Effects of Hydroelectric Dam Operations on the Restoration Potential of Snake River Fall Chinook Salmon (Oncorhynchus tshawytscha) Spawning Habitat Final Report, October 2005 - September 2007.

This report describes research conducted by the Pacific Northwest National Laboratory for the Bonneville Power Administration (BPA) as part of the Fish and Wildlife Program directed by the Northwest Power and Conservation Council. The study evaluated the restoration potential of Snake River fall Chinook salmon spawning habitat within the impounded lower Snake River. The objective of the research was to determine if hydroelectric dam operations could be modified, within existing system constraints (e.g., minimum to normal pool levels; without partial removal of a dam structure), to increase the amount of available fall Chinook salmon spawning habitat in the lower Snake River. Empirical and modeled physical habitat data were used to compare potential fall Chinook salmon spawning habitat in the Snake River, under current and modified dam operations, with the analogous physical characteristics of an existing fall Chinook salmon spawning area in the Columbia River. The two Snake River study areas included the Ice Harbor Dam tailrace downstream to the Highway 12 bridge and the Lower Granite Dam tailrace downstream approximately 12 river kilometers. These areas represent tailwater habitat (i.e., riverine segments extending from a dam downstream to the backwater influence from the next dam downstream). We used a reference site, indicative of current fall Chinook salmon spawning areas in tailwater habitat, against which to compare the physical characteristics of each study site. The reference site for tailwater habitats was the section extending downstream from the Wanapum Dam tailrace on the Columbia River. Fall Chinook salmon spawning habitat use data, including water depth, velocity, substrate size and channelbed slope, from the Wanapum reference area were used to define spawning habitat suitability based on these variables. Fall Chinook salmon spawning habitat suitability of the Snake River study areas was estimated by applying the Wanapum reference reach habitat suitability criteria to measured and modeled habitat data from the Snake River study areas. Channel morphology data from the Wanapum reference reach and the Snake River study areas were evaluated to identify geomorphically suitable fall Chinook salmon spawning habitat. The results of this study indicate that a majority of the Ice Harbor and Lower Granite study areas contain suitable fall Chinook salmon spawning habitat under existing hydrosystem operations. However, a large majority of the currently available fall Chinook salmon spawning habitat in the Ice Harbor and Lower Granite study areas is of low quality. The potential for increasing, through modifications to hydrosystem operations (i.e., minimum pool elevation of the next downstream dam), the quantity or quality of fall Chinook salmon spawning habitat appears to be limited. Estimates of the amount of potential fall Chinook salmon spawning habitat in the Ice Harbor study area decreased as the McNary Dam forebay elevation was lowered from normal to minimum pool elevation. Estimates of the amount of potential fall Chinook salmon spawning habitat in the Lower Granite study area increased as the Little Goose Dam forebay elevation was lowered from normal to minimum pool elevation; however, 97% of the available habitat was categorized within the range of lowest quality. In both the Ice Harbor and Lower Granite study areas, water velocity appears to be more of a limiting factor than water depth for fall Chinook salmon spawning habitat, with both study areas dominated by low-magnitude water velocity. The geomorphic suitability of both study areas appears to be compromised for fall Chinook salmon spawning habitat, with the Ice Harbor study area lacking significant bedforms along the longitudinal thalweg profile and the Lower Granite study area lacking cross-sectional topographic diversity. To increase the quantity of available fall Chinook salmon spawning habitat in the Ice Harbor and Lower Granite study area, modifications to hydroelectric dam operations beyond those evaluated in this study likely would be necessary. Modifications may include operational and structural changes, such as lowering downstream dam forebay elevations to less than minimum pool. There is a large amount of uncertainty as to whether or not such modifications could increase the quantity of available fall Chinook salmon spawning habitat in the Ice Harbor and Lower Granite study area. The results from this study provide some certainty that the quantity and quality of fall Chinook salmon spawning habitat within the lower Snake River are not likely to be increased within the existing hydroelectric dam operations

Evaluation of Salmon Spawning Below Bonneville Dam, Annual Report October 2005 - September 2006.

Since FY 2000, scientists at Pacific Northwest National Laboratory (PNNL) have conducted research to assess the extent of spawning by chum salmon (Oncorhynchus keta) and fall Chinook salmon (O. tshawytscha) in the lower mainstem Columbia River. Their work supports a larger project funded by the Bonneville Power Administration (BPA) aimed at characterizing the physical habitat used by mainstem fall Chinook and chum salmon populations. Multiple collaborators in addition to PNNL are involved in the BPA project--counterparts include the Washington Department of Fish and Wildlife (WDFW), U.S. Fish and Wildlife Service (USFWS), Pacific States Marine Fisheries Commission (PSMFC), U.S. Geological Survey (USGS), and Oregon Department of Fish and Wildlife (ODFW). Data resulting from the individual tasks each agency conducts are providing a sound scientific basis for developing strategies to operate the Federal Columbia River Power System (FCRPS) in ways that will effectively protect and enhance the chum and tule fall Chinook salmon populations--both listed as threatened under the Endangered Species Act (ESA). Fall Chinook salmon, thought to originate from Bonneville Hatchery, were first noted to be spawning downstream of Bonneville Dam by WDFW biologists in 1993. Known spawning areas include gravel beds on the Washington side of the river near Hamilton Creek and near Ives Island. Limited surveys of spawning ground were conducted in the area around Ives and Pierce islands from 1994 through 1997. Based on those surveys, it is believed that fall Chinook salmon are spawning successfully in this area. The size of this population from 1994 to 1996 was estimated at 1800 to 5200 fish. Chum salmon also have been documented spawning downstream of Bonneville Dam. Chum salmon were listed as threatened under the ESA in March 1999. At present there is a need to determine the number of fall Chinook and chum salmon spawning downstream of Bonneville Dam, the characteristics of their spawning areas, and the flows necessary to ensure their long-term survival. Ongoing discussions regarding the minimum and maximum flows will result in optimal spawning habitat usage and survival of embryos of both species. Collection of additional data as part of this project will ensure that established flow guidelines are appropriate and provide adequate protection for the species of concern. This is consistent with the high priority placed by the Northwest Power and Conservation Council Independent Scientific Advisory Board and the salmon managers on determining the importance of mainstem habitats to the production of salmon in the Columbia River Basin. Thus, there is a need to better understand the physical habitat variables used by mainstem fall Chinook and chum salmon populations and the effects of hydropower project operations on spawning and incubation. Pacific Northwest National Laboratory was asked to participate in the cooperative study during FY 2000. Since then, we have focused on (1) investigating the interactions between groundwater and surface water near fall Chinook and chum salmon spawning areas; (2) providing in-season hyporheic temperature data and assisting state agencies with emergence timing estimates; (3) locating and mapping deep-water fall Chinook salmon spawning areas; and (4) providing support to the WDFW for analysis of stranding data. Work conducted during FY 2006 addressed these same efforts. This report documents the studies and tasks performed by PNNL during FY 2006. Chapter 1 provides a description of the searches conducted for deepwater redds--adjacent to Pierce and Ives islands for fall Chinook salmon and near the Interstate 205 bridge for chum salmon. The chapter also provides data on redd location, information about habitat associations, and estimates of total spawning populations. Chapter 2 documents the collection of data on riverbed and river temperatures and water surface elevations, from the onset of spawning to the end of emergence, and the provision of those data in-season to fisheries management agencies to assist with emergence timing estimates and evaluations of redd dewatering. Technical assistance provided to the WDFW and PSMFC in evaluation of stranding data is summarized in Chapter 3

Development of a Conceptual Chum Salmon Emergence Model for Ives Island

The objective of the study described herein was to develop a conceptual model of chum salmon emergence that was based on empirical water temperature of the riverbed and river in specific locations where chum salmon spawn in the Ives Island area. The conceptual model was developed using water temperature data that have been collected in the past and are currently being collected in the Ives Island area. The model will be useful to system operators who need to estimate the complete distribution of chum salmon emergence (first emergence through final emergence) in order to balance chum salmon redd protection and power system operation

Total Dissolved Gas Monitoring in Chum Salmon Spawning Gravels Below Bonneville Dam

At the request of the U.S. Army Corps of Engineers (Portland District), Pacific Northwest National Laboratory (PNNL) conducted research to determine whether total dissolved gas concentrations are elevated in chum salmon redds during spring spill operations at Bonneville Dam. The study involved monitoring the total dissolved gas levels at egg pocket depth and in the river at two chum salmon spawning locations downstream from Bonneville Dam. Dissolved atmospheric gas supersaturation generated by spill from Bonneville Dam may diminish survival of chum (Oncorhynchus keta) salmon when sac fry are still present in the gravel downstream from Bonneville Dam. However, no previous work has been conducted to determine whether total dissolved gas (TDG) levels are elevated during spring spill operations within incubation habitats. The guidance used by hydropower system managers to provide protection for pre-emergent chum salmon fry has been to limit TDG to 105% after allowing for depth compensation. A previous literature review completed in early 2006 shows that TDG levels as low as 103% have been documented to cause mortality in sac fry. Our study measured TDG in the incubation environment to evaluate whether these levels were exceeded during spring spill operations. Total dissolved gas levels were measured within chum salmon spawning areas near Ives Island and Multnomah Falls on the Columbia River. Water quality sensors screened at egg pocket depth and to the river were installed at both sites. At each location, we also measured dissolved oxygen, temperature, specific conductance, and water depth to assist with the interpretation of TDG results. Total dissolved gas was depth-compensated to determine when levels were high enough to potentially affect sac fry. This report provides detailed descriptions of the two study sites downstream of Bonneville Dam, as well as the equipment and procedures employed to monitor the TDG levels at the study sites. Results of the monitoring at both sites are then presented in both text and graphics. The findings and recommendations for further research are discussed, followed by a listing of the references cited in the report

Methods for Assessing the Relative Amounts of Groundwater Discharge into the Columbia River and Measurement of Columbia River Gradients at the Hanford Site’s 300 Area

This report summarizes FY08 activities conducted under the Remediation and Closure Sciences Project

Effects of Total Dissolved Gas on Chum Salmon Fry Incubating in the Lower Columbia River

This report describes research conducted by Pacific Northwest National Laboratory in FY 2007 for the U.S. Army Corps of Engineers, Portland District, to characterize the effects of total dissolved gas (TDG) on the incubating fry of chum salmon (Onchorhynchus keta) in the lower Columbia River. The tasks conducted and results obtained in pursuit of three objectives are summarized: * to conduct a field monitoring program at the Ives Island and Multnomah Falls study sites, collecting empirical data on TDG to obtain a more thorough understanding of TDG levels during different river stage scenarios (i.e., high-water year versus low-water year) * to conduct laboratory toxicity tests on hatchery chum salmon fry at gas levels likely to occur downstream from Bonneville Dam * to sample chum salmon sac fry during Bonneville Dam spill operations to determine if there is a physiological response to TDG levels. Chapter 1 discusses the field monitoring, Chapter 2 reports the findings of the laboratory toxicity tests, and Chapter 3 describes the field-sampling task. Each chapter contains an objective-specific introduction, description of the study site and methods, results of research, and discussion of findings. Literature cited throughout this report is listed in Chapter 4. Additional details on the study methdology and results are provided in Appendixes A through D

Total Dissolved Gas Effects on Incubating Chum Salmon Below Bonneville Dam

At the request of the U.S. Army Corps of Engineers (USACE; Portland District), Pacific Northwest National Laboratory (PNNL) undertook a project in 2006 to look further into issues of total dissolved gas (TDG) supersaturation in the lower Columbia River downstream of Bonneville Dam. In FY 2008, the third year of the project, PNNL conducted field monitoring and laboratory toxicity testing to both verify results from 2007 and answer some additional questions about how salmonid sac fry respond to elevated TDG in the field and the laboratory. For FY 2008, three objectives were 1) to repeat the 2006-2007 field effort to collect empirical data on TDG from the Ives Island and Multnomah Falls study sites; 2) to repeat the static laboratory toxicity tests on hatchery chum salmon fry to verify 2007 results and to expose wild chum salmon fry to incremental increases in TDG, above those of the static test, until external symptoms of gas bubble disease were clearly present; and 3) to assess physiological responses to TDG levels in wild chum salmon sac fry incubating below Bonneville Dam during spill operations. This report summarizes the tasks conducted and results obtained in pursuit of the three objectives. Chapter 1 discusses the field monitoring, Chapter 2 reports the findings of the laboratory toxicity tests, and Chapter 3 describes the field-sampling task. Each chapter contains an objective-specific introduction, description of the study site and methods, results of research, and discussion of findings. Literature cited throughout this report is listed in Chapter 4. Additional details on the monitoring methodology and results are provided in Appendices A and B included on the compact disc bound inside the back cover of the printed version of this report

Investigation of the Hyporheic Zone at the 300 Area,Hanford Site

The Remediation Task of the Science and Technology (S&T) Project is intended to provide research to meet several objectives concerning the discharge of groundwater contamination into the river at the 300 Area of the Hanford Site. This report serves to meet the research objectives by developing baseline data for future evaluation of remedial technologies, evaluating the effects changing river stage on near-shore groundwater chemistry, improving estimates of contaminant flux to the river, providing estimates on the extent of contaminant discharge areas along the shoreline, and providing data to support computer models used to evaluate remedial alternatives. This report summarizes the activities conducted to date and provides an overview of data collected through July 2006. Recent geologic investigations (funded through other U. S. Department of Energy (DOE) programs) have provided a more complete geologic interpretation of the 300 Area and a characterization of the vertical extent of uranium contamination. Extrapolation of this geologic interpretation into the hyporheic zone is possible, but there is little data to provide corroboration. Penetration testing was conducted along the shoreline to develop evidence to support the extrapolation of the mapping of the geologic facies. In general, this penetration testing provided evidence supporting the extrapolation of the most recent geologic interpretation, but it also provided some higher resolution detail on the shape of the layer than constrains contaminant movement. Information on this confining layer will provide a more detailed estimate of the area of river bed that has the potential to be impacted by uranium discharge to the river from groundwater transport. Water sampling in the hyporheic zone has provided results that illustrate the degree of mixing that occurs in the hyporheic zone. Uranium concentrations measured at individual sampling locations can vary by several orders of magnitude depending on the river and near-shore aquifer elevations. It is shown in this report that the concentrations of all the measured constituents in water samples collected from the hyporheic zone vary according to the ratio of groundwater and river water in the sample. One important aspect of this is that specific conductance provides a sensitive indicator of the relative contribution of groundwater and river water in a particular sample. This is because of the large difference is specific conductance of groundwater (~400 μS/cm) and river water (~130 μS/cm). It appears that in the hyporheic zone, advection of contaminates occurs very quickly, and variations in concentrations are a function of dilution rather than any chemistry effects caused by the difference in water chemistry between groundwater and river water

In Situ Hydraulic Testing and Water Quality Sampling in the Hyporheic Zone of the Columbia River, Hanford Reach, Washington

Several chemical and radiological contaminants are present in an unconfined aquifer underlying the U.S. Department of Energy\u27s Hanford Site in southeast Washington State. Hexavalent chromium [Cr(VI)], previously used as an anticorrosive in plutonium production reactors on the shoreline of the Columbia River, is of particular concern because of its conservative nature, toxicity to humans and aquatic life, and proximity to protected salmon spawning habitat. Hydrogeologic data are abundant from the unconfined aquifer, but are lacking from the hyporheic zone through which Cr(VI) is transported into the river. A hydrogeologic study was conducted near one known Cr(VI) plume to determine the concentration and extent of Cr(VI), effect of anisotropy on transport of Cr(VI) into the river, and the relationship between changing river stage and water quality within the hyporheic zone. Forty-one piezometers were installed along a 4,000 m reach of the river at depths from 0.2 m to 2.0 m below the riverbed. The piezometers were used to sample Cr(VI), specific conductance, dissolved oxygen, and temperature. Cr(VI) concentrations ranged from undetectable to \u3e0.7 mg/L, with 75% of the samples above the federal standards for protection of aquatic life and 25% above federal drinking water standards. Vertical hydraulic gradients ranged from -0.01 to +0.30. Hydraulic conductivity values, estimated using slug tests, ranged from 2.8 x 10–5 cm/s to 4.3 x 10-2 cm/s and were largest in areas with high Cr(VI) concentrations. Specific discharge values were estimated using borehole dilution and ranged from 4.0 x 10-3 cm/s to 1.5 x 10-1 cm/s. In general, an inverse correlation was determined for river stage versus Cr(VI) and other water quality parameters; further investigation determined the relationship to be hysteretic. Results showed that 0.044 kg/d Cr(VI) entered the river, and the concentration of Cr(VI) in the Columbia River downstream of the 100D Area was 1.8 x 10-7 mg/L . This study produced results which will allow managers to make better risk-based decisions on Cr(VI) impacts to the biota living in the hyporheic zone

Evaluation of Salmon Spawning Below Bonneville Dam Annual Report October 2006 - September 2007.

From 1999 through 2007, the Fish and Wildlife Program of the Bonneville Power Administration funded a project to determine the number of fall Chinook and chum salmon spawning downstream of Bonneville Dam, the characteristics of their spawning areas, and the flows necessary to ensure their long-term survival. Data were collected to ensure that established flow guidelines are appropriate and provide adequate protection for the species of concern. The projects objectives are consistent with the high priority placed by the Northwest Power and Conservation Council Independent Scientific Advisory Board and the salmon managers on determining the importance of mainstem habitats to the production of salmon in the Columbia River Basin. Because of the influence of mainstem habitat on salmon production, there is a continued need to better understand the physical habitat variables used by mainstem fall Chinook and chum salmon populations and the effects of hydropower project operations on spawning and incubation. During FY 2007, Pacific Northwest National Laboratory focused on (1) locating and mapping deep-water fall Chinook salmon and chum salmon spawning areas, (2) investigating the interaction between groundwater and surface water near fall Chinook and chum salmon spawning areas, and (3) providing in-season hyporheic temperature and water surface elevation data to assist state agencies with emergence timing and redd dewatering estimates. This report documents the studies and tasks performed by PNNL during FY 2007. Chapter 1 provides a description of the searches conducted for deepwater redds-adjacent to Pierce and Ives islands for fall Chinook salmon and near the Interstate 205 bridge for chum salmon. The chapter also provides data on redd location, information about habitat associations, and estimates of total spawning populations. Chapter 2 documents the collection of data on riverbed and river temperatures and water surface elevations, from the onset of spawning to the end of emergence, and the provision of those data in-season to fisheries management agencies to assist with emergence timing estimates and evaluations of redd dewatering