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5312. [Image] Annual survey of abundance and distribution of age 0 shortnose and Lost River suckers in Upper Klamath Lake
One chapter of a seven chapter annual report from 1999 examining ecological issues regarding the shortnose and Lost River sucker populations in Upper Klamath Lake and Williamson River.Citation Citation
- Title:
- Annual survey of abundance and distribution of age 0 shortnose and Lost River suckers in Upper Klamath Lake
- Author:
- Oregon Cooperative Wildlife Research Unit
- Year:
- 2000, 2005
One chapter of a seven chapter annual report from 1999 examining ecological issues regarding the shortnose and Lost River sucker populations in Upper Klamath Lake and Williamson River.
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5315. [Image] The Water Report - The role of science in the ESA
Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. See the full report at http://www.thewaterreport.com/Citation -
Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. Includes bibliographical references. See the full report at http://www.thewaterreport.com/
Citation Citation
- Title:
- The Water Report - Critical habitat, bull trout and politics
- Author:
- Envirotech Publications
- Year:
- 2005, 2008, 2006
Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. Includes bibliographical references. See the full report at http://www.thewaterreport.com/
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5317. [Image] Upper Klamath Basin bull trout conservation strategy : part 1, a conceptual framework for recovery, final
EXECUTIVE SUMMARY This document presents the framework of a plan to reverse the decline of bull trout (Salvelinus confluentus) populations in the Klamath Basin. If successful, we expect bull trout ...Citation Citation
- Title:
- Upper Klamath Basin bull trout conservation strategy : part 1, a conceptual framework for recovery, final
- Author:
- Light, Jeffrey
- Year:
- 1996, 2008, 2005
EXECUTIVE SUMMARY This document presents the framework of a plan to reverse the decline of bull trout (Salvelinus confluentus) populations in the Klamath Basin. If successful, we expect bull trout to recover to a level where they will have a reasonable chance of long-term viability. The work is the collective effort of fish biologists, foresters, other natural resource management professionals, and local landowners representing a diverse array of interests and organizations. Together, these individuals have worked for several years to gather information pertaining to the distribution and status of Klamath bull trout populations and threats to their persistence. The members of the Bull Trout Working Group share the common desire to restore bull trout populations while at the same time sustaining their respective land use interests in the Klamath Basin. This approach provides incentives to all the interested parties to seek agreement on solutions, encouraging cooperative work on an otherwise ambitious and daunting task. The following few pages summarize the plan. Each area is covered again in greater detail in the body of the document. The goals established by the Bull Trout Working Group for this recovery plan are to (1) Secure existing bull trout populations, and (2) Expand the populations to some of their former range and numbers. We pursue these goals with a three step approach of assessment, implementation, and evaluation. We begin with a review of the distribution and status of bull trout generally, then specifically within the Klamath Basin. Next we present available data and interpretations supporting our conclusions regarding the type, magnitude, and extent of physical and biological factors or concerns that may hamper bull trout persistence. Land and fish management activities that contribute to these problem situations are then identified. This is followed by a blueprint for stepwise development and implementation of practical solutions. Finally, a monitoring plan is proposed to measure the success of the recovery efforts. The Klamath Basin Bull trout populations represent a valuable biological resource. These populations exist at the southern edge of the species' distribution, and have distinctive genetic character. In the Upper Klamath River Basin, bull trout are presently found as resident forms in eight isolated headwater streams within six small drainages. (4Headwater streams' in this document refers to very small streams, rather than rivers which are the headwaters for larger rivers). These streams occur in three general locations: they are tributaries of the Sprague River, of the Sycan River and of Upper Klamath Lake. Together, the known populations occupy approximately 23 miles (37 km) of perennial streams. Formerly, bull trout may have occurred in the mainstems of these systems (Gilbert 1897. Dambacher et al. 1992, Roger Smith, ODFW, pers. coram. 1994). In addition to existing populations, other populations are known to have recently occupied nearby streams (Cherry and Coyote creeks, the Upper Sycan River). Estimated current population sizes in each drainage range between 133 and 1,293, indicating that populations are low enough to warrant concern. These population sizes are smaller than the minimum viable population sizes predicted by conservation biology theory. A substantial risk of extirpation via natural disturbance cycles and stochastic events exists for such small populations. Streams that are presently inhabited by bull trout are typically small and spring-fed with steep gradients. They originate in the higher elevations of mountains within the Upper Klamath Basin and flow through forests where land uses range from wilderness and national parkland to commercial forestry and grazing. Eventually, these tributaries or their mainstem receiving waters leave the forest and flow through broad sagebrush-covered valleys or marshes where they widen and flatten. Here livestock grazing and agriculture are the dominant land uses. An assessment of the current situation regarding Klamath Basin bull trout was performed using existing and new information on life history, distribution, habitat requirements by lifestage, environmental requirements, exotic species interactions, angling pressure, land use interactions, habitat fragmentation, population fragmentation and many other factors. Basin-specific information on each of these factors was collected and analyzed, complemented by a thorough review of the literature. Past, present and possible future distributions of bull trout were examined. Particular emphasis was placed on determining the nature and extent of biotic interactions, because this potential agent of bull trout decline has not been thoroughly addressed in other works. Analysis of the assembled information resulted in the identification of several specific natural and anthropogenic factors which are thought to limit the distribution and persistence of bull trout. Habitat quality and quantity are affected by land use to some degree in all currently inhabited bull trout streams except upper Sun Creek. Generally, habitat conditions vary from fair to good in existing bull trout streams. We identified several land uses that have reduced habitat quality. Principal among the abiotic factors of concern is fine sediment loading from (1) road erosion, (2) stream bank and adjacent ground disturbance by livestock, and (3) Bull Trout Document - Final - - 6 - 26-Jan-96 stream-adjacent hillslope erosion from logging. Second among the abiotic factors of concern is elevated temperature. Other concerns include diminished large woody debris (LWD) recruitment, declining bank integrity, low flows, changes in stream morphology, and blocked or hindered fish passage. The relative importance of each of these factors or concerns differs by watershed, or by location within a watershed. In most cases, information on specific issues and their locations is available with sufficient resolution to allow land managers to develop action plans to address them. Possible exceptions may include Deming Creek, where Watershed Analysis has not yet been performed. Based on the assessment results to date, the following strategy was developed to address limiting factors and concerns. Competitive and genetic interactions with non-native brook trout (Salvelinus fontinalis) and brown trout (Salmo trutta) were found to be important biotic factors currently threatening the persistence of bull trout in the Klamath Basin. This conclusion was based on the almost pervasive presence of these exotic competitors and the significance of their negative interactions as determined from the literature and from local observations in headwater streams. Temperature may be a significant issue, especially for juvenile rearing, although the temperature tolerances of bull trout are not well understood. Habitat fragmentation and alteration appear to have been major issues in the past, resulting in population fragmentation, particularly at lower elevations and in larger streams where bull trout may have ranged historically. These final two factors appear less important than exotic competitors or temperature for bull trout in the current limited ranges in headwater streams, though they are important in mainstems and larger tributaries. They will need to be addressed if large scale restoration is undertaken. With the exceptions of temperature and fine sediment, brook trout have habitat requirements and environmental tolerances similar to bull trout, and they thrive in many Klamath Basin headwater streams while bull trout do not. Brown trout pose a competitive threat similar to that posed by brook trout, but the mechanisms of displacement and the areas where they occur differ. Even in environments unaltered by land management, such as Sun Creek within Crater Lake National Park, exotic trout are displacing bull trout. This conclusion is consistent with findings throughout the west, where competition with exotic species has clearly had a major effect on bull trout range, resulting in widespread declines in bull trout distribution. Changes in habitat may have altered competitive interactions between bull trout and other salmonids, both directly and indirectly. Since changes in environmental factors can exacerbate competition issues in sensitive populations, habitat condition remains a concern. Near-term, mid-term, and long-term strategy for Recovery of Bull Trout Populations Our approach to recovery of the Klamath basin's bull trout populations is a two-phase effort corresponding to near- and mid-term objectives, and an examination of possible long-term recovery objectives. It entails securing and maintaining existing populations followed by expansion into former headwater and downstream habitats, and ultimately the possibility of connecting tributaries with mainstem linkages. Assessment, research and monitoring needs associated with each phase were identified (see main body of text). Specific project details such as funding, work schedules, participant responsibilities, specific actions, implementation methods and costs are not presented but are to be developed collectively by the Bull Trout Working Group. Phase 1: Securing existing populations This phase of the recovery plan focuses on the six small drainages where bull trout populations are known to exist today. Here we wish to prevent further decline of individual populations as a step toward securing the viability of the Klamath Basin metapopulation(s).1 This is accomplished by addressing biotic and abiotic factors that threaten the persistence of these populations. The most immediate threat is the continued presence of non-native salmonids. Localized areas of habitat degradation or alteration from sediment inputs and shade removal are an additional serious concern. It may be feasible to isolate bull trout populations above barriers, followed by eradication of brook and brown trout within each isolated stream reach. This approach will be tested early in Phase 7, with particular attention to unforeseen consequences on the ecology of the test streams. Assuming it is viable, this approach will become the focus of Phases 1 & 2, in parallel with habitat enhancement efforts. Habitat enhancement is generally feasible, particularly in areas where roads or livestock are the issues. Where needed, such habitat enhancement efforts are expected to be completed as part of Phases 1&2. It will be necessary to understand the distribution of genetic variation among existing sub-populations of bull trout in order to embark on a well 1 For an understanding of metapopulation considerations, see the body of the text, in particular the section on 'Metapopulations and sub-populations' on page 60. Bull Trout Document - Final - - 7 - 26-Jan-96 directed range expansion program. Baseline data would be essential for genetic monitoring activities and for the development of stocks for establishing new sub-populations in subsequent phases. If successful, the actions taken in Phase 1 are expected to eliminate the direct threats to existing bull trout sub-populations posed by non-native salmonids. Parallel efforts to improve the in-stream physical environment to ensure habitat is suitable for bull trout are expected to eliminate proximate environmental threats to existing bull trout sub-populations. This effort will require that abiotic limiting factors and concerns be addressed via land management activities, most of which fall within the realm of forest land management. Timber harvest and regeneration, roads (construction, use, and maintenance), and livestock grazing programs are considered. Immediate actions may take the form of road erosion abatement, including road abandonment and revegetation. Some of these actions can be accomplished when a particular unit is harvested, while others may be pursued as independent restoration activities (e.g., livestock management plans, culvert replacements). Presently, no in-stream fish habitat improvement projects have been proposed, and none are foreseen for stream reaches affected by this phase of the recovery plan. Most of the concerns related to livestock are focused within the riparian zone. Some riparian locations are much more sensitive than others, for example the large meadow in Long Creek. Actions to address these concerns will vary by landowner and location, and may range from complete riparian exclosure to short-term grazing to continuous but moderate access. The preferred actions will depend on the success of these various strategies in bringing about the desired response of the channel and fish habitat, and can be expected to change as recovery of riparian areas progresses. Effectiveness monitoring will be invaluable for measuring the success of these efforts, and in adapting our management strategy during the implementation. No water diversion concerns have been identified for this phase of the plan, except for Deming Creek, where screening of irrigation ditches may be warranted. Some additional fish management actions may also be applicable in Phase 7, for example to continue to monitor compliance with existing no kill regulations in bull trout streams. Other pertinent fish management issues have been addressed already, for example the cessation of exotic trout stocking (brook, brown or non-native rainbow) in bull trout streams. Phase 2: Expanding the range of bull trout within headwater streams In Phase 2, bull trout populations are refounded in headwater streams which now support brook trout, e.g. Calahan and Cherry creeks, or possibly in creeks without fish, e.g. Sheep Creek on the North Fork Sprague. This serves to expand the number of sub-populations, increases the number of refugia, and increases the overall size of the Klamath metapopulation(s). This is a major step in the establishment of viable metapopulations; by increasing the number of sub-populations, the effect of the loss or decline of any particular sub-population is reduced, making the metapopulation(s) more resilient to natural disturbance, variations in breeding success, disease outbreaks and other stochastic factors. Phase 2 consists of two parts: Phase 2a, in which sub-populations are founded in streams which only recently lost bull trout (e.g. Cherry Creek, Coyote Creek and the upper Sycan River) and Phase 2b, in which sub-populations are founded in other suitable headwater habitat, as indicated by the presence of thriving brook trout sub-populations (e.g. Sevenmile Creek, Calahan Creek, Annie Creek, Camp Creek, Jackson Creek, Deep Creek and Corral Creek). Both parts of Phase 2 are accomplished in much the same way as Phase 7: Barriers are constructed to exclude brook trout and brown trout, then the exotic species are eradicated above the barriers. Bull trout populations are then founded with human-introduced bull trout, whether via transplantation from wild sources or from a hatchery. Care must be exercised to maintain adequate genetic diversity in the founded sub-populations as establishment of genetically healthy populations is a non-trivial task. An inherent risk in newly created sub-populations is the loss of genetic variation (founder effect), which if great enough can reduce the vigor of the population and its long-term viability. As in Phase 7, stresses from abiotic factors, such as excessive delivery of fine sediment, low flows, or warm water temperatures, need to be reduced in parallel with the removal of exotics. Streamside roads, road crossings, low flows in upper reaches, and livestock are situations of concern in many of the streams, and warm temperatures are in some. Also as in phase 7, monitoring for the presence of exotics, bull trout population parameters, and abiotic factors is an important follow-up activity to track and ensure long-term success. In addition, genetic monitoring of newly founded populations is indicated. Bull Trout Document - Final - -8- 26-Jan-96 A possible future direction after Phase 2 Once Phase 2 is complete, the Bull Trout Working Group will pause to assess the efforts completed and plan future efforts. If phases 1 and 2 are successful, there will be significant numbers of bull trout in various tributaries, but possibly little genetic exchange between them. Bull trout range may still be restricted to headwater streams. During the evaluation and reassessment of the recovery effort, the group will re-consider the long-term recovery objectives. Based on what we know now, two possible recovery objectives are likely to be considered. The first such possible objective is the establishment of natural movement corridors between adjacent headwater streams, thereby establishing complete and viable metapopulation(s) of bull trout within the Upper Klamath Basin. Connectivity between headwater streams would allow volitional movement of bull trout. Movement would allow dispersal, founding of new sub-populations, and interbreeding between sub-populations, within the local sub-basin. Establishing natural movement corridors between headwater streams may require that selected reaches of larger tributaries or even portions of mainstem rivers be restored to suitable habitat for bull trout. This would be an ambitious undertaking, which may be infeasible. It might require the elimination or exclusion of exotics, the removal of man-made barriers which prevent movement between streams, or alterations in current land use to reduce anthropogenically induced fine sediment loads, low flows, warm stream temperatures, or changes in channel morphology. The change in focus from headwater streams to larger tributaries represents an escalation in the scale and complexity of the restoration effort. Exclusion of exotics is much more difficult. Land use effects, whether from water diversions or livestock grazing are often more significant. The second possible objective of future efforts after Phase 2 is to attemp to re-establish fluvial populations of bull trout in selected mainstem rivers of the Upper Klamath Basin, in such a way as to connect the sub-populations of each metapopulation. Fluvial bull trout are far larger than stream resident bull trout, and have much higher fecundity as a result. This gives them a tremendous advantage in breeding, whether in founding new sub-populations, or augmenting existing sub-populations. By establishing a fluvial form of bull trout in the Upper Klamath Basin, overall viability of the metapopulation(s) should be greatly increased. Timeline for implementation A prototype Phase 1 implementation is likely to be completed within 2-5 years. Full implementation of Phase 1 may take many years, but the bulk of the work could be completed in 10-20 years. Further assessment work and some aspects of Phase 2 will be accomplished concurrent with Phase 1 efforts over the next several years, but may require 5-10 years before being well underway. Specific timelines for individual projects in phases 1 and 2 and the overall recovery effort will be developed by the Bull Trout Working Group. Summary and prognosis for bull trout populations in the Upper Klamath River Basin If our analysis is accurate, the Klamath Basin's native bull trout populations are imperiled, yet their future need not be bleak. They persist today as a handful of isolated sub-populations in small, headwater streams. If a fluvial life history form existed, as it may have at one time in the Wood River2, no longer occurs or is a very small (i.e., undetectable) component of the current Klamath River Basin population. Gene flow between these sub-populations has apparently ceased. Individual population sizes are small enough to be near or below minimum viable levels as defined by current theorists in conservation biology. Competition from introduced brook and brown trout is widespread, with severe long-term consequences. Habitat conditions vary from stream to stream, depending on the nature and extent of land uses around and downstream of the bull trout tributaries. Fine sediment inputs and elevated stream temperatures are the principal habitat issue. Water withdrawals, altered channels and flood plains, and other anthropogenic influences have contributed to loss of mainstem fluvial habitat, and may have ultimately resulted in habitat fragmentation, followed by isolation of the remaining populations. Together, these conditions do not bode well for the longevity of native bull trout populations. We believe concerted efforts to resolve the identified problems can achieve the goals of maintaining, and possibly restoring, Klamath bull trout populations. Further, we believe that without attention, one or more of the identified limiting factors will almost certainly spell an end to most or all of the sub-populations in the basin. 2 A 330 mm specimen was collected from Fort Creek, a tributary to the Wood River, in 1876. Cited in Cavendar 1978; Smithsonian Accession Number 16793. Bull Trout Document - Final - -9 - 26-Jan-96
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"September 1997"; Includes bibliographical references (p. 24)
Citation Citation
- Title:
- Research information needs on terrestrial vertebrate species of the interior Columbia River basin and northern portions of the Klamath and Great basins: research, development, and application database
- Author:
- Marcot, Bruce G.
- Year:
- 1997, 2005, 2004
"September 1997"; Includes bibliographical references (p. 24)
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Summary In summary, we found that federal agencies have taken steps to improve collaboration as a way to reduce conflicts that often occur between species protections and other resource uses, but that ...
Citation Citation
- Title:
- Endangered Species Act : successes and challenges in agency collaboration and the use of scientific information in the decision making process : testimony before the Subcommittee on Fisheries, Wildlife and Water, Committee on Environment and Public Works, United States Senate / statement of Robin M. Nazzaro
- Author:
- Nazzaro, Robin M
- Year:
- 2005, 2007
Summary In summary, we found that federal agencies have taken steps to improve collaboration as a way to reduce conflicts that often occur between species protections and other resource uses, but that more could be done to promote routine use of collaboration and clarify agencies' responsibilities under the Endangered Species Act. In September 2003, we reported on efforts taken by the Department of Defense (DOD) to coordinate with other federal land managers in order to reduce the impact of species protections on military activities. We found several cases where such efforts were successful. For example, at the Barry M. Goldwater range in Arizona, Air Force officials worked with officials at FWS and the National Park Service to enhance food sources for the endangered Sonoran pronghorn in locations away from military training areas. As a result, the Air Force was able to minimize the impact of restrictions on training missions due to the presence of the pronghorn. However, such cases were few and far between because, among other things, there were no procedures or centralized information sources for facilitating such collaboration. In March 2004, we reported on collaboration that takes place pursuant to section 7(a)(2) of the act?referred to as the consultation process?in the Pacific Northwest. In this area, large numbers of protected species and vast amounts of federal land conspire to make balancing species protection and resource use a contentious endeavor. We found that steps the Services and other federal agencies had taken made the consultation process run smoother and contributed to improved interagency relationships. However, some problems have persisted. For example, some agencies disagree with the Services about when consultation is necessary and how much analysis is required to determine potential impacts on protected species. In each of these reports, we made recommendations intended to further improve collaboration among federal agencies with regard to balancing species protections and other resource uses, and?in the March 2004 report?to resolve disagreements about the consultations process. DOD and FWS have begun discussing an implementation strategy to improve collaboration regarding species protection on military and other federal lands and development of a training program. With regard to the consultation process, while FWS and NMFS have continued to take steps to expand their collaboration processes, the agencies did not believe that disagreements about the consultation process require additional steps. They believe that current training and guidance is sufficient to address questions about the process. With regard to the use of science, we have found that FWS generally used the best available information in key Endangered Species Act decisions, although the agency was not always integrating new research into ongoing species management decisions. In addition, we identified concerns with the adequacy of the information available to make critical habitat decisions. In December 2002, we reported on many aspects of the decision making for species protections regarding the Mojave Desert tortoise. We found that the decision to list the tortoise as threatened, its critical habitat designation, and the recommended steps in the species' recovery plan, were based on the best available information. However, despite over $100 million in expenditures on recovery actions and research over the past 25 years, it is still unclear what the status of the tortoise is and what effect, if any, recovery actions are having on the species because research has not been coordinated in a way to provide essential management information. Such information is critically important as some of the protective actions, such as restrictions on grazing and off road vehicle use, are vigorously opposed by interest groups who question whether they are necessary for the tortoise's recovery. Accordingly, we recommended that FWS better link land management decisions with research results to ensure that conservation actions and land use restrictions actually benefit the tortoise. In response, FWS recently established a new office with a tortoise recovery coordinator and plans to create an advisory committee to ensure that monitoring and recovery actions are fed back into management decisions. In August 2003, we found that, similar to the decision making regarding the tortoise, FWS decisions about listing species for protection under the act were generally based on the best available information. However, while most critical habitat designations also appeared to be based on the best available information, there were concerns about the adequacy of the information available at the time these decisions are made. Specifically, critical habitat decisions require detailed information of a species' life history and habitat needs and the economic impacts of such decisions?information that is often not available and that FWS is unable to gather before it is obligated under the act to make the decision. As a result, we recommended that the Secretary of the Interior clarify how and when critical habitat should be designated and identify if any policy, regulatory, or legislative changes are required to enable the department to make better informed designations. FWS has not responded to our recommendation.
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1 Acknowledgements 2 3 The completion of this work in large part can be attributed to the efforts of the 4 U.S. Fish and Wildlife Service Arcata Field Office staff and in particular to Mr. 5 Thomas Shaw ...
Citation Citation
- Title:
- Evaluation of Interim Instream Flow Needs in the Klamath River Phase II Final Report
- Author:
- Hardy, Thomas B; Addley. R. Craig
- Year:
- 2001, 2008, 2005
1 Acknowledgements 2 3 The completion of this work in large part can be attributed to the efforts of the 4 U.S. Fish and Wildlife Service Arcata Field Office staff and in particular to Mr. 5 Thomas Shaw for providing much of the supporting site-specific field data, 6 habitat mapping, and fisheries data used in the analyses. The efforts of the 7 various Tribal fisheries personnel were critical in supplying additional fisheries 8 collection data, and intensive site substrate and cover mapping. In particular, the 9 efforts of Tim Hayden, Charlie Chamberlain and Mike Belchik. USGS personnel 10 from the Midcontinent Ecological Science Center also provided valuable 11 assistance and field data used in the cross section based hydraulic and habitat 12 modeling. Mr. Gary Smith and Mike Rode of the California Department of Fish 13 and Game also provided critical information on site-specific habitat suitability 14 criteria and conceptual foundations for the escape cover analysis used in the 15 habitat simulations. Much of this work was also supported by work of Tim 16 Harden (Harden and Associates). The Bureau of Reclamation also provided 17 valuable input during the Phase II study process on Klamath Project operations. 18 A special thanks is also given to Mr. Mike Deas (U.C. Davis) for providing water 19 temperature simulations below Iron Gate Dam. The Technical Team also 20 provided critical input and review of all technical elements of this work as well as 21 providing reviews of the report. Finally, the completion of this work would not 22 have been possible without the tireless efforts of Jennifer Ludlow, Mark 23 Winkelaar, James Shoemaker, Shannon Clemens, Jerilyn Brunson, William 24 Bradford, Sarah Blake, Brandy Blank, Matt Combes, Leon Basdekas, and Aaron 25 Hardy at the Institute for Natural Systems Engineering, Utah State University. 26 27 Executive Summary 28 29 Previous instream flow recommendations developed as part of Phase I (Hardy, 30 1999) recommended interim instream flows in the main stem Klamath River 31 based on analyses of hydrology data. At that time, site-specific data suitable for 32 analysis and evaluation using habitat based modeling were not available. This 33 report details the analytical approach and modeling results from site-specific 34 studies conducted within the main stem Klamath River below Iron Gate Dam 35 downstream to the estuary. Study results are utilized to make revised interim 36 instream flow recommendations necessary to protect the aquatic resources 37 within the main stem Klamath River between Iron Gate and the estuary. This 38 report also makes specific recommendations for future research needs as part of 39 the on-going strategic instream flow studies being undertaken by the U.S. Fish 40 and Wildlife Service and collaborating private, local, state, federal, and tribal 41 entities. 42 43 This report was developed for the Department of the Interior (DOI) who provided 44 access to a technical review team composed of representatives of the U.S. Fish 45 and Wildlife Service, Bureau of Reclamation, Bureau of Indian Affairs, U.S. 46 Geological Survey, and the National Marine Fisheries Service. The technical Draft - Subject to Change 1 review team also included participation by the Yurok, Hoopa Valley, and Karuk 2 Tribes given the Departments trust responsibilities and the California Department 3 of Fish and Game as the state level resource management agency. The 4 technical review team provided invaluable assistance in the review of methods 5 and results used in the analysis, provided comments on draft sections of the 6 report, and provided data and supporting material for use in completion of the 7 Phase II report. In addition, several agencies and private individuals provided 8 written comments on the Preliminary Draft Report, which have been addressed in 9 this report where appropriate. 10 11 This report is organized to follow the general process used to implement the 12 technical studies. It first provides important background information on the 13 historical and current conditions of the anadromous species, highlights factors 14 that have contributed to their decline, provides an overview of the Phase I study 15 process and its principal findings. The report then continues with a description of 16 the Phase II technical study process. Key sections address methods and 17 findings for each technical component such as study design, study site selection, 18 field methods, analytical approaches, summary results, and recommended 19 instream flows. 20 21 The Phase II study relied on state-of-the-art field data collection methodologies 22 and modeling of physical habitat for target species and life stages of anadromous 23 fish. The field methods were directed toward achieving a three-dimensional 24 representation of each study site that incorporated between 0.6 to over one mile 25 of river depending on the specific study site. At each study site, a spatially 26 explicit substrate and vegetation map was developed and then integrated with 27 the three-dimensional channel topography in GIS. Fieldwork also involved 28 collection of hydraulic calibration data and fish observation data. The later 29 information was used in the development of habitat suitability criteria, conceptual 30 habitat model development and implementation, and habitat model validation 31 efforts. 32 33 Hydrology in the main stem Klamath River below Iron Gate Dam was estimated 34 differently for different purposes in Phase II. For example, we used simulated 35 unimpaired inflows (i.e., no depletions) to Upper Klamath Lake routed to Iron 36 Gate Dam with no Klamath Project imposed water demands. This simulated 37 scenario represents the best available estimates of the unimpaired flows below 38 Iron Gate Dam for the purposes of this study. The remaining flow scenarios 39 included the use of Upper Klamath Lake net inflows, historical Klamath Project 40 water demands, and the USFWS Biological Opinion (2000) target Upper Klamath 41 Lake water elevations. These scenarios represent different potential operational 42 flow scenarios as points of reference to the instream flow recommendations 43 developed as part of Phase II. Differences between these simulated flow 44 scenarios required the use of different models and/or modeling assumptions. 45 The assumptions and modeling tools are described in the appropriate technical 46 sections of the report. The estimated hydrology at each study site was used in Draft - Subject to Change 1 both the physical habitat modeling and temperature simulations using the USGS 2 Systems Impact Assessment Model (SIAM) or its components. 3 4 Physical habitat modeling at each study site relied on two-dimensional hydraulic 5 simulations that were coupled to three-dimensional habitat models. The 6 analytical form of the habitat models varied for spawning, fry, and 'juveniles' (i.e., 7 pre-smolts). These modeling results were compared to available 1-dimensional 8 cross section based hydraulic and habitat modeling at study sites that overlapped 9 between existing USFWS/USGS and Phase II studies. 10 11 Habitat suitability criteria for target species and life stages of anadromous fish 12 were developed from site-specific data for Chinook spawning, Chinook fry, and 13 steelhead 1+. These curves were validated both by field observations using the 14 habitat modeling results as well as by comparison to results from an individual 15 based bioenergetics model for drift feeding salmonids developed at USU. A 16 separate procedure was developed to obtain habitat suitability curves for Chinook 17 juvenile (i.e., pre-smolts), steelhead fry, and coho fry based on available 18 literature data. This approach used a systematic process to construct an 19 'envelope' habitat suitability curve that encompassed the available literature 20 curves. The overall process included a validation component that compared the 21 habitat versus discharge relationships between envelope curves to the site- 22 specific curves for Chinook spawning, Chinook fry, and steelhead 1+. The results 23 validated the use of the envelope curves for use as interim criteria pending 24 further research and development of site-specific curves for these species and 25 life stages within the Klamath River. 26 27 Habitat modeling involved the integration of substrate and cover mapping with 28 the three-dimensional topography and hydraulic properties at each study site with 29 the habitat suitability curves. Habitat modeling was undertaken for Chinook 30 spawning, fry, and juveniles, coho fry and juveniles, and steelhead fry and 31 steelhead 1+. Different habitat models were developed for spawning, fry, and 32 juveniles. The study generated a salmonid fry habitat model that incorporated a 33 distance to escape cover that also required sufficient depth within the escape 34 cover in order for it to be utilized at a given flow rate. This model also 35 incorporated quantitative differences in the type of escape cover. 36 37 The habitat modeling results for each species and life stage were validated 38 against the spatial distribution of each species and life stage surveyed at study 39 sites at different flow rates. These results generally demonstrated that the 40 integrated habitat modeling was validated for the study in terms of spawning and 41 fry life stages. Our assessment of the pre-smolt or juvenile life stage results is 42 that they are consistent for the existing habitat model assumptions. However, we 43 discuss what we perceive to be inherent biases in these results (juveniles) based 44 on the existing habitat model structure and make specific recommendations of 45 what additional work would likely improve the results for this particular life stage. 46 Draft - Subject to Change jjj 1 Temperature simulations based on the unimpaired flow regime below Iron Gate 2 Dam were conducted with HEC5Q as part of the SIAM applications. These 3 results supported the findings in Phase I that flows lower than ~ 1000 cfs during 4 the late summer would likely increase the environmental risk to anadromous 5 species due to almost continual exposure to chronic temperature thresholds. We 6 believe that these simulation results show that there is very little flexibility for 7 reservoir operations at Iron Gate Dam to mitigate deleterious flow dependent 8 temperature effects. This finding has previously been reported by the USGS 9 (Bartholow 1995) and Deas (1999). 10 11 The integration of the habitat modeling with the unimpaired hydrology was used 12 to develop habitat reference values for target species and life stages at each 13 study reach on a monthly basis for flow exceedence ranges between 10 and 90 14 percent. The reference habitat value was computed as the percent of maximum 15 habitat associated with the unimpaired flow values for each species and life 16 stage on a monthly basis. This reference habitat value was used as one 'target' 17 condition to guide the selection of monthly flow recommendations at a given 18 exceedence flow level. 19 20 The flow recommendation process also employed a prioritization of species and 21 life stages to be considered within the year and/or within a specific month. The 22 prioritization of life stages was taken from the life history sequence of 23 anadromous species (i.e., spawning, fry, and then juveniles). The initial priority 24 order for species was defined as Chinook, then coho, and finally steelhead. It is 25 stressed that this initial prioritization was used to conceptually simplify the flow 26 recommendation process only, and that all species and life stages were 27 examined as part of the overall analysis. The process then relied on an iterative 28 procedure to select target flows for each month at a given exceedence level. 29 This procedure attempted to pick a target flow that would simultaneously 30 preserve the underlying characteristics of the seasonal unimpaired hydrograph at 31 that exceedence flow, the underlying relationship of the unimpaired hydrograph 32 between all exceedence flow levels, while striving to maximize habitat for the 33 priority species and life stages relative to the unimpaired habitat reference 34 conditions. The corresponding monthly flow rates at each exceedence level 35 were then used to compute the percent of maximum habitat for all other species 36 and life stages in a given month. These values were then compared to their 37 respective unimpaired habitat values to ensure that adequate protection of 38 habitat for non-priority species and life stages remained reasonable. 39 40 The flow recommendations developed in the Iron Gate to Shasta River Reach 41 were 'propagated' downstream to each successive reach by addition of the reach 42 gains as presently defined by the USGS in their MODSIM module of SIAM. It is 43 recognized that these reach gains reflect existing depletions in tributary systems 44 (e.g., Shasta and Scott Rivers) but are the only estimates presently available for 45 use in the simulation models for the system. The flow recommendations for each 46 river reach were then used to compute the percent of maximum habitat on a Draft - Subject to Change 1 monthly basis for each species and life stage. The recommended flow based 2 calculation of percent of maximum habitat for each species and life stage was 3 then compared against the associated unimpaired flow based habitat values. 4 5 Although flow recommendations were developed for the 10 to 90 percent 6 exceedence range (i.e., nine water year types), five water year types were 7 identified representing Critically Dry, Dry, Average, Wet, and Extremely Wet 8 inflow conditions for Upper Klamath Lake. These water year classifications 9 parallel those developed for the Trinity River and were used as operational 10 definitions in the Phase I report. Furthermore, the USBR KPSIM model was 11 modified to use this five-water year type format for simulating operations under 12 different instream flow requirements below Iron Gate Dam. The 90, 70, 50, 30, 13 and 10 percent exceedence flow levels were assigned to each of these water 14 year types, respectively (i.e., critically dry to extremely wet). This assignment 15 was used to demonstrate several key points regarding the use of 16 recommendations at this level of resolution (i.e., five water year types) and how 17 the existing operational models for the Klamath Project simulate flow scenarios. 18 19 These five water year type dependent recommendations were utilized in the U.S. 20 Bureau of Reclamation's Klamath Project Simulation Module (KPSIM) to simulate 21 project operations over the 1961 to 1997 period of record. This analysis 22 confirmed that the project could be operated to achieve these recommendations 23 in all but 19 of the 468 simulated months in this period of record. These results 24 also highlighted that an alternative water year 'classification' strategy for 25 specifying instream flows should be considered in lieu of a five water year type 26 scheme. We provide a specific recommendation of how this could be 27 approached based on the instream flow recommendations developed in Phase II. 28 29 30 Draft - Subject to Change