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• 1. [Image] Klamath River water quality and acoustic Doppler current profiler data from Link River Dam to Keno Dam, 2007

  	Klamath River Water Quality and Acoustic Doppler Current Profiler Data from Link River Dam to Keno Dam, 2007 By Annett B. Sullivan, Michael L. Deas, Jessica Asbill, Julie D. Kirshtein, Kenna Butler, Roy ...
  	Citation × Citation Citation Abstract Copy Title: Klamath River water quality and acoustic Doppler current profiler data from Link River Dam to Keno Dam, 2007 Author: Sullivan, Annett B. (Annett Brigitte), 1970- Year: 2008 Klamath River Water Quality and Acoustic Doppler Current Profiler Data from Link River Dam to Keno Dam, 2007 By Annett B. Sullivan, Michael L. Deas, Jessica Asbill, Julie D. Kirshtein, Kenna Butler, Roy E. Wellman, Marc A. Stewart, and Jennifer Vaughn Abstract In 2007, the U.S. Geological Survey, Watercourse Engineering, and Bureau of Reclamation began a project to construct and calibrate a water quality and hydrodynamic model of the 21-mile reach of the Klamath River from Link River Dam to Keno Dam. To provide a basis for this work, data collection and experimental work were planned for 2007 and 2008. This report documents sampling and analytical methods and presents data from the first year of work. To determine water velocities and discharge, a series of cross-sectional acoustic Doppler current profiler (ADCP) measurements were made on the mainstem and four canals on May 30 and September 19, 2007. Water quality was sampled weekly at five mainstem sites and five tributaries from early April through early November, 2007. Constituents reported here include field parameters (water temperature, pH, dissolved oxygen concentration, specific conductance); total nitrogen and phosphorus; particulate carbon and nitrogen; filtered orthophosphate, nitrite, nitrite plus nitrate, ammonia, organic carbon, iron, silica, and alkalinity; specific UV absorbance at 254 nm; phytoplankton and zooplankton enumeration and species identification; and bacterial abundance and morphological subgroups. The ADCP measurements conducted in good weather conditions in May showed that four major canals accounted for most changes in discharge along the mainstem on that day. Direction of velocity at measured locations was fairly homogeneous across the channel, while velocities were generally lowest near the bottom, and highest near surface, ranging from 0.0 to 0.8 ft/s. Measurements in September, made in windy conditions, raised questions about the effect of wind on flow. Most nutrient and carbon concentrations were lowest in spring, increased and remained elevated in summer, and decreased in fall. Dissolved nitrite plus nitrate and nitrite had a different seasonal cycle and were below detection or at low concentration in summer. Many nutrient and carbon concentrations were similar at the top and bottom of the water column, though ammonia and particulate carbon showed more variability in summer. Averaged over the season, particulate carbon and particulate nitrogen decreased in the downstream direction, while ammonia and orthophosphate concentrations increased in the downstream direction. At most sites, bacteria, phytoplankton, and zooplankton populations reached their maximums in summer. Large bacterial cells made up most of the bacteria biovolume, though cocci were the most numerous bacteria type. The cocci were smaller than the filter pore sizes used to separate dissolved from particulate matter in this study. Phytoplankton biovolumes were dominated by the blue-green alga Aphanizomenonflos aquae most of the sampling season, though a spring diatom bloom occurred. Phytoplankton biovolumes were generally highest at the upstream Link River and Railroad Bridge sites and decreased in the downstream direction. Zooplankton populations were dominated by copepods in early spring, and by cladocerans and rotifers in summer, with rotifers more common farther downstream. l Title: Klamath River water quality and acoustic Doppler current profiler data from Link River Dam to Keno Dam, 2007 Author: Sullivan, Annett B. (Annett Brigitte), 1970- Year: 2008 Klamath River Water Quality and Acoustic Doppler Current Profiler Data from Link River Dam to Keno Dam, 2007 By Annett B. Sullivan, Michael L. Deas, Jessica Asbill, Julie D. Kirshtein, Kenna Butler, Roy E. Wellman, Marc A. Stewart, and Jennifer Vaughn Abstract In 2007, the U.S. Geological Survey, Watercourse Engineering, and Bureau of Reclamation began a project to construct and calibrate a water quality and hydrodynamic model of the 21-mile reach of the Klamath River from Link River Dam to Keno Dam. To provide a basis for this work, data collection and experimental work were planned for 2007 and 2008. This report documents sampling and analytical methods and presents data from the first year of work. To determine water velocities and discharge, a series of cross-sectional acoustic Doppler current profiler (ADCP) measurements were made on the mainstem and four canals on May 30 and September 19, 2007. Water quality was sampled weekly at five mainstem sites and five tributaries from early April through early November, 2007. Constituents reported here include field parameters (water temperature, pH, dissolved oxygen concentration, specific conductance); total nitrogen and phosphorus; particulate carbon and nitrogen; filtered orthophosphate, nitrite, nitrite plus nitrate, ammonia, organic carbon, iron, silica, and alkalinity; specific UV absorbance at 254 nm; phytoplankton and zooplankton enumeration and species identification; and bacterial abundance and morphological subgroups. The ADCP measurements conducted in good weather conditions in May showed that four major canals accounted for most changes in discharge along the mainstem on that day. Direction of velocity at measured locations was fairly homogeneous across the channel, while velocities were generally lowest near the bottom, and highest near surface, ranging from 0.0 to 0.8 ft/s. Measurements in September, made in windy conditions, raised questions about the effect of wind on flow. Most nutrient and carbon concentrations were lowest in spring, increased and remained elevated in summer, and decreased in fall. Dissolved nitrite plus nitrate and nitrite had a different seasonal cycle and were below detection or at low concentration in summer. Many nutrient and carbon concentrations were similar at the top and bottom of the water column, though ammonia and particulate carbon showed more variability in summer. Averaged over the season, particulate carbon and particulate nitrogen decreased in the downstream direction, while ammonia and orthophosphate concentrations increased in the downstream direction. At most sites, bacteria, phytoplankton, and zooplankton populations reached their maximums in summer. Large bacterial cells made up most of the bacteria biovolume, though cocci were the most numerous bacteria type. The cocci were smaller than the filter pore sizes used to separate dissolved from particulate matter in this study. Phytoplankton biovolumes were dominated by the blue-green alga Aphanizomenonflos aquae most of the sampling season, though a spring diatom bloom occurred. Phytoplankton biovolumes were generally highest at the upstream Link River and Railroad Bridge sites and decreased in the downstream direction. Zooplankton populations were dominated by copepods in early spring, and by cladocerans and rotifers in summer, with rotifers more common farther downstream. l Close

• 2. [Image] Undepleted natural flow of the upper Klamath River : natural inflow to, natural losses from, and natural outfall of Upper Klamath Lake to the Link River and of Lower Klamath Lake to the Klamath River at Keno

  	A monthly natural flow history was determined for the 1949 to 2000 period at the Keno gage of the Upper Klamath River basin in south-central Oregon. Included within the evaluation is an assessment of natural ...
  	Citation × Citation Citation Abstract Copy Title: Undepleted natural flow of the upper Klamath River : natural inflow to, natural losses from, and natural outfall of Upper Klamath Lake to the Link River and of Lower Klamath Lake to the Klamath River at Keno Author: United States. Bureau of Reclamation. Denver Office. Technical Service Center Year: 2005, 2004 A monthly natural flow history was determined for the 1949 to 2000 period at the Keno gage of the Upper Klamath River basin in south-central Oregon. Included within the evaluation is an assessment of natural flows for the same period at the outfall of Upper Klamath Lake, which forms the head of the Link River at Klamath Falls, Oregon. Flow past the Link River gage is tributary to the Klamath River above Lower Klamath Lake. These natural flows were determined using standard and accepted methods. Records used in developing this analysis were derived from stream-gaging records and from climatic records for stations within and adjacent to the study area. Information was also obtained from published maps and reports, and file documents of the Klamath Area Office. Currently, received comments are being addressed and evaluation of elements related to these comments is in progress. The objective of this report is to provide a representative estimate of the monthly natural flow of the Upper Klamath River. Such an estimate is of the natural flow that would typically have occurred without the water-resources developments in the Upper Klamath Basin. A water-budget assessment was used in the determination of the natural flows. The assessment includes results from an evaluation of present-day irrigation depletions, and losses from reclaimed marshland, that have changed the natural inflow to, and resulting natural outfall from, Upper Klamath Lake. Also evaluated were losses to the natural inflow that would have been incurred due to pre-development marshland and evaporation associated with Upper Klamath Lake. The natural outfall from the lake comprised the natural flow of the Link River at Klamath Falls and also the consequent natural inflow to Lower Klamath Lake. Therefore, a similar evaluation was also completed for Lower Klamath Lake to estimate the natural flow of the Klamath River at Keno. The water-budget assessment was designed to simulate each lake as a natural water body within a stream-connected two-lake system. Much of the assessment was completed using Excel. Title: Undepleted natural flow of the upper Klamath River : natural inflow to, natural losses from, and natural outfall of Upper Klamath Lake to the Link River and of Lower Klamath Lake to the Klamath River at Keno Author: United States. Bureau of Reclamation. Denver Office. Technical Service Center Year: 2005, 2004 A monthly natural flow history was determined for the 1949 to 2000 period at the Keno gage of the Upper Klamath River basin in south-central Oregon. Included within the evaluation is an assessment of natural flows for the same period at the outfall of Upper Klamath Lake, which forms the head of the Link River at Klamath Falls, Oregon. Flow past the Link River gage is tributary to the Klamath River above Lower Klamath Lake. These natural flows were determined using standard and accepted methods. Records used in developing this analysis were derived from stream-gaging records and from climatic records for stations within and adjacent to the study area. Information was also obtained from published maps and reports, and file documents of the Klamath Area Office. Currently, received comments are being addressed and evaluation of elements related to these comments is in progress. The objective of this report is to provide a representative estimate of the monthly natural flow of the Upper Klamath River. Such an estimate is of the natural flow that would typically have occurred without the water-resources developments in the Upper Klamath Basin. A water-budget assessment was used in the determination of the natural flows. The assessment includes results from an evaluation of present-day irrigation depletions, and losses from reclaimed marshland, that have changed the natural inflow to, and resulting natural outfall from, Upper Klamath Lake. Also evaluated were losses to the natural inflow that would have been incurred due to pre-development marshland and evaporation associated with Upper Klamath Lake. The natural outfall from the lake comprised the natural flow of the Link River at Klamath Falls and also the consequent natural inflow to Lower Klamath Lake. Therefore, a similar evaluation was also completed for Lower Klamath Lake to estimate the natural flow of the Klamath River at Keno. The water-budget assessment was designed to simulate each lake as a natural water body within a stream-connected two-lake system. Much of the assessment was completed using Excel. Close

• 3. [Image] Biological opinion Klamath Project operations

  	"May 31, 2002."; Includes bibliographical references.
  	Citation × Citation Citation Abstract Copy Title: Biological opinion Klamath Project operations Author: United States.; National Marine Fisheries Service. Year: 2002, 2008, 2005 "May 31, 2002."; Includes bibliographical references. Title: Biological opinion Klamath Project operations Author: United States.; National Marine Fisheries Service. Year: 2002, 2008, 2005 "May 31, 2002."; Includes bibliographical references. Close

• 4. [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

• 5. [Image] Natural flow of the upper Klamath River

  	Executive Summary Executive Summary This report presents details of the investigation and results in estimating the natural flow of the upper Klamath River at Keno, Oregon. The area investigated includes ...
  	Citation × Citation Citation Abstract Copy Title: Natural flow of the upper Klamath River Author: United States. Bureau of Reclamation. Klamath Basin Area Office Year: 2005, 2008 Executive Summary Executive Summary This report presents details of the investigation and results in estimating the natural flow of the upper Klamath River at Keno, Oregon. The area investigated includes the Klamath River Basin above Keno, Oregon, primarily in Klamath County, with some areas of Siskiyou and Modoc Counties in California. The study area includes the Sprague, Williamson, and Wood River basins, as well as Upper Klamath and Lower Klamath Lakes. Objectives The current purpose of this study is to provide an estimate of the monthly natural flows in the upper Klamath River at Keno. This estimate of the natural flow represents typical flow without agricultural development in the Upper Klamath River Basin, including its tributaries. Study Approach This study used a water budget approach to assess the agricultural depletions and alterations to the natural flow. The approach was to evaluate the changes of agriculture from predevelopment conditions, estimate the effects of these changes, and restore the water budget to natural conditions by reversing the effects of agricultural development. Records used in this empirical assessment were derived from both stream gaging flow histories and from climatological records for stations within and adjacent to the study area. Water Budget Description The water budget assessment of the watershed as a natural system includes an evaluation of hydrological changes related to agricultural development above the Keno gage. The water budget assessment includes: ? Natural inflow from the Sprague, Williamson, and Wood Rivers to Upper Klamath Lake ? Predevelopment evapotranspiration losses from marshes surrounding Upper Klamath Lake ? Predevelopment evaporation losses of the Upper Klamath Lake ? Natural flow at the outlet of Upper Klamath Lake into the Link River at Klamath Falls ? Resulting natural flow at Keno The processes developed in the water budget to evaluate the natural outflow of Upper Klamath Lake accounts for factors related to water resources developments XI Natural Flow of the Upper Klamath River in the watershed that have affected inflow to the lake, and for losses due to natural condition of the lake. The water budget assessment of the watershed as a natural system includes an evaluation of hydrological changes related to agricultural development above the Keno gage. The results of the water budget assessment are given as average annual flows for two important stream gages, one located on the Link River at Klamath Falls and the other on the Klamath River at Keno. Evaluation of Predevelopment Conditions An evaluation of predevelopment conditions included an evaluation of changes to Upper Klamath Lake, agricultural developments in the Wood River, Sprague River, and Williamson River watersheds. Several basic elements were considered in this study: ? How had development changed the system ? Was information available about conditions before the changes occurred ? Were data available to assist in estimating changes to the natural system Evaluation of Current Conditions Period of Record The period of record considered in this investigation is the 52 years from 1949 to 2000. This period of record was chosen because hydrologic and climatological data were limited for the pre-1949 period and data beyond 2000 were not available when the study began. The water year convention (October through September) is used in this report. Crop and Marshland Evapotranspiration Analysis The modified Blaney-Criddle method was used to determine potential net evapotranspiration (ET) from crops, marshlands, and riparian zones. The method is empirical and the calculated values were adjusted based on other recent study findings and water limiting considerations. To estimate net ET water consumption by this method requires the following data: ? Location of irrigated lands, marshlands, and riparian zones ? Types of crops and number of acres for each crop ? Types and acreages of marshland and riparian vegetation, both existing and predevelopment ? Monthly precipitation and monthly average temperature for the period of record for each area Methods to Estimate Natural Flows Natural streamflow development included adjustment of gaged streamflow to natural flow, restoration of missing streamflow and climate data, making natural streamflow estimates in ungaged watersheds, assessing groundwater XII Executive Summary contributions, and estimating transit losses. Not all of these procedures were appropriate or possible in all subbasins of the study area. Records of historic flow may be adjusted to natural flow using crop net consumptive use and marshland evapotranspiration: natural flow = gaged flow + crop net consumptive use - reclaimed natural marshland net evapotranspiration Correlation analysis was used to restore missing values from monthly-value data records used in this study. The method is different from linear least-squares regression estimation. Data records used in this study include precipitation and average temperature histories, in addition to hydrologic records of streamflow and lake stage. Also, natural streamflow histories are required in ungaged watersheds to assess the natural inflow to Upper Klamath Lake. Sparse monthly flow records for streams heading on the east flank of the Cascades and flowing into the Wood River Valley or Pelican Bay area of Upper Klamath Lake required estimation techniques that used gaged histories from nearby river basins. These data were evaluated in statistical applications to yield natural flow estimates for these ungaged portions of the Klamath Basin. In a similar vein, groundwater contributions required temporal adjustments attributable to the climate signature evident in longer term records for similar groundwater discharges in neighboring watersheds. Transit losses for both surface water and groundwater contributions were also estimated in this study. Natural Lake Simulations Implementation of a water budget for Upper Klamath Lake required developing information about (1) the storage and inundation surface area characteristics of the lake, and (2) the discharge characteristics at the outflow point of the lake. These characteristics were evaluated in relation to the elevation, or stage, of the water surface of the lake. Additionally, discharge from the lake was also related to the stage. Estimating the outflow of a natural lake is accomplished using a water budget approach. A monthly summation of all elements in the water budget may be stated by the general form of the hydrologic equation: i = o + As where i = inflow to the lake o = outflow from the lake and As = change in storage of the lake XIII Natural Flow of the Upper Klamath River For Upper Klamath Lake, the month-to-month water budget accounts for natural inflow, storage of water within each lake, resulting estimated lake stage, and discharge from each lake. In addition, open water surface evaporation and groundwater discharge to the lake from the regional aquifer were estimated. The water budget assessment was designed to simulate the lake as a natural water body. Materials and Data Researched and Used Data Sources Records used in this analysis were derived from both stream gaging flow histories and from climatological records for stations within and adjacent to the study area. Information was also developed from published reports, file documents, and maps. Supporting information included documents from: ? Archives of the Bureau of Reclamation Klamath Basin Area Office ? Numerous U.S. Geological Survey (USGS) Water Supply Papers regarding stream gaging records ? Compact disk databases containing digital records of gaged flow, lake stage records, and meteorological data Anecdotal items from newspaper articles or clipped from magazines were also reviewed. These sources consisted of narratives of past events or conditions, transcripts of interviews, newspaper accounts, books, diaries, and historical journals. These provided an impression of predevelopment conditions that can be compared to the empirical and scientific information gleaned from other sources. Other reviewed materials included unpublished and out-of-print scientific reports, historical maps, letters, books, journals, and photographs. Modeling Tools Results of the water budget assessment were accomplished using Excel?, a sophisticated spreadsheet available in the Microsoft Office for Windows software package. This model was chosen over other models because this study is unique. The computational modules built as the study developed represent a custom application of Excel? to the solution of estimating the natural flow conditions in the Upper Klamath River Basin. Klamath River at Keno Gaging Station For the simulation period, 1949 to 2000, the water balance for the Upper Klamath River Basin at Keno is described below. The natural outflow (discharge) from Upper Klamath Lake at Link River was computed in the water balance. Discharge at Keno was then calculated using a correlation relationship developed between historic measured Link River and Keno flows. Table S-l presents the estimated water balance and outflow developed for the Link River and Keno gages. XIV Executive Summary Table S-1. Estimated inflow and outflow developed for Link River and Keno gages Upper Klamath Lake Acre-feet Average annual natural inflow Average annual natural net loss 1,605,000 210,000 Resulting average annual natural outflow 1,395,000 Link River to Keno Average annual natural inflow 1,485,000 Resulting average annual natural outflow at Keno gage 1,306,000 Other Factors Considered The focus of this study is agricultural development in the Upper Klamath River Basin and its effects on natural flow conditions. Other watershed factors have changed since predevelopment. Some of these factors were considered, but are unaccounted-for in the assessment, such as changes in forest conditions or an extension of the flow histories before 1949. Model Review and Sensitivity Analysis Although this study uses best available hydrologic methods and data to either measure or estimate all inflows and outflows to the system, additional concerns have arisen in completing the work. Relationships regarding the significance of uncertainty are likely to be spatially and temporally variable. The key factor is the relative importance of each module in the transit losses suffered by inflows to the natural system. The significance of these influences to model sensitivity is related to time of year or length of time over which flows are evaluated. Model sensitivity is related to uncertainty in data regarding the most significant transit losses; namely, marsh evapotranspiration and open water evaporation. The natural flows developed at Keno are realized, in part, through a statistical rule based model rather than a physically based model. This construct within the model is for the segment from the Link River gage below Upper Klamath Lake, to the Keno gage below Lower Klamath Lake. Thus, sensitivity in testing the spatial and temporal variables within the Link River to Keno reach that affect the flow at Keno is problematic. xv Natural Flow of the Upper Klamath River Summary Development of the natural flows at the Keno gage was accomplished using a spreadsheet modeling approach to resolve the water budget for the Upper Klamath River Basin under undeveloped watershed conditions. The resulting flow duration for simulated natural average monthly flows for Keno gage are described in Table S-2. The percentiles represent the flow exceedence ranges in monthly natural flow estimates at Keno solely due to record length. These percentiles are estimates for modeled baseline conditions and do not reflect data uncertainties for possible changes in evaporation, evapotranspiration, or other factors. Table S-2. Summary of simulated monthly flows at Keno in cfs % Time <= Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sept Annual % Time >= 10 648 1088 1216 1408 1647 1577 1670 1408 1168 631 520 560 1188 90 20 769 1159 1352 1472 1767 1689 2017 1721 1358 822 578 616 1429 80 30 857 1255 1453 1667 1925 1907 2125 2051 1664 964 706 720 1528 70 40 974 1342 1625 1845 2016 2040 2477 2280 1890 1228 767 746 1607 60 50 1033 1455 1698 1964 2343 2133 2595 2649 2039 1349 873 854 1773 50 60 1131 1523 1803 2072 2410 2360 3009 2827 2388 1478 998 955 1903 40 70 1224 1576 1984 2196 2615 2703 3146 3131 2657 1706 1154 1049 2169 30 80 1304 1739 2049 2399 2829 3115 3615 3385 3104 2210 1351 1210 2347 20 90 1488 1815 2319 2659 3294 3367 3877 3707 3460 2923 1684 1412 2511 10 A simplified flowchart depicting the overall sources of included inflow and outflow variables has been completed as figure S-l, with average annual values shown from each source. XVI Title: Natural flow of the upper Klamath River Author: United States. Bureau of Reclamation. Klamath Basin Area Office Year: 2005, 2008 Executive Summary Executive Summary This report presents details of the investigation and results in estimating the natural flow of the upper Klamath River at Keno, Oregon. The area investigated includes the Klamath River Basin above Keno, Oregon, primarily in Klamath County, with some areas of Siskiyou and Modoc Counties in California. The study area includes the Sprague, Williamson, and Wood River basins, as well as Upper Klamath and Lower Klamath Lakes. Objectives The current purpose of this study is to provide an estimate of the monthly natural flows in the upper Klamath River at Keno. This estimate of the natural flow represents typical flow without agricultural development in the Upper Klamath River Basin, including its tributaries. Study Approach This study used a water budget approach to assess the agricultural depletions and alterations to the natural flow. The approach was to evaluate the changes of agriculture from predevelopment conditions, estimate the effects of these changes, and restore the water budget to natural conditions by reversing the effects of agricultural development. Records used in this empirical assessment were derived from both stream gaging flow histories and from climatological records for stations within and adjacent to the study area. Water Budget Description The water budget assessment of the watershed as a natural system includes an evaluation of hydrological changes related to agricultural development above the Keno gage. The water budget assessment includes: ? Natural inflow from the Sprague, Williamson, and Wood Rivers to Upper Klamath Lake ? Predevelopment evapotranspiration losses from marshes surrounding Upper Klamath Lake ? Predevelopment evaporation losses of the Upper Klamath Lake ? Natural flow at the outlet of Upper Klamath Lake into the Link River at Klamath Falls ? Resulting natural flow at Keno The processes developed in the water budget to evaluate the natural outflow of Upper Klamath Lake accounts for factors related to water resources developments XI Natural Flow of the Upper Klamath River in the watershed that have affected inflow to the lake, and for losses due to natural condition of the lake. The water budget assessment of the watershed as a natural system includes an evaluation of hydrological changes related to agricultural development above the Keno gage. The results of the water budget assessment are given as average annual flows for two important stream gages, one located on the Link River at Klamath Falls and the other on the Klamath River at Keno. Evaluation of Predevelopment Conditions An evaluation of predevelopment conditions included an evaluation of changes to Upper Klamath Lake, agricultural developments in the Wood River, Sprague River, and Williamson River watersheds. Several basic elements were considered in this study: ? How had development changed the system ? Was information available about conditions before the changes occurred ? Were data available to assist in estimating changes to the natural system Evaluation of Current Conditions Period of Record The period of record considered in this investigation is the 52 years from 1949 to 2000. This period of record was chosen because hydrologic and climatological data were limited for the pre-1949 period and data beyond 2000 were not available when the study began. The water year convention (October through September) is used in this report. Crop and Marshland Evapotranspiration Analysis The modified Blaney-Criddle method was used to determine potential net evapotranspiration (ET) from crops, marshlands, and riparian zones. The method is empirical and the calculated values were adjusted based on other recent study findings and water limiting considerations. To estimate net ET water consumption by this method requires the following data: ? Location of irrigated lands, marshlands, and riparian zones ? Types of crops and number of acres for each crop ? Types and acreages of marshland and riparian vegetation, both existing and predevelopment ? Monthly precipitation and monthly average temperature for the period of record for each area Methods to Estimate Natural Flows Natural streamflow development included adjustment of gaged streamflow to natural flow, restoration of missing streamflow and climate data, making natural streamflow estimates in ungaged watersheds, assessing groundwater XII Executive Summary contributions, and estimating transit losses. Not all of these procedures were appropriate or possible in all subbasins of the study area. Records of historic flow may be adjusted to natural flow using crop net consumptive use and marshland evapotranspiration: natural flow = gaged flow + crop net consumptive use - reclaimed natural marshland net evapotranspiration Correlation analysis was used to restore missing values from monthly-value data records used in this study. The method is different from linear least-squares regression estimation. Data records used in this study include precipitation and average temperature histories, in addition to hydrologic records of streamflow and lake stage. Also, natural streamflow histories are required in ungaged watersheds to assess the natural inflow to Upper Klamath Lake. Sparse monthly flow records for streams heading on the east flank of the Cascades and flowing into the Wood River Valley or Pelican Bay area of Upper Klamath Lake required estimation techniques that used gaged histories from nearby river basins. These data were evaluated in statistical applications to yield natural flow estimates for these ungaged portions of the Klamath Basin. In a similar vein, groundwater contributions required temporal adjustments attributable to the climate signature evident in longer term records for similar groundwater discharges in neighboring watersheds. Transit losses for both surface water and groundwater contributions were also estimated in this study. Natural Lake Simulations Implementation of a water budget for Upper Klamath Lake required developing information about (1) the storage and inundation surface area characteristics of the lake, and (2) the discharge characteristics at the outflow point of the lake. These characteristics were evaluated in relation to the elevation, or stage, of the water surface of the lake. Additionally, discharge from the lake was also related to the stage. Estimating the outflow of a natural lake is accomplished using a water budget approach. A monthly summation of all elements in the water budget may be stated by the general form of the hydrologic equation: i = o + As where i = inflow to the lake o = outflow from the lake and As = change in storage of the lake XIII Natural Flow of the Upper Klamath River For Upper Klamath Lake, the month-to-month water budget accounts for natural inflow, storage of water within each lake, resulting estimated lake stage, and discharge from each lake. In addition, open water surface evaporation and groundwater discharge to the lake from the regional aquifer were estimated. The water budget assessment was designed to simulate the lake as a natural water body. Materials and Data Researched and Used Data Sources Records used in this analysis were derived from both stream gaging flow histories and from climatological records for stations within and adjacent to the study area. Information was also developed from published reports, file documents, and maps. Supporting information included documents from: ? Archives of the Bureau of Reclamation Klamath Basin Area Office ? Numerous U.S. Geological Survey (USGS) Water Supply Papers regarding stream gaging records ? Compact disk databases containing digital records of gaged flow, lake stage records, and meteorological data Anecdotal items from newspaper articles or clipped from magazines were also reviewed. These sources consisted of narratives of past events or conditions, transcripts of interviews, newspaper accounts, books, diaries, and historical journals. These provided an impression of predevelopment conditions that can be compared to the empirical and scientific information gleaned from other sources. Other reviewed materials included unpublished and out-of-print scientific reports, historical maps, letters, books, journals, and photographs. Modeling Tools Results of the water budget assessment were accomplished using Excel?, a sophisticated spreadsheet available in the Microsoft Office for Windows software package. This model was chosen over other models because this study is unique. The computational modules built as the study developed represent a custom application of Excel? to the solution of estimating the natural flow conditions in the Upper Klamath River Basin. Klamath River at Keno Gaging Station For the simulation period, 1949 to 2000, the water balance for the Upper Klamath River Basin at Keno is described below. The natural outflow (discharge) from Upper Klamath Lake at Link River was computed in the water balance. Discharge at Keno was then calculated using a correlation relationship developed between historic measured Link River and Keno flows. Table S-l presents the estimated water balance and outflow developed for the Link River and Keno gages. XIV Executive Summary Table S-1. Estimated inflow and outflow developed for Link River and Keno gages Upper Klamath Lake Acre-feet Average annual natural inflow Average annual natural net loss 1,605,000 210,000 Resulting average annual natural outflow 1,395,000 Link River to Keno Average annual natural inflow 1,485,000 Resulting average annual natural outflow at Keno gage 1,306,000 Other Factors Considered The focus of this study is agricultural development in the Upper Klamath River Basin and its effects on natural flow conditions. Other watershed factors have changed since predevelopment. Some of these factors were considered, but are unaccounted-for in the assessment, such as changes in forest conditions or an extension of the flow histories before 1949. Model Review and Sensitivity Analysis Although this study uses best available hydrologic methods and data to either measure or estimate all inflows and outflows to the system, additional concerns have arisen in completing the work. Relationships regarding the significance of uncertainty are likely to be spatially and temporally variable. The key factor is the relative importance of each module in the transit losses suffered by inflows to the natural system. The significance of these influences to model sensitivity is related to time of year or length of time over which flows are evaluated. Model sensitivity is related to uncertainty in data regarding the most significant transit losses; namely, marsh evapotranspiration and open water evaporation. The natural flows developed at Keno are realized, in part, through a statistical rule based model rather than a physically based model. This construct within the model is for the segment from the Link River gage below Upper Klamath Lake, to the Keno gage below Lower Klamath Lake. Thus, sensitivity in testing the spatial and temporal variables within the Link River to Keno reach that affect the flow at Keno is problematic. xv Natural Flow of the Upper Klamath River Summary Development of the natural flows at the Keno gage was accomplished using a spreadsheet modeling approach to resolve the water budget for the Upper Klamath River Basin under undeveloped watershed conditions. The resulting flow duration for simulated natural average monthly flows for Keno gage are described in Table S-2. The percentiles represent the flow exceedence ranges in monthly natural flow estimates at Keno solely due to record length. These percentiles are estimates for modeled baseline conditions and do not reflect data uncertainties for possible changes in evaporation, evapotranspiration, or other factors. Table S-2. Summary of simulated monthly flows at Keno in cfs % Time <= Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sept Annual % Time >= 10 648 1088 1216 1408 1647 1577 1670 1408 1168 631 520 560 1188 90 20 769 1159 1352 1472 1767 1689 2017 1721 1358 822 578 616 1429 80 30 857 1255 1453 1667 1925 1907 2125 2051 1664 964 706 720 1528 70 40 974 1342 1625 1845 2016 2040 2477 2280 1890 1228 767 746 1607 60 50 1033 1455 1698 1964 2343 2133 2595 2649 2039 1349 873 854 1773 50 60 1131 1523 1803 2072 2410 2360 3009 2827 2388 1478 998 955 1903 40 70 1224 1576 1984 2196 2615 2703 3146 3131 2657 1706 1154 1049 2169 30 80 1304 1739 2049 2399 2829 3115 3615 3385 3104 2210 1351 1210 2347 20 90 1488 1815 2319 2659 3294 3367 3877 3707 3460 2923 1684 1412 2511 10 A simplified flowchart depicting the overall sources of included inflow and outflow variables has been completed as figure S-l, with average annual values shown from each source. XVI 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