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• 1. [Article] Water quality effects of hyporheic processing

  "PB2000-107420."

  Citation × Citation Citation Abstract Copy Title: Water quality effects of hyporheic processing Author: Wigington, P.J., Landers, Dixon, Fernald, Alexander "PB2000-107420." Title: Water quality effects of hyporheic processing Author: Wigington, P.J., Landers, Dixon, Fernald, Alexander "PB2000-107420." Close

• 2. [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

• 3. [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

• 4. [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

• 5. [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

• 6. [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

• 7. [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

• 8. [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

• 9. [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

• 10. [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

• 11. [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

• 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] Monitoring Restoration in South Sister Creek : The Effect of Stream Enhancement Structures on Water Temperature

  This pilot study of South Sister Creek (8 km length) examined stream-scale (i.e., longitudinal trends) and sub-reach scale (less than 100 m) water temperature. Hourly summer temperature time-series data ...

  Citation × Citation Citation Abstract Copy Title: Monitoring Restoration in South Sister Creek : The Effect of Stream Enhancement Structures on Water Temperature Author: Harewood, Alessandra Greer This pilot study of South Sister Creek (8 km length) examined stream-scale (i.e., longitudinal trends) and sub-reach scale (less than 100 m) water temperature. Hourly summer temperature time-series data were gathered at four to seven locations along South Sister Creek in 2006, 2012, and 2013 and were used to explore whether restoration projects (in 2007 to 2011) affected stream temperature. Calculated seven-day maximum temperatures were cooler in post-treatment years (2012 and 2013) than the pre-treatment year (2006) at all four multi-year sites with the greatest differences near the mouth of the creek (4 to 5ºC cooler). While median stream temperature values were highest in 2013 for all four of the multi-year sites, the upper quartiles of measured hourly temperature for 2006 compared to 2012 and 2013 indicated more extreme high temperatures in 2006 than in subsequent years. Cross-correlation between stream and air temperature were used as an indicator of hyporheic flow. All peak CCF coefficients indicated a strong (.70) positive correlation in the early summer period between air and stream temperature, with lags ranging from 3 to 6 hours between peak air temperature and peak stream temperature. In the late summer period, most sites demonstrated lower correlations and longer lag times, patterns consistent with greater groundwater influence during low summer flows. There was no observable difference between pre- and post-treatment air-stream temperature cross correlation relationships. At a sub-reach scale, sites with more in-stream structural complexity -- including designed structures -- displayed greater spatial temperature variability than bedrock dominated reaches with simpler geomorphology. Title: Monitoring Restoration in South Sister Creek : The Effect of Stream Enhancement Structures on Water Temperature Author: Harewood, Alessandra Greer This pilot study of South Sister Creek (8 km length) examined stream-scale (i.e., longitudinal trends) and sub-reach scale (less than 100 m) water temperature. Hourly summer temperature time-series data were gathered at four to seven locations along South Sister Creek in 2006, 2012, and 2013 and were used to explore whether restoration projects (in 2007 to 2011) affected stream temperature. Calculated seven-day maximum temperatures were cooler in post-treatment years (2012 and 2013) than the pre-treatment year (2006) at all four multi-year sites with the greatest differences near the mouth of the creek (4 to 5ºC cooler). While median stream temperature values were highest in 2013 for all four of the multi-year sites, the upper quartiles of measured hourly temperature for 2006 compared to 2012 and 2013 indicated more extreme high temperatures in 2006 than in subsequent years. Cross-correlation between stream and air temperature were used as an indicator of hyporheic flow. All peak CCF coefficients indicated a strong (.70) positive correlation in the early summer period between air and stream temperature, with lags ranging from 3 to 6 hours between peak air temperature and peak stream temperature. In the late summer period, most sites demonstrated lower correlations and longer lag times, patterns consistent with greater groundwater influence during low summer flows. There was no observable difference between pre- and post-treatment air-stream temperature cross correlation relationships. At a sub-reach scale, sites with more in-stream structural complexity -- including designed structures -- displayed greater spatial temperature variability than bedrock dominated reaches with simpler geomorphology. Close

• 14. [Article] Fire meets inland water via burned wood: and then what?

  This is the publisher’s final pdf. The article is copyrighted by the Society for Freshwater Science and published by The University of Chicago Press. It can be found at: http://www.freshwater-science.o...

  Citation × Citation Citation Abstract Copy Title: Fire meets inland water via burned wood: and then what? Author: Merten, Eric C., Warren, Dana R., Vaz, Pedro G., et al. This is the publisher’s final pdf. The article is copyrighted by the Society for Freshwater Science and published by The University of Chicago Press. It can be found at: http://www.freshwater-science.org/Journal/Access-FWS.cfm Title: Fire meets inland water via burned wood: and then what? Author: Merten, Eric C., Warren, Dana R., Vaz, Pedro G., et al. This is the publisher’s final pdf. The article is copyrighted by the Society for Freshwater Science and published by The University of Chicago Press. It can be found at: http://www.freshwater-science.org/Journal/Access-FWS.cfm Close

• 15. [Article] Spatiotemporal dynamics and drivers of stream pCO₂ in a headwater mountain catchment in the Cascade Mountains, Oregon

  We examined the spatial and temporal variability of stream carbon dioxide (CO₂) and the drivers of these variations in a headwater catchment. To examine temporal variation and drivers, we measured stream ...

  Citation × Citation Citation Abstract Copy Title: Spatiotemporal dynamics and drivers of stream pCO₂ in a headwater mountain catchment in the Cascade Mountains, Oregon Author: Dosch, Nicholas T. We examined the spatial and temporal variability of stream carbon dioxide (CO₂) and the drivers of these variations in a headwater catchment. To examine temporal variation and drivers, we measured stream and hyporheic pCO₂ at high temporal resolution over 11 months in a 95.9-ha forested headwater catchment in the Western Cascades of Central Oregon, USA. Stream and hyporheic pCO₂ showed high seasonal and event-scale variability with distinct stream and hyporheic dynamics during storm discharge events. Hyporheic exchange flow exported 37.5 kg-C yr⁻¹ per watershed hectare (confidence interval 4.0-122.3 kg-C ha⁻¹ yr⁻¹) from the riparian zone to the stream. Summing CO₂ evasion and downstream advection suggests that one third of inorganic carbon export originated in the hyporheic zone. Hyporheic exchange flow had greatest influence over stream pCO₂ during low and high baseflow, while CO₂ evasion had greatest influence during storm discharge events. These findings suggest that the hyporheic zone actively participates in carbon cycling in this headwater stream and continuously replenishes stream CO₂. To examine spatial variation and drivers, we measured stream CO₂ at monthly intervals from July 2013 through July 2014 at 38 locations across the 6400-ha HJ Andrews Experimental Forest. Stream pCO₂ was consistently supersaturated with respect to atmospheric concentrations. Stream pCO₂ ranged from atmospheric (~400 μatm) to 20 times atmospheric concentrations (8150 μatm) and exhibited strong spatial and temporal variability. The distribution of pCO₂ over the study period was different in small and large streams within the drainage network. At the watershed scale, pCO₂ decreased with distance downstream. At the reach scale, we did not detect clear patterns in the downstream direction. However, individual transects displayed persistent profile shape, with consistent high and low pCO₂ locations. We found negative relationships between stream pCO₂ and stream discharge, mean velocity and the carbon dioxide gas transfer velocity. Stream pCO₂ exhibited changes over short distances, with large changes in pCO₂ over less than 50 m. Longitudinal variability indicates spatial variability of in-stream controls on pCO₂ at this scale. Stream pCO₂ shows generally higher concentrations during the summer and lower concentrations in the winter, with considerable intrannual variability. Title: Spatiotemporal dynamics and drivers of stream pCO₂ in a headwater mountain catchment in the Cascade Mountains, Oregon Author: Dosch, Nicholas T. We examined the spatial and temporal variability of stream carbon dioxide (CO₂) and the drivers of these variations in a headwater catchment. To examine temporal variation and drivers, we measured stream and hyporheic pCO₂ at high temporal resolution over 11 months in a 95.9-ha forested headwater catchment in the Western Cascades of Central Oregon, USA. Stream and hyporheic pCO₂ showed high seasonal and event-scale variability with distinct stream and hyporheic dynamics during storm discharge events. Hyporheic exchange flow exported 37.5 kg-C yr⁻¹ per watershed hectare (confidence interval 4.0-122.3 kg-C ha⁻¹ yr⁻¹) from the riparian zone to the stream. Summing CO₂ evasion and downstream advection suggests that one third of inorganic carbon export originated in the hyporheic zone. Hyporheic exchange flow had greatest influence over stream pCO₂ during low and high baseflow, while CO₂ evasion had greatest influence during storm discharge events. These findings suggest that the hyporheic zone actively participates in carbon cycling in this headwater stream and continuously replenishes stream CO₂. To examine spatial variation and drivers, we measured stream CO₂ at monthly intervals from July 2013 through July 2014 at 38 locations across the 6400-ha HJ Andrews Experimental Forest. Stream pCO₂ was consistently supersaturated with respect to atmospheric concentrations. Stream pCO₂ ranged from atmospheric (~400 μatm) to 20 times atmospheric concentrations (8150 μatm) and exhibited strong spatial and temporal variability. The distribution of pCO₂ over the study period was different in small and large streams within the drainage network. At the watershed scale, pCO₂ decreased with distance downstream. At the reach scale, we did not detect clear patterns in the downstream direction. However, individual transects displayed persistent profile shape, with consistent high and low pCO₂ locations. We found negative relationships between stream pCO₂ and stream discharge, mean velocity and the carbon dioxide gas transfer velocity. Stream pCO₂ exhibited changes over short distances, with large changes in pCO₂ over less than 50 m. Longitudinal variability indicates spatial variability of in-stream controls on pCO₂ at this scale. Stream pCO₂ shows generally higher concentrations during the summer and lower concentrations in the winter, with considerable intrannual variability. Close

• 16. [Article] Heat fluxes in the hyporheic zone of a gravel bar on the Willamette River, Oregon

  Increased water temperatures and thermal loading due to anthropogenic inputs has been shown to negatively impact the lifecycles of aquatic organisms in riverine systems (Poole and Berman 2001; Hannah, ...

  Citation × Citation Citation Abstract Copy Title: Heat fluxes in the hyporheic zone of a gravel bar on the Willamette River, Oregon Author: Squeochs, Graysen M. Increased water temperatures and thermal loading due to anthropogenic inputs has been shown to negatively impact the lifecycles of aquatic organisms in riverine systems (Poole and Berman 2001; Hannah, Malcolm et al. 2004; Quinn, Gagne et al. 2004). The studies enclosed in this thesis evaluate and quantify the heat fluxes within the hyporheic zone of a young unvegetated gravel bar on the Willamette River. The first study evaluated the application of the fiber optic distributed temperature sensing (DTS) system for thermal characterization of the shallow subsurface. The second study utilized data collected via the fiber optic DTS system, combined with data collected by thermistor probes, to calculate an energy balance for the hyporheic zone of the gravel bar. Lessons learned from the first study were that the fiber optic DTS system proved to be a flexible, high data-yielding, temperature monitoring system, but was not without limitations. The system flexibility allowed for the simultaneous temperature measurement of a 180 m² area (river and alcove combined sampling area) and multiple 2 m vertical temperature profiles with vertical resolutions of 0.022 m. Measurements made at the finest resolution of the DTS unit resulted in an increased amount of measurement variability when compared to a more traditional temperature measurement technique. An additional limitation was that the measurement sensor, the fiber optic cable, was inherently very fragile. Our recommendation for future studies is that special considerations must be taken to minimize damage to the fiber cable and signal loss. Nonetheless, the fiber optic DTS system provided an unprecedented view into the shallow subsurface. In the second study, we observed the amplitude of the thermal signal from the river decrease along a hyporheic flow path, while the net hyporheic temperature increased. Contrary to what other studies had found, no hyporheic cooling was observed. Using a simple layer control volume approach, we determined that ground-surface heating was a primary source of heat, via vadose zone storage and transport, for the hyporheic zone. The overlying conclusion of this thesis is that young, unvegetated, gravel bars on the Willamette River similar to the one examined in these studies, may increase the temperature within the hyporheic zone. Therefore, the geometry and the development of vegetation on gravel bars should be considered with regard to river engineering and planning. Title: Heat fluxes in the hyporheic zone of a gravel bar on the Willamette River, Oregon Author: Squeochs, Graysen M. Increased water temperatures and thermal loading due to anthropogenic inputs has been shown to negatively impact the lifecycles of aquatic organisms in riverine systems (Poole and Berman 2001; Hannah, Malcolm et al. 2004; Quinn, Gagne et al. 2004). The studies enclosed in this thesis evaluate and quantify the heat fluxes within the hyporheic zone of a young unvegetated gravel bar on the Willamette River. The first study evaluated the application of the fiber optic distributed temperature sensing (DTS) system for thermal characterization of the shallow subsurface. The second study utilized data collected via the fiber optic DTS system, combined with data collected by thermistor probes, to calculate an energy balance for the hyporheic zone of the gravel bar. Lessons learned from the first study were that the fiber optic DTS system proved to be a flexible, high data-yielding, temperature monitoring system, but was not without limitations. The system flexibility allowed for the simultaneous temperature measurement of a 180 m² area (river and alcove combined sampling area) and multiple 2 m vertical temperature profiles with vertical resolutions of 0.022 m. Measurements made at the finest resolution of the DTS unit resulted in an increased amount of measurement variability when compared to a more traditional temperature measurement technique. An additional limitation was that the measurement sensor, the fiber optic cable, was inherently very fragile. Our recommendation for future studies is that special considerations must be taken to minimize damage to the fiber cable and signal loss. Nonetheless, the fiber optic DTS system provided an unprecedented view into the shallow subsurface. In the second study, we observed the amplitude of the thermal signal from the river decrease along a hyporheic flow path, while the net hyporheic temperature increased. Contrary to what other studies had found, no hyporheic cooling was observed. Using a simple layer control volume approach, we determined that ground-surface heating was a primary source of heat, via vadose zone storage and transport, for the hyporheic zone. The overlying conclusion of this thesis is that young, unvegetated, gravel bars on the Willamette River similar to the one examined in these studies, may increase the temperature within the hyporheic zone. Therefore, the geometry and the development of vegetation on gravel bars should be considered with regard to river engineering and planning. Close

• 17. [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

• 18. [Article] Carbon dynamics in the hyporheic zone of a headwater mountain stream in the Cascade Mountains, Oregon

  This study investigated carbon dynamics in the hyporheic zone of a steep, forested catchment in the Cascade Mountains of western Oregon, USA. Water samples were collected monthly from a headwater stream ...

  Citation × Citation Citation Abstract Copy Title: Carbon dynamics in the hyporheic zone of a headwater mountain stream in the Cascade Mountains, Oregon Author: Corson-Rikert, Hayley A. This study investigated carbon dynamics in the hyporheic zone of a steep, forested catchment in the Cascade Mountains of western Oregon, USA. Water samples were collected monthly from a headwater stream and well network during baseflow conditions from July to December 2013 and again in March 2014. We also sampled during one fall storm event, collecting pre-storm, rising leg, and extended high flow samples. The well network is located at the base of Watershed 1 (WS1) of the H.J. Andrews Experimental Forest and spans the full width of the floodplain (~14 m) along a 29 m reach of stream. We measured pH, temperature, water level, major anions, major cations, DOC, DIC, and total alkalinity. Flow paths, travel time to wells and hydraulic conductivity were available from previous studies. During baseflow periods, hyporheic DOC decreased with median travel time through the subsurface. DIC concentrations increased with travel time, but the magnitude of this increase in DIC was too large to be explained by metabolism of stream water DOC. This suggests that there are additional sources of DIC and/or DOC in the subsurface, and that hyporheic DIC concentrations are not well linked to stream-source DOC. The most likely supplemental sources of DIC to hyporheic water are soil CO₂ and microbial respiration of DOC leached from buried particulate organic matter and from overlying soils. Overall, the hyporheic zone appears to be a source of DIC to the stream. In summer, the hyporheic zone is likely isolated from vertical infiltration or lateral inflow of soil water, and particulate organic carbon is not present in stream water. Thus, spatial patterns in hyporheic zone biogeochemistry must result from underlying spatial patterns in hyporheic flowpaths, groundwater inputs, and buried particulate organic carbon. With the transition to the rainy season throughout the fall and early winter, vertical infiltration and leaching of accumulated solutes from the overlying soil appear to become important sources of carbon that help explain patterns in hyporheic zone biogeochemistry. During a small November storm event, DOC and nitrate concentrations in the stream displayed clockwise hysteresis. Travel time appeared to be associated with both nitrate and DOC response patterns in the hyporheic zone. In wells with long travel times, DOC and nitrate concentrations showed a clockwise hysteresis pattern that mimicked and even exceeded that observed in the stream. We hypothesize that these solutes were flushed from overlying soils into the hyporheic zone via vertically infiltrating rainwater. In wells with short travel times, we observed only a small peak in DOC and nitrate concentrations during the storm, potentially due to lateral infiltration of stream water later in the event. Overall, temporal patterns in hyporheic solute chemistry during the November storm differed from patterns we observed in the well network. This suggests that whole-watershed processes that controlled stream water chemistry during this storm event were different than those that controlled solute concentrations in the hyporheic zone. Nonetheless, the hyporheic zone must have been linked to the stream. That measurements in our well network reveal a very different response between the stream and the hyporheic zone suggests that: 1) Our hyporheic zone is not representative of stream-hyporheic riparian processes that occur within the larger watershed, or 2) Hillslope-stream or within-stream processes dominate during storms, and at these times the influence of the hyporheic zone on the stream is much weaker than during baseflow. During both baseflow and storm periods, the hydrology of the WS1 system is complex – hyporheic exchange flows follow extended, non-linear flow paths through a heterogeneous subsurface and may be augmented by lateral inflows of groundwater and, during storms, vertical infiltration of soil water. Our results from both baseflow and storm sampling suggest that a complex set of physical mechanisms and biogeochemical processes influence carbon transport and transformation within this hyporheic environment. Title: Carbon dynamics in the hyporheic zone of a headwater mountain stream in the Cascade Mountains, Oregon Author: Corson-Rikert, Hayley A. This study investigated carbon dynamics in the hyporheic zone of a steep, forested catchment in the Cascade Mountains of western Oregon, USA. Water samples were collected monthly from a headwater stream and well network during baseflow conditions from July to December 2013 and again in March 2014. We also sampled during one fall storm event, collecting pre-storm, rising leg, and extended high flow samples. The well network is located at the base of Watershed 1 (WS1) of the H.J. Andrews Experimental Forest and spans the full width of the floodplain (~14 m) along a 29 m reach of stream. We measured pH, temperature, water level, major anions, major cations, DOC, DIC, and total alkalinity. Flow paths, travel time to wells and hydraulic conductivity were available from previous studies. During baseflow periods, hyporheic DOC decreased with median travel time through the subsurface. DIC concentrations increased with travel time, but the magnitude of this increase in DIC was too large to be explained by metabolism of stream water DOC. This suggests that there are additional sources of DIC and/or DOC in the subsurface, and that hyporheic DIC concentrations are not well linked to stream-source DOC. The most likely supplemental sources of DIC to hyporheic water are soil CO₂ and microbial respiration of DOC leached from buried particulate organic matter and from overlying soils. Overall, the hyporheic zone appears to be a source of DIC to the stream. In summer, the hyporheic zone is likely isolated from vertical infiltration or lateral inflow of soil water, and particulate organic carbon is not present in stream water. Thus, spatial patterns in hyporheic zone biogeochemistry must result from underlying spatial patterns in hyporheic flowpaths, groundwater inputs, and buried particulate organic carbon. With the transition to the rainy season throughout the fall and early winter, vertical infiltration and leaching of accumulated solutes from the overlying soil appear to become important sources of carbon that help explain patterns in hyporheic zone biogeochemistry. During a small November storm event, DOC and nitrate concentrations in the stream displayed clockwise hysteresis. Travel time appeared to be associated with both nitrate and DOC response patterns in the hyporheic zone. In wells with long travel times, DOC and nitrate concentrations showed a clockwise hysteresis pattern that mimicked and even exceeded that observed in the stream. We hypothesize that these solutes were flushed from overlying soils into the hyporheic zone via vertically infiltrating rainwater. In wells with short travel times, we observed only a small peak in DOC and nitrate concentrations during the storm, potentially due to lateral infiltration of stream water later in the event. Overall, temporal patterns in hyporheic solute chemistry during the November storm differed from patterns we observed in the well network. This suggests that whole-watershed processes that controlled stream water chemistry during this storm event were different than those that controlled solute concentrations in the hyporheic zone. Nonetheless, the hyporheic zone must have been linked to the stream. That measurements in our well network reveal a very different response between the stream and the hyporheic zone suggests that: 1) Our hyporheic zone is not representative of stream-hyporheic riparian processes that occur within the larger watershed, or 2) Hillslope-stream or within-stream processes dominate during storms, and at these times the influence of the hyporheic zone on the stream is much weaker than during baseflow. During both baseflow and storm periods, the hydrology of the WS1 system is complex – hyporheic exchange flows follow extended, non-linear flow paths through a heterogeneous subsurface and may be augmented by lateral inflows of groundwater and, during storms, vertical infiltration of soil water. Our results from both baseflow and storm sampling suggest that a complex set of physical mechanisms and biogeochemical processes influence carbon transport and transformation within this hyporheic environment. Close

• 19. [Article] Passage, migration behavior, and autoecology of adult Pacific lamprey at Winchester Dam and within the North Umpqua River Basin, Oregon, USA

  The extensive reduction in adult Pacific lamprey (Entosphenus tridentatus) counts at many hydroelectric dams in the northwestern USA signals a substantial decline in lamprey numbers across the entire region ...

  Citation × Citation Citation Abstract Copy Title: Passage, migration behavior, and autoecology of adult Pacific lamprey at Winchester Dam and within the North Umpqua River Basin, Oregon, USA Author: Lampman, Ralph Tatsuo The extensive reduction in adult Pacific lamprey (Entosphenus tridentatus) counts at many hydroelectric dams in the northwestern USA signals a substantial decline in lamprey numbers across the entire region in the past 40 to 50 years. Among the many potential causes of this decline, obstruction of migration routes has likely played a substantial role. Within the North Umpqua River basin in southwest Oregon, USA, I focused on the following three research goals: 1) to describe the passage efficiency and migration routes of adult Pacific lamprey at Winchester Dam; 2) to evaluate the seasonal movement patterns of adult Pacific lamprey and their use of holding habitat at Winchester Dam in relation to temperature conditions; and 3) to portray the diversity of upstream migratory behaviors of adult Pacific lamprey and the environmental factors that influence these behaviors. This radio telemetry study was conducted between March 2009 and August 2011 with a combination of fixed stations and manual tracking. Passage efficiency was low in both years (8% and 19%, respectively), and all tagged lamprey that successfully passed the dam used routes other than the fish ladder. Lamprey that migrated early within the run and those with relatively small tags had higher passage rates and traveled further than the other groups of lamprey. Lamprey released above of the dam or those that passed the dam on their own distributed themselves widely in the upstream environment, suggesting that the dam deterred their upstream migration. Using mark-recapture data for the two years, the adult Pacific lamprey population upstream of Winchester Dam was estimated at 960 (95% C.I. [188, 4760]) in 2009 and 556 (95% C.I. [110, 2798]) in 2010, which was considerably lower than historical counts at the dam (between 14,532-46,785 in 1965-1971). Most tagged lamprey that did not pass the dam remained at the base of the dam at the end of the summer migration (63% in 2009 and 67% in 2010). Types of habitat most frequently used by lamprey downstream from the dam included the dam surface (wooden structures with crevices), interface zones between fast and slow water, and highway bridge pilings. The lamprey movement changed considerably between August and September, and the frequency of movements decreased sharply during this period. Tagged lamprey were detected using thermal refuges immediately downstream of the dam that were 0.4 to 2.8 C° colder than the mean river temperature at the dam, and this temperature differential increased as the season progressed. Lamprey may be seeking overwintering habitat associated with hyporheic exchange flows at the dam towards the end of the summer season after their display of heightened activity early in the summer. Ninety-five percent of the overall upstream migration took place during the first spring/summer period, and only small-scale upstream movements were observed during the winter and second spring/summer (4% and 1%, respectively). The rate of upstream migration (median) was the fastest during the initial migration phase and was 1.9 km/day (ranging from 0.3 to 11.0 km/day) for tagged lamprey released above Winchester Dam. During winter, 71% of the lamprey remained in the same location where they initiated holding. Multiple regression analysis indicated that the total upstream distance traveled by individual lamprey was most strongly related to presence/absence of Winchester Dam, relative tag size, and water temperature and photoperiod conditions at release. The presence of Winchester Dam, large relative tag size, and high water temperature / short photoperiod conditions at release significantly reduced upstream migration distance. Title: Passage, migration behavior, and autoecology of adult Pacific lamprey at Winchester Dam and within the North Umpqua River Basin, Oregon, USA Author: Lampman, Ralph Tatsuo The extensive reduction in adult Pacific lamprey (Entosphenus tridentatus) counts at many hydroelectric dams in the northwestern USA signals a substantial decline in lamprey numbers across the entire region in the past 40 to 50 years. Among the many potential causes of this decline, obstruction of migration routes has likely played a substantial role. Within the North Umpqua River basin in southwest Oregon, USA, I focused on the following three research goals: 1) to describe the passage efficiency and migration routes of adult Pacific lamprey at Winchester Dam; 2) to evaluate the seasonal movement patterns of adult Pacific lamprey and their use of holding habitat at Winchester Dam in relation to temperature conditions; and 3) to portray the diversity of upstream migratory behaviors of adult Pacific lamprey and the environmental factors that influence these behaviors. This radio telemetry study was conducted between March 2009 and August 2011 with a combination of fixed stations and manual tracking. Passage efficiency was low in both years (8% and 19%, respectively), and all tagged lamprey that successfully passed the dam used routes other than the fish ladder. Lamprey that migrated early within the run and those with relatively small tags had higher passage rates and traveled further than the other groups of lamprey. Lamprey released above of the dam or those that passed the dam on their own distributed themselves widely in the upstream environment, suggesting that the dam deterred their upstream migration. Using mark-recapture data for the two years, the adult Pacific lamprey population upstream of Winchester Dam was estimated at 960 (95% C.I. [188, 4760]) in 2009 and 556 (95% C.I. [110, 2798]) in 2010, which was considerably lower than historical counts at the dam (between 14,532-46,785 in 1965-1971). Most tagged lamprey that did not pass the dam remained at the base of the dam at the end of the summer migration (63% in 2009 and 67% in 2010). Types of habitat most frequently used by lamprey downstream from the dam included the dam surface (wooden structures with crevices), interface zones between fast and slow water, and highway bridge pilings. The lamprey movement changed considerably between August and September, and the frequency of movements decreased sharply during this period. Tagged lamprey were detected using thermal refuges immediately downstream of the dam that were 0.4 to 2.8 C° colder than the mean river temperature at the dam, and this temperature differential increased as the season progressed. Lamprey may be seeking overwintering habitat associated with hyporheic exchange flows at the dam towards the end of the summer season after their display of heightened activity early in the summer. Ninety-five percent of the overall upstream migration took place during the first spring/summer period, and only small-scale upstream movements were observed during the winter and second spring/summer (4% and 1%, respectively). The rate of upstream migration (median) was the fastest during the initial migration phase and was 1.9 km/day (ranging from 0.3 to 11.0 km/day) for tagged lamprey released above Winchester Dam. During winter, 71% of the lamprey remained in the same location where they initiated holding. Multiple regression analysis indicated that the total upstream distance traveled by individual lamprey was most strongly related to presence/absence of Winchester Dam, relative tag size, and water temperature and photoperiod conditions at release. The presence of Winchester Dam, large relative tag size, and high water temperature / short photoperiod conditions at release significantly reduced upstream migration distance. Close

• 20. [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