ObjectiveBecause predation is thought to be the primary source of natural mortality for juvenile salmon first entering the ocean, we sought to identify regions where, on average, stock-specific spatial overlap between the distribution of threatened and endangered juvenile Chinook Salmon Oncorhynchus tshawytscha and abundant fish-eating seabirds (common murres Uria aalge and sooty shearwaters Ardenna grisea) suggests the greatest potential for ocean predation risk to juvenile Chinook Salmon.MethodsThe relative abundance and spatial distribution of seabird predators and juvenile Chinook Salmon were quantified as part of long-term ecosystem surveys during May 2003-2012 and June 2003-2022. Genetic stock identification methods were used to assign individual fish to their respective stock groups. Stock-specific species distribution models then generated maps and indices of average annual spatial overlap between predators and prey within the survey area.ResultThere is unequivocal evidence for spatial overlap between common murres, sooty shearwaters, and five genetic groups of interior and lower Columbia River juvenile Chinook Salmon. We found strongly positive (>= 0.70) spatial correlations between predator and prey densities in both May and June, although spatial overlap was, in general, greater during May. The region of highest spatial overlap occurred on the inner continental shelf between the Columbia River mouth (46.2 degrees N) and Grays Harbor (47.0 degrees N), a region at the beginning of the juvenile salmon migratory pathway that is strongly affected by freshwater outflow from the river.ConclusionOur findings support the idea that ocean avian predation during early marine residence has the potential to affect marine survival of juvenile Chinook Salmon and should be further investigated to better inform and implement ecological models and possible recovery actions for Chinook Salmon populations of the Columbia River basin.

First recognized as threatened with extinction in 1999, native winter steelhead Oncorhynchus mykiss from Oregon's Upper Willamette River (UWR) declined to a record-low 543 adult fish in 2017. This anadromous species has been seriously affected by habitat loss caused by impassable dams, intense predation from pinnipeds, and water pollution. Genetic and ecological risks posed by non-native hatchery steelhead may also limit recovery. Here we used 15 microsatellite markers to investigate the genetic composition of naturally-produced juvenile O. mykiss, collected from the most downstream UWR location and other sites throughout the upper basin. Our results, based on 1012 individuals, identified some natural production by summer steelhead released by ongoing hatchery programs, but even greater influence from discontinued non-native winter steelhead hatchery programs. Genetic influence from hatchery programs was nearly absent in above-dam habitats, but concentrated in below-dam habitats and rivers stocked with hatchery steelhead. Although informative, our microsatellite data lacked sufficient power to assign individual fish to hybrid classes, and we urge caution when interpreting similar results from few loci. Taken together, our findings suggest that fish sorting facilities can assist with the conservation of steelhead populations reintroduced above dams, and that hatchery programs can have a lasting genetic influence over naturally-spawning populations, even after stocking has ceased. To conserve the genetic integrity of native UWR steelhead, we recommend that managers consider the lineage of steelhead used for reintroductions, continue to implement policies that limit genetic risks from existing hatchery programs and explore ways to alleviate persistent risks from discontinued programs.

Columbia 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.

In response to petitions to list coho salmon Oncorhynchus kisutch under the U.S. Endangered Species Act (ESA), the National Marine Fisheries Service (NMFS) initiated a status review of coho salmon in the Pacific Northwest and formed a Biological Review Team (BRT) to conduct the review. The BRT identified six evolutionarily significant units (ESUs), or "species" under the ESA, for coho salmon and evaluated the risk of extinction for these ESUs. Identification of these ESUs was based on genetic, life history, biogeographic, geologic, and environmental information. The six ESUs encompass coho salmon habitats from the southern limit of their range in Monterey Bay to tributaries flowing into the north end of the Strait of Georgia. Both qualitative and quantitative information were used to assess extinction risks faced by these ESUs. This information indicated a latitudinal trend in stock health, with coho salmon in the southernmost ESUs facing the greatest risks and those in the northern ESUs facing fewer risks. Based on this latitudinal trend in stock health, and on present conservation efforts, NMFS proposed listing three coho salmon ESUs south of the Columbia River as threatened under the ESA. Of the three remaining ESUs, only one was not proposed for listing. The other two were identified as "candidate" species, for which listing may be warranted in the future. Since the NMFS proposed listings, the three southernmost ESUs have been listed as "threatened" under the ESA and the fate of the remaining candidate ESUs are being determined as of this printing.

Migration patterns of juvenile Columbia River Chinook salmon (Oncorhynchus tshawytscha) differ among stocks and life history types, creating diverse marine distributions of these fish. This results in different stocks being subject to different ocean conditions during their first summer of marine residence, a time that is critical for their survival. Understanding their early marine distributions, and the conditions that affect their survival, may enhance conservation efforts for these stocks, many of which are protected under the Endangered Species Act. We analyzed juvenile Chinook salmon samples collected in trawls made from 2011 to 2015 off the southeastern (SE) Alaskan panhandle, and off the coasts of Washington and Oregon. We used genetic stock identification techniques to estimate stock proportions of juvenile Chinook salmon in each of these areas. Results indicated that most juvenile Chinook salmon in our SE Alaska coast study area in July originate from Columbia River spring-run stocks. We found a significant relationship in catch per unit effort (CPUE) over all stocks between the SE Alaska and the Washington and Oregon coast samples. In 2011, CPUE for Columbia River spring-run stocks for the SE Alaska coast was lower than for the Washington and Oregon coast, suggesting a differing level of marine mortality that year. We also found a significant relationship between juvenile CPUE of interior Columbia River spring-run stocks off the SE Alaska coast and adult counts at Bonneville Dam two years later. Our results provide marine life history, performance and survival information that supports management and recovery efforts for Columbia River Chinook salmon.

Considerable effort towards conservation has contributed to the recovery of historically depleted pinniped populations worldwide. However, in several locations where pinnipeds have increased, they have been blamed for preventing the recovery of commercially valuable fish species through predation. Prompted by increasing pinniped abundance within the Columbia River (CR), USA, over a 6-year period, we used passive integrated transponder tags to measure the survival of adult spring-run Chinook salmon (Oncorhynchus tshawytscha) through the estuary and lower CR to Bonneville Dam (river kilometre 234). We estimated 51 751 – 224 705 salmon died annually within this reach from sources other than harvest. Mixed-effects logistic regression modelling identified pinniped predation as the most likely source of this mortality. The odds of survival was estimated to decrease by 32% (95% CI: 6%–51%) for every additional 467 sea lions (Zalophus californianus and Eumetopias jubatus) present within the CR and to increase by 32% (95% CI: 8%–61%) for every increase of 1.5 in the log of American shad (Alosa sapidissima), a potential prey item for sea lions.

Estuarine habitats provide rearing opportunities for the juvenile life stage of anadromous fishes. Because survival is positively correlated with juvenile performance, these estuarine habitats play an important role in population abundance and productivity. To provide information for the recovery of several depressed stocks of Chinook salmon in the Columbia River Basin, we sought to identify the factors that explain variability in performance. Using otolith-derived estimates of juvenile somatic growth rate as an index of recent performance, we observed a negative nonlinear relationship between growth rate and day of year, and a decreasing and increasing trend of growth rate over the 8years of this study and distance from the river mouth respectively. Using a generalised linear modelling approach, we found that variability in juvenile somatic growth rate was best explained by where and when individuals were collected, their body size, contaminant loads, stock of origin, and whether a fish was hatchery produced or unmarked. Lastly, we argue that a considerable improvement to the growth rate of juveniles in estuarine habitats is physiologically possible. The results of this 8-year study provide a baseline of the performance of juvenile Chinook salmon to evaluate habitat restoration programs and to compare against future anthropogenic conditions.

Variations in marine prey availability and nutritional quality can affect juvenile salmon growth and survival during early ocean residence. Salmon growth, and hence survival, may be related to the onset of piscivory, but there is limited knowledge on the interplay between the prey field, environment, and salmon ontogeny. Subyearling Chinook Salmon (Oncorhynchus tshawytscha) and their potential prey were sampled in coastal waters off Willapa Bay, USA to explore this issue. Three seasonal prey assemblages were identified, occurring in spring (May), early summer (June – July), and late summer (August – September). The onset of piscivory, based on salmon stomach contents, fatty acids, and stable isotopes occurred later in 2011 compared to 2012, and coincided with the appearance of Northern Anchovy (Engraulis mordax). Salmon fork length (FL) and carbon isotope values (δ13C) increased with a fatty acid biomarker for marine phytoplankton and decreased with a freshwater marker, indicating dietary carbon sources changed as salmon emigrated from the Columbia River. Salmon FL also increased with nitrogen isotope ratios (δ15N), trophic position, and a fatty acid marker for piscivory – a consequence of the ontogenetic shift in diet to fish. Salmon grew faster and obtained larger size and condition by September 2011 compared to 2012, which was related to inter-annual differences in ocean conditions and the duration over which Northern Anchovy were available. Our results support the idea that juvenile salmon growth depends on the onset and duration of piscivory, suggesting both of these factors may be important components of lifetime growth and fitness.

We investigated the spatial and temporal variability of the fish community and the density, size, and genetic stock composition of juvenile Chinook Salmon Oncorhynchus tshawytscha in shallow tidal freshwater habitats of the Columbia River. We sought to address data gaps related to juvenile Chinook Salmon in this portion of the Columbia River and thereby inform habitat restoration efforts. We examined fish communities, juvenile salmon life history characteristics, and relationships between salmon density and habitat conditions by using beach seine data collected over a 63-month period (2007-2012) from two tidal freshwater areas: the Sandy River delta (river kilometer [rkm] 188-202) and the lower river reach (rkm 110-141). We found few differences in the fish community across the two study areas. Fish community patterns were largely attributable to seasonal changes as opposed to spatial gradients and habitat types. Juvenile Chinook Salmon were the most common salmon species in our catches; this species was the only salmonid encountered during all four seasons. Chinook Salmon density differed among three distinct habitat strata (main channel, off-channel, and wetland channel), but FL and genetic stock composition did not. Across all habitat strata, environmental covariates (mean percent tree cover, dissolved oxygen level, and mean percent emergent vegetation) were positively associated with juvenile Chinook Salmon density. Although comparisons of environmental metrics and salmon density helped to establish a quantitative relationship between biotic and abiotic conditions, we found that juvenile salmon occupied a range of habitats. Our findings support a strategy that involves restoring a diversity of shallow tidal freshwater habitats to facilitate the recovery of threatened and endangered salmon populations in the Columbia River basin.

The degree to which fine-scale habitat use by salmonid species and stocks varies within habitat types such as estuaries is not fully resolved. We sampled shallow shoreline and deeper main-stem channel habitats in the Columbia River estuary over 3 years to compare salmon species composition, migration timing, density, size, and production type (hatchery or natural). Results indicated a high degree of spatial heterogeneity in habitat occupancy by the five salmonid species that are native to the basin. Salmonid communities at two channel habitat sites were much more similar to each other than to the community at a shoreline site. Salmonids sampled at the shoreline site were primarily subyearling Chinook Salmon Oncorhynchus tshawytscha and Chum Salmon O. keta and yearling Coho Salmon O. kisutch, with few other salmonids present. In contrast, channel habitat contained a higher diversity of salmon species, with samples representing all species of anadromous salmonids, including Sockeye Salmon O. nerka and steelhead O. mykiss. Salmonids in deeper channel habitat were generally larger than salmonids found along the shore, and the proportion of hatchery-origin salmon was also higher in deep channel habitats. On a per-area basis, we also found much higher densities of salmon along the shoreline than in channel habitats. For Chinook Salmon, habitat use also differed by genetic stock of origin: upper-river stocks primarily used deeper channels, while lower-river populations used both channel and shoreline areas. We concluded that sampling at both habitat types is required to fully encompass the migration patterns of all salmon evolutionarily significant units in the Columbia River basin. These spatial and temporal variations in salmon timing and density have ramifications for feeding, growth, and competitive interactions. This study provides information that is relevant for conservation efforts targeting specific fish populations and efforts to evaluate the potential impacts of in-water activities in the Columbia River estuary.

Ocean currents or temperature may substantially influence migration behavior in many marine species. However, high-resolution data on animal movement in the marine environment are scarce; therefore, analysts and managers must typically rely on unvalidated assumptions regarding movement, behavior, and habitat use. We used a spatially explicit, individual-based model of early marine migration with two stocks of yearling Chinook salmon to quantify the influence of external forces on estimates of swim speed, consumption, and growth. Model results suggest that salmon behaviorally compensate for changes in the strength and direction of ocean currents. These compensations can result in salmon swimming several times farther than their net movement (straight-line distance) would indicate. However, the magnitude of discrepancy between compensated and straight-line distances varied between oceanographic models. Nevertheless, estimates of relative swim speed among fish groups were less sensitive to the choice of model than estimates of absolute individual swim speed. By comparing groups of fish, this tool can be applied to management questions, such as how experiences and behavior may differ between groups of hatchery fish released early vs. later in the season. By taking into account the experiences and behavior of individual fish, as well as the influence of physical ocean processes, our approach helps illuminate the "black box" of juvenile salmon behavior in the early marine phase of the life cycle.

Conservation genetics studies are frequently conducted on Pacific salmon Oncorhynchus spp. to delineate their population structure and to quantify their genetic diversity, especially for populations that have experienced declines in abundance and are subject to anthropogenic activities. One such group of salmonids is steelhead O. mykiss (anadromous Rainbow Trout) from the Willamette River, a tributary of the Columbia River. Within the Willamette River there are multiple steelhead life history and run-timing types, some of which originated from nonnative populations. Late winter-run steelhead and Rainbow Trout are native to the Willamette River, whereas early winter-run and summer-run steelhead have been introduced into the system via releases from artificial propagation efforts. We conducted genetic analyses of Willamette River steelhead to determine the effect that nonnative steelhead released into the Willamette River basin have had on the genetic population structure of native steelhead. We found genetic differentiation among the samples that separated steelhead into four population groups that corresponded to run type. Possibly due to local adaptation, the native run type has retained its genetic distinctiveness from the introduced types, despite there being opportunities for gene flow among all types. Introduced early winter-run steelhead appear to be the origin of steelhead inhabiting certain Willamette River tributaries where native steelhead did not historically spawn.

We documented two life history strategies for juvenile salmonids as expressed in off-channel tidal freshwater habitats of the Columbia River: (i) active migrations by upper river Chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss) during the primary spring and summer migration periods and (ii) overwinter rearing in tidal freshwater habitats by coho salmon (Oncorhynchus kisutch) and naturally produced Chinook salmon mostly from lower river sources. During spring–summer 2007–2008, acoustic-tagged fish originating above Bonneville Dam (rkm 234) had short residence times in off-channel areas (rkm 192–203): median 2.5 and 2.6 h for yearling (mean lengths 134 and 158 mm) and 3.0 and 3.4 h for subyearling (104 and 116 mm) Chinook salmon and 2.5 h for yearling steelhead (215 mm). The percentage of fish in off-channel areas out of the total in the main- and off-channels areas was highest for yearling Chinook salmon (8.1% and 9.3% for 2007 and 2008, respectively) and lowest for steelhead (4.0% for 2008) and subyearling Chinook salmon (3.6% and 6.1% for 2007 and 2008, respectively). In late January and early February 2010, 2011, and 2012, we captured and tagged yearling Chinook and coho salmon occupying off-channel tidal freshwater habitats. Median residence times in off-channel areas were 11.6–25.5 days for juvenile Chinook (106, 115, and 118 mm, respectively by year) and 11.2 days for coho salmon (116 mm). This study is the first to estimate residence times for juvenile salmonids specifically in off-channel areas of tidal fresh water and, most importantly, residence times for Chinook salmon expressing a life history of overwintering in tidal fresh water. The findings support restoration of shallow off-channel habitats in tidal freshwater portions of the Columbia River.

Juvenile salmon transitioning from freshwater to marine environments experience high variation in growth and survival, yet the specific causes of this variation are poorly understood. Size at and timing of ocean entry may contribute to this variation because they influence both the availability of prey and vulnerability to predators. To explore this issue, we used stock assignments based on genetic stock identification and internal tags to document the stock-specific size and timing of juvenile hatchery and presumed wild Columbia River Chinook Salmon Oncorhynchus tshawytscha and steelhead O. mykiss at ocean entry during 2007-2011. We found that juvenile salmon and steelhead had consistent stock-specific capture dates, with lower-river stocks typically having earlier timing than those originating farther upstream. Mean size also varied among stocks and was related to hatchery practices. Hatchery yearling Chinook Salmon and steelhead were consistently larger than wild fish from the same stocks, although timing in the estuary was similar. In contrast, hatchery subyearling Chinook Salmon were of similar size to wild fish but entered the ocean up to a month earlier. We evaluated the potential importance of these traits on early marine growth by estimating stock-specific growth rates for Chinook Salmon caught in estuarine and ocean habitats. Growth rates were related to relative ocean entry timing, with lower growth rates for stocks that had only recently arrived in marine waters. Our results demonstrate that stocks within a single basin can differ in their size and timing of ocean entry, life history traits that contribute to early marine growth and potentially to the survival of juvenile salmon. Our results also highlight the necessity of considering stock-specific variation in life history traits to understand salmon ecology and survival across the entire life cycle.

We used microsatellite DNA data and genetic stock identification methods to delineate the temporal and spatial distributions of juvenile Chinook Salmon Oncorhynchus tshawytscha occupying coastal habitats extending from central Oregon to northern Washington. Juveniles were collected in trawl surveys conducted during spring, summer, and autumn over 15 years. Distributions (mean latitude and distance from shore) differed between yearling and subyearling life history types and between stocks; many of these differences were consistent across years. Yearlings were nearly all (98%) from Columbia River sources, and only 6% were naturally produced. In late May, yearlings from the lower Columbia and Willamette rivers were farther north than other yearlings, likely due to the early spring timing of their releases from hatcheries and subsequent out-migration from the Columbia River. However, yearling distributions in late June reflected known migration behaviors. Yearlings from interior Columbia and Snake River sources were farthest north by June, whereas yearlings from other stocks were more spread out in latitude. Subyearlings sampled in early summer were also largely from the Columbia River (98%), but greater percentages of subyearlings from coastal rivers were present during the fall (24%). In contrast to yearlings, natural production accounted for nearly one-third of subyearlings. Subyearlings of most stocks tended to remain relatively near their point of sea entry throughout the summer. Subyearlings from the Snake River fall-run stock and upper Columbia River summer-fall-run stock exhibited diverse distributions that included both southward and northward dispersal. Overall, distributions of Chinook Salmon stocks and life history types reflected differences in migration behavior but also reflected the influence of environmental factors and hatchery practices.

The underlying causes of mortality during critical life stages of fish are not well understood, nor is it clear if these causes are similar for naturally versus artificially propagated (i.e. hatchery) individuals. To assess the importance of selective mortality related to production type (hatchery vs. naturally produced) and size at and timing of marine entry, we compared attributes of juvenile Chinook salmon Oncorhynchus tshawytscha from the upper Columbia River summer- and fall-run genetic stock group captured in the Columbia River estuary with back-calculated attributes of survivors captured in marine waters. We used genetic stock identification, otolith chemistry and structure, and physical tags to determine stock of origin, size at and timing of marine entry, and production type. Fish emigrated from fresh water in May to September and the majority of fish collected in the estuary (87%) had arrived within 3 d of capture. In 1 of 2 yr, timing of marine entry for both production types differed between the estuary and ocean: the ocean catch included a greater proportion of juveniles that emigrated in late July than the estuary catch. There was no evidence of selective mortality of smaller juveniles during early marine residence in hatchery or natural juveniles, but the mean percentage (+/- SE) of hatchery fish in ocean collections was 16 +/- 5.8% less than in the estuary, which could indicate reduced survival compared to naturally produced fish. Results from this study highlight the need to understand the effects of hatchery rearing and how hatchery propagation may influence survival during later critical life-history transitions.

We examined the hypotheses that density and morphometric condition of subyearling juvenile Chinook Salmon Oncorhynchus tshawytscha would decline during periods of high water temperature in the lower Columbia River and estuary. The hypotheses were tested using salmon density measurements and a condition anomaly calculated from residuals of the length-weight linear regression based on 5,536 subyearlings collected from brackish estuarine and tidal freshwater (TFW) habitats. We captured Chinook Salmon at all temperatures encountered (4.2-23.5 degrees C). In the TFW zone, densities were highest at optimal temperatures and lowest at suboptimal and supraoptimal temperatures; in the estuary, density did not differ among temperature regimes. Fish condition was lowest in winter, when temperatures were suboptimal, and highest in summer, when temperatures were supraoptimal. Pairwise comparisons of fish condition between periods of optimal temperature (spring) and supraoptimal or stressful temperature (summer) showed little change in the estuary but a large, positive increase with temperature in the TFW zone. Similarly, we examined seasonal differences in the condition of 50-60-mm fry and again found condition to be lowest in winter and highest in summer. Finally, using genetic information, we identified stock-specific differences in migration timing and concluded that most large yearlings and many subyearlings migrated in late winter or spring and therefore were never exposed to high temperatures. Other prevalent stocks persisted in the estuary during periods of elevated temperature; however, the condition of those fish also tended to be higher or neutral in summer than in spring. High temperatures appeared to influence migration timing, as evidenced by reduced density in TFW reaches during summer. However, we found little support for the hypothesis that condition of juvenile Chinook Salmon is reduced during periods of high water temperature in the lower Columbia River and estuary.

Research on regulatory mechanisms in biological populations often focuses on environmental covariates. An integrated approach that combines environmental indices with organismal-level information can provide additional insight on regulatory mechanisms. Survival of spring/summer Snake River Chinook salmon (Oncorhynchus tshawytscha) is consistently low whereas some adjacent populations with similar life histories experience greater survival. It is not known if populations with differential survival respond similarly during early marine residence, a critical period in the life history. Ocean collections, genetic stock identification, and otolith analyses were combined to evaluate the growth-mortality and match-mismatch hypotheses during early marine residence of spring/summer Snake River Chinook salmon. Interannual variation in juvenile attributes, including size at marine entry and marine growth rate, was compared with estimates of survival and physical and biological metrics. Multiple linear regression and multi-model inference were used to evaluate the relative importance of biological and physical metrics in explaining interannual variation in survival. There was relatively weak support for the match-mismatch hypothesis and stronger evidence for the growth-mortality hypothesis. Marine growth and size at capture were strongly, positively related to survival, a finding similar to spring Chinook salmon from the Mid-Upper Columbia River. In hindcast models, basin-scale indices (Pacific Decadal Oscillation (PDO) and the North Pacific Gyre Oscillation (NPGO)) and biological indices (juvenile salmon catch-per-unit-effort (CPUE) and a copepod community index (CCI)) accounted for substantial and similar portions of variation in survival for juvenile emigration years 1998-2008 (R-2 > 0.70). However, in forecast models for emigration years 2009-2011, there was an increasing discrepancy between predictions based on the PDO (50-448% of observed value) compared with those based on the NPGO (68-212%) or biological indices (CPUE and CCI: 83-172%). Overall, the PDO index was remarkably informative in earlier years but other basin-scale and biological indices provided more accurate indications of survival in recent years.

The community of trophically transmitted marine parasites of juvenile coho (Oncorhynchus kisutch) and Chinook (Oncorhynchus tshawytscha) salmon across 8 years (2002–2009) was related to indices of physical and biological ocean conditions and adult returns. When the biomass of lipid-poor, southern origin copepods in the coastal ocean was high during juvenile salmon outmigration from fresh water (April–June), yearling coho and Chinook salmon harbored a different trophically transmitted parasite fauna and exhibited lower survival compared with years when the southern copepod biomass was low. As copepods are key intermediate hosts in many marine parasite life cycles, these results support a trophic linkage between the copepod community and salmon prey. Interannual variation in the parasite community was correlated with survival of coho salmon (r = −0.67) measured 1 year later and adult returns of Upper Columbia River summer and fall Chinook salmon (r = −0.94) 3 years from the time of ocean entry.

Extensive efforts are underway to restore and conserve nearshore shallow water habitats in the Columbia River estuary with the intent of increasing the estuary's capacity to provide food, refuge, and other crucial ecosystem functions for juvenile salmon. Juvenile Chinook Salmon Oncorhynchus tshawytscha, including those from the five Evolutionarily Significant Units listed as threatened or endangered under the U. S. Endangered Species Act, are particularly expected to benefit from the habitat improvements. However, information on the temporal and spatial estuarine distributions of juveniles from specific populations or stocks is lacking and impedes restoration planning for at-risk salmon. We conducted a series of surveys to sample juvenile Chinook Salmon occupying shallow-water habitats with sandy beaches in six hydrogeomorphic reaches across the tidal freshwater portion of the estuary and also at one long-term reference site near the estuary mouth. Sites were sampled bimonthly over 26 months during 2010-2012 to capture seasonal patterns of stock-specific habitat use. Genetic stock identification analyses were conducted on the samples using microsatellite DNA loci and genotypic data representing spawning populations from throughout the Columbia River basin. We identified three tidal freshwater areas that could be distinguished by genetic stock composition. Lower tidal freshwater reaches were dominated by fall-run juveniles from West Cascade tributaries (>70%), upper reaches had a large proportion of fish from the upper Columbia River summer-fall stock (>60%), and middle reaches were characterized by greater stock diversity with no single stock contributing more than 30% in each reach. Stock-specific juvenile habitat use differed by season, life history type, and between natural and hatchery-produced fish. Data from this study provide improved descriptions of the near-shore estuary habitat use of several Columbia River genetic stocks of Chinook Salmon that can assist managers in the design and selection of estuary restoration projects.