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• 1. [Image] Water quality and nutrient loading in the Klamath River between Keno, Oregon and Seiad Valley, California from 1996-1998

  	ABSTRACT A water quality study was performed in the mainstem Klamath River from Keno, Oregon to Seiad Valley, California during 1996 through 1998. Four sites within the study area were continuously ...
  	Citation × Citation Citation Abstract Copy Title: Water quality and nutrient loading in the Klamath River between Keno, Oregon and Seiad Valley, California from 1996-1998 Author: Campbell, S. G Year: 2001, 2007, 2005 ABSTRACT A water quality study was performed in the mainstem Klamath River from Keno, Oregon to Seiad Valley, California during 1996 through 1998. Four sites within the study area were continuously monitored using multiparameter recorders. Water quality sampling was also performed at these four locations in 1996 and 1997. Additional water quality sampling sites were added in 1998 for a total of 8 locations between Keno and Seiad. Temperature ranged from near zero ?C to >25 ?C with cooler temperatures in early spring and fall, and maximum temperatures occurring in July and August of each year. Dissolved oxygen concentration ranged from near zero mg/L to >13 mg/L with highest DO occurring in early spring and fall and lowest DO occurring in mid-summer. Air temperature was generally highly correlated with water temperature with r values ranging from 0.8 to 0.9 during the study period from 1996-1998. Water temperature in the study area exceeded chronic (>16?C) and acute (>22?C) criteria for salmonids during the summer months. Although chronic DO (<7 mg/L) criteria were exceeded throughout most of the study area during the summer, in the free-flowing river below Iron Gate Dam the acute DO (<5.5 mg/L) criteria were not exceeded. Nonpoint source pollution in the form of agricultural return flows, industrial, or sewage effluent entering the stream may have resulted in higher ammonia and total organic nitrogen concentrations at the upstream locations in the Klamath River study area (Keno and J.C. Boyle Powerplant). Nitrification of ammonia and organic nitrogen seemed to result in higher concentrations of nitrate in the downstream Klamath River (Iron Gate Dam). Total phosphorus concentration stayed relatively stable through the reservoirs in the study area, but decreased in the downstream direction between Iron Gate Dam and Seiad. Ortho-phosphorus concentrations increased longitudinally through the reservoirs, then decreased in the downstream direction between Iron Gate Dam and Seiad. An increase in ortho-phosphorus concentration can indicate internal cycling occurring in the reservoirs as well as photosynthesis. On an annual basis total phosphorus loading increased longitudinally from up- to downstream between Keno and Seiad. The increase was statistically significant (p = .03) indicating that the reservoirs in series in the Klamath River study area do not function as a nutrient sink. However, during the summer there was no statistically significant difference in total P loading when Keno, Iron Gate and Seiad locations were compared, therefore, the reservoirs may act as a nutrient sink seasonally. The Klamath River study locations were generally nitrogen limited, although at Keno, a regular change from N limitation to P limitation occurred during the fall of all three years of the study. When the Klamath River annual nutrient loading values are compared to other rivers in the vicinity, the Carson, Truckee, and Long Tom Rivers also appear to be nutrient enriched. The Carson and South Yamhill Rivers seem to be N limited systems and the Wood, Long Tom, Snake and Truckee Rivers seem to be P limited systems. Implementing management strategies for reservoir operations to improve water quality and reduce nutrient concentration or loading in the Klamath River study area to benefit anadromous fisheries may be difficult and expensive. However, improving the thermal regime in spring to benefit YOY salmonids may be possible as is short-term relief in fate summer for over-summering species. Decreases in nutrient concentration or loading accomplished through best management practices in the water shed may allow general protection of water resources in the Klamath Basin for future needs. Title: Water quality and nutrient loading in the Klamath River between Keno, Oregon and Seiad Valley, California from 1996-1998 Author: Campbell, S. G Year: 2001, 2007, 2005 ABSTRACT A water quality study was performed in the mainstem Klamath River from Keno, Oregon to Seiad Valley, California during 1996 through 1998. Four sites within the study area were continuously monitored using multiparameter recorders. Water quality sampling was also performed at these four locations in 1996 and 1997. Additional water quality sampling sites were added in 1998 for a total of 8 locations between Keno and Seiad. Temperature ranged from near zero ?C to >25 ?C with cooler temperatures in early spring and fall, and maximum temperatures occurring in July and August of each year. Dissolved oxygen concentration ranged from near zero mg/L to >13 mg/L with highest DO occurring in early spring and fall and lowest DO occurring in mid-summer. Air temperature was generally highly correlated with water temperature with r values ranging from 0.8 to 0.9 during the study period from 1996-1998. Water temperature in the study area exceeded chronic (>16?C) and acute (>22?C) criteria for salmonids during the summer months. Although chronic DO (<7 mg/L) criteria were exceeded throughout most of the study area during the summer, in the free-flowing river below Iron Gate Dam the acute DO (<5.5 mg/L) criteria were not exceeded. Nonpoint source pollution in the form of agricultural return flows, industrial, or sewage effluent entering the stream may have resulted in higher ammonia and total organic nitrogen concentrations at the upstream locations in the Klamath River study area (Keno and J.C. Boyle Powerplant). Nitrification of ammonia and organic nitrogen seemed to result in higher concentrations of nitrate in the downstream Klamath River (Iron Gate Dam). Total phosphorus concentration stayed relatively stable through the reservoirs in the study area, but decreased in the downstream direction between Iron Gate Dam and Seiad. Ortho-phosphorus concentrations increased longitudinally through the reservoirs, then decreased in the downstream direction between Iron Gate Dam and Seiad. An increase in ortho-phosphorus concentration can indicate internal cycling occurring in the reservoirs as well as photosynthesis. On an annual basis total phosphorus loading increased longitudinally from up- to downstream between Keno and Seiad. The increase was statistically significant (p = .03) indicating that the reservoirs in series in the Klamath River study area do not function as a nutrient sink. However, during the summer there was no statistically significant difference in total P loading when Keno, Iron Gate and Seiad locations were compared, therefore, the reservoirs may act as a nutrient sink seasonally. The Klamath River study locations were generally nitrogen limited, although at Keno, a regular change from N limitation to P limitation occurred during the fall of all three years of the study. When the Klamath River annual nutrient loading values are compared to other rivers in the vicinity, the Carson, Truckee, and Long Tom Rivers also appear to be nutrient enriched. The Carson and South Yamhill Rivers seem to be N limited systems and the Wood, Long Tom, Snake and Truckee Rivers seem to be P limited systems. Implementing management strategies for reservoir operations to improve water quality and reduce nutrient concentration or loading in the Klamath River study area to benefit anadromous fisheries may be difficult and expensive. However, improving the thermal regime in spring to benefit YOY salmonids may be possible as is short-term relief in fate summer for over-summering species. Decreases in nutrient concentration or loading accomplished through best management practices in the water shed may allow general protection of water resources in the Klamath Basin for future needs. Close

• 2. [Image] Evaluation of interim instream flow needs in the Klamath River : Phase I, final report

  	"August 5, 1999"
  	Citation × Citation Citation Abstract Copy Title: Evaluation of interim instream flow needs in the Klamath River : Phase I, final report Author: United States. Dept. of the Interior Year: 1999, 2005 "August 5, 1999" Title: Evaluation of interim instream flow needs in the Klamath River : Phase I, final report Author: United States. Dept. of the Interior Year: 1999, 2005 "August 5, 1999" Close

• 3. [Image] Klamath District and Klamath Project annual history, 1948

  	Ill., maps (some color), photographs; Includes organization of Klamath District with official correspondence and description of the Klamath project, an organization chart, fiscal year financials, photographs, ...
  	Citation × Citation Citation Abstract Copy Title: Klamath District and Klamath Project annual history, 1948 Author: United States. Bureau of Reclamation Year: 1948, 2008, 2006 Ill., maps (some color), photographs; Includes organization of Klamath District with official correspondence and description of the Klamath project, an organization chart, fiscal year financials, photographs, maps, charts and tables of crop and livestock yields and water storage and distribution, etc.; Includes index; Title covers: calendar years for 1946-1948; Description is based on: Klamath District and Klamath Project Annual History for 1946; Dates of the beginning year(s) of publication are derived from the May 1, 1903 to December 31, 1912, History of the Klamath Project and from the volume information on later volumes (v. 35) Klamath District and Klamath Project Annual history for 1945, dated December 1, 1946 Title: Klamath District and Klamath Project annual history, 1948 Author: United States. Bureau of Reclamation Year: 1948, 2008, 2006 Ill., maps (some color), photographs; Includes organization of Klamath District with official correspondence and description of the Klamath project, an organization chart, fiscal year financials, photographs, maps, charts and tables of crop and livestock yields and water storage and distribution, etc.; Includes index; Title covers: calendar years for 1946-1948; Description is based on: Klamath District and Klamath Project Annual History for 1946; Dates of the beginning year(s) of publication are derived from the May 1, 1903 to December 31, 1912, History of the Klamath Project and from the volume information on later volumes (v. 35) Klamath District and Klamath Project Annual history for 1945, dated December 1, 1946 Close

• 4. [Image] Klamath Project annual history, 1949

  	Ill., maps (some color), photographs; Includes fiscal year financials, photographs, maps, crop and livestock yields, irrigation and drainage and irrigation pumping plant operations, WPA camp maintenance, ...
  	Citation × Citation Citation Abstract Copy Title: Klamath Project annual history, 1949 Author: United States. Bureau of Reclamation Year: 1949, 2008 Ill., maps (some color), photographs; Includes fiscal year financials, photographs, maps, crop and livestock yields, irrigation and drainage and irrigation pumping plant operations, WPA camp maintenance, etc.; Title covers: calendar years for 1949 - 1952; Description is based on: Klamath Project annual history for 1949; Dates of the beginning year(s) of publication are derived from May 1, 1903 to December 31, 1912, History of the Klamath Project and from the volume information on later volumes (v. 35) Klamath District and Klamath Project Annual history for 1945, dated December 1, 1946 Title: Klamath Project annual history, 1949 Author: United States. Bureau of Reclamation Year: 1949, 2008 Ill., maps (some color), photographs; Includes fiscal year financials, photographs, maps, crop and livestock yields, irrigation and drainage and irrigation pumping plant operations, WPA camp maintenance, etc.; Title covers: calendar years for 1949 - 1952; Description is based on: Klamath Project annual history for 1949; Dates of the beginning year(s) of publication are derived from May 1, 1903 to December 31, 1912, History of the Klamath Project and from the volume information on later volumes (v. 35) Klamath District and Klamath Project Annual history for 1945, dated December 1, 1946 Close

• 5. [Image] Annual project history: Klamath Project, Oregon-California 1954

  	Ill., maps (some color), photographs; Includes fiscal year financials, maps, photographs, agricultural economics and crop yield, some grazing financial information with cost of water usage, tables for ...
  	Citation × Citation Citation Abstract Copy Title: Annual project history: Klamath Project, Oregon-California 1954 Author: United States. Bureau of Reclamation Year: 1954, 2008, 2006 Ill., maps (some color), photographs; Includes fiscal year financials, maps, photographs, agricultural economics and crop yield, some grazing financial information with cost of water usage, tables for irrigation and drainage and water storage and distributions, list of steam gaging stations, weather conditions, list of evaporation stations, quality of irrigation water at pumping plants, etc.; Title covers: calendar years for 1954-1962; Description is based on: Annual project history: Klamath Project, Oregon-California 1954; Dates of the beginning year(s) of publication are derived from May 1, 1903 to December 31, 1912, History of the Klamath Project and from the volume information on later volumes (v. 35) Klamath District and Klamath Project annual history for 1945, dated December 1, 1946 Title: Annual project history: Klamath Project, Oregon-California 1954 Author: United States. Bureau of Reclamation Year: 1954, 2008, 2006 Ill., maps (some color), photographs; Includes fiscal year financials, maps, photographs, agricultural economics and crop yield, some grazing financial information with cost of water usage, tables for irrigation and drainage and water storage and distributions, list of steam gaging stations, weather conditions, list of evaporation stations, quality of irrigation water at pumping plants, etc.; Title covers: calendar years for 1954-1962; Description is based on: Annual project history: Klamath Project, Oregon-California 1954; Dates of the beginning year(s) of publication are derived from May 1, 1903 to December 31, 1912, History of the Klamath Project and from the volume information on later volumes (v. 35) Klamath District and Klamath Project annual history for 1945, dated December 1, 1946 Close

• 6. [Image] Evaluation of Interim Instream Flow Needs in the Klamath River Phase II Final Report

  	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 Citation Abstract Copy 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 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 Close

• 7. [Image] Klamath Project annual history, 1951

  	Ill., maps (some color), photographs; Includes fiscal year financials, photographs, maps, crop and livestock yields, irrigation and drainage and irrigation pumping plant operations, WPA camp maintenance, ...
  	Citation × Citation Citation Abstract Copy Title: Klamath Project annual history, 1951 Author: United States. Bureau of Reclamation Year: 1951, 2008, 2007 Ill., maps (some color), photographs; Includes fiscal year financials, photographs, maps, crop and livestock yields, irrigation and drainage and irrigation pumping plant operations, WPA camp maintenance, etc.; Title covers: calendar years for 1949 - 1952; Description is based on: Klamath Project annual history for 1949; Dates of the beginning year(s) of publication are derived from May 1, 1903 to December 31, 1912, History of the Klamath Project and from the volume information on later volumes (v. 35) Klamath District and Klamath Project Annual history for 1945, dated December 1, 1946 Title: Klamath Project annual history, 1951 Author: United States. Bureau of Reclamation Year: 1951, 2008, 2007 Ill., maps (some color), photographs; Includes fiscal year financials, photographs, maps, crop and livestock yields, irrigation and drainage and irrigation pumping plant operations, WPA camp maintenance, etc.; Title covers: calendar years for 1949 - 1952; Description is based on: Klamath Project annual history for 1949; Dates of the beginning year(s) of publication are derived from May 1, 1903 to December 31, 1912, History of the Klamath Project and from the volume information on later volumes (v. 35) Klamath District and Klamath Project Annual history for 1945, dated December 1, 1946 Close

• 8. [Image] Klamath District and Klamath Project annual history, 1946

  	Ill., maps (some color), photographs; Includes organization of Klamath District with official correspondence and description of the Klamath project, an organization chart, fiscal year financials, photographs, ...
  	Citation × Citation Citation Abstract Copy Title: Klamath District and Klamath Project annual history, 1946 Author: United States. Bureau of Reclamation Year: 1946, 2008, 2006 Ill., maps (some color), photographs; Includes organization of Klamath District with official correspondence and description of the Klamath project, an organization chart, fiscal year financials, photographs, maps, charts and tables of crop and livestock yields and water storage and distribution, etc.; Includes index; Title covers: calendar years for 1946-1948; Description is based on: Klamath District and Klamath Project Annual History for 1946; Dates of the beginning year(s) of publication are derived from the May 1, 1903 to December 31, 1912, History of the Klamath Project and from the volume information on later volumes (v. 35) Klamath District and Klamath Project Annual history for 1945, dated December 1, 1946 Title: Klamath District and Klamath Project annual history, 1946 Author: United States. Bureau of Reclamation Year: 1946, 2008, 2006 Ill., maps (some color), photographs; Includes organization of Klamath District with official correspondence and description of the Klamath project, an organization chart, fiscal year financials, photographs, maps, charts and tables of crop and livestock yields and water storage and distribution, etc.; Includes index; Title covers: calendar years for 1946-1948; Description is based on: Klamath District and Klamath Project Annual History for 1946; Dates of the beginning year(s) of publication are derived from the May 1, 1903 to December 31, 1912, History of the Klamath Project and from the volume information on later volumes (v. 35) Klamath District and Klamath Project Annual history for 1945, dated December 1, 1946 Close

• 9. [Image] Klamath Project annual history, 1950

  	Ill., maps (some color), photographs; Includes fiscal year financials, photographs, maps, crop and livestock yields, irrigation and drainage and irrigation pumping plant operations, WPA camp maintenance, ...
  	Citation × Citation Citation Abstract Copy Title: Klamath Project annual history, 1950 Author: United States. Bureau of Reclamation Year: 1950, 2008, 2007 Ill., maps (some color), photographs; Includes fiscal year financials, photographs, maps, crop and livestock yields, irrigation and drainage and irrigation pumping plant operations, WPA camp maintenance, etc.; Title covers: calendar years for 1949 - 1952; Description is based on: Klamath Project annual history for 1949; Dates of the beginning year(s) of publication are derived from May 1, 1903 to December 31, 1912, History of the Klamath Project and from the volume information on later volumes (v. 35) Klamath District and Klamath Project Annual history for 1945, dated December 1, 1946 Title: Klamath Project annual history, 1950 Author: United States. Bureau of Reclamation Year: 1950, 2008, 2007 Ill., maps (some color), photographs; Includes fiscal year financials, photographs, maps, crop and livestock yields, irrigation and drainage and irrigation pumping plant operations, WPA camp maintenance, etc.; Title covers: calendar years for 1949 - 1952; Description is based on: Klamath Project annual history for 1949; Dates of the beginning year(s) of publication are derived from May 1, 1903 to December 31, 1912, History of the Klamath Project and from the volume information on later volumes (v. 35) Klamath District and Klamath Project Annual history for 1945, dated December 1, 1946 Close

• 10. [Image] Klamath District and Klamath Project annual history, 1947

  	Ill., maps (some color), photographs; Includes organization of Klamath District with official correspondence and description of the Klamath project, an organization chart, fiscal year financials, photographs, ...
  	Citation × Citation Citation Abstract Copy Title: Klamath District and Klamath Project annual history, 1947 Author: United States. Bureau of Reclamation Year: 1947, 2008, 2004 Ill., maps (some color), photographs; Includes organization of Klamath District with official correspondence and description of the Klamath project, an organization chart, fiscal year financials, photographs, maps, charts and tables of crop and livestock yields and water storage and distribution, etc.; Includes index; Title covers: calendar years for 1946-1948; Description is based on: Klamath District and Klamath Project Annual History for 1946; Dates of the beginning year(s) of publication are derived from the May 1, 1903 to December 31, 1912, History of the Klamath Project and from the volume information on later volumes (v. 35) Klamath District and Klamath Project Annual history for 1945, dated December 1, 1946 Title: Klamath District and Klamath Project annual history, 1947 Author: United States. Bureau of Reclamation Year: 1947, 2008, 2004 Ill., maps (some color), photographs; Includes organization of Klamath District with official correspondence and description of the Klamath project, an organization chart, fiscal year financials, photographs, maps, charts and tables of crop and livestock yields and water storage and distribution, etc.; Includes index; Title covers: calendar years for 1946-1948; Description is based on: Klamath District and Klamath Project Annual History for 1946; Dates of the beginning year(s) of publication are derived from the May 1, 1903 to December 31, 1912, History of the Klamath Project and from the volume information on later volumes (v. 35) Klamath District and Klamath Project Annual history for 1945, dated December 1, 1946 Close