Limitations of biotelemetry technology available in 2001 prompted the U.S. Army Corps of Engineers Portland District to develop a new acoustic telemetry system to monitor survival of juvenile salmonids through the Columbia River to the Pacific Ocean. Eight years later, the Juvenile Salmon Acoustic Telemetry System (JSATS) consists of microacoustic transmitters (12 mm long, 0.43 g weight in air), autonomous and cabled receiving systems, and data management and processing applications. Transmitter pulse rate can be user‐defined and as configured for this case study was set at 5 seconds, with an estimated tag life of 30 days and detection range of 300 m. Before JSATS development, no technology existed to study movement and survival of fish smaller than 10 g migrating long distances from freshwater and into saltwater. In a 2008 study comparing detection probabilities, travel times, and survival of 4,140 JSATS‐tagged and 48,433 passive integrated transponder (PIT)‐tagged yearling Chinook salmon (Oncorhynchus tshawytscha; mean fork length 133.9 and 135.3 mm, for JSATS and PIT‐tagged fish, respectively) migrating the Snake and Columbia rivers to the Pacific, the JSATS provided survival estimates at more locations with greater precision, using less than one‐tenth as many tagged fish as the traditional PIT‐tag system. While designed to be optimized for juvenile salmonid survival assessment in the Columbia River basin, JSATS technology may be used in a variety of environments. Information regarding different acoustic telemetry systems from various vendors is presented and discussed relative to the nonproprietary JSATS.

A substantial percentage of the Pacific salmon Oncorhynchus spp. and steelhead O. mykiss smolts that emigrate to the ocean each year are smaller than 110 mm (fork length). However, relatively few researchers have implanted acoustic transmitters in fish of this size, and none have reported minimum fish lengths below 110 mm for which the tag burden did not negatively influence growth or survival. The influence of a surgically implanted acoustic microtransmitter and a passive integrated transponder (PIT) tag on the growth and survival of hatchery‐reared juvenile Chinook salmon was examined over a period of 30 d. Growth and survival were compared between treatment (tagged) and control (untagged) fish within three size‐groups (80–89, 90–99, and 100–109 mm). The acoustic microtransmitter and PIT tag implanted in our study had a combined weight of 0.74 g; the combined tag burden for implanted fish ranged from 4.5% to 15.7%. The results indicated that growth and survival among implanted juvenile Chinook salmon were size dependent. Significant differences in growth rate and survival were observed between treatment and control fish in the 80–89‐mm group. The survival of implanted fish smaller than 11.1 g (tag burden, >6.7%) and the growth of fish smaller than 9.0 g (tag burden, >8.2%) were negatively affected by the implantation or presence of an acoustic microtransmitter and PIT tag. The results of this study will aid researchers in determining the minimum fish size suitable for use in acoustic telemetry studies that estimate the short‐term (30‐d) survival and growth of juvenile salmonids.

We applied acoustic telemetry methods to characterize migration pathways and estimate associated travel times and survival probabilities for juvenile Chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss migrating downstream through the Columbia River estuary (from river kilometer [rkm] 86 to rkm 8). Acoustic‐tagged fish were detected as migrating in the navigation channel and in off‐channel areas at each of the estuarine reaches we examined during May–August 2010. However, the majority of fish traveled in the main navigation channel from rkm 86 to rkm 37, at which point most fish left the river‐influenced navigation channel; crossed a broad, shallow tidal flat; and migrated the final 37 km in a secondary channel, which was characterized as having greater tidal transport than the navigation channel. The pathway used by acoustic‐tagged smolts to migrate through the estuary affected their rate of travel. In most reaches, navigation channel migrants traveled significantly faster than fish that migrated through off‐channel areas. Contrary to observations from previous studies, smolts that migrated through off‐channel areas at a slower rate did not experience lower survival than their cohorts that used the navigation channel. Although no significant differences in survival probability were observed between navigation channel migrants and off‐channel migrants, areas of high mortality were identified between rkm 37 and rkm 8. Dispersion of juvenile salmonids into multiple pathways during downstream migration can be beneficial in terms of increased expression of life history diversity and resiliency to environmental perturbations. Our results, which document juvenile salmon migration pathways and associated travel time and survival through a large estuary, can be used to focus future research and management activities in areas identified as having high mortality and therefore can be used to aid in the recovery of Endangered Species Act‐listed salmon populations.

Steelhead (Oncorhynchus mykiss) populations have declined throughout their range in the last century and many populations, including those of the Snake River Basin are listed under the Endangered Species Act of 1973. The reasons for their decline are many and complex, but include habitat loss and degradation, overharvesting, and dam construction. The 2008 Biological Opinion calls for an increase in the abundance of female steelhead through an increase in iteroparity (i.e., repeat spawning) and this can be realized through a combination of reconditioning and in-river survival of migrating kelts. The goal of this study is to provide the data necessary to inform fisheries managers and dam operators of Snake River kelt migration patterns, survival, and routes of dam passage. Steelhead kelts (n = 487) were captured and implanted with acoustic transmitters and passive integrated transponder (PIT)-tags at the Lower Granite Dam (LGR) Juvenile Fish Facility and at weirs located in tributaries of the Snake and Clearwater rivers upstream of LGR. Kelts were monitored as they moved downstream through the Federal Columbia River Power System (FCRPS) by 15 autonomous and 3 cabled acoustic receiver arrays. Cabled receiver arrays deployed on the dam faces allowed for three-dimensional tracking of fish as they approached the dam face and were used to determine the route of dam passage. Overall, 27.3% of the kelts tagged in this study successfully migrated to Martin Bluff (rkm 126, as measured from the mouth of the Columbia River), which is located downstream of all FCRPS dams. Within individual river reaches, survival per kilometer estimates ranged from 0.958 to 0.999; the lowest estimates were observed in the immediate forebay of FCRPS dams. Steelhead kelts tagged in this study passed over the spillway routes (spillway weirs, traditional spill bays) in greater proportions and survived at higher rates compared to the few fish passed through powerhouse routes (turbines and juvenile bypass systems). The results of this study provide information about the route of passage and subsequent survival of steelhead kelts that migrated through the Snake and Columbia rivers from LGR to Bonneville Dam in 2013. These data may be used by fisheries managers and dam operators to identify potential ways to increase the survival of kelts during their seaward migrations. Passage Times and Travel Rates Forebay residence and tailrace egress times were consistent among LGR, LGS, and LMN in 2013. Median forebay residence times were less than 2.00 hours at all dams and median tailrace egress times were approximately 0.50 hours. Median project passage time in this study ranged from 2.00 (LMN) to 3.06 (LGR) hours. Overall, passage times were lowest for fish that passed LMN. Of the kelts captured and tagged in the tributaries, those released in Fish Creek, which migrated the greatest distance through fluvial habitats, travelled fastest to Red Wolf Bridge (rkm 743; median = 88.2 vi Many people made valuable contributions to this study and deserve acknowledgment.

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Acoustic telemetry is one of the primary technologies for studying the behavior and survival of fishes throughout the world. The size and performance of the transmitter are key limiting factors. The newly developed injectable transmitter is the first acoustic transmitter that can be implanted via injection instead of surgery. A two-part field study was conducted to evaluate the performance of the injectable transmitter and its effect on the survival of implanted fish. The injectable transmitter performed well and similarly to the proceeding generation of commercially-available JSATS transmitters tested concurrently. Snake River subyearling Chinook salmon smolts implanted with the injectable transmitter had a higher survival probability from release to each of eleven downstream detection arrays, because reach-specific survival estimates were significantly higher for the injectable group in three of the eleven reaches examined. Overall, the injectable group had a 0.263 (SE = 0.017) survival probability over the entire 500 km study area compared to 0.199 (0.012) for the surgically implanted group. The reduction in size and ability to implant the new transmitter via injection has reduced the tag or tagging effect bias associated with studying small fishes. The information gathered with this new technology is helping to evaluate the impacts of dams on fishes.

American eel are likely to encounter and pass through hydropower turbines, particularly during the downstream spawning migration, where exposure to stressors can potentially lead to injuries and mortality. Previous research has recovered dead eels downstream of hydropower facilities and, for some fish, injuries were easily attributed to blade strike; however, others showed no external signs of injury suggesting that other stressors, such as rapid decompression may be a potential source of mortality. For this research, yellow– and silver-phase American eel were held and allowed to acclimate to 172 kPa (absolute pressure) in hyper/hypobaric hydro-chambers for about 1 d. After acclimation, the state of buoyancy was determined prior to exposure to a rapid decompression simulating pressures encountered during hydroturbine passage. Fish were then examined for signs of barotrauma. Eel did not attain a state of neutral buoyancy but rather maintained negative buoyancy suggesting that eels, and possibly other benthic species, likely maintain a state of negative buoyancy to facilitate occupancy on or near the substrate. Additionally, eel were found to be resilient to rapid decompression, displaying no instantaneous mortality and minimal injuries, suggesting that barotrauma is not likely a major concern for American eel passing downstream through hydroturbines.

Strontium isotopes (87Sr/86Sr) recorded in the otoliths of Pacific Salmon (Oncorhynchus spp.) are commonly used to identify natal origin. For species that migrate at or soon after emergence, the embryonic region of the otolith provides the only record of provenance. However, maternal contribution of Sr from the yolk can confound the isotopic signature of the natal site. We experimentally quantified maternal and exogenous diet contributions to otolith 87Sr/86Sr over embryonic development in Kokanee salmon (O. nerka). Eggs from two populations in isotopically distinct lakes were incubated and reared in a common water source. Timing of developmental events and proportional contribution from yolk to otolith 87Sr/86Sr differed significantly between the two populations. We suggest that the magnitude of difference in 87Sr/86Sr between yolk and water, the relative concentrations of Sr and Ca in these isotopic sources, and population-specific effects on otolith growth and composition contribute to this variation. Understanding how these factors affect otolith 87Sr/86Sr could extend the use of otolith geochemistry for determining provenance to species and populations in which natal site rearing is limited.