Salmon Population Dynamics Research Articles

Estimating the benefits of floodplain restoration to juvenile Chinook salmon in the upper San Francisco Estuary, United States, under future climate scenarios

Many river systems within the Central Valley of California have been disconnected from their floodplains, hypothesized to be partially responsible for declining Chinook salmon populations (Oncorhynchus tshawytscha). The primary floodplain of the system, Yolo By‐Pass (known regionally as “Yolo Bypass”), offered an opportunity to examine whether improved connectivity between the floodplain and river could limit negative climate change effects on salmon populations. Specifically, the top of the floodplain (Fremont Weir) is being modified to provide Sacramento River Chinook salmon better access to floodplain rearing habitat. We estimated restoration effects on the Yolo By‐Pass flood regime now and under future climate scenarios using flow rating curves. Additionally, we used temperature and flow‐specific effects on Chinook salmon population dynamics within the Yolo By‐Pass and Sacramento River complex to describe how the restoration project and climate change may interact to affect juvenile Chinook salmon biomass production. Our results indicate that the Fremont Weir restoration project will extend the frequency, timing, and duration of Yolo By‐Pass flooding. Our production model indicates that the modification will result in greater salmon entrainment rates into the Yolo By‐Pass, where salmon growth rates, survival rates, and biomass production were higher when compared to the Sacramento River main stem. The project appears to benefit all regional runs of Chinook salmon, which should help support life history diversity. Our results suggest that the weir modification should benefit native fish from the Central Valley that use floodplain habitat and that these benefits may be resilient to challenges created by a changing climate.

Six decades of ecohydrological research connecting landscapes and riverscapes in the Girnock Burn, Scotland: Atlantic salmon population and habitat dynamics in a changing world

AbstractLong‐term data are crucial for understanding ecological responses to climate and land use change; they are also vital evidence for informing management. As a migratory fish, Atlantic salmon are sentinels of both global and local environmental change. This paper reviews the main insights from six decades of research in an upland Scottish stream (Girnock Burn) inhabited by a spring Atlantic salmon population dominated by multi‐sea‐winter fish. Research began in the 1960s providing a census of returning adults, juvenile emigrants and in‐stream production of Atlantic salmon. Early research pioneered new monitoring techniques providing new insights into salmon ecology and population dynamics. These studies underlined the need for interdisciplinary approaches for understanding salmon interactions with physical, chemical and biological components of in‐stream habitats at different life‐stages. This highlighted variations in catchment‐scale hydroclimate, hydrology, geomorphology and hydrochemistry as essential to understanding freshwater habitats in the wider landscape context. Evolution of research has resulted in a remarkable catalogue of novel findings underlining the value of long‐term data that increases with time as modelling tools advance to leverage more insights from “big data”. Data are available on fish numbers, sizes and ages across multiple life stages, extending over many decades and covering a wide range of stock levels. Combined with an unusually detailed characterization of the environment, these data have enabled a unique process‐based understanding of the controls and bottlenecks on salmon population dynamics across the entire lifecycle and the consequences of declining marine survival and ova deposition. Such powerful datasets, methodological enhancements and the resulting process understanding have informed and supported the development of fish population assessment tools which have been applied to aid management of threatened salmon stocks at large‐catchment, regional and national scales. Many pioneering monitoring and modelling approaches developed have been applied internationally. This history shows the importance of integrating discovery science with monitoring for informing policy development and assessing efficacy of management options. It also demonstrates the need to continue to resource long‐term sites, which act as a focus for inter‐disciplinary research and innovation, and where the overall value of the research greatly exceeds the costs of individual component parts.

Status of a stocked Atlantic salmon population in Lake Huron

In 2011, the Michigan Department of Natural Resources (MDNR) expanded stocking of Atlantic salmon (Salmo salar) in Lake Huron to enhance fishing opportunities following Chinook salmon (Oncorhynchus tshawytscha) abundance declines. Currently, little is known about the population produced from this stocking. We fit an assessment model to harvest data from Michigan jurisdictional waters to estimate Atlantic salmon population dynamics and abundance. Because of potential biases in MDNR creel survey harvest estimates, a survey was e-mailed to online purchasers of a 2019 Michigan fishing license asking about where and when Atlantic salmon were harvested to correct creel harvest estimates. Anglers were also asked about catch-and-release angling and tested on their ability to identify Lake Huron salmonids. Creel harvest estimates overlapped spatially and temporally with 42% of survey reported Atlantic salmon harvest. After correcting creel harvest estimates, total abundance of Atlantic salmon in 2019 was estimated at approximately 392,000 fish with a peak abundance of approximately 406,000 fish. Anglers released 27% of caught fish and correctly identified Atlantic salmon 28% of the time. To assess the occurrence of food resource competition, differences in condition (i.e., expected weight at length) were evaluated. Condition was higher in later years than in earlier years despite abundance increases. Our results suggested that past stocking established a population of approximately 400,000 Atlantic salmon with evidence suggesting that fish were finding sufficient food resources. Future Atlantic salmon management efforts may be improved by quantifying post-stocking survival rates and other sources (e.g., charter, Canadian) of harvest.

Adult spawners: A critical period for subarctic Chinook salmon in a changing climate.

Concurrent, distribution-wide abundance declines of some Pacific salmon species, including Chinook salmon (Oncorhynchus tshawytscha), highlights the need to understand how vulnerability at different life stages to climate stressors affects population dynamics and fisheries sustainability. Yukon River Chinook salmon stocks are among the largest subarctic populations, near the northernmost extent of the species range. Existing research suggests that Yukon River Chinook salmon population dynamics are largely driven by factors occurring between the adult spawner life stage and their offspring's first summer at sea (second year post-hatching). However, specific mechanisms sustaining chronic poor productivity are unknown, and there is a tremendous sense of urgency to understand causes, as declines of these stocks have taken a serious toll on commercial, recreational, and indigenous subsistence fisheries. Therefore, we leveraged multiple existing datasets spanning parent and juvenile stages of life history in freshwater and marine habitats. We analyzed environmental data in association with the production of offspring that survive to the marine juvenile stage (juveniles per spawner). These analyses suggest more than 45% of the variability in the production of juvenile Chinook salmon is associated with river temperatures or water discharge levels during the parent spawning migration. Over the past two decades, parents that experienced warmer water temperatures and lower discharge in the mainstem Yukon River produced fewer juveniles per spawning adult. We propose the adult spawner life stage as a critical period regulating population dynamics. We also propose a conceptual model that can explain associations between population dynamics and climate stressors using independent data focused on marine nutrition and freshwater heat stress. It is sobering to consider that some of the northernmost Pacific salmon habitats may already be unfavorable to these cold-water species. Our findings have immediate implications, given the common assumption that northern ranges of Pacific salmon offer refugia from climate stressors.

Synchrony in population dynamics of juvenile Atlantic salmon: analyzing spatiotemporal variation and the influence of river flow and demography

Dispersal and shared environmental conditions can both synchronize the dynamics of local populations, but disentangling their relative influence on dynamics is challenging. We used a Bayesian approach to estimate the synchrony of a metapopulation of Atlantic salmon (Salmo salar) composed of 18 populations in Brittany, France, including a 24-year time series of the abundances of juveniles. We estimated the spatial synchrony at a regional and local spatial scale over the study period. We found a strong regional synchrony despite spatiotemporal variability of local synchrony in the abundance of juveniles. We then explored the drivers of synchrony, including environmental conditions (aspects of river flow) and abundance of adult breeders. This revealed that summer low-flow conditions seemed to synchronize the abundances of juveniles more than the synchrony in the abundance of adult breeders, suggesting a Moran effect. Given that drought conditions are expected to become more common with climate change, our work highlights the potentially strong synchronizing effect of summer low flow on the dynamics of local salmon populations and the benefits of considering synchrony at multiple scales.

Impacts of run‐of‐river hydropower on coho salmon (Oncorhynchus kisutch): the role of density‐dependent survival

AbstractPredicting whether anthropogenic sources of mortality have negative consequences at the level of population dynamics is challenged by mechanisms like density‐dependent survival that can amplify or offset the loss of individuals from anthropogenic disturbances. Run‐of‐river (RoR) hydropower is a growing industry that can cause frequent mortality of salmonid fry through rapid reductions in streamflow, leading to stranding on dewatered shores. However, whether individual‐level impacts reduce population growth rates or increase local extinction risk is difficult to predict. We used a stochastic stage‐structured matrix model to evaluate how the timing and magnitude of anthropogenic flow fluctuations impacted population abundance and extinction risk of coho salmon (Oncorhynchus kisutch), which spend up to 1.5 yr in many streams regulated by RoR hydropower. We additionally assessed how the timing (spring, winter) and strength (weak, moderate, high) of natural density‐dependent bottlenecks experienced by salmon in freshwaters tempers or amplifies the potential for RoR‐induced mortality to scale to emergent population dynamics. We compared population sizes and the 45‐yr probability of quasi‐extinction under 12 scenarios that varied the frequency (0–20 events per year) and magnitude (1–10% mortality per event) of RoR‐induced flow fluctuations, as well as the timing and strength of density‐dependent bottlenecks occurring during the first year in freshwater. We found that even mild flow fluctuations by RoR hydropower can impact coho salmon population dynamics, especially if density dependence is weak or occurs early in freshwater residency (spring). When density dependence was strong and during winter, the potential for population‐level impact was lessened, but populations still declined by 13–42% when RoR‐induced mortality was severe (5–10%) or frequent (10–20 events/yr). We conclude that strong density‐dependent survival bottlenecks could partially mitigate the loss of fry from anthropogenic flow fluctuations, especially if bottlenecks occur late in freshwater residency, but not for all intensities of flow fluctuations. Even with strong density dependence in winter, our models predict declining populations by up to 70% under strong and very frequent flow fluctuations, which should serve to caution those tasked with regulating flows in streams affected by RoR hydropower.

Redefining the oceanic distribution of Atlantic salmon

Determining the mechanisms driving range-wide reductions in Atlantic salmon marine survival is hindered by an insufficient understanding of their oceanic ecology and distribution. We attached 204 pop-up satellite archival tags to post-spawned salmon when they migrated to the ocean from seven European areas and maiden North American salmon captured at sea at West Greenland. Individuals migrated further north and east than previously reported and displayed increased diving activity near oceanographic fronts, emphasizing the importance of these regions as feeding areas. The oceanic distribution differed among individuals and populations, but overlapped more between geographically proximate than distant populations. Dissimilarities in distribution likely contribute to variation in growth and survival within and among populations due to spatio-temporal differences in environmental conditions. Climate-induced changes in oceanographic conditions will alter the location of frontal areas and may have stock-specific effects on Atlantic salmon population dynamics, likely having the largest impacts on southern populations.

Evaluating Fish Rescue as a Drought Adaptation Strategy Using a Life Cycle Modeling Approach for Imperiled Coho Salmon

AbstractProjected intensification of drought as a result of climate change may reduce the capacity of streams to rear fish, exacerbating the challenge of recovering salmonid populations listed under the Endangered Species Act. Without management intervention, some stocks will likely go extinct as stream drying and fragmentation reduce juvenile survival to unsustainable levels. To offset drought‐related mortality, fish rescue programs have proliferated, whereby juvenile salmonids are captured and transferred to off‐site rearing facilities. However, the efficacy of this potential conservation tool remains poorly understood. We developed a life cycle model to examine the implications of fish rescue on the abundance of Coho Salmon Oncorhynchus kisutch across serial life stages. The simulation model examines scenarios with varying quantities of rescued fish, time in captivity, drought severity, and reduced smolt‐to‐adult return rates. Our results indicate that fish rescue can increase the abundance of adults and lower extinction risk, particularly for fish held in captivity for a full year. However, fish rescue can also decrease the abundance of adults and increase extinction risk if fish are held only for summer and there is limited winter habitat. We found that when fish rescue did increase returns, it functioned more like a stock enhancement program than a drought mitigation tool and it would likely lead to consecutive generations of captive rearing, which has been shown to have negative effects on fitness. We translated our model into an R Shiny application (https://shiny.wdfw‐fish.us/CohoPopulationDynamics/) that allows users to explore how fish rescue affects Coho Salmon population dynamics through customized parameterization of the model to represent different systems or different assumptions about the effects of fish rescue.

Correction: Climate and competition influence sockeye salmon population dynamics across the Northeast Pacific Ocean

Correction: Climate and competition influence sockeye salmon population dynamics across the Northeast Pacific Ocean

Climate and competition influence sockeye salmon population dynamics across the Northeast Pacific Ocean

Pacific salmon productivity is influenced by ocean conditions and interspecific interactions, yet their combined effects are poorly understood. Using data from 47 North American sockeye salmon (Oncorhynchus nerka) populations, we present evidence that the magnitude and direction of climate and competition effects vary over large spatial scales. In the south, a warm ocean and abundant salmon competitors combined to strongly reduce sockeye productivity, whereas in the north, a warm ocean substantially increased productivity and offset the negative effects of competition at sea. From 2005 to 2015, the approximately 82 million adult pink salmon (Oncorhynchus gorbuscha) produced annually from hatcheries were estimated to have reduced the productivity of southern sockeye salmon by ∼15%, on average. In contrast, for sockeye at the northwestern end of their range, the same level of hatchery production was predicted to have reduced the positive effects of a warming ocean by ∼50% (from a ∼10% to a ∼5% increase in productivity, on average). These findings reveal spatially dependent effects of climate and competition on sockeye productivity and highlight the need for international discussions about large-scale hatchery production.

Implementing Ecosystem-Based Management Principles in the Design of a Salmon Ocean Ecology Program

Two decades have passed since the initiation of the National Oceanic and Atmospheric Administration’s research program aimed at advancing the understanding of estuary and ocean ecology of U.S. West Coast Pacific salmon (Oncorhynchus spp.). In this review and prospectus, we summarize key findings from this program and describe a plan for transitioning it to better support Ecosystem-Based Management (EBM). While we focus on salmon research, our approach applies to research design generally. Our path forward involves increasing understanding of ecosystem processes to improve the dependability of scenario testing under novel conditions. Over the past two decades, we developed a conceptual model for how climate, predators, prey, fisheries, and human activities influence salmon. Knowledge gaps we identified from our conceptual model include limited understanding of salmon distributions, behavior, maturation dynamics, and population dynamics, and salmon interactions with predators, competitors, and prey during winter. We consider emerging risks and vulnerabilities facing salmon and propose analysis frameworks for evaluating them. Increased predator populations, coupled with climate change, pose increasing threats to West Coast salmon and will require new strategies and actions to mitigate their negative impacts. We propose research to support the development of decision-support tools to evaluate tradeoffs associated with alternative management strategies and to inform an adaptive ecosystem management system to improve the resilience of salmon populations and salmon-dependent fisheries.

Environmental and behavioral controls on juvenile Chinook salmon migration pathways in the Columbia River estuary

Juvenile Chinook salmon population dynamics in the Columbia River estuary are influenced by physical processes, hatchery practices, and behavioral decision-making. To better understand how environmental forcing and swimming behavior influence estuarine migration and travel times, we developed an individual-based model (IBM) that uses 3-D outputs from a hydrodynamic model to simulate Lagrangian transport as well as swimming and bioenergetics sub-models to simulate active swimming and growth. Simulations were run in 2010 during the migration seasons for yearling and subyearling Chinook salmon. For both life history types, alternative behaviors were simulated, from random walks to behaviors that optimized efficient system migration for yearling Chinook salmon and growth for subyearling Chinook salmon. Simulation results compared well against observed data on travel times and common migration pathways; the simulated travel times for both yearling and subyearling Chinook salmon were within several hours of the observed travel times. In general, residence times and pathways were largely driven by river discharge and the phase of the tide. During periods of greater river discharge, simulated estuarine residence times were reduced and variability across individuals was minimal. The timing of estuarine exit was closely tied to the phase of the tide, with most simulated individuals exiting the system during the ebb phase. While travel times were largely driven by flow velocities, swimming behavior was likewise important. Simulated yearling Chinook salmon behaviors that optimized movement with surrounding flows resulted in reduced estuarine residence times when compared to passive and random walk behaviors. Similarly, simulated subyearling Chinook salmon behaviors that optimized growth directed individuals to shallow peripheral habitats, resulting in longer residence times and higher growth rates. Even if potentially important factors such as predator avoidance were not included, this IBM provides an informative tool to model migration pathways, growth, and residence times of juvenile salmon in an estuarine environment and could be used to inform management decisions by evaluating various scenarios.

CLIMATE CHANGES AND CURRENT STATE OF BIOTA IN THE RUSSIAN WATERS OF THE FAR-EASTERN SEAS

Discussion about limiting influence of climate conditions on dynamics of the pacific salmon populations and generally on biological resources of the Far-Eastern Seas is continuing. Multifactor impacts of climate and oceanographic conditions on populations and communities are concluded that cannot be described only by climatic indices and anomalies of the surface water temperature in the ocean in winter. Dynamics of the fish and invertebrates populations in various regions of the Far-Eastern Seas show a positive effect of climate warming on state and sustainability of the resource base for fisheries.

Comparing abundance‐based and tag‐based estimates of coho salmon marine survival

AbstractObtaining reliable estimates of marine survival is essential for understanding anadromous salmon population dynamics. Two common approaches to estimating marine survival are (a) dividing abundance of returning adult salmon abundance by abundance of smolts from the same cohort, or (b) tagging a portion of the migrating smolts and estimating the return rate of tagged adults. This study compared these two approaches to estimating marine survival for coho salmon, Oncorhynchus kisutch (Walbaum), across multiple years in three California streams. Abundance‐based survival estimates were higher than tag‐based estimates; average estimates for the two techniques differed from 1.5‐fold to 7.4‐fold across streams. One likely cause for these divergent estimates is migration of juveniles from natal habitat before smolt trapping begins, resulting in an underestimate of smolt abundance and an overestimate of marine survival rate for the abundance‐based method. Estimates of marine survival obtained from abundance estimates and tag returns are not directly comparable.

Evidence for spatial coherence in time trends of marine life history traits of Atlantic salmon in the North Atlantic

AbstractA hierarchical Bayesian life cycle model is presented that considers spatial covariation of marine life history traits of Atlantic salmon (Salmo salar) populations in the North Atlantic. The model is based on a collective analysis of the dynamics of 13 stock units (SUs) from two continental stock groups (CSGs) in North America and Southern Europe in a single hierarchical model over the period 1971–2014. The model sets up a new assessment framework for Atlantic salmon stocks. It also provides a framework to investigate the drivers of changes in Atlantic salmon population dynamics including disentangling the effects of fisheries from those of environmental factors in a hierarchy of spatial scales. It is used to test the hypothesis of a strong spatial synchrony in marine life history dynamics of Atlantic salmon populations. The trends in two key parameters associated with the early marine phase of the life cycle are estimated: (i) the marine survival during the first summer–autumn spent at sea and (ii) the proportion of fish maturing after the first winter at sea. The results provide evidence of a decline in the marine survival together with an increase in the proportion of fish that mature after the first winter at sea, common to all SUs. Our results show an increased coherence in the covariations of trends in these two marine life history traits related to geographic proximity of SUs which support the hypothesis of a coherent response of geographically proximate Atlantic salmon populations that likely share similar migration routes.

Assessing long-term changes in sex ratios of Pacific herring in Prince William Sound, Alaska

The Pacific herring (Clupea pallasii) population in Prince William Sound, Alaska suffered a sudden collapse in 1993 and has failed to recover. No consensus has been reached for the causes of the collapse, but hypotheses span a range of ecological, environmental, and anthropogenic drivers. During the course of investigations into changes in PWS herring and salmon population dynamics and fisheries we discovered that the observed percentage of male herring in spawning biomass estimates appeared to increase since the mid-1980s. Using available data (1983–2015) we analysed sex ratios of herring caught in close proximity to the spring spawn using various gear types. In recent years, the overall sex ratio of Pacific herring in PWS has been skewed towards males (>60%), but only if samples from cast nets are included, which generally catch spawning fish. In contrast, purse seine samples, generally collected days to weeks prior to the spawn, had relatively equal sex ratios. Age also affected the sex ratio, with a higher proportion of older fish being females. Using an age-structured simulation model, we illustrate that overestimating the number of males in the population can lead to biases in estimated model parameters (such as vulnerability at age) and as a result, biases in the inferred age composition of the population, and other derived quantities. After accounting for differences in sampling gears to improve estimated sex ratios, we recommend that future work focus attention on separating spatial and temporal differences in sex ratios of this otherwise much-studied population.

Sockeye salmon population dynamics over the past 4000\xa0years in Upper Russian Lake, south-central Alaska

Stable nitrogen isotope (δ15N) data from sediment cores taken in clear-water Upper Russian Lake (Kenai River Watershed, Alaska, USA) indicate that sockeye salmon (Oncorhynchus nerka) populations varied significantly over the past 4000 years, with a prominent ~ 650-year period of lower salmon abundance from ~ 100 BCE to 550 CE. Sediment characteristics during this ~ 650-year interval reflect glacial sediment input, which may have contributed to the salmon decline by degrading spawning habitat and reducing carrying capacity. The decline, however, coincides with large reductions in sockeye salmon abundance identified previously in Karluk and Akalura lakes on Kodiak Island, > 400 km southwest, supporting the possibility of regionally synchronous, multi-centennial production regimes that may originate from shifts in oceanographic conditions such as biological productivity in the northeastern Pacific Ocean. Under such a scenario, coincidence with watershed glacial activity indicates a common driver, i.e. regional climate change. Climate conditions that led to significant glacial advances in this part of the Kenai Peninsula (cold and/or wet conditions) may have also created unfavorable ocean conditions during critical periods in the marine phase for these stocks of Gulf of Alaska sockeye salmon. Future climate projections and management strategies should focus on how climate regimes impact not only prey availability for salmon at sea, but also local conditions for spawners and juveniles.

Influence of body condition on the population dynamics of Atlantic salmon with consideration of the potential impact of sea lice.

Atlantic salmon Salmo salar is an iconic species of high conservation and economic importance. At sea, individuals typically are subject to sea lice infestation, which can have detrimental effects on their host. Over recent decades, the body condition and marine survival in NE Atlantic stocks have generally decreased, reflected in fewer adults returning to rivers, which is partly attributable to sea lice. We developed a deterministic stage-structured population model to assess condition-mediated population dynamics resulting in changing fecundity, age at sexual maturation and marine survival rate. The model is parameterized using data from the North Esk system, north-east Scotland. Both constant and density-dependent juvenile survival rates are considered. We show that even small sea lice-mediated changes in mean body condition of MSW can cause substantial population declines, whereas 1SW condition is less influential. Density dependence alleviates the condition-mediated population effect. The resilience of the population to demographic perturbations declines as adult condition is reduced. Indirect demographic changes in salmonid life-history traits (e.g., body condition) are often considered unimportant for population trajectory. The model shows that Atlantic salmon population dynamics can be highly responsive to sea lice-mediated effects on adult body condition, thus highlighting the importance of non-lethal parasitic long-term effects.

Science Advancements Key to Increasing Management Value of Life Stage Monitoring Networks for Endangered Sacramento River Winter-Run Chinook Salmon in California

A robust monitoring network that provides quantitative information about the status of imperiled species at key life stages and geographic locations over time is fundamental for sustainable management of fisheries resources. For anadromous species, management actions in one geographic domain can substantially affect abundance of subsequent life stages that span broad geographic regions. Quantitative metrics (e.g., abundance, movement, survival, life history diversity, and condition) at multiple life stages are needed to inform how management actions (e.g., hatcheries, harvest, hydrology, and habitat restoration) influence salmon population dynamics. The existing monitoring network for endangered Sacramento River winter-run Chinook Salmon (SRWRC, Oncorhynchus tshawytscha) in California’s Central Valley was compared to conceptual models developed for each life stage and geographic region of the life cycle to identify relevant SRWRC metrics. We concluded that the current monitoring network was insufficient to diagnose when (life stage) and where (geographic domain) chronic or episodic reductions in SRWRC cohorts occur, precluding within- and among-year comparisons. The strongest quantitative data exist in the Upper Sacramento River, where abundance estimates are generated for adult spawners and emigrating juveniles. However, once SRWRC leave the upper river, our knowledge of their identity, abundance, and condition diminishes, despite the juvenile monitoring enterprise. We identified six system-wide recommended actions to strengthen the value of data generated from the existing monitoring network to assess resource management actions: (1) incorporate genetic run identification; (2) develop juvenile abundance estimates; (3) collect data for life history diversity metrics at multiple life stages; (4) expand and enhance real-time fish survival and movement monitoring; (5) collect fish condition data; and (6) provide timely public access to monitoring data in open data formats. To illustrate how updated technologies can enhance the existing monitoring to provide quantitative data on SRWRC, we provide examples of how each recommendation can address specific management issues

Salish Sea Chinook salmon exhibit weaker coherence in early marine survival trends than coastal populations

AbstractIdentifying factors that influence anadromous Pacific salmon (Oncorhynchus spp.) population dynamics is complicated by their diverse life histories and large geographic range. Over the last several decades, Chinook salmon (O. tshawytscha) populations from coastal areas and the Salish Sea have exhibited substantial variability in abundance. In some cases, populations within the Salish Sea have experienced persistent declines that have not rebounded. We analyzed a time series of early marine survival from 36 hatchery Chinook salmon populations spanning ocean entry years 1980–2008 to quantify spatial and temporal coherence in survival. Overall, we observed higher inter‐population variability in survival for Salish Sea populations than non‐Salish Sea populations. Annual survival patterns of Salish Sea populations covaried over smaller spatial scales and exhibited less synchrony among proximate populations relative to non‐Salish Sea populations. These results were supported by multivariate autoregressive state space (MARSS) models which predominantly identified region‐scale differences in survival trends between northern coastal, southern coastal, Strait of Georgia, and Puget Sound population groupings. Furthermore, Dynamic Factor Analysis (DFA) of regional survival trends showed that survival of southern coastal populations was associated with the North Pacific Gyre Oscillation, a large‐scale ocean circulation pattern, whereas survival of Salish Sea populations was not. In summary, this study demonstrates that survival patterns in Chinook salmon are likely determined by a complex hierarchy of processes operating across a broad range in spatial and temporal scales, presenting challenges to the management of mixed‐stock fisheries.