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• 1. [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

• 2. [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

• 3. [Article] Green River CE-QUAL-W2 Project: A Hydrodynamic and Water Quality Study of the Green River King County, Washington

  This report describes the data processing and model calibration performed for a hydrodynamic and water quality model of the Green River, located in King County, Washington. Figure 1 shows the location ...

  Citation × Citation Citation Abstract Copy Title: Green River CE-QUAL-W2 Project: A Hydrodynamic and Water Quality Study of the Green River King County, Washington Author: Kraft, Tim, Annear, Robert Leslie, Berger, Chris, Wells, Scott A. Year: 2004 This report describes the data processing and model calibration performed for a hydrodynamic and water quality model of the Green River, located in King County, Washington. Figure 1 shows the location of the river, and the limits of the section of river that was modeled. The Green River flows from its headwaters in the Cascade Mountain foothills through the King County, Washington communities of Auburn, Kent, and Tukwila before discharging into the Duwamish River. Two sections of the river were modeled in this project. The Middle Green River begins in the Cascade Mountain foothills east of Tacoma, and continues downstream to the city of Auburn, WA. The Lower Green River continues from Auburn to the confluence with the Duwamish River, in the town of Tukwila. The Green/Duwamish River system is unique in that it flows through a heavily urbanized and industrialized environment yet supports a large salmon population (Green/Duwamish Ecosystem Restoration Study, 2003). To protect the river and its prime salmon habitat, King County and the US Army Corps of Engineers have joined together on a study to identify and implement strategies for restoring and protecting the Green/Duwamish River System and its tributaries (Green/Duwamish Ecosystem Restoration Study, 2003). As part of the Green-Duwamish Watershed Water Quality Assessment Program, King County contracted with Portland State University to develop a hydrodynamic and water quality model for the Lower and Middle Green River. This model will be used in Total Maximum Daily Load (TMDL) development, in assessing current water quality conditions in the river, and as a planning tool for evaluating the impacts of future development in the basin. Title: Green River CE-QUAL-W2 Project: A Hydrodynamic and Water Quality Study of the Green River King County, Washington Author: Kraft, Tim, Annear, Robert Leslie, Berger, Chris, Wells, Scott A. Year: 2004 This report describes the data processing and model calibration performed for a hydrodynamic and water quality model of the Green River, located in King County, Washington. Figure 1 shows the location of the river, and the limits of the section of river that was modeled. The Green River flows from its headwaters in the Cascade Mountain foothills through the King County, Washington communities of Auburn, Kent, and Tukwila before discharging into the Duwamish River. Two sections of the river were modeled in this project. The Middle Green River begins in the Cascade Mountain foothills east of Tacoma, and continues downstream to the city of Auburn, WA. The Lower Green River continues from Auburn to the confluence with the Duwamish River, in the town of Tukwila. The Green/Duwamish River system is unique in that it flows through a heavily urbanized and industrialized environment yet supports a large salmon population (Green/Duwamish Ecosystem Restoration Study, 2003). To protect the river and its prime salmon habitat, King County and the US Army Corps of Engineers have joined together on a study to identify and implement strategies for restoring and protecting the Green/Duwamish River System and its tributaries (Green/Duwamish Ecosystem Restoration Study, 2003). As part of the Green-Duwamish Watershed Water Quality Assessment Program, King County contracted with Portland State University to develop a hydrodynamic and water quality model for the Lower and Middle Green River. This model will be used in Total Maximum Daily Load (TMDL) development, in assessing current water quality conditions in the river, and as a planning tool for evaluating the impacts of future development in the basin. Close

• 4. [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

• 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