Federal Columbia River Power System Research Articles

Assessing seasonal and biological indices of juvenile Chinook Salmon for freshwater decision triggers that increase ocean survival

Decision triggers, used in adaptive management frameworks to decide when a specific management action will be implemented, are often informed by monitoring data. The identification and application of decision triggers is highly relevant to endangered fishes migrating through regulated rivers, as examined in the current study. The main goal was to determine whether seasonal patterns of behavioral, physical, and physiological indices of juveniles were related to subsequent smolt-to-adult return (SAR) survival and, if so, to determine whether these indices could be used to guide decisions related to the mitigation strategy of the juvenile fish transportation program in the Federal Columbia River Power System (Pacific Northwest, USA). Hatchery yearling Chinook Salmon (Oncorhynchus tshawytscha Walbaum in Artedi, 1792) were collected over the migration season at 3 dams in the hydrosystem and measured for fork length, wet mass, Fulton’s K (or condition factor), Na+/K+-ATPase (NKA) activity (or smoltification index), and % dry mass (or index of energetic reserves and smoltification). We estimated SAR survival from passive integrated transponder-tagged fish representative of our field samples and assessed its relationship to our fish indices, as well as indices of transported vs run-of-river passage and distance of sampling site to ocean. SAR survival was associated to interaction effects between juvenile fish transportation and % dry mass or NKA activity. Transported hatchery Chinook Salmon with dry mass <23% of whole fish wet mass and NKA activity >7 µmol ADP mg protein−1 h−1 showed greater SAR survival than their run-of-river counterparts. Fish with the highest predicted SAR survival had been transported and had fish indices consistent with smolts that were more developed (i.e., lower % dry mass and higher NKA activity). Furthermore, our results on % dry mass provided support for the hypothesis that greater lipid content increases fish buoyancy leading to greater susceptibility to predation. The buoyancy effect is expected to be greatest in hatchery fish. Overall, this study shows that decision triggers based on biological indices of migrating fish are potentially useful tools for in-season management.

The Abundance and Distribution of Hatchery and Naturally Produced Chinook Salmon in Columbia River Estuary Nearshore Habitat

AbstractColumbia River hatcheries release millions of juvenile Chinook Salmon Oncorhynchus tshawytscha to support fisheries and mitigate for historical productivity declines from dam construction and upriver habitat losses. Recent federal biological opinions for Federal Columbia River Power System operations also have mandated restoration of estuarine rearing habitats to mitigate for mortality of naturally produced (NP) salmon at main‐stem dams. We compared genetic stock compositions, distributions, abundances, and length frequencies of hatchery‐marked and unmarked Chinook Salmon to evaluate the extent of hatchery influence on nearshore estuarine habitat use and the potential for interactions between hatchery‐origin (HO) and NP salmon. Cumulative Chinook Salmon releases from all hatcheries in 2010 and 2011 dictated estuarine stock composition, abundance, and life histories during the spring–summer migration peak. Naturally produced salmon from the lower Columbia River populations, including many fry migrants, were most abundant, but larger HO juveniles also frequented nearshore sites, where their total biomass often equaled or exceeded that of NP fish. Large releases of a single stock of origin (Spring Creek Group fall run) in April and May created sharp pulses in the estuary entry timing of fingerling‐sized salmon and dominated abundance and stock composition at some sites. Successive releases from scores of hatcheries during spring and early summer ensured a consistent presence of HO salmon near shore, regardless of the habitat‐specific residence times of individual fish. Overall, the historical replacement of diverse wild populations with fewer hatchery stocks of a narrow size range and migration timing has intensified nearshore habitat use during the spring–summer migration peak and reduced life history variation of Columbia River Chinook Salmon. Such changes could undermine the fish conservation goals of both hatchery mitigation and estuary restoration programs.

Passage and Survival of Juvenile Salmonid Smolts through Dams in the Columbia and Snake Rivers, 2010–2018

AbstractMinimizing the mortality and migration time of juvenile salmon (smolts) that pass through dams is a long‐standing objective in the pursuit of salmon recovery in the Columbia River basin. We compiled and analyzed 40 acoustic tag studies of juvenile salmonid that were performed between 2010 and 2018 at seven of the eight hydroelectric projects in the Federal Columbia River Power System. We found that the use of nonturbine routes decreased monotonically moving downstream from the Snake River to the main‐stem Columbia River dams and associated mortality differed substantially between the dams in the two rivers. Spillways were the predominant passage route at the main‐stem Columbia River dams. In contrast, passage was more common through the surface weirs and juvenile bypass systems at the dams in the Snake River, which generally provided higher survival. The observed stocks exhibited variable passage behaviors and mortalities, and the estimated probability that an individual would pass through all eight dams in the system without using a turbine route was 0.31, 0.47, and 0.60 for subyearling Chinook Salmon Oncorhynchus tshawytscha, yearling Chinook Salmon, and steelhead O. mykiss, respectively. Although subyearling Chinook Salmon were generally more likely to pass through a turbine route, they also experienced less turbine‐associated mortality than did the other stocks, especially steelhead. Notably, the proportion of smolts that passed through the spillway relative to the proportion of water through the spillway was lowest at Bonneville Dam, the largest and lowermost dam in the system. Bonneville Dam also stood out as having the highest proportion of smolts passing through turbines, but it was among the locations with the lowest rates of turbine‐associated mortality.

Achieving Productivity to Recover and Restore Columbia River Stream‐Type Chinook Salmon Relies on Increasing Smolt‐To‐Adult Survival

AbstractWe analyzed and compared productivity and survival rates of populations of stream‐type Chinook Salmon Oncorhynchus tshawytscha from the upper and middle ranges of their distribution in the Columbia River basin. These two groups of populations undergo vastly different exposures during migration through the Federal Columbia River Power System (FCRPS). Declines of the Snake River populations, listed as threatened under the U.S. Endangered Species Act, have been associated with the development and operation of the FCRPS. In contrast, John Day River stream‐type Chinook Salmon populations, which were less affected by the FCRPS, have declined to a lesser extent and are not listed. Smolt‐to‐adult survival rates (SARs) accounted for a majority of the variation in life cycle survival rates of Snake River Chinook Salmon. Productivity declined to 13% and 44% of historical productivity levels for Snake River and John Day River populations, respectively. A synthesis of previous studies contrasting anthropogenic impacts between the two regions supports the conclusion that FCRPS impacts explain the large difference in population productivity. Our results suggest that SARs of 4% would result in an expected productivity of up to 70% of historical levels (a SAR level consistent with regional restoration objectives). The SARs have been shown to be highly influenced by conditions within the FCRPS (e.g., water velocity and passage through dam powerhouses). Marine conditions also influence SARs; however, meaningful management actions are only available to affect conditions within the FCRPS. Given the importance of SARs to overall life cycle productivity, recovery and restoration strategies need to prioritize actions that have potential to substantially increase SARs by addressing the significant impacts of main‐stem dams. This study highlights the importance of considering river management options in the face of increasingly variable and warming ocean conditions.

The Fight Over Columbia Basin Salmon Spills and the Future of the Lower Snake River Dams

One of the nation’s most longstanding environmental-energy conflicts concerns the plight of numerous Columbia Basin salmon species which must navigate the Federal Columbia River Power System (FCRPS), a series of hydroelectric dams that make the basin one of the most highly developed in the world. Although the FCRPS dams produce a considerable amount of low-cost hydropower, the mortalities they cause due to the construction and operation of FCRPS dams led to Endangered Species Act listings for the basin’s salmon. Since those listings a quarter-century ago, the federal government has struggled to produce biological opinions that can survive judicial scrutiny, repeatedly failing to do so. The latest round of litigation resulted in renewed directive from the federal district court of Oregon to revise the current biological opinion and to spill water at several dams in the interim to facilitate salmon migration. The directive to spill was upheld by the Ninth Circuit in 2018, but the U.S. House of Representatives quickly voted to overturn that decision, and the Senate now has the matter under consideration. This article considers the latest round of Columbia Basin salmon litigation and the threat of congressional intervention. We also examine the fate of four Snake River FCRPS dams that have proved particularly hazardous to listed salmon. These dams provide no flood control, easily replaceable power, and barge navigation for which there are also ready substitutes. The article maintains that since these four dams can pass no reasonable cost-benefit test, Congress should not act to revise the court-ordered spills but instead order the lower Snake River dams removed, which would begin the restoration the listed Snake River salmon and result in the transformation of the economy of the Snake Basin in eastern Washington and Oregon, and in Idaho.

Still Crying Out for a 'Major Overhaul' after All These Years Salmon and the Fourth Failed Biological Opinion on Columbia Basin Hydroelectric Operations

For nearly four decades, national policy has been to restore Columbia Basin salmon devastated by the construction and operation of the Federal Columbia River Power System (FCRPS). In the 1980 Northwest Power Act, Congress declared that salmon restoration was a national priority, and that it would be funded largely through federal hydropower sales. A basinwide plan approved by the Northwest states began the restoration effort in 1982, but since that plan did not focus on wild salmon restoration, it was eclipsed by federal biological opinions (BiOps) after several salmon species were listed under the Endangered Species in the early 1990s. There followed a seemingly endless series of court challenges to the adequacy of the BiOps, most of which succeeded.Although we discuss all of the Columbia Basin ESA salmon court decisions over the last quarter-century, we focus on the 2016 decision, a remarkable 149-page opinion that is a paragon of close judicial review. Judge Michael Simon became the third consecutive federal judge to find the federal BiOp on FCRPS hydroelectric operations wanting, but he did so in much greater detail and scope than did his predecessors. The result was a judicial opinion that could produce substantial changes in the way the federal government approaches ESA compliance of the world’s largest integrated hydroelectric system. Like his predecessors, Judge Simon faulted the federal government for failing to ensure that the mitigation measures in its FCRPS BiOp were “reasonably certain to occur.” In addition, among other shortcomings, he determined that the BiOp failed to 1) employ a proper standard of species recovery in its BiOp, 2) account for the effects of climate change on the mitigation measures in its BiOp, and 3) prepare a programmatic environmental impact statement on the cumulative effects of those measures and reasonable alternatives. Implementation of the Simon opinion, if carried out faithfully, could substantially improve prospects for the recovery of the thirteen ESA-listed salmon runs. The opinion also may establish important ESA precedent concerning the species jeopardy that BiOps are to avoid, the critical habitat that BiOps are supposed to protect, and the relationship between BiOp implementation and procedures necessary to satisfy the National Environmental Policy Act (NEPA). Concerning the latter, perhaps the most arresting aspect of the Simon opinion was the directive that NEPA required an environmental impact statement evaluating the alternative of breaching the four federal dams on the Lower Snake River. However, while a court may order the FCRPS agencies to consider dam breaching as a NEPA alternative, neither the agencies nor a court have authority to order dam breaching, a matter that in the case of federal dams lies exclusively with Congress.

Establishing and using study criteria to ensure the rigor and robustness of survival compliance testing at hydroelectric dams

An elaborate set of criteria have been developed by fish managers and regulators to assure the accuracy, precision, representativeness, and robustness of survival compliance studies coordinated within the Federal Columbia River Power System in the northwestern USA. Dam passage survival, defined as survival from the dam face to the tailrace mixing zone, must be ≥96 % for spring out migrating juvenile salmonids [i.e., yearling Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss)] and ≥93 % for summer outmigrants (i.e., subyearling Chinook salmon). Survival must be estimated with a standard error ≤1.5 %. However, these quantitative benchmarks are only part of a multifaceted set of criteria, including representative dam operations, river discharge levels, and fish selection, along with tests of model validity that must be satisfied. These criteria are illustrated using acoustic-tag survival compliance studies conducted at The Dalles Dam on the Columbia River, 2010–2012. The results suggest evaluation criteria for survival compliance tests must balance the needs for rigor and robustness with the ability to reasonably perform the tests in naturally varying riverine systems.

Status after 5 Years of Survival Compliance Testing in the Federal Columbia River Power System (FCRPS)

AbstractSurvival studies of juvenile Pacific salmon Oncorhynchus spp. implanted with acoustic tags have been conducted at hydroelectric dams within the Federal Columbia River Power System in the Columbia and Snake rivers between 2010 and 2014 to assess compliance with the dam passage survival standards stipulated in the 2008 Biological Opinion. For juvenile yearling Chinook Salmon O. tshawytscha and steelhead O. mykiss that migrate downstream in the spring, dam passage survival (defined as survival from the upstream dam face to the tailrace mixing zone) must be ≥ 96%, and for subyearling Chinook Salmon that migrate downstream in summer, dam passage survival must be ≥ 93%. Precision requirement stipulates a standard error ≤ 1.5% (i.e., a 95% confidence interval of ± 3%). A total of 29 compliance tests have been conducted at six of eight main‐stem dams in the Federal Columbia River Power System, using over 109,000 acoustic‐tagged salmonid smolts. Of these 29 compliance studies, 23 met the survival standards and 26 met the precision requirements. Of the six dams evaluated to date, individual survival estimates range from 0.9597 to 0.9868 for yearling Chinook Salmon, from 0.9534 to 0.9952 for steelhead, and from 0.9076 to 0.9789 for subyearling Chinook Salmon. Averages across the six dams exceed the survival standards for all three migrant populations.Received November 9, 2015; accepted February 16, 2016 Published online June 27, 2016

Short-Term Hydropower Optimization and Assessment of Operational Flexibility

Hydroelectric power systems are largely characterized by variability and uncertainty in water resource obligations. Market volatility and the growing number of operational obligations for flood control, navigation, environmental obligations, and ancillary services (including load-balancing requirements for renewable resources) further the need to quantify sources of uncertainty. The variations caused by these factors require the hydropower system to have enough upward and downward flexibility for control technologies, such as dynamic optimal control load-following, unit commitment, or automatic generation, to be effective. Therefore, it is increasingly important to identify measures of operational flexibility to better manage uncertainty and operational obligations. The objective of this paper is to present and discuss approaches for assessment of operational flexibility as a function of dynamic states and control input and how the available operational flexibility can be used by hydropower producers in a comprehensive optimization reformulation to accommodate business procedures to drive the system in an efficient, safe, and interpretable way. The authors consider simple metrics such as power capability and its derivatives as indicators for upward flexibility and effective energy storage capability for downward flexibility. Test results based on the Federal Columbia River power system (FCRPS), managed by the Bonneville Power Administration, Army Corps of Engineers, and Bureau of Reclamation, are presented and demonstrate how operational flexibility can be assessed and that role it plays in short-term operations.

Short-term management of hydropower reservoirs under meteorological uncertainty by means of multi-stage optimization

Abstract Uncertainty in meteorology, market volatility and balancing requirements for introducing renewable energy resources into the power grid, environmental obligations require robust management of non-intermittent energy sources such as hydropower. In this paper, a probalistic management system is shown and its performance is discussed in relation to the deterministic one. In the system, scenario trees enable to setup a multi-stage stochastic optimization approach as the mathematical formulation of the short-term system management. The Federal Columbia River Power System (FCRPS), managed by the Bonneville Power Administration, the US Army Corps of Engineers and the Bureau of Reclamation, serves as a large-scale test case for the application of the management system and proves that the stochastic approach is feasible and verify the operational applicability within a real-time environment.

The Energy Authority Optimizes Water Routing and Hydroelectric Generation on the Columbia River

We describe a software application that enables owners of generation output from a virtualized Federal Columbia River Power System to safely operate the system, while also shaping the generation to meet their energy and economic needs. The application, the Optimizer, employs modern operations research techniques to convert a highly nonlinear problem into a linear one to create a robust solution for the six-dam system on an hourly basis, over a 10-day time horizon, and within a few minutes. The Optimizer helps to simultaneously manage and optimize the generation portfolios for 13 utilities in a stringent time frame around the clock, and enables hydroelectric (i.e., hydro) planners to ensure that the operation of the river meets all the requirements for flood control, fish management, electrical reliability, safe dam operations, and recreation under high degrees of uncertainty. The Optimizer allows utilities to integrate renewable, environmentally friendly wind and solar generation into their resource portfolio with hydro generation, and empowers these utilities to rapidly make decisions and adapt to changing conditions. We estimate that this project will reap benefits of $765–$952 million between 2011 and 2028.

Assessment of Subyearling Chinook Salmon Survival through the Federal Hydropower Projects in the Main‐Stem Columbia River

AbstractHigh survival through hydropower projects is an essential element in the recovery of Pacific salmon Oncorhynchus spp. populations in the Columbia River. High dam passage survival is also a regulatory requirement under the 2008 Biological Opinion (BiOp; established under the Endangered Species Act) on Federal Columbia River Power System operation. The BiOp requires dam passage survival to be at least 0.96 and at least 0.93 for spring and summer out‐migrating juvenile salmonids, respectively, and to be estimated with an SE of 0.015 or lower. An innovative virtual/paired‐release design was used to estimate dam passage survival, which was defined as survival from the upstream face of a dam to the tailrace mixing zone. A coordinated four‐dam study was conducted during the 2012 summer out‐migration using 14,026 subyearling Chinook Salmon O. tshawytscha out‐migrants with surgically implanted acoustic micro‐transmitter tags. The release–recapture design consisted of 9 different release locations and 14 different detection arrays. Each of the four estimates of dam passage survival exceeded BiOp requirements, with values ranging from 0.9414 to 0.9747 (SE = 0.0031–0.0114). The virtual/paired‐release design illustrated here has potential applicability wherever dam passage survival of migrant juvenile fish stocks must be estimated.Received November 21, 2013; accepted March 13, 2014

Evaluating river management during seaward migration to recover Columbia River stream-type Chinook salmon considering the variation in marine conditions

Evidence suggests Snake River stream-type Chinook salmon (Oncorhynchus tshawytscha) experience substantial delayed mortality in the marine environment as a result of their outmigration experience through the Federal Columbia River Power System (FCRPS). We analyzed mortality patterns using methods that incorporated downriver reference populations passing fewer dams, and temporal approaches that were independent of reference populations. Our results from the alternative spatial and temporal methods consistently corroborated with spawner–recruit residuals and smolt-to-adult survival rate data sets, indicating that Snake River salmon survived about one quarter as well as the reference populations. Temporal analysis indicated that a high percentage (76%) of Snake River juvenile salmon that survived the FCRPS subsequently died in the marine environment as a result of their outmigration experience. Through this and previous studies, it is evident that delayed hydrosystem mortality increases with the number of powerhouse passages and decreases with the speed of outmigration. Therefore, a promising conservation approach would be to explore management experiments that evaluate these relationships by increasing managed spill levels at the dams during the spring migration period.

Short-term management of hydropower assets of the Federal Columbia River Power System

We focus on the short-term optimization of large-scale hydropower systems with a mixture of storage reservoirs and run-of-the-river projects. If sufficient operational flexibility is available within the operational constraints, the system is capable of balancing the transmission network by compensating for load fluctuations and power production of other renewables such as solar and wind resources. The proposed optimization model is based on a nonlinear system representation of the hydropower system for forecasting state trajectories over a forecast horizon in combination with nonlinear programming for computing optimal release trajectories for specific hydropower projects. We present the application of a deterministic version of the approach to the short-term management of the Federal Columbia River Power System in the Pacific Northwest of the USA during the chum spawning season. An assessment of the computational performance of the approach for different optimization algorithms shows a superior performance of the Interior Point OPTimizer (IPOPT) in combination with the HSL/MA27 linear equation solver. In particular, the scaling properties are promising and will enable an extension of the deterministic approach towards a multi-stage stochastic optimization for taking into account the forecast uncertainty.

Assessing compliance with fish survival standards: a case study at Rock Island Dam, Washington

Abstract Safe fish passage through hydroprojects is of paramount importance in the Pacific Northwest of the United States where anadromous runs of salmon smolts pass through as many as nine dams on the Columbia River on their way to the ocean. Minimum survival standards through the dams or hydroprojects (i.e., reservoir and dam) have been established by the 2008 Federal Columbia River Power System (FCRPS) Biological Opinion or by Habitat Conservation Plans (HCPs) in order to protect salmon stocks. These federal requirements have prompted the need to conduct scientifically and statistically rigorous and precise smolt survival studies at federally and publicly operated hydroprojects throughout the Snake-Columbia River Basin. Successful studies have been the cooperative results of regulators, hydro managers, fish biologists, engineers, and biometricians working together to conduct these high value investigations. Rock Island Dam, Washington, is used as a case study where a total of 17 release-recapture studies were conducted over a nine-year period on three salmonid species to assess compliance with HCP survival standards.

Development of external and neutrally buoyant acoustic transmitters for juvenile salmon turbine passage evaluation

Fish can sustain injury or mortality when they pass through hydroelectric facilities. To develop a method to monitor the passage and survival of juvenile salmonids without bias through turbines within the Federal Columbia River Power System, we developed and fabricated two designs of neutrally buoyant transmitters: Type A (sutured to the dorsal musculature of the fish anterior to the dorsal fin) and Type B (two-part design attached with wire pushed through the dorsal musculature, ventral to the dorsal fin). To determine the efficacy of the two designs under non-turbine passage-related conditions, fish had one of the tags attached and were held for 14 days to determine any potential effects of the tags on growth, survival and tissue damage. We also evaluated the attachment method by monitoring tag retention. These two neutrally buoyant tag designs were compared to nontagged individuals and those surgically implanted with current Juvenile Salmon Acoustic Telemetry System (JSATS) transmitters and passive integrated responder (PIT) tags. In addition, two suture materials (Monocryl and Vicryl Rapide) were tested for attachment of Type A tags. When compared with non-tagged individuals, fish tagged with Type A tags did not differ significantly with respect to growth or mortality over a 14-d holding period. However, fish tagged with Type B transmitters had lower growth rates than the nontagged controls or other tag treatments. The efficacy of two designs was also compared to nontagged individuals under shear exposure. Fish were exposed to a submerged, 6.35-cm-diameter water jet at velocities ranging from 3.0 to 12.2 m/s in a water flume to simulate turbine conditions within the Columbia River basin. Throughout the shear exposure study, no mortalities or tag loss were observed. There was also no significant difference in the rates of shear injury between untagged fish and fish tagged with Type A or Type B tags. When tissue damage was assessed for tagged individuals exposed to shear forces, those tagged with Type A tags showed lower rates and severity of injury when compared to Type B-tagged fish. Overall, Type A tags may be a viable tag design for juvenile Chinook salmon passing through hydropower facilities.

Trends in organic pollutants and lipids in juvenile Snake River spring Chinook salmon with different outmigrating histories through the Lower Snake and Middle Columbia Rivers

A three-year field study was conducted from 2006 to 2008 to monitor the spatial and temporal trends of organic pollutants in migrating juvenile Snake River spring Chinook salmon ( Oncorhynchus tshawytscha) sampled from the Lower Snake and Middle Columbia River Basins. Specifically, hatchery-reared juvenile salmon were monitored as they navigated the Federal Columbia River Power System (FCRPS) by either transport barge (Barged) or remained in the river (In-River) from Lower Granite Dam to a terminal collection dam, either John Day Dam or Bonneville Dam. Levels of polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and organochlorine (OC) pesticides were detected in the bodies of both In-River and Barged salmon during the 2006, 2007 and 2008 outmigrating season. At the terminal dam, In-River fish had greater concentrations of persistent organic pollutants POPs than Barged salmon. Of the POPs detected, dichlorodiphenyltrichloroethanes (DDTs) were found at the greatest concentrations in the salmon bodies. These elevated lipid-normalized concentrations in the In-River fish were due to lipid depletion in all years as well as increased exposure to POPs in some years as indicated by an increase in wet weight contaminant concentrations. Salmon were also exposed to polycyclic aromatic hydrocarbons (PAHs) as indicated by the phenanthrene (PHN) signal for biliary fluorescent aromatic compounds (FACs) at the hatcheries or prior to Lower Granite Dam. There were detectable levels of biliary FACs as fish migrated downstream or were barged to the terminal dam. Therefore, the potential exists for these organic pollutants and lipid levels to cause adverse effects and should be included as one of the variables to consider when examining the effects of the FCRPS on threatened and endangered juvenile salmon.

A Cabled Acoustic Telemetry System for Detecting and Tracking Juvenile Salmon: Part 1. Engineering Design and Instrumentation

In 2001 the U.S. Army Corps of Engineers, Portland District (OR, USA), started developing the Juvenile Salmon Acoustic Telemetry System, a nonproprietary sensing technology, to meet the needs for monitoring the survival of juvenile salmonids through eight large hydroelectric facilities within the Federal Columbia River Power System (FCRPS). Initial development focused on coded acoustic microtransmitters and autonomous receivers that could be deployed in open reaches of the river for detection of the juvenile salmonids implanted with microtransmitters as they passed the autonomous receiver arrays. In 2006, the Pacific Northwest National Laboratory began the development of an acoustic receiver system for deployment at hydropower facilities (cabled receiver) for detecting fish tagged with microtransmitters as well as tracking them in two or three dimensions for determining route of passage and behavior as the fish passed at the facility. The additional information on route of passage, combined with survival estimates, is used by the dam operators and managers to make structural and operational changes at the hydropower facilities to improve survival of fish as they pass the facilities through the FCRPS.

A Cabled Acoustic Telemetry System for Detecting and Tracking Juvenile Salmon: Part 2. Three-Dimensional Tracking and Passage Outcomes

In Part 1 of this paper, we presented the engineering design and instrumentation of the Juvenile Salmon Acoustic Telemetry System (JSATS) cabled system, a nonproprietary sensing technology developed by the U.S. Army Corps of Engineers, Portland District (Oregon, USA) to meet the needs for monitoring the survival of juvenile salmonids through the hydroelectric facilities within the Federal Columbia River Power System. Here in Part 2, we describe how the JSATS cabled system was employed as a reference sensor network for detecting and tracking juvenile salmon. Time-of-arrival data for valid detections on four hydrophones were used to solve for the three-dimensional (3D) position of fish surgically implanted with JSATS acoustic transmitters. Validation tests demonstrated high accuracy of 3D tracking up to 100 m upstream from the John Day Dam spillway. The along-dam component, used for assigning the route of fish passage, had the highest accuracy; the median errors ranged from 0.02 to 0.22 m, and root mean square errors ranged from 0.07 to 0.56 m at distances up to 100 m. For the 2008 case study at John Day Dam, the range for 3D tracking was more than 100 m upstream of the dam face where hydrophones were deployed, and detection and tracking probabilities of fish tagged with JSATS acoustic transmitters were higher than 98%. JSATS cabled systems have been successfully deployed on several major dams to acquire information for salmon protection and for development of more “fish-friendly” hydroelectric facilities.

Survey of Pathogens in Hatchery Chinook Salmon with Different Out‐Migration Histories through the Snake and Columbia Rivers

The operation of the Federal Columbia River Power System (FCRPS) has negatively affected threatened and endangered salmonid populations in the Pacific Northwest. Barging Snake River spring Chinook salmon Oncorhynchus tshawytscha through the FCRPS is one effort to mitigate the effect of the hydrosystem on juvenile salmon out-migration. However, little is known about the occurrence and transmission of infectious agents in barged juvenile salmon relative to juvenile salmon that remain in-river to navigate to the ocean. We conducted a survey of hatchery-reared spring Chinook salmon at various points along their out-migration path as they left their natal hatcheries and either migrated in-river or were barged through the FCRPS. Salmon kidneys were screened by polymerase chain reaction for nine pathogens and one family of water molds. Eight pathogens were detected; the most prevalent were Renibacterium salmoninarum and infectious hematopoietic necrosis virus. Species in the family Saprolegniaceae were also commonly detected. Pathogen prevalence was significantly greater in fish that were barged through the FCRPS than in fish left to out-migrate in-river. These results suggest that the transmission of infectious agents to susceptible juvenile salmon occurs during the barging process. Therefore, management activities that reduce pathogen exposure during barging may increase the survival of juvenile Chinook salmon after they are released.