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• 1. [Article] Impacts of Columbia River Discharge on Salmonid Habitat: 2. Changes in Shallow-Water Habitat

  This is the second part of an investigation that analyzes human alteration of shallow-water habitat (SWH) available to juvenile salmonids in the tidal Lower Columbia River. Part 2 develops a one-dimensional, ...

  Citation × Citation Citation Abstract Copy Title: Impacts of Columbia River Discharge on Salmonid Habitat: 2. Changes in Shallow-Water Habitat Author: Jay, David A., Kukulka, Tobias Year: 2003 This is the second part of an investigation that analyzes human alteration of shallow-water habitat (SWH) available to juvenile salmonids in the tidal Lower Columbia River. Part 2 develops a one-dimensional, subtidal river stage model that explains ~90% of the stage variance in the tidal river. This model and the tidal model developed in part 1 (Kukulka and Jay, 2003) uncouple the nonlinear interaction of river tides and river stage by referring both to external forcing by river discharge, ocean tides, and atmospheric pressure. Applying the two models, daily high-water levels were predicted for a reach from rkm-50 to rkm-90 during 1974 to 1998, the period of contemporary management. Predicted water levels were related to the bathymetry and topography to determine the changes in shallow-water habitat area (SWHA) caused by flood control dikes and altered flow management. Model results suggest that diking and a >40% reduction of peak flows have reduced SWHA by ~62% during the crucial spring freshet period during which juvenile salmon use of SWHA is maximal. Taken individually, diking and flow cycle alteration reduced spring freshet SWHA by 52% and 29%, respectively. SWHA has been both displaced to lower elevations and modified in its character because tidal range has increased. Our models of these processes are economical for the very long simulations (seasons to centuries) needed to understand historic changes and climate impacts on SWH. Through analysis of the nonlinear processes controlling surface elevation in a tidal river, we have identified some of the mechanisms that link freshwater discharge to SWH and salmonid survival. Title: Impacts of Columbia River Discharge on Salmonid Habitat: 2. Changes in Shallow-Water Habitat Author: Jay, David A., Kukulka, Tobias Year: 2003 This is the second part of an investigation that analyzes human alteration of shallow-water habitat (SWH) available to juvenile salmonids in the tidal Lower Columbia River. Part 2 develops a one-dimensional, subtidal river stage model that explains ~90% of the stage variance in the tidal river. This model and the tidal model developed in part 1 (Kukulka and Jay, 2003) uncouple the nonlinear interaction of river tides and river stage by referring both to external forcing by river discharge, ocean tides, and atmospheric pressure. Applying the two models, daily high-water levels were predicted for a reach from rkm-50 to rkm-90 during 1974 to 1998, the period of contemporary management. Predicted water levels were related to the bathymetry and topography to determine the changes in shallow-water habitat area (SWHA) caused by flood control dikes and altered flow management. Model results suggest that diking and a >40% reduction of peak flows have reduced SWHA by ~62% during the crucial spring freshet period during which juvenile salmon use of SWHA is maximal. Taken individually, diking and flow cycle alteration reduced spring freshet SWHA by 52% and 29%, respectively. SWHA has been both displaced to lower elevations and modified in its character because tidal range has increased. Our models of these processes are economical for the very long simulations (seasons to centuries) needed to understand historic changes and climate impacts on SWH. Through analysis of the nonlinear processes controlling surface elevation in a tidal river, we have identified some of the mechanisms that link freshwater discharge to SWH and salmonid survival. Close

• 2. [Article] Salmon at River's End: The Role of the Estuary in the Decline and Recovery of Columbia River salmon

  The continued decline of Columbia River salmon (Oncorhynchus spp.) populations has long focused concerns on habitat changes upriver, particularly the effects of large hydroelectric dams. Increasing evidence ...

  Citation × Citation Citation Abstract Copy Title: Salmon at River's End: The Role of the Estuary in the Decline and Recovery of Columbia River salmon Author: Bottom, Daniel L., Simenstad, Charles A., Burke, Jennifer, Baptista, Antonio M., Jay, David A., Jone, Kim K., Casillas, Edmundo, Schiewe, Michael H. Year: 2005 The continued decline of Columbia River salmon (Oncorhynchus spp.) populations has long focused concerns on habitat changes upriver, particularly the effects of large hydroelectric dams. Increasing evidence that ocean conditions strongly influence salmon production, however, has raised questions about the importance of the estuarine environment to salmon and whether the hydropower system has affected estuarine-rearing habitats. In response to Northwest Power Planning Council recommendations, we initiated a review of what is known about the effects of the hydroelectric system on the hydrology, habitats, and ecology of the Columbia River estuary. Our goal was to develop recommendations for improving estuarine conditions or to identify research that may be needed before appropriate salmon-management changes can be defined. Our review and analyses addressed four major questions: (1) What habitats and processes support native salmon populations during the estuarine phase of their life cycle? (2) Have changes to the estuary had a significant role in salmon decline? (3) What have been the impacts of flow regulation on the hydrology, habitat, and biological interactions in the estuarine ecosystem? (4) What estuarine conditions are necessary to maintain salmonid diversity in the Columbia River basin? Title: Salmon at River's End: The Role of the Estuary in the Decline and Recovery of Columbia River salmon Author: Bottom, Daniel L., Simenstad, Charles A., Burke, Jennifer, Baptista, Antonio M., Jay, David A., Jone, Kim K., Casillas, Edmundo, Schiewe, Michael H. Year: 2005 The continued decline of Columbia River salmon (Oncorhynchus spp.) populations has long focused concerns on habitat changes upriver, particularly the effects of large hydroelectric dams. Increasing evidence that ocean conditions strongly influence salmon production, however, has raised questions about the importance of the estuarine environment to salmon and whether the hydropower system has affected estuarine-rearing habitats. In response to Northwest Power Planning Council recommendations, we initiated a review of what is known about the effects of the hydroelectric system on the hydrology, habitats, and ecology of the Columbia River estuary. Our goal was to develop recommendations for improving estuarine conditions or to identify research that may be needed before appropriate salmon-management changes can be defined. Our review and analyses addressed four major questions: (1) What habitats and processes support native salmon populations during the estuarine phase of their life cycle? (2) Have changes to the estuary had a significant role in salmon decline? (3) What have been the impacts of flow regulation on the hydrology, habitat, and biological interactions in the estuarine ecosystem? (4) What estuarine conditions are necessary to maintain salmonid diversity in the Columbia River basin? Close

• 3. [Article] Impacts of Columbia River Discharge on Salmonid Habitat: 1. A Nonstationary Fluvial Tide Model

  This is the first part of a two-part investigation that applies nonstationary time series analysis methods and the St. Venant equations to the problem of understanding juvenile salmonid access to favorable ...

  Citation × Citation Citation Abstract Copy Title: Impacts of Columbia River Discharge on Salmonid Habitat: 1. A Nonstationary Fluvial Tide Model Author: Jay, David A., Kukulka, Tobias Year: 2003 This is the first part of a two-part investigation that applies nonstationary time series analysis methods and the St. Venant equations to the problem of understanding juvenile salmonid access to favorable shallow-water habitat in a tidal river. Habitat access is a function of river stage, tidal range, and the distribution of bed elevation. Part 1 models nonstationary tidal properties: species amplitudes and phases and tidal range. Part 2 models low-frequency river stage in the Lower Columbia River and reconstructs historical water levels, using the tidal model from part 1. To incorporate the nonstationary frictional effects of variable river discharge into the tidal model, we decompose the tidal wave into tidal species and calculate daily tidal range. Our one-dimensional tidal model is based on analytic wave solutions to the linearized St. Venant equation and uses six coefficients per tidal species to represent the upstream evolution of the frictionally damped tidal wave. The form of the coefficients is derived from the St. Venant equations, but their values are determined objectively from the data. About 50 station-years of surface elevation data collected (1981-2000) below Bonneville Dam (235 km from the ocean) were processed with a wavelet filter bank to retrieve time series of tidal species properties. A min-max filter was used to estimate daily tidal range. Tidal range, diurnal, and semidiurnal amplitudes were predicted with mean root mean square errorsmm, which is significantly more accurate than predictions obtained from harmonic analysis. Thus despite the compact form of our solution, we model nonstationary fluvial tidal properties with a high level of accuracy. Title: Impacts of Columbia River Discharge on Salmonid Habitat: 1. A Nonstationary Fluvial Tide Model Author: Jay, David A., Kukulka, Tobias Year: 2003 This is the first part of a two-part investigation that applies nonstationary time series analysis methods and the St. Venant equations to the problem of understanding juvenile salmonid access to favorable shallow-water habitat in a tidal river. Habitat access is a function of river stage, tidal range, and the distribution of bed elevation. Part 1 models nonstationary tidal properties: species amplitudes and phases and tidal range. Part 2 models low-frequency river stage in the Lower Columbia River and reconstructs historical water levels, using the tidal model from part 1. To incorporate the nonstationary frictional effects of variable river discharge into the tidal model, we decompose the tidal wave into tidal species and calculate daily tidal range. Our one-dimensional tidal model is based on analytic wave solutions to the linearized St. Venant equation and uses six coefficients per tidal species to represent the upstream evolution of the frictionally damped tidal wave. The form of the coefficients is derived from the St. Venant equations, but their values are determined objectively from the data. About 50 station-years of surface elevation data collected (1981-2000) below Bonneville Dam (235 km from the ocean) were processed with a wavelet filter bank to retrieve time series of tidal species properties. A min-max filter was used to estimate daily tidal range. Tidal range, diurnal, and semidiurnal amplitudes were predicted with mean root mean square errorsmm, which is significantly more accurate than predictions obtained from harmonic analysis. Thus despite the compact form of our solution, we model nonstationary fluvial tidal properties with a high level of accuracy. Close

• 4. [Article] The Dynamics of the Columbia River Estuarine Ecosystem: Volume I and Volume II, CREDDP

  Integrates results from the CREDDP studies into a comprehensive synthesis. Includes physical setting and processes; relationships between physical and biological processes and among functional groups of ...

  Citation × Citation Citation Abstract Copy Title: The Dynamics of the Columbia River Estuarine Ecosystem: Volume I and Volume II, CREDDP Author: Simenstad, Charles A., Jay, David A., McIntire, C. David, Nehlsen, Willa, Sherwood, Christopher R., Small, Lawrence F. Year: 1984 Integrates results from the CREDDP studies into a comprehensive synthesis. Includes physical setting and processes; relationships between physical and biological processes and among functional groups of organisms; species, biomass and productivity per habitat type per region. Approximately 360 pages per volume. Title: The Dynamics of the Columbia River Estuarine Ecosystem: Volume I and Volume II, CREDDP Author: Simenstad, Charles A., Jay, David A., McIntire, C. David, Nehlsen, Willa, Sherwood, Christopher R., Small, Lawrence F. Year: 1984 Integrates results from the CREDDP studies into a comprehensive synthesis. Includes physical setting and processes; relationships between physical and biological processes and among functional groups of organisms; species, biomass and productivity per habitat type per region. Approximately 360 pages per volume. Close

• 5. [Article] Maintaining Safe, Efficient and Sustainable Intermodal Transport Through the Port of Portland

  About $15 billion of freight passes annually through the Lower Columbia River (LCR) navigation channel to reach Portland and Vancouver, where most of it connects with land transport. This commerce plays ...

  Citation × Citation Citation Abstract Copy Title: Maintaining Safe, Efficient and Sustainable Intermodal Transport Through the Port of Portland Author: Jay, David A., Pan, Jiayi Year: 2011 About $15 billion of freight passes annually through the Lower Columbia River (LCR) navigation channel to reach Portland and Vancouver, where most of it connects with land transport. This commerce plays a vital role in sustaining the regional economy and connecting Oregon to the global economy. The timely connection of truck and rail transport with vessels is vital, especially for export traffic. This link is susceptible to disruption if water depths in the navigation channel are shallower than expected, leading to delays and/or draft limitations. Moreover, ship drafts have increased in recent decades, 25% of the vessels calling in the river sail with a draft close to the channel depth at low water, and these carry roughly 70% of the cargo. A large vessel may have as little as 0.6 m bed clearance when it passes through a low-tide point in the river, which each vessel in transit must do. Thus, prediction and real-time communication of water level to vessels is vital to safety as well as efficiency. This has been implemented through the LOADMAX system, consisting of telemetered water-level gauges and a forecast model. Moreover, the dilemma has been made more critical by changes in the river – low water levels in the river channel between Wauna and Vancouver have decreased 0.3-1.2 m since 1940. The rate of decrease depends on location and riverflow, but appears to have accelerated in the last decade. The reasons for this decrease are not understood. For perspective, an ongoing 0.9 m channel deepening will cost about $150 million when completed, so unintended decreases in water depths are expensive as well as potentially dangerous. Lower water levels in the river also increase carbon emissions, because smaller loads mean more land and vessel transport trips. Further, navigation and salmon habitat restoration are closely connected. Dredging is used to maintain the channel, and habitat restoration is an integral part of the channel deepening. New dredging strategies are needed to maintain the newly deepened channel, but dredging that removes material permanently from the river may, further lower water levels, limiting possibilities for habitat restoration and reducing bed clearance for large ships. These problems will be exacerbated by future decreases in summer river flows due to climate change. Title: Maintaining Safe, Efficient and Sustainable Intermodal Transport Through the Port of Portland Author: Jay, David A., Pan, Jiayi Year: 2011 About $15 billion of freight passes annually through the Lower Columbia River (LCR) navigation channel to reach Portland and Vancouver, where most of it connects with land transport. This commerce plays a vital role in sustaining the regional economy and connecting Oregon to the global economy. The timely connection of truck and rail transport with vessels is vital, especially for export traffic. This link is susceptible to disruption if water depths in the navigation channel are shallower than expected, leading to delays and/or draft limitations. Moreover, ship drafts have increased in recent decades, 25% of the vessels calling in the river sail with a draft close to the channel depth at low water, and these carry roughly 70% of the cargo. A large vessel may have as little as 0.6 m bed clearance when it passes through a low-tide point in the river, which each vessel in transit must do. Thus, prediction and real-time communication of water level to vessels is vital to safety as well as efficiency. This has been implemented through the LOADMAX system, consisting of telemetered water-level gauges and a forecast model. Moreover, the dilemma has been made more critical by changes in the river – low water levels in the river channel between Wauna and Vancouver have decreased 0.3-1.2 m since 1940. The rate of decrease depends on location and riverflow, but appears to have accelerated in the last decade. The reasons for this decrease are not understood. For perspective, an ongoing 0.9 m channel deepening will cost about $150 million when completed, so unintended decreases in water depths are expensive as well as potentially dangerous. Lower water levels in the river also increase carbon emissions, because smaller loads mean more land and vessel transport trips. Further, navigation and salmon habitat restoration are closely connected. Dredging is used to maintain the channel, and habitat restoration is an integral part of the channel deepening. New dredging strategies are needed to maintain the newly deepened channel, but dredging that removes material permanently from the river may, further lower water levels, limiting possibilities for habitat restoration and reducing bed clearance for large ships. These problems will be exacerbated by future decreases in summer river flows due to climate change. Close

• 6. [Article] Applications of Remote Sensing to the Study of Estuarine Physics: Suspended Sediment Dynamics in the Columbia River Estuary

  Estuarine circulation and its associated transport processes drive the environmental integrity of many near-shore habitats (the coastal ocean, rivers, estuaries and emergent wetlands). A thorough understanding ...

  Citation × Citation Citation Abstract Copy Title: Applications of Remote Sensing to the Study of Estuarine Physics: Suspended Sediment Dynamics in the Columbia River Estuary Author: Hudson, Austin Scott Year: 2014 Estuarine circulation and its associated transport processes drive the environmental integrity of many near-shore habitats (the coastal ocean, rivers, estuaries and emergent wetlands). A thorough understanding and consideration of this circulation is, therefore, vital in the proper management of these habitats. The aim of this study is to bring together theory and new satellite observations in the Columbia River Estuary to increase our understanding of estuarine circulation and transport. Surface reflectance measurements gathered by the Moderate Imaging Spectroradiometer (MODIS) are first compared to in situ observations to develop an empirical model for remotely derived surface turbidity. Results indicate that MODIS data significantly correlate with in situ measurements of turbidity throughout the CRE (R2 = 0.96). Remote estimates of turbidity are then used to explore the physical processes that drive their spatial distribution. Although the response to different hydrodynamic conditions varies throughout the system, global levels of turbidity are most sensitive to fluvial and tidal inputs and increase during spring tides and high river flow. As a result, the turbidity field has temporal cycles that are consistent with the frequency of these processes. The location of the estuarine turbidity maximum (ETM) is highly dynamic and typically migrates downstream as the tidal velocity or river flow increases. The ETM becomes trapped near the Megler Bridge (river kilometer 20), however, and the presence of strong topography in this region suggests there exists an interaction between bottom topography and sediment transport. A 2-D semi-analytical model, developed herein from the simplified Navier-Stokes equations, confirms that topographic features exhibit substantial influence on longitudinal turbidity distributions. The model considers the coupled, tidally-averaged velocity (composed of gravitational circulation, internal tidal asymmetry, and river flow) and salinity fields and assumes a condition of morphodynamic equilibrium to estimate the distribution of sediment for arbitrary channel configurations. Model simulations demonstrate that topographic highs tend to increase local seaward sediment fluxes, and that topographic lows increase local landward sediment fluxes. Sediment flux convergence near topographic highs compresses the local turbidity distribution, whereas flux divergence near topographic lows dilates the distribution and, under appropriate conditions, produces multiple ETMs. In summary a combination of the model and satellite data has given valuable new insights into the sediment dynamics of estuarine environments; in particular, both show that turbidity distribution and ETM location vary considerably with tidal and river flow conditions, fluctuating on a variety of timescales, and are heavily influenced by bottom topography. Title: Applications of Remote Sensing to the Study of Estuarine Physics: Suspended Sediment Dynamics in the Columbia River Estuary Author: Hudson, Austin Scott Year: 2014 Estuarine circulation and its associated transport processes drive the environmental integrity of many near-shore habitats (the coastal ocean, rivers, estuaries and emergent wetlands). A thorough understanding and consideration of this circulation is, therefore, vital in the proper management of these habitats. The aim of this study is to bring together theory and new satellite observations in the Columbia River Estuary to increase our understanding of estuarine circulation and transport. Surface reflectance measurements gathered by the Moderate Imaging Spectroradiometer (MODIS) are first compared to in situ observations to develop an empirical model for remotely derived surface turbidity. Results indicate that MODIS data significantly correlate with in situ measurements of turbidity throughout the CRE (R2 = 0.96). Remote estimates of turbidity are then used to explore the physical processes that drive their spatial distribution. Although the response to different hydrodynamic conditions varies throughout the system, global levels of turbidity are most sensitive to fluvial and tidal inputs and increase during spring tides and high river flow. As a result, the turbidity field has temporal cycles that are consistent with the frequency of these processes. The location of the estuarine turbidity maximum (ETM) is highly dynamic and typically migrates downstream as the tidal velocity or river flow increases. The ETM becomes trapped near the Megler Bridge (river kilometer 20), however, and the presence of strong topography in this region suggests there exists an interaction between bottom topography and sediment transport. A 2-D semi-analytical model, developed herein from the simplified Navier-Stokes equations, confirms that topographic features exhibit substantial influence on longitudinal turbidity distributions. The model considers the coupled, tidally-averaged velocity (composed of gravitational circulation, internal tidal asymmetry, and river flow) and salinity fields and assumes a condition of morphodynamic equilibrium to estimate the distribution of sediment for arbitrary channel configurations. Model simulations demonstrate that topographic highs tend to increase local seaward sediment fluxes, and that topographic lows increase local landward sediment fluxes. Sediment flux convergence near topographic highs compresses the local turbidity distribution, whereas flux divergence near topographic lows dilates the distribution and, under appropriate conditions, produces multiple ETMs. In summary a combination of the model and satellite data has given valuable new insights into the sediment dynamics of estuarine environments; in particular, both show that turbidity distribution and ETM location vary considerably with tidal and river flow conditions, fluctuating on a variety of timescales, and are heavily influenced by bottom topography. Close

• 7. [Article] Hydrodynamic and Water Quality Modeling of the Chehalis River Using CE-QUAL-W2

  The Chehalis River Basin is located in the southwest region of Washington State, originating in the Olympic Mountains and flowing to Grays Harbor and the Pacific Ocean. The Chehalis River is over 125 miles, ...

  Citation × Citation Citation Abstract Copy Title: Hydrodynamic and Water Quality Modeling of the Chehalis River Using CE-QUAL-W2 Author: Van Glubt, Sarah Year: 2017 The Chehalis River Basin is located in the southwest region of Washington State, originating in the Olympic Mountains and flowing to Grays Harbor and the Pacific Ocean. The Chehalis River is over 125 miles, exists within five counties, and flows through agricultural, residential, industrial, and forest land areas. Four major rivers discharge to the Chehalis River, as well as many smaller creeks, five wastewater treatment plants, and groundwater flows. Flooding is a major problem in the relatively flat areas surrounding the cities of Chehalis and Centralia, with severe consequences for property, safety and transportation. As a result, construction of a flood-control dam in the upper basin has been proposed. One major concern of constructing a dam is the potentially severe impacts to fish health and habitat. The Chehalis River has routinely violated water quality standards for primarily temperature and dissolved oxygen, and has had multiple water quality and Total Maximum Daily Load studies beginning in 1990. CE-QUAL-W2, a two-dimensional (longitudinal and vertical) hydrodynamic and water quality model, was used to simulate the Chehalis River, including free flowing river stretches and stratified (in summer) lake-like stretches. The goals of this research were to assess the flood retention structure's impacts to water quality, as well as river responses to potential climate change scenarios. In order to use the model to achieve these goals, calibration to field data for flow, temperature, and water quality constituents was performed. This involved developing meteorological data, riparian shading data, and flow, temperature, water quality records for all tributaries during the calibration period of January 1, 2013 to December 31, 2014. System cross-sectional geometry data were also required for the model grid. Because of the short travel time in the river, the model was sensitive to boundary condition data, wind speed, bathymetry, nutrient kinetics, and algae, epiphyton, and zooplankton kinetics. Future conditions showed predictions of warmer water temperatures and slight changes to water quality conditions on the river. As fish in the area prefer cooler water temperatures, this could pose a threat to fish health and habitat. Flood retention structures also showed impacts to river temperature and water quality. Structures with the purpose of flood retention only (only operating during times of flooding) gave model predictions for daily maximum temperature higher than structures that employed flood retention and flow augmentation (operating during all times of the year). This suggested the management of flow passage or retention by the dam is important for water quality on the river. As this research continues improvements will be made, particularly to temperature and water quality constituents. Additional data for the system would be beneficial to this process. Model predictions of temperature were sensitive to meteorological data, including cloud cover, which were largely estimated based on solar radiation. Additional meteorological data throughout the basin would be useful to temperature results. Temperature results were also sensitive to the model bathymetry, and additional investigations into segments widths and water depths may improve temperature predictions. Water quality constituent data were largely lacking for the system. Many estimation techniques and approximations were used for input water quality constituents for the model upstream boundary and tributaries when little or no data were available, introducing uncertainty to the model. It was not possible to calibrate pH to field data because alkalinity data were essentially unavailable. However, other constituents had good agreement between model predictions and field data, including dissolved oxygen, nitrates, total phosphorus, and total suspended solids. Title: Hydrodynamic and Water Quality Modeling of the Chehalis River Using CE-QUAL-W2 Author: Van Glubt, Sarah Year: 2017 The Chehalis River Basin is located in the southwest region of Washington State, originating in the Olympic Mountains and flowing to Grays Harbor and the Pacific Ocean. The Chehalis River is over 125 miles, exists within five counties, and flows through agricultural, residential, industrial, and forest land areas. Four major rivers discharge to the Chehalis River, as well as many smaller creeks, five wastewater treatment plants, and groundwater flows. Flooding is a major problem in the relatively flat areas surrounding the cities of Chehalis and Centralia, with severe consequences for property, safety and transportation. As a result, construction of a flood-control dam in the upper basin has been proposed. One major concern of constructing a dam is the potentially severe impacts to fish health and habitat. The Chehalis River has routinely violated water quality standards for primarily temperature and dissolved oxygen, and has had multiple water quality and Total Maximum Daily Load studies beginning in 1990. CE-QUAL-W2, a two-dimensional (longitudinal and vertical) hydrodynamic and water quality model, was used to simulate the Chehalis River, including free flowing river stretches and stratified (in summer) lake-like stretches. The goals of this research were to assess the flood retention structure's impacts to water quality, as well as river responses to potential climate change scenarios. In order to use the model to achieve these goals, calibration to field data for flow, temperature, and water quality constituents was performed. This involved developing meteorological data, riparian shading data, and flow, temperature, water quality records for all tributaries during the calibration period of January 1, 2013 to December 31, 2014. System cross-sectional geometry data were also required for the model grid. Because of the short travel time in the river, the model was sensitive to boundary condition data, wind speed, bathymetry, nutrient kinetics, and algae, epiphyton, and zooplankton kinetics. Future conditions showed predictions of warmer water temperatures and slight changes to water quality conditions on the river. As fish in the area prefer cooler water temperatures, this could pose a threat to fish health and habitat. Flood retention structures also showed impacts to river temperature and water quality. Structures with the purpose of flood retention only (only operating during times of flooding) gave model predictions for daily maximum temperature higher than structures that employed flood retention and flow augmentation (operating during all times of the year). This suggested the management of flow passage or retention by the dam is important for water quality on the river. As this research continues improvements will be made, particularly to temperature and water quality constituents. Additional data for the system would be beneficial to this process. Model predictions of temperature were sensitive to meteorological data, including cloud cover, which were largely estimated based on solar radiation. Additional meteorological data throughout the basin would be useful to temperature results. Temperature results were also sensitive to the model bathymetry, and additional investigations into segments widths and water depths may improve temperature predictions. Water quality constituent data were largely lacking for the system. Many estimation techniques and approximations were used for input water quality constituents for the model upstream boundary and tributaries when little or no data were available, introducing uncertainty to the model. It was not possible to calibrate pH to field data because alkalinity data were essentially unavailable. However, other constituents had good agreement between model predictions and field data, including dissolved oxygen, nitrates, total phosphorus, and total suspended solids. Close

• 8. [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

• 9. [Article] A Comparison of Five Models for Estimating Clear-Sky Solar Radiation

  Many agencies in the USA are developing management approaches to address water quality concerns and threatened and endangered species habitat requirements in water bodies. Many of these water bodies are ...

  Citation × Citation Citation Abstract Copy Title: A Comparison of Five Models for Estimating Clear-Sky Solar Radiation Author: Annear, Robert Leslie, Wells, Scott A. Year: 2007 Many agencies in the USA are developing management approaches to address water quality concerns and threatened and endangered species habitat requirements in water bodies. Many of these water bodies are water quality limited for temperature. Factors influencing stream temperature include: streamside vegetation, topographic shading, inflows and outflows, stream width, stream depth, light extinction and solar radiation. One of the key driving factors in estimating a water body heat budget is calculating the amount of solar radiation incident on the water surface. Even though it is preferable to measure clear-sky solar radiation, many temperature models rely on theoretical estimates of clear-sky solar radiation. The literature on estimating short-wave solar radiation by calculating the position of the sun and attenuating the radiation through the atmosphere was reviewed. As a first step in relating water temperature to solar radiation, several empirical solar radiation models were calibrated to data at seventeen sites around the United States for clear-sky days. Sensitivity analyses were conducted and differences between the models were examined. Results indicated that the more complex models for calculating solar radiation resulted in better estimates of clear-sky solar radiation once they were calibrated to data. When no data were available, models with one or no calibration parameters did reasonably well at estimating clear-sky solar radiation. Title: A Comparison of Five Models for Estimating Clear-Sky Solar Radiation Author: Annear, Robert Leslie, Wells, Scott A. Year: 2007 Many agencies in the USA are developing management approaches to address water quality concerns and threatened and endangered species habitat requirements in water bodies. Many of these water bodies are water quality limited for temperature. Factors influencing stream temperature include: streamside vegetation, topographic shading, inflows and outflows, stream width, stream depth, light extinction and solar radiation. One of the key driving factors in estimating a water body heat budget is calculating the amount of solar radiation incident on the water surface. Even though it is preferable to measure clear-sky solar radiation, many temperature models rely on theoretical estimates of clear-sky solar radiation. The literature on estimating short-wave solar radiation by calculating the position of the sun and attenuating the radiation through the atmosphere was reviewed. As a first step in relating water temperature to solar radiation, several empirical solar radiation models were calibrated to data at seventeen sites around the United States for clear-sky days. Sensitivity analyses were conducted and differences between the models were examined. Results indicated that the more complex models for calculating solar radiation resulted in better estimates of clear-sky solar radiation once they were calibrated to data. When no data were available, models with one or no calibration parameters did reasonably well at estimating clear-sky solar radiation. Close

• 10. [Article] Willamette River Basin Temperature TMDL Model: Model Calibration

  The State of Oregon Department of Environmental Quality (DEQ) is developing a TMDL for temperature in the Willamette River basin shown in Figure 1. The study area included the Willamette River and all ...

  Citation × Citation Citation Abstract Copy Title: Willamette River Basin Temperature TMDL Model: Model Calibration Author: Berger, Chris, McKillip, Michael Lee, Annear, Robert Leslie, Khan, Sher Jamal, Wells, Scott A. Year: 2004 The State of Oregon Department of Environmental Quality (DEQ) is developing a TMDL for temperature in the Willamette River basin shown in Figure 1. The study area included the Willamette River and all major tributaries (except the Tualatin River where a TMDL process was already concluded). A large section of the Columbia River was also modeled to provide adequate boundary representation of tidal flows in the lower Willamette River. The Willamette River below the Oregon City Falls in the Portland metropolitan area has a typical diurnal tidal range of 1 m. The development of a dynamic model of temperature and hydrodynamics of the entire river basin incorporating shading were primary requirements of this modeling study. The model would be used by DEQ to set temperature limits on point source dischargers and to evaluate the impact of management strategies on river temperatures to improve fish habitat. Some of these strategies included modifications of the dam at the Willamette River Falls south of Portland and channel reconfigurations. The river basin model was originally divided into several reaches. Individual models were developed for each reach. The models were set-up for each section of the Willamette basin as described in Annear et al. (2004a), the models were calibrated to field data and management strategies were evaluated as described in Annear et al (2004b). This report outlines the model calibration of each of these model sections or elements for both the calibration time periods. The calibration period for each model section differs due to the availability of boundary condition data. The model management simulation scenarios (Annear et al, 2004b) also required boundary condition data that extended past the calibration periods. Title: Willamette River Basin Temperature TMDL Model: Model Calibration Author: Berger, Chris, McKillip, Michael Lee, Annear, Robert Leslie, Khan, Sher Jamal, Wells, Scott A. Year: 2004 The State of Oregon Department of Environmental Quality (DEQ) is developing a TMDL for temperature in the Willamette River basin shown in Figure 1. The study area included the Willamette River and all major tributaries (except the Tualatin River where a TMDL process was already concluded). A large section of the Columbia River was also modeled to provide adequate boundary representation of tidal flows in the lower Willamette River. The Willamette River below the Oregon City Falls in the Portland metropolitan area has a typical diurnal tidal range of 1 m. The development of a dynamic model of temperature and hydrodynamics of the entire river basin incorporating shading were primary requirements of this modeling study. The model would be used by DEQ to set temperature limits on point source dischargers and to evaluate the impact of management strategies on river temperatures to improve fish habitat. Some of these strategies included modifications of the dam at the Willamette River Falls south of Portland and channel reconfigurations. The river basin model was originally divided into several reaches. Individual models were developed for each reach. The models were set-up for each section of the Willamette basin as described in Annear et al. (2004a), the models were calibrated to field data and management strategies were evaluated as described in Annear et al (2004b). This report outlines the model calibration of each of these model sections or elements for both the calibration time periods. The calibration period for each model section differs due to the availability of boundary condition data. The model management simulation scenarios (Annear et al, 2004b) also required boundary condition data that extended past the calibration periods. Close