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• 21. [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

• 22. [Article] Groundwater Flow Model.zip

  Citation × Citation Citation Abstract Copy Title: Groundwater Flow Model.zip Author: Squeochs, Graysen M. Title: Groundwater Flow Model.zip Author: Squeochs, Graysen M. Close

• 23. [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

• 24. [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

• 25. [Article] Infiltration and temperature characterization of a wastewater hyporheic discharge system

  The Clean Water Act imposes Total Maximum Daily Load (TMDL) limits on pollutant concentrations within wastewater effluent; in Oregon, thermal discharge is one of the pollutants subject to regulation. ...

  Citation × Citation Citation Abstract Copy Title: Infiltration and temperature characterization of a wastewater hyporheic discharge system Author: Stewart, Ryan D. The Clean Water Act imposes Total Maximum Daily Load (TMDL) limits on pollutant concentrations within wastewater effluent; in Oregon, thermal discharge is one of the pollutants subject to regulation. The City of Woodburn, Oregon, funded a series of pilot scale studies to investigate the utility of natural systems to reduce wastewater effluent temperature. The research discussed here examined the groundwater response to an unlined, 0.15 hectare wetland used to infiltrate treated wastewater into the subsurface and the potential efficacy of an upscaled discharge system. An array of geotechnical holes and monitoring wells were placed around the wetland and were equipped with pressure transducers. Groundwater level, water temperature, and water chemistry were then monitored for 1.5 years. These data were used to calibrate a series of numerical models, which were in turn utilized to assess the rate, flow direction, and spatial extent of infiltration from the wetland. Results suggest that the water table rises to the level of the wetland, and that infiltration occurs primarily through lateral flow from the wetland. Numerically-simulated and observational data found maximum water displacement velocities of 1.5 m/day in the horizontal direction, and 0.1 m/day in the vertical direction. Next, the numerical groundwater simulation model was used to predict how infiltration rate would be affected by moving from a pilot-scale to a large-scale system. It was determined that because a large percentage of flow occurs laterally through the perimeter, the specific infiltration rate will decrease as wetland area increases, due to a smaller perimeter-to-area ratio. Simulations estimated that the water displacement velocity for the large-scale (5.5 hectare) system was 0.06 m/day in the vertical direction and 0.4 m/day along the perimeter. These results were deemed consistent with a water budget performed on a separate inundated portion of the floodplain. Finally, the observed temperature and numerical simulations were used to simulate the subsurface temperature profile. It is predicted that the heat which enters the subsurface spreads out beyond a radius of 20 - 50m, and the wastewater will have its temperature transition from having daily fluctuations to seasonal fluctuations, before eventually reaching steady state. Further, it was found that mean annual temperature is a function of the distance from the wetland, thus effectively dispersing the thermal load to the river across the entire year. In an effort to translate these results to other locations, two sets of non-dimensional numbers were formulated. The first set of parameters examines the potential for cooling due to conductive losses to the atmosphere, and may indicate systems where the hydraulic retention time will be sufficient to partially or fully cool the wastewater. The second set of non-dimensional numbers provides a means by which a site's potential for hyporheic discharge may be assessed, by comparing hydraulic retention time against infiltration capacity. Altogether, the results suggest that infiltration wetland systems will reduce the peak wastewater discharge temperatures, and thus enable the City of Woodburn and other wastewater agencies to comply with their permit requirements through use of wetland recharge systems. Title: Infiltration and temperature characterization of a wastewater hyporheic discharge system Author: Stewart, Ryan D. The Clean Water Act imposes Total Maximum Daily Load (TMDL) limits on pollutant concentrations within wastewater effluent; in Oregon, thermal discharge is one of the pollutants subject to regulation. The City of Woodburn, Oregon, funded a series of pilot scale studies to investigate the utility of natural systems to reduce wastewater effluent temperature. The research discussed here examined the groundwater response to an unlined, 0.15 hectare wetland used to infiltrate treated wastewater into the subsurface and the potential efficacy of an upscaled discharge system. An array of geotechnical holes and monitoring wells were placed around the wetland and were equipped with pressure transducers. Groundwater level, water temperature, and water chemistry were then monitored for 1.5 years. These data were used to calibrate a series of numerical models, which were in turn utilized to assess the rate, flow direction, and spatial extent of infiltration from the wetland. Results suggest that the water table rises to the level of the wetland, and that infiltration occurs primarily through lateral flow from the wetland. Numerically-simulated and observational data found maximum water displacement velocities of 1.5 m/day in the horizontal direction, and 0.1 m/day in the vertical direction. Next, the numerical groundwater simulation model was used to predict how infiltration rate would be affected by moving from a pilot-scale to a large-scale system. It was determined that because a large percentage of flow occurs laterally through the perimeter, the specific infiltration rate will decrease as wetland area increases, due to a smaller perimeter-to-area ratio. Simulations estimated that the water displacement velocity for the large-scale (5.5 hectare) system was 0.06 m/day in the vertical direction and 0.4 m/day along the perimeter. These results were deemed consistent with a water budget performed on a separate inundated portion of the floodplain. Finally, the observed temperature and numerical simulations were used to simulate the subsurface temperature profile. It is predicted that the heat which enters the subsurface spreads out beyond a radius of 20 - 50m, and the wastewater will have its temperature transition from having daily fluctuations to seasonal fluctuations, before eventually reaching steady state. Further, it was found that mean annual temperature is a function of the distance from the wetland, thus effectively dispersing the thermal load to the river across the entire year. In an effort to translate these results to other locations, two sets of non-dimensional numbers were formulated. The first set of parameters examines the potential for cooling due to conductive losses to the atmosphere, and may indicate systems where the hydraulic retention time will be sufficient to partially or fully cool the wastewater. The second set of non-dimensional numbers provides a means by which a site's potential for hyporheic discharge may be assessed, by comparing hydraulic retention time against infiltration capacity. Altogether, the results suggest that infiltration wetland systems will reduce the peak wastewater discharge temperatures, and thus enable the City of Woodburn and other wastewater agencies to comply with their permit requirements through use of wetland recharge systems. Close

• 26. [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

• 27. [Article] Lateral cavities in streams : flow structure and mean residence times from channel hydraulics, morphology, and computational fluid dynamics

  Surface transient storage (STS) and hyporheic transient storage (HTS) have functional significance in stream ecology and hydrology. Both provide refugia for aquatic communities and their longer mean residence ...

  Citation × Citation Citation Abstract Copy Title: Lateral cavities in streams : flow structure and mean residence times from channel hydraulics, morphology, and computational fluid dynamics Author: Jackson, Tracie R. (Tracie Robin) Surface transient storage (STS) and hyporheic transient storage (HTS) have functional significance in stream ecology and hydrology. Both provide refugia for aquatic communities and their longer mean residence times (compared to the main flow) increase the potential for biogeochemical reactions that can improve water quality. As STS and HTS have different storage and mass exchange mechanisms, hydrologists have proposed quantitatively separating STS from HTS to better predict solute fate and transport in streams. In addition, more accurate estimates of mass exchange parameters, such as mean residence times, are needed for STS and HTS. At present, effective solute transport parameters are estimated either from empirical relationships or by parameterizing effective transport metrics in solute transport models, resulting in empirical and nontransferrable parameters and an approximate equifinality in optimized numerical solutions. Through the development of relationships using field-measureable hydraulic and morphologic parameters, transient storage mass exchange parameters can be better constrained in solute transport models. To develop mass exchange relationships for transient storage, this dissertation focuses on the study of a prevalent and widelyrecognized type of STS termed lateral cavities. Lateral cavities have flow fields characterized by a recirculation region comprised of one or more gyres and a shear layer that spans the entire entrance. The goals of this dissertation are: (1) to develop a classification scheme that categorizes different types of STS in fluvial systems in order to quantitatively separate STS from HTS; and (2) to develop accurate estimates of mass exchange parameters (i.e., mean residence times) for lateral cavities in order to better understand and quantify solute transport and dispersion in fluvial systems. There are six major contributions of this work to the hydrology community. First, to quantitatively separate STS from HTS, a fluid-mechanics-based classification scheme is presented that identifies and categorizes different types of STS based on their characteristic mean flow structure. The classification scheme will allow for the systematic study of different STS types and development of predictive mean residence time relationships. Second, the best estimate of lateral cavity mean residence time, which represents the mean residence time of the primary gyre, is the first characteristic time of exponential decay. Third, a cavity shape factor--ratio of the square root of cavity width and depth to the cavity length--represents the degree of cavity equidimensionality and best quantifies the effect of cavity shape on mean residence time. Fourth, two roughness factors have good correlations with normalized mean residence time when computed using the median grain diameter of sediments measured in the shear layer: ratio of median grain diameter to channel depth and ratio of shear velocity to mean channel velocity. Fifth, mean residence time relationships are derived for lateral cavities in open channel flows with hydraulically smooth beds and for lateral cavities in gravel-bed rivers and streams. The mean residence time relationships are applicable for lateral cavities over a range of geometry, shape, roughness, and flow conditions. Sixth, cavity configuration (e.g., series or parallel) has a greater influence on breakthrough curve shape and transport parameters than the number of lateral cavities present. Therefore, the configuration and interaction of transient storage zones must be considered to accurately quantify stream solute transport and is a missing component in current solute transport theory. Title: Lateral cavities in streams : flow structure and mean residence times from channel hydraulics, morphology, and computational fluid dynamics Author: Jackson, Tracie R. (Tracie Robin) Surface transient storage (STS) and hyporheic transient storage (HTS) have functional significance in stream ecology and hydrology. Both provide refugia for aquatic communities and their longer mean residence times (compared to the main flow) increase the potential for biogeochemical reactions that can improve water quality. As STS and HTS have different storage and mass exchange mechanisms, hydrologists have proposed quantitatively separating STS from HTS to better predict solute fate and transport in streams. In addition, more accurate estimates of mass exchange parameters, such as mean residence times, are needed for STS and HTS. At present, effective solute transport parameters are estimated either from empirical relationships or by parameterizing effective transport metrics in solute transport models, resulting in empirical and nontransferrable parameters and an approximate equifinality in optimized numerical solutions. Through the development of relationships using field-measureable hydraulic and morphologic parameters, transient storage mass exchange parameters can be better constrained in solute transport models. To develop mass exchange relationships for transient storage, this dissertation focuses on the study of a prevalent and widelyrecognized type of STS termed lateral cavities. Lateral cavities have flow fields characterized by a recirculation region comprised of one or more gyres and a shear layer that spans the entire entrance. The goals of this dissertation are: (1) to develop a classification scheme that categorizes different types of STS in fluvial systems in order to quantitatively separate STS from HTS; and (2) to develop accurate estimates of mass exchange parameters (i.e., mean residence times) for lateral cavities in order to better understand and quantify solute transport and dispersion in fluvial systems. There are six major contributions of this work to the hydrology community. First, to quantitatively separate STS from HTS, a fluid-mechanics-based classification scheme is presented that identifies and categorizes different types of STS based on their characteristic mean flow structure. The classification scheme will allow for the systematic study of different STS types and development of predictive mean residence time relationships. Second, the best estimate of lateral cavity mean residence time, which represents the mean residence time of the primary gyre, is the first characteristic time of exponential decay. Third, a cavity shape factor--ratio of the square root of cavity width and depth to the cavity length--represents the degree of cavity equidimensionality and best quantifies the effect of cavity shape on mean residence time. Fourth, two roughness factors have good correlations with normalized mean residence time when computed using the median grain diameter of sediments measured in the shear layer: ratio of median grain diameter to channel depth and ratio of shear velocity to mean channel velocity. Fifth, mean residence time relationships are derived for lateral cavities in open channel flows with hydraulically smooth beds and for lateral cavities in gravel-bed rivers and streams. The mean residence time relationships are applicable for lateral cavities over a range of geometry, shape, roughness, and flow conditions. Sixth, cavity configuration (e.g., series or parallel) has a greater influence on breakthrough curve shape and transport parameters than the number of lateral cavities present. Therefore, the configuration and interaction of transient storage zones must be considered to accurately quantify stream solute transport and is a missing component in current solute transport theory. Close

• 28. [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

• 29. [Article] Ecosystem respiration increases with biofilm growth and bed forms: Flume measurements with resazurin

  This is the publisher’s final pdf. The published article is copyrighted by the American Geophysical Union and can be found at: http://agupubs.onlinelibrary.wiley.com/agu/jgr/journal/10.1002/%28ISSN%292...

  Citation × Citation Citation Abstract Copy Title: Ecosystem respiration increases with biofilm growth and bed forms: Flume measurements with resazurin Author: Singer, Gabriel A., Ribot, Miquel, Agell, Gemma, Argerich, Alba, Battin, Tom J., Marti, Eugénia, Haggerty, Roy This is the publisher’s final pdf. The published article is copyrighted by the American Geophysical Union and can be found at: http://agupubs.onlinelibrary.wiley.com/agu/jgr/journal/10.1002/%28ISSN%292169-8961/. Title: Ecosystem respiration increases with biofilm growth and bed forms: Flume measurements with resazurin Author: Singer, Gabriel A., Ribot, Miquel, Agell, Gemma, Argerich, Alba, Battin, Tom J., Marti, Eugénia, Haggerty, Roy This is the publisher’s final pdf. The published article is copyrighted by the American Geophysical Union and can be found at: http://agupubs.onlinelibrary.wiley.com/agu/jgr/journal/10.1002/%28ISSN%292169-8961/. Close

• 30. [Article] Nutrient uptake in a stream affected by hydropower plants: comparison between stream channels and diversion canals

  This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Springer and can be found at: http://link.springer.com/journal/10750.

  Citation × Citation Citation Abstract Copy Title: Nutrient uptake in a stream affected by hydropower plants: comparison between stream channels and diversion canals Author: Izagirre, Oihana, Marti, Eugenia, Argerich, Alba, Elosegi, Arturo This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Springer and can be found at: http://link.springer.com/journal/10750. Title: Nutrient uptake in a stream affected by hydropower plants: comparison between stream channels and diversion canals Author: Izagirre, Oihana, Marti, Eugenia, Argerich, Alba, Elosegi, Arturo This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Springer and can be found at: http://link.springer.com/journal/10750. Close