BASIN TABLE 2-7 Continued Factor Impact to habitat Impact to fish Commercial No impact to habitat Repeated reduction in spawning exploitation stock below levels needed for sustained support of the population results in reduction in production of juveniles Climate change By changing flow volumes and Reduction in habitat availability water temperatures, climate and amount would reduce fish change would affect the productivity; increases in late- availability, amount, and summer temperatures could quality of riverine habitat increase the frequency and available magnitude of mortality events areas, partly served by the Klamath Project of the USBR. Rivers are alluvial streams flowing across valley floors blanketed with alluvium that includes fine materials as well as gravels. A prominent feature of the upper basin is Upper Klamath Lake, a natural temporary holding area for runoff before it exits downstream through the Link River. The Link River Dam serves as a partial valve on the lake. The lower Klamath River passes through a moun- tainous area that has little agriculture but that is graced with steep forested slopes. Unlike the upper basin, the river is confined between bedrock walls and has a relatively steep gradient with a gravel bed. These two physical provinces of the Klamath River basin host differing fish populations. The upper basin includes the lake and its several species of suckers (including the federally endangered shortnose and Lost River suckers), and tributary streams served as spawning areas for steelhead, coho salmon, and Chinook salmon, but dams in the system have cut off these streams from direct ocean access for fishes. The lower Klamath River and its tributaries served as habitat for several species of trout, salmon, and sturgeon among many other species. Dams now limit their access to the system to the area downstream from John C. Boyle Dam except for those fish able to ascend the fish ladder on the dam. A variety of human factors, including changes to the basin hydrology, construction of dams, introduction of contaminants, logging of riparian forests, and fishing have contributed to the decline in the populations of many native fishes. Natural environmental changes, including those related to drought and flood frequencies and water temperature, are likely also to have affected populations of fishes. Where once the runs of anadromous species numbered in the millions of fish, present observations reveal less than 10% of historical numbers. Coho salmon are federally listed as a threatened species.

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2 HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER BASIN In an effort to understand these conditions and to improve them for the enhancement of fish populations, the USBR commissioned two models that were to provide insight to flows in the Klamath River and their effects on fish habitat: a reconstruction of what “natural” flows might have been like without dams in place (the Natural Flow Study), and a model to predict the distribution of fish habitats (the Instream Flow Study). These models oper- ate within the general physical matrix described in this chapter, and they deal with the fish populations defined here. The remainder of this report explores the products of these research models.