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• 1. [Image] Klamath Falls Resource Area resource management plan and environmental impact statement : final : Volume 3

  	Proposed resource management plan/final environmental impact statement for the Klamath Falls Resource Area
  	Citation × Citation Citation Abstract Copy Title: Klamath Falls Resource Area resource management plan and environmental impact statement : final : Volume 3 Author: United States. Bureau of Land Management. Klamath Falls Resource Area Office Year: 1994, 2005 Proposed resource management plan/final environmental impact statement for the Klamath Falls Resource Area Title: Klamath Falls Resource Area resource management plan and environmental impact statement : final : Volume 3 Author: United States. Bureau of Land Management. Klamath Falls Resource Area Office Year: 1994, 2005 Proposed resource management plan/final environmental impact statement for the Klamath Falls Resource Area Close

• 2. [Image] Influences of human activity on stream temperatures and existence of cold-water fish in streams with elevated temperature: report of a workshop: Independent Multidisciplinary Science Team, Corvallis, OR, October 5-6, 2000

  	Executive Summary The Independent Multidisciplinary Science Team (IMST) convened a panel of experts on stream temperature and fish ecology on October 5-6, 2000 for a scientific workshop on human influences ...
  	Citation × Citation Citation Abstract Copy Title: Influences of human activity on stream temperatures and existence of cold-water fish in streams with elevated temperature: report of a workshop: Independent Multidisciplinary Science Team, Corvallis, OR, October 5-6, 2000 Author: Independent Multidisciplinary Science Team (Oregon) Year: 2000, 2008, 2005 Executive Summary The Independent Multidisciplinary Science Team (IMST) convened a panel of experts on stream temperature and fish ecology on October 5-6, 2000 for a scientific workshop on human influences on stream temperature and responses by salmonids. The workshop was designed to review and discuss scientifically credible data and publications about 1) factors related to human activity that influence stream temperature and 2) behavioral, physical, and ecological mechanisms of cold water fish species for existing in streams with elevated temperatures. The goal of the workshop was to review empirical evidence and to identify points of agreement, disagreement, and knowledge gaps within the scientific community concerning the factors that influence stream temperature and fish responses to elevated temperatures. This information will assist the IMST in preparing a broader temperature report on Oregon's stream temperature water quality standards and their implementation. This report is prepared by the IMST. It was reviewed by workshop participants and revised by the IMST accordingly. The report includes abstracts of plenary presentations on factors that influence stream temperatures and fish responses, and the results of group discussions. The workshop participants focused on three main questions and were asked to list statements of agreement and disagreement, and to identify gaps in the scientific knowledge related to each question: ? How and where does riparian vegetation influence stream temperature? ? Do other changes in streams cause increases in stream temperature? ? How can apparently healthy fish populations exist in streams with temperatures higher than laboratory and field studies would indicate as healthy? The workshop participants provided answers to the questions in the form of bullets. The answers below represent the IMST's summation of the workshop findings and were reviewed by the participants. Several gaps in the scientific basis for specific questions or relationships were identified. The participants found no areas of disagreement for which technical information was available. They noted that any disagreements were not related to scientific interpretation, but were based on concerns or opinions about application, regulation, and management. How and where does riparian vegetation influence stream temperature? The influence of riparian vegetation on stream temperature is cumulative and complex, varying by site, over time, and across regions. Riparian vegetation can directly affect stream temperature by intercepting solar radiation and reducing stream heating. The influence of riparian shade in controlling temperature declines as streams widen in downstream reaches, but the role of riparian vegetation in providing water quality and fish habitat benefits continues to be important. Besides providing shade, riparian vegetation can also indirectly affect stream temperature by influencing microclimate, affecting channel morphology, affecting stream flow, influencing wind speed, affecting humidity, affecting soil temperature, using water, influencing air temperature, enhancing infiltration, and influencing thermal radiation. It is critical to know the site potential to understand what vegetation a site can support. There is not a good scientific understanding of how much vegetation shading is required to affect stream temperature. 1 This lack of understanding may be due to the spatial and temporal variability in landscape components, and the resulting variability in both the direct and indirect influences of vegetation on stream temperature. Therefore, it is difficult to generalize about the effects of vegetation on stream temperature. Do other changes in streams cause increases in stream temperature? The answer to this question is yes, other physical changes in the stream system can modify stream temperatures. Stream temperature is a product of complex interactions between geomorphology, soil, hydrology, vegetation, and climate within a watershed. Changes in these factors will result in changes in stream temperature. Human activities influence stream temperature by affecting one or more of four major components: riparian vegetation, channel morphology, hydrology, and surface/subsurface interactions. Stream systems vary substantially across the landscape, and site-specific information is critical to understanding stream temperature responses to human activities. How can apparently healthy fish populations exist in streams with temperatures higher than laboratory and field studies would indicate as healthy? Workshop participants identified several mechanisms that might explain the ability of fish populations to exist at higher than expected temperatures. The first mechanism was that the fish may have physiological adaptations to survive exposures to high temperatures. A second possibility was that stream habitats may contain cooler microhabitats that fish can occupy as refuge from higher temperatures. A third consideration is that ecological interactions may be different under differing thermal conditions resulting, for example, in changes in disease virulence or cumulative effects of stressors. Finally, since substantial differences exist between laboratory and field studies, it is difficult to apply results of laboratory studies to fish responses in the field. It is important to note that these proposed mechanisms are speculative and, as the list of gaps indicates, substantial experimental work is required to establish their influences on fish in different stream systems. Workshop Summaiy Workshop participants recognized gaps in the available science. Additional knowledge about human influences on stream temperatures and, consequently, influences on cold-water fish populations, will improve our ability to prevent further degradation of stream habitat and will enhance efforts geared towards the recovery of depressed fish populations. Even with these gaps, there was enough agreement on factors that influence stream temperature to indicate information is available to start developing and implementing management practices that are designed to reduce stream warming. It was suggested that managers should consider riparian vegetation, channel morphology, and hydrology, and should account for site differences. Title: Influences of human activity on stream temperatures and existence of cold-water fish in streams with elevated temperature: report of a workshop: Independent Multidisciplinary Science Team, Corvallis, OR, October 5-6, 2000 Author: Independent Multidisciplinary Science Team (Oregon) Year: 2000, 2008, 2005 Executive Summary The Independent Multidisciplinary Science Team (IMST) convened a panel of experts on stream temperature and fish ecology on October 5-6, 2000 for a scientific workshop on human influences on stream temperature and responses by salmonids. The workshop was designed to review and discuss scientifically credible data and publications about 1) factors related to human activity that influence stream temperature and 2) behavioral, physical, and ecological mechanisms of cold water fish species for existing in streams with elevated temperatures. The goal of the workshop was to review empirical evidence and to identify points of agreement, disagreement, and knowledge gaps within the scientific community concerning the factors that influence stream temperature and fish responses to elevated temperatures. This information will assist the IMST in preparing a broader temperature report on Oregon's stream temperature water quality standards and their implementation. This report is prepared by the IMST. It was reviewed by workshop participants and revised by the IMST accordingly. The report includes abstracts of plenary presentations on factors that influence stream temperatures and fish responses, and the results of group discussions. The workshop participants focused on three main questions and were asked to list statements of agreement and disagreement, and to identify gaps in the scientific knowledge related to each question: ? How and where does riparian vegetation influence stream temperature? ? Do other changes in streams cause increases in stream temperature? ? How can apparently healthy fish populations exist in streams with temperatures higher than laboratory and field studies would indicate as healthy? The workshop participants provided answers to the questions in the form of bullets. The answers below represent the IMST's summation of the workshop findings and were reviewed by the participants. Several gaps in the scientific basis for specific questions or relationships were identified. The participants found no areas of disagreement for which technical information was available. They noted that any disagreements were not related to scientific interpretation, but were based on concerns or opinions about application, regulation, and management. How and where does riparian vegetation influence stream temperature? The influence of riparian vegetation on stream temperature is cumulative and complex, varying by site, over time, and across regions. Riparian vegetation can directly affect stream temperature by intercepting solar radiation and reducing stream heating. The influence of riparian shade in controlling temperature declines as streams widen in downstream reaches, but the role of riparian vegetation in providing water quality and fish habitat benefits continues to be important. Besides providing shade, riparian vegetation can also indirectly affect stream temperature by influencing microclimate, affecting channel morphology, affecting stream flow, influencing wind speed, affecting humidity, affecting soil temperature, using water, influencing air temperature, enhancing infiltration, and influencing thermal radiation. It is critical to know the site potential to understand what vegetation a site can support. There is not a good scientific understanding of how much vegetation shading is required to affect stream temperature. 1 This lack of understanding may be due to the spatial and temporal variability in landscape components, and the resulting variability in both the direct and indirect influences of vegetation on stream temperature. Therefore, it is difficult to generalize about the effects of vegetation on stream temperature. Do other changes in streams cause increases in stream temperature? The answer to this question is yes, other physical changes in the stream system can modify stream temperatures. Stream temperature is a product of complex interactions between geomorphology, soil, hydrology, vegetation, and climate within a watershed. Changes in these factors will result in changes in stream temperature. Human activities influence stream temperature by affecting one or more of four major components: riparian vegetation, channel morphology, hydrology, and surface/subsurface interactions. Stream systems vary substantially across the landscape, and site-specific information is critical to understanding stream temperature responses to human activities. How can apparently healthy fish populations exist in streams with temperatures higher than laboratory and field studies would indicate as healthy? Workshop participants identified several mechanisms that might explain the ability of fish populations to exist at higher than expected temperatures. The first mechanism was that the fish may have physiological adaptations to survive exposures to high temperatures. A second possibility was that stream habitats may contain cooler microhabitats that fish can occupy as refuge from higher temperatures. A third consideration is that ecological interactions may be different under differing thermal conditions resulting, for example, in changes in disease virulence or cumulative effects of stressors. Finally, since substantial differences exist between laboratory and field studies, it is difficult to apply results of laboratory studies to fish responses in the field. It is important to note that these proposed mechanisms are speculative and, as the list of gaps indicates, substantial experimental work is required to establish their influences on fish in different stream systems. Workshop Summaiy Workshop participants recognized gaps in the available science. Additional knowledge about human influences on stream temperatures and, consequently, influences on cold-water fish populations, will improve our ability to prevent further degradation of stream habitat and will enhance efforts geared towards the recovery of depressed fish populations. Even with these gaps, there was enough agreement on factors that influence stream temperature to indicate information is available to start developing and implementing management practices that are designed to reduce stream warming. It was suggested that managers should consider riparian vegetation, channel morphology, and hydrology, and should account for site differences. Close

• 3. [Article] A Stable Isotopic Investigation of a Polar Desert Hydrologic System, McMurdo Dry Valleys, Antarctica

  The hydrologic system of the coastal McMurdo Dry Valleys, Antarctica, is defined by snow accumulation, glacier melt, stream flow, and retention in closed-basin, ice-covered lakes. During the austral summers ...

  Citation × Citation Citation Abstract Copy Title: A Stable Isotopic Investigation of a Polar Desert Hydrologic System, McMurdo Dry Valleys, Antarctica Author: Gooseff, Michael N., Lyons, W. Berry, McKnight, Diane M., Vaughn, Bruce H., Fountain, Andrew G., Dowling, Carolyn Year: 2006 The hydrologic system of the coastal McMurdo Dry Valleys, Antarctica, is defined by snow accumulation, glacier melt, stream flow, and retention in closed-basin, ice-covered lakes. During the austral summers from 1993-1996 and 1999-2000 to 2002-2003, fresh snow, snow pits, glacier ice, stream water, and lake waters were sampled for the stable isotopes deuterium (D) and 18O in order to resolve sources of meltwater and the interactions among the various hydrologic reservoirs in the dry valleys. This data set provides a survey of the distribution of natural water isotope abundances within the well-defined dry valley hydrologic system in Taylor Valley, which extends 20 km inland from McMurdo Sound. The three major Taylor Valley lakes are not connected to one another hydrologically, and their levels are maintained by glacial meltwater inflow and perennial ice-cover sublimation. At the valley scale, glacial ice, snow, stream, and lake waters become more depleted in delta D with increasing distance from McMurdo Sound (further inland). Snow pack in glacial accumulation zones is heterogeneous, likely a result of varying storm sources (continental versus coastal), and, in general, snow pits, fresh snow samples, and glacier ice are more depleted than stream waters. Within the lake basins, glacial ice source waters are depleted by as much as 111ppm delta D and 20 ppm delta 18O compared to lake waters. These results demonstrate the importance of in-stream fractionation at the valley scale. In-stream fractionation occurs through direct evaporation from the channel and hyporheic exchange with isotopically enriched waters in the near-stream subsurface during transport from the glacial source to lake. Furthermore, the results show that lake waters directly reflect their glacial ice sources, despite fractionation during stream transport. Inter-annual comparisons of lake profiles suggest that lake waters are directly influenced by the isotopic composition and amount of stream flow during a season. Title: A Stable Isotopic Investigation of a Polar Desert Hydrologic System, McMurdo Dry Valleys, Antarctica Author: Gooseff, Michael N., Lyons, W. Berry, McKnight, Diane M., Vaughn, Bruce H., Fountain, Andrew G., Dowling, Carolyn Year: 2006 The hydrologic system of the coastal McMurdo Dry Valleys, Antarctica, is defined by snow accumulation, glacier melt, stream flow, and retention in closed-basin, ice-covered lakes. During the austral summers from 1993-1996 and 1999-2000 to 2002-2003, fresh snow, snow pits, glacier ice, stream water, and lake waters were sampled for the stable isotopes deuterium (D) and 18O in order to resolve sources of meltwater and the interactions among the various hydrologic reservoirs in the dry valleys. This data set provides a survey of the distribution of natural water isotope abundances within the well-defined dry valley hydrologic system in Taylor Valley, which extends 20 km inland from McMurdo Sound. The three major Taylor Valley lakes are not connected to one another hydrologically, and their levels are maintained by glacial meltwater inflow and perennial ice-cover sublimation. At the valley scale, glacial ice, snow, stream, and lake waters become more depleted in delta D with increasing distance from McMurdo Sound (further inland). Snow pack in glacial accumulation zones is heterogeneous, likely a result of varying storm sources (continental versus coastal), and, in general, snow pits, fresh snow samples, and glacier ice are more depleted than stream waters. Within the lake basins, glacial ice source waters are depleted by as much as 111ppm delta D and 20 ppm delta 18O compared to lake waters. These results demonstrate the importance of in-stream fractionation at the valley scale. In-stream fractionation occurs through direct evaporation from the channel and hyporheic exchange with isotopically enriched waters in the near-stream subsurface during transport from the glacial source to lake. Furthermore, the results show that lake waters directly reflect their glacial ice sources, despite fractionation during stream transport. Inter-annual comparisons of lake profiles suggest that lake waters are directly influenced by the isotopic composition and amount of stream flow during a season. Close

• 4. [Article] Modeling Effects of Channel Complexity and Hyporheic Flow on Stream Temperatures

  Stream temperatures are affected by multiple forcing functions, including surface heat exchange (including solar radiation, evaporation, conduction, and net long wave radiation) and hyporheic flows. Each ...

  Citation × Citation Citation Abstract Copy Title: Modeling Effects of Channel Complexity and Hyporheic Flow on Stream Temperatures Author: Berger, Chris, Wells, Scott A. Year: 2007 Stream temperatures are affected by multiple forcing functions, including surface heat exchange (including solar radiation, evaporation, conduction, and net long wave radiation) and hyporheic flows. Each of these forcing functions is directly influenced by the level of channel complexity in the stream channel and riparian shading. The interrelationship between channel complexity, hyporheic flow and stream temperature is highly complex, and efforts to manage for habitat diversity by managing channel complexity could result in unintended consequences on stream temperature. When planning modifications to stream channel complexity, consideration should be given to the effects such moderations could have on stream temperatures. Urbanization has impacted many steams due to the construction of bank protections, levees, vegetation removal, etc. Such activities have eliminated side channels and reduced stream braiding, thereby reducing the overall channel complexity. Hulse et al. (2002) developed maps showing the channel configurations of the Willamette River in Oregon, USA in the years 1850 and 1995. These maps show a significant reduction in channel complexity in the intervening years. More complex stream channels provide greater habitat diversity and thus, are generally more desirable from a wildlife management perspective. Therefore, management of streams for increased channel complexity is gaining in popularity. Knowing that stream channel complexity has diminished over time, an important question to consider is ‘what were stream temperatures before we altered the natural channels?’ This is an important issue in determining what natural conditions were and how we have strayed from these so-called ‘natural’ conditions as a result of channelization, dam building, and changes to the riparian vegetation and deforestation. Current Total Maximum Daily Load’s (TMDL) rely on determining a ‘natural’ condition. In order to develop an understanding of what that is, a hydrodynamic and water quality computer simulation model has been applied to Oregon’s Willamette River with several levels of channel complexity and varying rates of hyporheic flows. Adapting the model used to develop TMDL’s for temperature in the Willamette River, the effects of present and past channel complexity on water temperatures was determined. The model used to develop the TMDL was the U. S. Army Corps of Engineers dynamic 2-D model CE-QUAL-W2, which consists of directly coupled hydrodynamic and water quality transport models and simulates parameters such as temperature, algae concentration, dissolved oxygen concentration, pH, nutrient concentrations and residence time. The model also incorporates a dynamic shading algorithm for both vegetative and topographic shading on water bodies. Title: Modeling Effects of Channel Complexity and Hyporheic Flow on Stream Temperatures Author: Berger, Chris, Wells, Scott A. Year: 2007 Stream temperatures are affected by multiple forcing functions, including surface heat exchange (including solar radiation, evaporation, conduction, and net long wave radiation) and hyporheic flows. Each of these forcing functions is directly influenced by the level of channel complexity in the stream channel and riparian shading. The interrelationship between channel complexity, hyporheic flow and stream temperature is highly complex, and efforts to manage for habitat diversity by managing channel complexity could result in unintended consequences on stream temperature. When planning modifications to stream channel complexity, consideration should be given to the effects such moderations could have on stream temperatures. Urbanization has impacted many steams due to the construction of bank protections, levees, vegetation removal, etc. Such activities have eliminated side channels and reduced stream braiding, thereby reducing the overall channel complexity. Hulse et al. (2002) developed maps showing the channel configurations of the Willamette River in Oregon, USA in the years 1850 and 1995. These maps show a significant reduction in channel complexity in the intervening years. More complex stream channels provide greater habitat diversity and thus, are generally more desirable from a wildlife management perspective. Therefore, management of streams for increased channel complexity is gaining in popularity. Knowing that stream channel complexity has diminished over time, an important question to consider is ‘what were stream temperatures before we altered the natural channels?’ This is an important issue in determining what natural conditions were and how we have strayed from these so-called ‘natural’ conditions as a result of channelization, dam building, and changes to the riparian vegetation and deforestation. Current Total Maximum Daily Load’s (TMDL) rely on determining a ‘natural’ condition. In order to develop an understanding of what that is, a hydrodynamic and water quality computer simulation model has been applied to Oregon’s Willamette River with several levels of channel complexity and varying rates of hyporheic flows. Adapting the model used to develop TMDL’s for temperature in the Willamette River, the effects of present and past channel complexity on water temperatures was determined. The model used to develop the TMDL was the U. S. Army Corps of Engineers dynamic 2-D model CE-QUAL-W2, which consists of directly coupled hydrodynamic and water quality transport models and simulates parameters such as temperature, algae concentration, dissolved oxygen concentration, pH, nutrient concentrations and residence time. The model also incorporates a dynamic shading algorithm for both vegetative and topographic shading on water bodies. Close

• 5. [Article] Changes in hyporheic exchange flow following experimental wood removal in a small, low-gradient stream

  This is the publisher’s final pdf. The published article is copyrighted by the American Geophysical Union and can be found at: http://www.agu.org/journals/wr/.

  Citation × Citation Citation Abstract Copy Title: Changes in hyporheic exchange flow following experimental wood removal in a small, low-gradient stream Author: Haggerty, Roy, Edwards, Richard T., LaNier, Justin, Wondzell, Steven M., Woodsmith, Richard D. This is the publisher’s final pdf. The published article is copyrighted by the American Geophysical Union and can be found at: http://www.agu.org/journals/wr/. Title: Changes in hyporheic exchange flow following experimental wood removal in a small, low-gradient stream Author: Haggerty, Roy, Edwards, Richard T., LaNier, Justin, Wondzell, Steven M., Woodsmith, Richard D. This is the publisher’s final pdf. The published article is copyrighted by the American Geophysical Union and can be found at: http://www.agu.org/journals/wr/. Close

• 6. [Article] Determining in-channel (dead zone) transient storage by comparing solute transport in a bedrock channel–alluvial channel sequence, Oregon

  This is the publisher’s final pdf. The published article is copyrighted by the American Geophysical Union and can be found at: http://www.agu.org/journals/wr/.

  Citation × Citation Citation Abstract Copy Title: Determining in-channel (dead zone) transient storage by comparing solute transport in a bedrock channel–alluvial channel sequence, Oregon Author: Haggerty, Roy, Gooseff, Michael N., LaNier, Justin, Kokkeler, Kenneth This is the publisher’s final pdf. The published article is copyrighted by the American Geophysical Union and can be found at: http://www.agu.org/journals/wr/. Title: Determining in-channel (dead zone) transient storage by comparing solute transport in a bedrock channel–alluvial channel sequence, Oregon Author: Haggerty, Roy, Gooseff, Michael N., LaNier, Justin, Kokkeler, Kenneth This is the publisher’s final pdf. The published article is copyrighted by the American Geophysical Union and can be found at: http://www.agu.org/journals/wr/. Close

• 7. [Article] A fluid-mechanics based classification scheme for surface transient storage in riverine environments: quantitatively separating surface from hyporheic transient storage

  This is the publisher’s final pdf. The published article is copyrighted by Copernicus Publications and can be found at: [http://publications.copernicus.org/.

  Citation × Citation Citation Abstract Copy Title: A fluid-mechanics based classification scheme for surface transient storage in riverine environments: quantitatively separating surface from hyporheic transient storage Author: Jackson, T. R., Haggerty, R., Apte, Sourabh V. This is the publisher’s final pdf. The published article is copyrighted by Copernicus Publications and can be found at: [http://publications.copernicus.org/. Title: A fluid-mechanics based classification scheme for surface transient storage in riverine environments: quantitatively separating surface from hyporheic transient storage Author: Jackson, T. R., Haggerty, R., Apte, Sourabh V. This is the publisher’s final pdf. The published article is copyrighted by Copernicus Publications and can be found at: [http://publications.copernicus.org/. Close

• 8. [Article] Spatial and Temporal Variability of Macroinvertebrates in Spawning and Non-Spawning Habitats during a Salmon Run in Southeast Alaska

  This is the publisher’s final pdf. The published article is copyrighted by PLoS ONE and can be found at: http://www.plosone.org/home.action.

  Citation × Citation Citation Abstract Copy Title: Spatial and Temporal Variability of Macroinvertebrates in Spawning and Non-Spawning Habitats during a Salmon Run in Southeast Alaska Author: Merritt, Richard W., Campbell, Emily Y., Benbow, M. Eric, Cummins, Kenneth W. This is the publisher’s final pdf. The published article is copyrighted by PLoS ONE and can be found at: http://www.plosone.org/home.action. Title: Spatial and Temporal Variability of Macroinvertebrates in Spawning and Non-Spawning Habitats during a Salmon Run in Southeast Alaska Author: Merritt, Richard W., Campbell, Emily Y., Benbow, M. Eric, Cummins, Kenneth W. This is the publisher’s final pdf. The published article is copyrighted by PLoS ONE and can be found at: http://www.plosone.org/home.action. Close

• 9. [Article] Geomorphic controls on hyporheic exchange flow in mountain streams

  Simulations of stream-subsurface water exchange (hyporheic exchange) using a three-dimensional steady state groundwater flow model and a particle tracking model in unconstrained and constrained reaches ...

  Citation × Citation Citation Abstract Copy Title: Geomorphic controls on hyporheic exchange flow in mountain streams Author: Kasahara, Tamao Simulations of stream-subsurface water exchange (hyporheic exchange) using a three-dimensional steady state groundwater flow model and a particle tracking model in unconstrained and constrained reaches of small (2nd-order) and intermediate (5th-order) mountain streams were conducted to estimate the effects of geomorphic features on the extent, volume and residence time of hyporheic exchange flow. Study sites were located in the Lookout Creek drainage in the western Cascades of Oregon. Stream water and water table elevations and saturated hydraulic conductivity were collected from four field sites. Steps were the dominant geomorphic features creating vertical complexity in 2nd-order streams and dominating hyporheic exchange flow. The removal of steps from the simulation models of 2nd-order stream reduced the total volume of hyporheic exchange by 54 %. Furthermore, hyporheic exchange flows resulting from steps had relatively short residence times. Horizontal complexity, resulting from secondary channels and channel splits, had strong effects on hyporheic exchange, as did vertically extensive features, such as riffles, in 5th-order streams. Removal of secondary channels, channel splits and riffles from the simulation models reduced hyporheic exchange flow by 25 %, 30 % and 40 %, respectively. Secondary channels contributed to hyporheic exchange with relatively long residence time, where as channel splits and riffles contributed to hyporheic exchange with short residence time. Thus, multiple features strongly contributed to the creation of hyporheic exchange flow and drove various types of the exchange flows. Also, the simulation results and stream survey showed that the interactions between multiple features, for example secondary channels and riffles, enhanced hyporheic exchange. Because horizontally extensive features were important in driving hyporheic exchange flow in the studied unconstrained reaches, the width of the valley floor strongly controlled hyporheic exchange flow in 5th-order streams. Geomorphic controls on hyporheic exchange flow differed between the two stream sizes sampled. Second-order streams had a single key geomorphic feature (i.e. steps) influencing the hyporheic exchange flow, whereas multiple geomorphic features (i.e. riffles, secondary channels and channel splits) were important in 5 b-order streams. As a result, residence time distribution of hyporheic exchange flow was narrow in 2nd- order stream and wide in 5th-order stream. Title: Geomorphic controls on hyporheic exchange flow in mountain streams Author: Kasahara, Tamao Simulations of stream-subsurface water exchange (hyporheic exchange) using a three-dimensional steady state groundwater flow model and a particle tracking model in unconstrained and constrained reaches of small (2nd-order) and intermediate (5th-order) mountain streams were conducted to estimate the effects of geomorphic features on the extent, volume and residence time of hyporheic exchange flow. Study sites were located in the Lookout Creek drainage in the western Cascades of Oregon. Stream water and water table elevations and saturated hydraulic conductivity were collected from four field sites. Steps were the dominant geomorphic features creating vertical complexity in 2nd-order streams and dominating hyporheic exchange flow. The removal of steps from the simulation models of 2nd-order stream reduced the total volume of hyporheic exchange by 54 %. Furthermore, hyporheic exchange flows resulting from steps had relatively short residence times. Horizontal complexity, resulting from secondary channels and channel splits, had strong effects on hyporheic exchange, as did vertically extensive features, such as riffles, in 5th-order streams. Removal of secondary channels, channel splits and riffles from the simulation models reduced hyporheic exchange flow by 25 %, 30 % and 40 %, respectively. Secondary channels contributed to hyporheic exchange with relatively long residence time, where as channel splits and riffles contributed to hyporheic exchange with short residence time. Thus, multiple features strongly contributed to the creation of hyporheic exchange flow and drove various types of the exchange flows. Also, the simulation results and stream survey showed that the interactions between multiple features, for example secondary channels and riffles, enhanced hyporheic exchange. Because horizontally extensive features were important in driving hyporheic exchange flow in the studied unconstrained reaches, the width of the valley floor strongly controlled hyporheic exchange flow in 5th-order streams. Geomorphic controls on hyporheic exchange flow differed between the two stream sizes sampled. Second-order streams had a single key geomorphic feature (i.e. steps) influencing the hyporheic exchange flow, whereas multiple geomorphic features (i.e. riffles, secondary channels and channel splits) were important in 5 b-order streams. As a result, residence time distribution of hyporheic exchange flow was narrow in 2nd- order stream and wide in 5th-order stream. Close

• 10. [Article] Patterns in stream geomorphology and implications for hyporheic exchange flow

  Longitudinal water surface profiles from high-gradient mountain streams provide useful indicators of the relative potential for hyporheic exchange flow in stream reaches with varying morphology. The spacing ...

  Citation × Citation Citation Abstract Copy Title: Patterns in stream geomorphology and implications for hyporheic exchange flow Author: Anderson, Justin K. Longitudinal water surface profiles from high-gradient mountain streams provide useful indicators of the relative potential for hyporheic exchange flow in stream reaches with varying morphology. The spacing between slope breaks in step-pool and pool-riffle streams provides a geomorphic scaling metric that indicates how the length of average hyporheic flow paths change throughout the river continuum. Twelve stream reaches were randomly selected and surveyed in the Lookout Creek basin at the H.J. Andrews Experimental Forest in the western Cascades Mountains of Oregon. Stream reach morphology was examined for patterns that are expressed over a continuum ranging from headwater to mid-order streams that can be predicted from easily measured drainage basin characteristics. Simple and multiple linear regression models were used to predict changes in lateral complexity in stream reaches, and to predict how the general shape of the water surface profile changes as drainage basin area increases from 0.6 km² to 62.3 km². Patterns in the lateral complexity of stream reaches were associated with the degree of channel confinement in valley segments, and longitudinal patterns in bed configuration were strongly associated with the position of a stream reach within the river continuum. Stream reach longitudinal profiles were evaluated to determine how patterns in slope breaks change throughout the portion of the river continuum represented by the study area. Channel units were defined according to slope categories for flat water, steep water, and step units (FLATs, STEEPs and STEPs). A set of regression models was used to predict how slope break spacing and the general shape of the water surface profile change as drainage basin area increases from 0.6 km² to 62.3 km². Output from these regression equations was tested against independent field data to evaluate model performance. The models generally performed well. Longitudinal transects of piezometers were installed along the thalweg of a second order, and a third order stream reach. Longitudinal profiles in the piezometer transects were surveyed, and piezometers were used to measure hydraulic head in stream beds. Data were used to test a theoretical model that predicts downwelling where stream profiles are convex, and upwelling where stream profiles are concave. Overall, the shape of the water surface profile explained 38% of the variation in the distribution of hydraulic pressure head in the streambed. Results demonstrated the usefulness of quantifying the magnitude of concavities and convexities in stream profiles. A metric for expressing the average water surface concavity (AWSC) is proposed. I demonstrated that this metric could be useful for comparing the potential for hyporheic exchange in stream reaches with varying degrees of stream profile roughness. Results showed a decreasing trend in AWSC as drainage basin area increased. Upwelling and downwelling zones were identified in piezometer transects, and their longitudinal lengths were measured. The lengths of downwelling zones were compared to the spacing between slope breaks in the water surface profile. Average lengths of downwelling zones and FLAT channel slope units increased with increasing basin area at a similar rate, indicating that slope break spacing was a useful indicator for average downwelling zone length. My results demonstrate that patterns in stream morphology are useful for predicting patterns in hyporheic exchange flow throughout the river continuum. I suggest that the potential for gravity driven exchange flow decreases along the river continuum as AWSC decreases. I also suggest that the frequency of hydrologic exchange between the stream and the hyporheic zone decreases, and that the average length of hyporheic flow paths increase, across the river continuum. Title: Patterns in stream geomorphology and implications for hyporheic exchange flow Author: Anderson, Justin K. Longitudinal water surface profiles from high-gradient mountain streams provide useful indicators of the relative potential for hyporheic exchange flow in stream reaches with varying morphology. The spacing between slope breaks in step-pool and pool-riffle streams provides a geomorphic scaling metric that indicates how the length of average hyporheic flow paths change throughout the river continuum. Twelve stream reaches were randomly selected and surveyed in the Lookout Creek basin at the H.J. Andrews Experimental Forest in the western Cascades Mountains of Oregon. Stream reach morphology was examined for patterns that are expressed over a continuum ranging from headwater to mid-order streams that can be predicted from easily measured drainage basin characteristics. Simple and multiple linear regression models were used to predict changes in lateral complexity in stream reaches, and to predict how the general shape of the water surface profile changes as drainage basin area increases from 0.6 km² to 62.3 km². Patterns in the lateral complexity of stream reaches were associated with the degree of channel confinement in valley segments, and longitudinal patterns in bed configuration were strongly associated with the position of a stream reach within the river continuum. Stream reach longitudinal profiles were evaluated to determine how patterns in slope breaks change throughout the portion of the river continuum represented by the study area. Channel units were defined according to slope categories for flat water, steep water, and step units (FLATs, STEEPs and STEPs). A set of regression models was used to predict how slope break spacing and the general shape of the water surface profile change as drainage basin area increases from 0.6 km² to 62.3 km². Output from these regression equations was tested against independent field data to evaluate model performance. The models generally performed well. Longitudinal transects of piezometers were installed along the thalweg of a second order, and a third order stream reach. Longitudinal profiles in the piezometer transects were surveyed, and piezometers were used to measure hydraulic head in stream beds. Data were used to test a theoretical model that predicts downwelling where stream profiles are convex, and upwelling where stream profiles are concave. Overall, the shape of the water surface profile explained 38% of the variation in the distribution of hydraulic pressure head in the streambed. Results demonstrated the usefulness of quantifying the magnitude of concavities and convexities in stream profiles. A metric for expressing the average water surface concavity (AWSC) is proposed. I demonstrated that this metric could be useful for comparing the potential for hyporheic exchange in stream reaches with varying degrees of stream profile roughness. Results showed a decreasing trend in AWSC as drainage basin area increased. Upwelling and downwelling zones were identified in piezometer transects, and their longitudinal lengths were measured. The lengths of downwelling zones were compared to the spacing between slope breaks in the water surface profile. Average lengths of downwelling zones and FLAT channel slope units increased with increasing basin area at a similar rate, indicating that slope break spacing was a useful indicator for average downwelling zone length. My results demonstrate that patterns in stream morphology are useful for predicting patterns in hyporheic exchange flow throughout the river continuum. I suggest that the potential for gravity driven exchange flow decreases along the river continuum as AWSC decreases. I also suggest that the frequency of hydrologic exchange between the stream and the hyporheic zone decreases, and that the average length of hyporheic flow paths increase, across the river continuum. Close

• 11. [Article] Economic analysis of restoration practices to improve water quality and fish habitat of a large river floodplain : a case study of the Willamette River, Oregon

  In- stream water temperature is one of the most important environmental factors associated with the decline in salmonid populations and their habitats in the Pacific Northwest. Most ecological restoration ...

  Citation × Citation Citation Abstract Copy Title: Economic analysis of restoration practices to improve water quality and fish habitat of a large river floodplain : a case study of the Willamette River, Oregon Author: Seedang, Saichon In- stream water temperature is one of the most important environmental factors associated with the decline in salmonid populations and their habitats in the Pacific Northwest. Most ecological restoration practices that attempt to reduce instream temperatures center on replanting or reestablishing riparian vegetation and increasing flows. However, in a large floodplain river like the Willamette, restoring hyporheic flow may also play an important role in reducing water temperature. The objective of this dissertation is to examine restoration practices that focus on the reduction of water temperatures in the upper mainstem Willamette River, Oregon, for the benefit of salmonid species. Economic information is developed to determine the cost-effectiveness of water temperature reduction strategies. The CEQUAL- W2 water temperature model is used to simulate the effects of upstream combinations of riparian shading and flow increments on downstream water temperatures. Costs associated with these strategies are estimated. These costs consist of the opportunity costs of losing agricultural production, and losing recreation due to flow releases from up-stream reservoirs. The effectiveness of each strategy in reducing water temperature and the associated costs are used to construct a cost-effectiveness frontier. The results indicate that the cumulative effects of shading and flows have little impact on temperature reduction downstream. Even when maximum available resources are allocated to investments in shade and flow increases they cannot lower summer water temperatures sufficiently to meet the state water temperature standard. However, the restoration practices selected from the cost-effectiveness frontiers method do provide ranges of achievable temperature reductions at minimum costs. These results are thus useful management tools when selecting policies to pursue water temperature goals. Hyporheic temperature reduction is also examined. Restoration practices associated with this type of cooling are done through removal/reconnection of the obstacles that are necessary to allow the process of re-creating dynamic channel complexity. The observed significant reduction of summer water temperatures associated with channel complexity indicates that this approach is more flexible in reducing temperature than approaches that rely on flow increments or/and shade. Although the costs associated with the hyporheic approach are substantial, the effects of such a long-term ecological improvement of floodplain habitat may substantially benefit salmonid populations. Title: Economic analysis of restoration practices to improve water quality and fish habitat of a large river floodplain : a case study of the Willamette River, Oregon Author: Seedang, Saichon In- stream water temperature is one of the most important environmental factors associated with the decline in salmonid populations and their habitats in the Pacific Northwest. Most ecological restoration practices that attempt to reduce instream temperatures center on replanting or reestablishing riparian vegetation and increasing flows. However, in a large floodplain river like the Willamette, restoring hyporheic flow may also play an important role in reducing water temperature. The objective of this dissertation is to examine restoration practices that focus on the reduction of water temperatures in the upper mainstem Willamette River, Oregon, for the benefit of salmonid species. Economic information is developed to determine the cost-effectiveness of water temperature reduction strategies. The CEQUAL- W2 water temperature model is used to simulate the effects of upstream combinations of riparian shading and flow increments on downstream water temperatures. Costs associated with these strategies are estimated. These costs consist of the opportunity costs of losing agricultural production, and losing recreation due to flow releases from up-stream reservoirs. The effectiveness of each strategy in reducing water temperature and the associated costs are used to construct a cost-effectiveness frontier. The results indicate that the cumulative effects of shading and flows have little impact on temperature reduction downstream. Even when maximum available resources are allocated to investments in shade and flow increases they cannot lower summer water temperatures sufficiently to meet the state water temperature standard. However, the restoration practices selected from the cost-effectiveness frontiers method do provide ranges of achievable temperature reductions at minimum costs. These results are thus useful management tools when selecting policies to pursue water temperature goals. Hyporheic temperature reduction is also examined. Restoration practices associated with this type of cooling are done through removal/reconnection of the obstacles that are necessary to allow the process of re-creating dynamic channel complexity. The observed significant reduction of summer water temperatures associated with channel complexity indicates that this approach is more flexible in reducing temperature than approaches that rely on flow increments or/and shade. Although the costs associated with the hyporheic approach are substantial, the effects of such a long-term ecological improvement of floodplain habitat may substantially benefit salmonid populations. Close

• 12. [Article] Quantifying spatial differences in metabolism in headwater streams

  This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by The Society for Freshwater Science and published by The University of Chicago Press. ...

  Citation × Citation Citation Abstract Copy Title: Quantifying spatial differences in metabolism in headwater streams Author: Haggerty, Roy, Argerich, Alba, Gonzalez-Pinzon, Ricardo This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by The Society for Freshwater Science and published by The University of Chicago Press. It can be found at: https://www.freshwater-science.org/Journal/Access-FWS.aspx Title: Quantifying spatial differences in metabolism in headwater streams Author: Haggerty, Roy, Argerich, Alba, Gonzalez-Pinzon, Ricardo This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by The Society for Freshwater Science and published by The University of Chicago Press. It can be found at: https://www.freshwater-science.org/Journal/Access-FWS.aspx Close

• 13. [Article] Influence of hyporheic flow and geomorphology on temperature of a large, gravel-bed river, Clackamas River, Oregon, USA

  The hyporheic zone influences the thermal regime of rivers, buffering temperature by storing and releasing heat over a range of timescales. We examined the relationship between hyporheic exchange and temperature ...

  Citation × Citation Citation Abstract Copy Title: Influence of hyporheic flow and geomorphology on temperature of a large, gravel-bed river, Clackamas River, Oregon, USA Author: Burkholder, Barbara K. The hyporheic zone influences the thermal regime of rivers, buffering temperature by storing and releasing heat over a range of timescales. We examined the relationship between hyporheic exchange and temperature along a 24-km reach of the lower Clackamas River, a large gravel-bed river in northwestern Oregon (median discharge = 75.7 m³/s; minimum mean monthly discharge = 22.7 m³/s in August 2006). With a simple mixing model, we estimated how much hyporheic exchange cools the river during hot summer months. Hyporheic exchange was primarily identified by temperature anomalies, which are patches of water that demonstrate at least a 1 °C temperature difference from the main channel. Forty hyporheic temperature anomalies were identified through field investigations and TIR (Thermal-Infrared-Radiometry) in summer 2006. The location of anomalies was associated with specific geomorphic features, primarily bar channels and bar heads that act as preferential pathways for hyporheic flow. Detailed field characterization and groundwater modeling on three Clackamas gravel bars indicate residence times of hyporheic water can vary from hours to weeks and months. This was largely determined by hydraulic conductivity, which is affected by how recently the gravel bar formed or was reworked. Upscaling of modeled discharges and hydrologic parameters from these bars to the other anomalies on the Clackamas network shows that hyporheic discharge from anomalies comprises a small fraction (<< 1 %) of mainstem discharge, resulting in small river cooling effects (0.012 °C). However, the presence of cooler patches of water within rivers can act as thermal refugia for fish and other aquatic organisms, making the creation or enhancement of hyporheic exchange an attractive method in restoring the thermal regime of rivers. Title: Influence of hyporheic flow and geomorphology on temperature of a large, gravel-bed river, Clackamas River, Oregon, USA Author: Burkholder, Barbara K. The hyporheic zone influences the thermal regime of rivers, buffering temperature by storing and releasing heat over a range of timescales. We examined the relationship between hyporheic exchange and temperature along a 24-km reach of the lower Clackamas River, a large gravel-bed river in northwestern Oregon (median discharge = 75.7 m³/s; minimum mean monthly discharge = 22.7 m³/s in August 2006). With a simple mixing model, we estimated how much hyporheic exchange cools the river during hot summer months. Hyporheic exchange was primarily identified by temperature anomalies, which are patches of water that demonstrate at least a 1 °C temperature difference from the main channel. Forty hyporheic temperature anomalies were identified through field investigations and TIR (Thermal-Infrared-Radiometry) in summer 2006. The location of anomalies was associated with specific geomorphic features, primarily bar channels and bar heads that act as preferential pathways for hyporheic flow. Detailed field characterization and groundwater modeling on three Clackamas gravel bars indicate residence times of hyporheic water can vary from hours to weeks and months. This was largely determined by hydraulic conductivity, which is affected by how recently the gravel bar formed or was reworked. Upscaling of modeled discharges and hydrologic parameters from these bars to the other anomalies on the Clackamas network shows that hyporheic discharge from anomalies comprises a small fraction (<< 1 %) of mainstem discharge, resulting in small river cooling effects (0.012 °C). However, the presence of cooler patches of water within rivers can act as thermal refugia for fish and other aquatic organisms, making the creation or enhancement of hyporheic exchange an attractive method in restoring the thermal regime of rivers. Close

• 14. [Article] Redd site selection and spawning habitat use by fall chinook salmon

  The spawning habitat associated with fall chinook salmon (Oncorhynchus tshawytscha) redd clusters was investigated in the Hanford Reach of the Columbia River. A conceptual spawning habitat model is proposed ...

  Citation × Citation Citation Abstract Copy Title: Redd site selection and spawning habitat use by fall chinook salmon Author: Geist, David R. The spawning habitat associated with fall chinook salmon (Oncorhynchus tshawytscha) redd clusters was investigated in the Hanford Reach of the Columbia River. A conceptual spawning habitat model is proposed that describes how geomorphic features of river channels create hydraulic processes, including hyporheic flows, that influence where salmon spawn in unconstrained reaches of large mainstem alluvial rivers. Spatial point pattern analysis of redds showed that redd clusters averaged approximately 10 hectares in area and their locations were consistent from year to year. The tendency to spawn in clusters suggests fall chinook salmon's use of spawning habitat is highly selective. Hydraulic characteristics of the redd clusters were significantly different than the habitat surrounding them. Velocity and lateral slope of the river bottom were the most important habitat variables in predicting redd site selection. While these variables explained a large proportion of the variance in redd site selection (86 to 96%), some unmeasured factors still accounted for a small percentage of actual spawning site selection. Further investigation showed that the magnitude and chemical characteristics of hyporheic discharge were different between and within two spawning areas. Apparently, fall chinook salmon used chemical and physical cues from the discharge to locate spawning areas. Traditional spawning habitat models could be improved if they: used spawning area-specific, rather than river-specific; spawning characteristics; incorporated hyporheic discharge measurements; and gave further consideration to the geomorphic features that are present in the unconstrained segments of large alluvial rivers. Ultimately the recovery of endangered fall chinook salmon will depend on how well we are able to recreate the characteristics once common in alluvial floodplains of large rivers. The results from this research can be used to better define the relationship between these physical habitat characteristics and fall chinook salmon spawning site selection, and provide more efficient use of limited recovery resources. Title: Redd site selection and spawning habitat use by fall chinook salmon Author: Geist, David R. The spawning habitat associated with fall chinook salmon (Oncorhynchus tshawytscha) redd clusters was investigated in the Hanford Reach of the Columbia River. A conceptual spawning habitat model is proposed that describes how geomorphic features of river channels create hydraulic processes, including hyporheic flows, that influence where salmon spawn in unconstrained reaches of large mainstem alluvial rivers. Spatial point pattern analysis of redds showed that redd clusters averaged approximately 10 hectares in area and their locations were consistent from year to year. The tendency to spawn in clusters suggests fall chinook salmon's use of spawning habitat is highly selective. Hydraulic characteristics of the redd clusters were significantly different than the habitat surrounding them. Velocity and lateral slope of the river bottom were the most important habitat variables in predicting redd site selection. While these variables explained a large proportion of the variance in redd site selection (86 to 96%), some unmeasured factors still accounted for a small percentage of actual spawning site selection. Further investigation showed that the magnitude and chemical characteristics of hyporheic discharge were different between and within two spawning areas. Apparently, fall chinook salmon used chemical and physical cues from the discharge to locate spawning areas. Traditional spawning habitat models could be improved if they: used spawning area-specific, rather than river-specific; spawning characteristics; incorporated hyporheic discharge measurements; and gave further consideration to the geomorphic features that are present in the unconstrained segments of large alluvial rivers. Ultimately the recovery of endangered fall chinook salmon will depend on how well we are able to recreate the characteristics once common in alluvial floodplains of large rivers. The results from this research can be used to better define the relationship between these physical habitat characteristics and fall chinook salmon spawning site selection, and provide more efficient use of limited recovery resources. Close

• 15. [Article] Surface Water and Groundwater Interactions in the Walla Walla River, Northeast Oregon, USA : A Multi-Method Field-Based Approach

  Surface water and groundwater interactions are a key component in the functioning of stream ecosystems. Exchange of water between the stream and the hyporheic zone creates habitat for aquatic organisms ...

  Citation × Citation Citation Abstract Copy Title: Surface Water and Groundwater Interactions in the Walla Walla River, Northeast Oregon, USA : A Multi-Method Field-Based Approach Author: Gryczkowski, Landon Surface water and groundwater interactions are a key component in the functioning of stream ecosystems. Exchange of water between the stream and the hyporheic zone creates habitat for aquatic organisms and serves as a control for stream biogeochemical, thermal, and flow processes. This study takes a multi-method field-based approach to gain a better understanding of exchange processes in the Walla Walla River, Northeast Oregon, USA, with focus on advancing methodologies, spatial and temporal exchange dynamics, fish ecology and habitat, and geomorphic controls on hyporheic exchange. Fiber-optic distributed temperature sensing (DTS) was used to identify, quantify, and map cold-water inflows at the meter scale. Analysis of the maximum and minimum daily temperature traces separated each cold-water inflow into either hyporheic or groundwater-derived. DTS identified a very active hyporheic zone in this system, with a near-equal importance of hyporheic and groundwater inflows. Approximately one-third of the 2-km study reach was influence by cold-water inflows, providing significant cooling in certain areas. Using piezometers in conjunction with DTS provided validation and supplementation of DTS results, increased the reliability of conclusions, and helped to identify and understand specific exchange processes. Piezometer data showed downwelling conditions (negative head differential) except immediately downstream of riffles, with head differentials becoming increasingly negative farther downstream from a riffle. Furthermore, head differentials increased in the negative direction from left bank to right bank, indicating lateral movement of groundwater and more loss of river water from the right bank. Nearest to riffles and river bends, head differentials remained more stable over time, which may indicate that geomorphic structures influence head variations locally, while aquifer levels and dynamics have an increasing influence farther from these structures. Seasonally, head differentials became increasingly negative through the summer into fall as aquifer levels decreased, and areas of the river that lost the most water to the subsurface tended to lose more water at a faster rate as the summer progressed. However, the seasonal trend of head differentials may be counteracted by decreasing bed permeability, yielding little or no temporal change in vertical flux of water through the streambed. During high-flow events, river losses to the subsurface decreased overall; in particular, areas with the greatest water loss at low flows showed reduced losses during high flows. High variability and lack of patterns in the response to high flow events suggests complexity in this process. Temperature-related variables from DTS data were combined with habitat-related variables to determine which variables best explain pool-scale salmonid abundance. Two snorkel surveys of 23 pools within the study reach were performed. The change in temperature across the pool showed the strongest overall relationship to salmonid abundance, particularly Chinook salmon. Chinook salmon showed a stronger preference for specific pools compared to steelhead/rainbow trout. The magnitude of cold-water inflows appears more important than the presence or proportion of the pool receiving cold-water inflows, and salmonid abundance was more strongly explained by hyporheic inflows compared to groundwater. Temperature variables increased in importance relative to habitat variables in the second snorkel sample compared to sample one. The highest river temperatures of the summer occurred between the two sample dates, and this may suggest that salmonids’ affinity for cold-water refuge was enhanced through behavioral adaptation following periods of high temperature approaching the lethal threshold. The combined use of DTS, continuous electrical resistivity/induced polarization profiling, LiDAR, aerial imagery analysis, and field surveys allowed for the quantification of many geomorphic and hydraulic variables known or hypothesized to contribute to surface water and groundwater exchange processes. Regression analysis was used to determine which of these variables best explain the presence and magnitude of both groundwater and hyporheic inflows. For the first time, the cross-sectional area of the hyporheic zone was estimated at high resolution at the reach scale, and decreasing hyporheic cross-sectional area best explained both the presence and magnitude of cold-water inflows of either type. Higher water surface slope and sinuosity/curvature were next in order of importance. The presence of hyporheic inflows was also explained by higher water surface slope, sinuosity, and Reynolds number, while the magnitude of hyporheic inflows was best explained by higher sinuosity. Groundwater inflows were also explained by higher width-to-depth ratio, higher water surface slope, decreasing distance from a stream bank to the bankfull or floodplain extent, and decreasing flow velocity. Lateral processes (e.g. sinuosity) and vertical processes (e.g. water surface slope) were found to be of comparable importance, but lateral processes better explained larger decreases in stream temperature, possibly because lateral subsurface flow paths are longer in distance and duration. Hydraulic conductivity variables did not show up among the most important variables likely because of the difficulty in estimating hydraulic conductivity at the meter scale using electrical geophysical tools. Title: Surface Water and Groundwater Interactions in the Walla Walla River, Northeast Oregon, USA : A Multi-Method Field-Based Approach Author: Gryczkowski, Landon Surface water and groundwater interactions are a key component in the functioning of stream ecosystems. Exchange of water between the stream and the hyporheic zone creates habitat for aquatic organisms and serves as a control for stream biogeochemical, thermal, and flow processes. This study takes a multi-method field-based approach to gain a better understanding of exchange processes in the Walla Walla River, Northeast Oregon, USA, with focus on advancing methodologies, spatial and temporal exchange dynamics, fish ecology and habitat, and geomorphic controls on hyporheic exchange. Fiber-optic distributed temperature sensing (DTS) was used to identify, quantify, and map cold-water inflows at the meter scale. Analysis of the maximum and minimum daily temperature traces separated each cold-water inflow into either hyporheic or groundwater-derived. DTS identified a very active hyporheic zone in this system, with a near-equal importance of hyporheic and groundwater inflows. Approximately one-third of the 2-km study reach was influence by cold-water inflows, providing significant cooling in certain areas. Using piezometers in conjunction with DTS provided validation and supplementation of DTS results, increased the reliability of conclusions, and helped to identify and understand specific exchange processes. Piezometer data showed downwelling conditions (negative head differential) except immediately downstream of riffles, with head differentials becoming increasingly negative farther downstream from a riffle. Furthermore, head differentials increased in the negative direction from left bank to right bank, indicating lateral movement of groundwater and more loss of river water from the right bank. Nearest to riffles and river bends, head differentials remained more stable over time, which may indicate that geomorphic structures influence head variations locally, while aquifer levels and dynamics have an increasing influence farther from these structures. Seasonally, head differentials became increasingly negative through the summer into fall as aquifer levels decreased, and areas of the river that lost the most water to the subsurface tended to lose more water at a faster rate as the summer progressed. However, the seasonal trend of head differentials may be counteracted by decreasing bed permeability, yielding little or no temporal change in vertical flux of water through the streambed. During high-flow events, river losses to the subsurface decreased overall; in particular, areas with the greatest water loss at low flows showed reduced losses during high flows. High variability and lack of patterns in the response to high flow events suggests complexity in this process. Temperature-related variables from DTS data were combined with habitat-related variables to determine which variables best explain pool-scale salmonid abundance. Two snorkel surveys of 23 pools within the study reach were performed. The change in temperature across the pool showed the strongest overall relationship to salmonid abundance, particularly Chinook salmon. Chinook salmon showed a stronger preference for specific pools compared to steelhead/rainbow trout. The magnitude of cold-water inflows appears more important than the presence or proportion of the pool receiving cold-water inflows, and salmonid abundance was more strongly explained by hyporheic inflows compared to groundwater. Temperature variables increased in importance relative to habitat variables in the second snorkel sample compared to sample one. The highest river temperatures of the summer occurred between the two sample dates, and this may suggest that salmonids’ affinity for cold-water refuge was enhanced through behavioral adaptation following periods of high temperature approaching the lethal threshold. The combined use of DTS, continuous electrical resistivity/induced polarization profiling, LiDAR, aerial imagery analysis, and field surveys allowed for the quantification of many geomorphic and hydraulic variables known or hypothesized to contribute to surface water and groundwater exchange processes. Regression analysis was used to determine which of these variables best explain the presence and magnitude of both groundwater and hyporheic inflows. For the first time, the cross-sectional area of the hyporheic zone was estimated at high resolution at the reach scale, and decreasing hyporheic cross-sectional area best explained both the presence and magnitude of cold-water inflows of either type. Higher water surface slope and sinuosity/curvature were next in order of importance. The presence of hyporheic inflows was also explained by higher water surface slope, sinuosity, and Reynolds number, while the magnitude of hyporheic inflows was best explained by higher sinuosity. Groundwater inflows were also explained by higher width-to-depth ratio, higher water surface slope, decreasing distance from a stream bank to the bankfull or floodplain extent, and decreasing flow velocity. Lateral processes (e.g. sinuosity) and vertical processes (e.g. water surface slope) were found to be of comparable importance, but lateral processes better explained larger decreases in stream temperature, possibly because lateral subsurface flow paths are longer in distance and duration. Hydraulic conductivity variables did not show up among the most important variables likely because of the difficulty in estimating hydraulic conductivity at the meter scale using electrical geophysical tools. Close

• 16. [Article] Heat balance of alcoves on the Willamette River, Oregon.

  Alcoves in some river systems are cooler than the mainstem of the river and provide thermal refugia for aquatic species. An energy balance and sensitivity analysis on 3 alcoves in the Willamette River, ...

  Citation × Citation Citation Abstract Copy Title: Heat balance of alcoves on the Willamette River, Oregon. Author: Bryenton, Andrew G. Alcoves in some river systems are cooler than the mainstem of the river and provide thermal refugia for aquatic species. An energy balance and sensitivity analysis on 3 alcoves in the Willamette River, Oregon indicate that alcove size and alcove flux determine the degree to which meteorological conditions affect the alcove water temperature. Large alcoves with a low alcove flux and large surface area are more sensitive to meteorological conditions (i.e., shade and wind). Small alcoves with a high alcove flux and small surface area are more sensitive to the temperature of emerging subsurface water than to meteorological conditions. The temperature of hyporheic water relative to the mainstem is determined by its residence time; longer flow paths disperse the diurnal signal and move hyporheic water into equilibrium with mean seasonal or annual subsurface temperatures. Floodplain restoration may increase alcove population in a river system thereby making it a potential credit trading tool for mitigating excess thermal loading in a heat stressed river. Title: Heat balance of alcoves on the Willamette River, Oregon. Author: Bryenton, Andrew G. Alcoves in some river systems are cooler than the mainstem of the river and provide thermal refugia for aquatic species. An energy balance and sensitivity analysis on 3 alcoves in the Willamette River, Oregon indicate that alcove size and alcove flux determine the degree to which meteorological conditions affect the alcove water temperature. Large alcoves with a low alcove flux and large surface area are more sensitive to meteorological conditions (i.e., shade and wind). Small alcoves with a high alcove flux and small surface area are more sensitive to the temperature of emerging subsurface water than to meteorological conditions. The temperature of hyporheic water relative to the mainstem is determined by its residence time; longer flow paths disperse the diurnal signal and move hyporheic water into equilibrium with mean seasonal or annual subsurface temperatures. Floodplain restoration may increase alcove population in a river system thereby making it a potential credit trading tool for mitigating excess thermal loading in a heat stressed river. Close

• 17. [Article] Bryenton, A_Thesis.pdf

  Citation × Citation Citation Abstract Copy Title: Bryenton, A_Thesis.pdf Author: Bryenton, Andrew G. Title: Bryenton, A_Thesis.pdf Author: Bryenton, Andrew G. Close

• 18. [Article] Appendix_E.zip

  Citation × Citation Citation Abstract Copy Title: Appendix_E.zip Author: Bryenton, Andrew G. Title: Appendix_E.zip Author: Bryenton, Andrew G. Close

• 19. [Article] Changes in hyporheic exchange flow following experimental large wood removal in a second order, low gradient stream, Chichagof Island, AK

  Hyporheic Exchange Flow (HEF) is driven by head gradients defined by the hydro-topography of the stream surface, which is controlled by the particular geomorphology of the stream. We quantified the impact ...

  Citation × Citation Citation Abstract Copy Title: Changes in hyporheic exchange flow following experimental large wood removal in a second order, low gradient stream, Chichagof Island, AK Author: La Nier, Justin Hyporheic Exchange Flow (HEF) is driven by head gradients defined by the hydro-topography of the stream surface, which is controlled by the particular geomorphology of the stream. We quantified the impact of large wood, which typically exerts a strong control on stream morphology, on HEF in a second order, low gradient (~1%), coastal Alaskan stream. Experimental removal of large wood (> 10 cm diameter) from Bambi Creek, a second order stream on Chichagof Island, AK demonstrated that the wood-forced pool-riffle morphology transitions to that of alternating pool-riffle sequences, and led to an increase in sediment stored in the reach (Smith et al., 1993). We constructed a series of five groundwater flow models (MODFLOW) spanning 16 years to examine the response of HEF, and we used particle tracking (MODPATH) to examine changes to the flow paths and residence times. Changes in the pattern of hyporheic upwelling and downwelling generally correspond to changes in the local hydro-topography over the five study periods and generally corresponded to locations of large wood removal. Reach total hyporheic exchange decreased from 0.96 to 0.87 L/s during loss of sediment storage, then increased to 1.22 L/s and again to 1.90 L/s for periods when sediment storage increased in the reach. The turnover length of hyporheic exchange for baseflow conditions decreased from 4.5 km to 2.3 km. The area of the streambed contributing to hyporheic flux increased over the study period, as well as the amount of hyporheic flow across meander bends. The median residence time of the hyporheic flowpaths increased from 8 to 11 hours by 4-years post removal then again to 14 hours by 16-years post-removal. Changes in the residence time probability and cumulative density functions for the models show an increase in late time portion of these functions at 4 years and 16 years post removal. The change in channel morphology from wood-forced pool-riffle to that of alternating pool-riffle sequences apparently increased the amount of hyporheic exchange. Title: Changes in hyporheic exchange flow following experimental large wood removal in a second order, low gradient stream, Chichagof Island, AK Author: La Nier, Justin Hyporheic Exchange Flow (HEF) is driven by head gradients defined by the hydro-topography of the stream surface, which is controlled by the particular geomorphology of the stream. We quantified the impact of large wood, which typically exerts a strong control on stream morphology, on HEF in a second order, low gradient (~1%), coastal Alaskan stream. Experimental removal of large wood (> 10 cm diameter) from Bambi Creek, a second order stream on Chichagof Island, AK demonstrated that the wood-forced pool-riffle morphology transitions to that of alternating pool-riffle sequences, and led to an increase in sediment stored in the reach (Smith et al., 1993). We constructed a series of five groundwater flow models (MODFLOW) spanning 16 years to examine the response of HEF, and we used particle tracking (MODPATH) to examine changes to the flow paths and residence times. Changes in the pattern of hyporheic upwelling and downwelling generally correspond to changes in the local hydro-topography over the five study periods and generally corresponded to locations of large wood removal. Reach total hyporheic exchange decreased from 0.96 to 0.87 L/s during loss of sediment storage, then increased to 1.22 L/s and again to 1.90 L/s for periods when sediment storage increased in the reach. The turnover length of hyporheic exchange for baseflow conditions decreased from 4.5 km to 2.3 km. The area of the streambed contributing to hyporheic flux increased over the study period, as well as the amount of hyporheic flow across meander bends. The median residence time of the hyporheic flowpaths increased from 8 to 11 hours by 4-years post removal then again to 14 hours by 16-years post-removal. Changes in the residence time probability and cumulative density functions for the models show an increase in late time portion of these functions at 4 years and 16 years post removal. The change in channel morphology from wood-forced pool-riffle to that of alternating pool-riffle sequences apparently increased the amount of hyporheic exchange. Close

• 20. [Article] Monitoring river restoration using fiber optic temperature measurements in a modeling framework

  The Middle Fork of the John Day River (MFJD) in Northeastern Oregon contains important spawning grounds for spring Chinook and summer steelhead of the Columbia River Basin. In the summer of 2008 phase ...

  Citation × Citation Citation Abstract Copy Title: Monitoring river restoration using fiber optic temperature measurements in a modeling framework Author: Huff, Julie A. The Middle Fork of the John Day River (MFJD) in Northeastern Oregon contains important spawning grounds for spring Chinook and summer steelhead of the Columbia River Basin. In the summer of 2008 phase one of a river restoration project was completed which included the addition of engineered log jams (ELJs) and scour pools. The restoration focuses on increasing habitat diversity and decreasing peak summer temperatures which, perhaps, had been degraded due to anthropogenic activities such as dredge mining, cattle grazing, channelization and deforestation. This study utilized Distributed Temperature Sensing (DTS) technology to measure the temperature the MFJD study site before and after restoration during the summer of 2008. The temperature data along with other physical and climatic data were modeled using a physically based stream temperature model which incorporated groundwater inflows and an average depth of hyporheic exchange over the entire study reach. The root mean square errors for the pre- and post-restoration model are 0.57°C and 0.47°C, respectively. An average depth of the thermal mass associated with hyporheic exchange was calculated within the model to be 11m for pre- restoration and 1.6m for post-restoration. It is unclear as to whether the hyporheic exchange increased due to restoration or is an artifact of high flows during the pre-restoration period. A statistical analysis was completed on the longitudinal temperature profiles of the MFJD to identify lengths of the river whose temperatures are different upstream and downstream. Groundwater inflow was defined as locations with cooler day time and night time temperatures than the surroundings whereas hyporheic discharge was defined as locations with cooler day time temperatures but warmer night time temperature than the surroundings. Statistically significant locations were highlighted for both pre- and post-restoration and equated to an average decrease in local temperature of 0.08°C pre-restoration and 1.18°C post-restoration. This equates to 0.004 m³/s and 0.012 m³/s of groundwater inflow for pre- and post-restoration, respectively. Again, these differences could be artifacts of high flows during pre-restoration and cannot conclusively be linked to the restoration efforts. However, the largest groundwater inflow (0.004 m³/s) can be associated with one ELJ structure and its corresponding scour pool. Title: Monitoring river restoration using fiber optic temperature measurements in a modeling framework Author: Huff, Julie A. The Middle Fork of the John Day River (MFJD) in Northeastern Oregon contains important spawning grounds for spring Chinook and summer steelhead of the Columbia River Basin. In the summer of 2008 phase one of a river restoration project was completed which included the addition of engineered log jams (ELJs) and scour pools. The restoration focuses on increasing habitat diversity and decreasing peak summer temperatures which, perhaps, had been degraded due to anthropogenic activities such as dredge mining, cattle grazing, channelization and deforestation. This study utilized Distributed Temperature Sensing (DTS) technology to measure the temperature the MFJD study site before and after restoration during the summer of 2008. The temperature data along with other physical and climatic data were modeled using a physically based stream temperature model which incorporated groundwater inflows and an average depth of hyporheic exchange over the entire study reach. The root mean square errors for the pre- and post-restoration model are 0.57°C and 0.47°C, respectively. An average depth of the thermal mass associated with hyporheic exchange was calculated within the model to be 11m for pre- restoration and 1.6m for post-restoration. It is unclear as to whether the hyporheic exchange increased due to restoration or is an artifact of high flows during the pre-restoration period. A statistical analysis was completed on the longitudinal temperature profiles of the MFJD to identify lengths of the river whose temperatures are different upstream and downstream. Groundwater inflow was defined as locations with cooler day time and night time temperatures than the surroundings whereas hyporheic discharge was defined as locations with cooler day time temperatures but warmer night time temperature than the surroundings. Statistically significant locations were highlighted for both pre- and post-restoration and equated to an average decrease in local temperature of 0.08°C pre-restoration and 1.18°C post-restoration. This equates to 0.004 m³/s and 0.012 m³/s of groundwater inflow for pre- and post-restoration, respectively. Again, these differences could be artifacts of high flows during pre-restoration and cannot conclusively be linked to the restoration efforts. However, the largest groundwater inflow (0.004 m³/s) can be associated with one ELJ structure and its corresponding scour pool. Close