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• 1. [Article] Differential use of salmon by vertebrate consumers: implications for conservation

  This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by PeerJ. The published article can be found at: https://peerj.com/

  Citation × Citation Citation Abstract Copy Title: Differential use of salmon by vertebrate consumers: implications for conservation Author: Allen, Jennifer M., Wilmers, Christopher C., Wheat, Rachel E., Levi, Taal This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by PeerJ. The published article can be found at: https://peerj.com/ Title: Differential use of salmon by vertebrate consumers: implications for conservation Author: Allen, Jennifer M., Wilmers, Christopher C., Wheat, Rachel E., Levi, Taal This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by PeerJ. The published article can be found at: https://peerj.com/ Close

• 2. [Article] Statistical analysis on otolith data of anadromous fishes

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Springer ...

  Citation × Citation Citation Abstract Copy Title: Statistical analysis on otolith data of anadromous fishes Author: Bean, David, Noakes, David L. G., Conrad, Robert, Gao, Yongwen To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Springer and can be found at: http://www.springer.com/?SGWID=0-102-0-0-0. Title: Statistical analysis on otolith data of anadromous fishes Author: Bean, David, Noakes, David L. G., Conrad, Robert, Gao, Yongwen To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Springer and can be found at: http://www.springer.com/?SGWID=0-102-0-0-0. Close

• 3. [Article] Variability in expression of anadromy by female Oncorhynchus mykiss within a river network

  We described and predicted spatial variation in marine migration (anadromy) of female Oncorhynchus mykiss in the John Day River watershed, Oregon. We collected 149 juvenile O. mykiss across 72 sites and ...

  Citation × Citation Citation Abstract Copy Title: Variability in expression of anadromy by female Oncorhynchus mykiss within a river network Author: Zimmerman, Christian E., Jordan, Chris E., McMillan, John R., Mills, Justin S., Dunham, Jason B., Reeves, Gordon H. We described and predicted spatial variation in marine migration (anadromy) of female Oncorhynchus mykiss in the John Day River watershed, Oregon. We collected 149 juvenile O. mykiss across 72 sites and identified locations used by anadromous females by assigning maternal origin (anadromous versus non-anadromous) to each juvenile. These assignments used comparisons of strontium to calcium ratios in otolith primordia and freshwater growth regions to indicate maternal origin. We used logistic regression to predict probability of anadromy in relation to mean annual stream runoff using data from a subset of individuals. This model correctly predicted anadromy in a second sample of individuals with a moderate level of accuracy (e.g., 68% correctly predicted with a 0.5 classification threshold). Residuals from the models were not spatially autocorrelated, suggesting that remaining variability in the expression of anadromy was due to localized influences, as opposed to broad-scale gradients unrelated to mean annual stream runoff. These results are important for the management of O. mykiss because anadromous individuals (steelhead) within the John Day River watershed are listed as a threatened species, and it is difficult to discern juvenile steelhead from non-anadromous individuals (rainbow trout) in the field. Our results provide a broad-scale description and prediction of locations supporting anadromy, and new insight for habitat restoration, monitoring, and research to better manage and understand the expression of anadromy in O. mykiss. Title: Variability in expression of anadromy by female Oncorhynchus mykiss within a river network Author: Zimmerman, Christian E., Jordan, Chris E., McMillan, John R., Mills, Justin S., Dunham, Jason B., Reeves, Gordon H. We described and predicted spatial variation in marine migration (anadromy) of female Oncorhynchus mykiss in the John Day River watershed, Oregon. We collected 149 juvenile O. mykiss across 72 sites and identified locations used by anadromous females by assigning maternal origin (anadromous versus non-anadromous) to each juvenile. These assignments used comparisons of strontium to calcium ratios in otolith primordia and freshwater growth regions to indicate maternal origin. We used logistic regression to predict probability of anadromy in relation to mean annual stream runoff using data from a subset of individuals. This model correctly predicted anadromy in a second sample of individuals with a moderate level of accuracy (e.g., 68% correctly predicted with a 0.5 classification threshold). Residuals from the models were not spatially autocorrelated, suggesting that remaining variability in the expression of anadromy was due to localized influences, as opposed to broad-scale gradients unrelated to mean annual stream runoff. These results are important for the management of O. mykiss because anadromous individuals (steelhead) within the John Day River watershed are listed as a threatened species, and it is difficult to discern juvenile steelhead from non-anadromous individuals (rainbow trout) in the field. Our results provide a broad-scale description and prediction of locations supporting anadromy, and new insight for habitat restoration, monitoring, and research to better manage and understand the expression of anadromy in O. mykiss. Close

• 4. [Article] Quantifying Salmon-Derived Nutrient Loads from the Mortality of Hatchery-Origin Juvenile Chinook Salmon in the Snake River Basin

  This is the publisher’s final pdf. The article is copyrighted by the American Fisheries Society and published by Taylor & Francis. It can be found at: http://www.tandfonline.com/toc/utaf20/current. To ...

  Citation × Citation Citation Abstract Copy Title: Quantifying Salmon-Derived Nutrient Loads from the Mortality of Hatchery-Origin Juvenile Chinook Salmon in the Snake River Basin Author: Warren, Dana R., McClure, Michelle M. This is the publisher’s final pdf. The article is copyrighted by the American Fisheries Society and published by Taylor & Francis. It can be found at: http://www.tandfonline.com/toc/utaf20/current. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. Title: Quantifying Salmon-Derived Nutrient Loads from the Mortality of Hatchery-Origin Juvenile Chinook Salmon in the Snake River Basin Author: Warren, Dana R., McClure, Michelle M. This is the publisher’s final pdf. The article is copyrighted by the American Fisheries Society and published by Taylor & Francis. It can be found at: http://www.tandfonline.com/toc/utaf20/current. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. Close

• 5. [Article] The Scientific Basis for Artificial Propagation in the Recovery of Wild Anadromous Salmonids in Oregon

  This report was prepared by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds

  Citation × Citation Citation Abstract Copy Title: The Scientific Basis for Artificial Propagation in the Recovery of Wild Anadromous Salmonids in Oregon Author: Independent Multidisciplinary Science Team (Or.) This report was prepared by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds Title: The Scientific Basis for Artificial Propagation in the Recovery of Wild Anadromous Salmonids in Oregon Author: Independent Multidisciplinary Science Team (Or.) This report was prepared by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds Close

• 6. [Article] Salmon Abundances and Effects of Harvest: Implications for Rebuilding Stocks of Wild Coho Salmon in Oregon

  This report was prepared by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds.

  Citation × Citation Citation Abstract Copy Title: Salmon Abundances and Effects of Harvest: Implications for Rebuilding Stocks of Wild Coho Salmon in Oregon Author: Independent Multidisciplinary Science Team (Or.) This report was prepared by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds. Title: Salmon Abundances and Effects of Harvest: Implications for Rebuilding Stocks of Wild Coho Salmon in Oregon Author: Independent Multidisciplinary Science Team (Or.) This report was prepared by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds. Close

• 7. [Article] Relationships among juvenile anadromous salmonids, their freshwater habitat, and landscape characteristics over multiple years and spatial scales in the Elk River, Oregon

  Research on the distribution of juvenile salmonids in streams has been dominated by studies examining small areas over short periods. However, information relevant to freshwater influences on population ...

  Citation × Citation Citation Abstract Copy Title: Relationships among juvenile anadromous salmonids, their freshwater habitat, and landscape characteristics over multiple years and spatial scales in the Elk River, Oregon Author: Burnett, Kelly M. Research on the distribution of juvenile salmonids in streams has been dominated by studies examining small areas over short periods. However, information relevant to freshwater influences on population persistence is likely to derive from longer-term, multi-scale studies. Relationships were examined among juvenile anadromous salmonids, their freshwater habitat, and landscape characteristics throughout the Elk River, Oregon over 7 years at multiple spatial scales. Ocean-type chinook salmon (Oncorhynchus tshawytscha), coho salmon (0. kisutch), coastal cutthroat trout (0. clarki) and winter-run steelhead (0. mykiss) comprised the salmonid assemblage. Habitat selection was quantified at stream system, valley segment, and channel unit scales by selection ratios estimated with bootstrapping methods. Unconstrained valleys in tributaries and pools in the mainstem were typically selected by each species except steelhead, which often avoided these. Valley segment types generally did not differ for characteristics routinely assessed in stream surveys. Thus, fish probably perceived other biotic or abiotic differences among valley segment types. Evidence suggested competition may have influenced selection by coho and chinook salmon. Discriminant analysis indicated that level of use by juvenile chinook salmon appeared related to valley segment type and spatial position. Unconstrained valleys, nearby valley segments, and valley segments with larger, deeper pools, containing more wood were most highly used by chinook salmon. Mean volume and maximum depth of pools were each directly related to catchment area, which explained more variation than landscape characteristics summarized at any of five spatial scales. At each scale except the most spatially extensive, wood density in valley segments was negatively related to the percent area in resistant rock types and positively related to the percent area in mature to old forests. The most variation was explained with these landscape variables summarized at an intermediate spatial scale (i.e., sub-catchment). Although spatial scales appeared similar in processes affecting wood density, finer scales omitted key source areas for wood delivery, and coarser scales included source areas less tightly coupled to wood dynamics in surveyed channels. If only 1 or 2 years of data or one spatial scale had been examined, as commonly occurs, conclusions may have differed substantially from those in this study. Title: Relationships among juvenile anadromous salmonids, their freshwater habitat, and landscape characteristics over multiple years and spatial scales in the Elk River, Oregon Author: Burnett, Kelly M. Research on the distribution of juvenile salmonids in streams has been dominated by studies examining small areas over short periods. However, information relevant to freshwater influences on population persistence is likely to derive from longer-term, multi-scale studies. Relationships were examined among juvenile anadromous salmonids, their freshwater habitat, and landscape characteristics throughout the Elk River, Oregon over 7 years at multiple spatial scales. Ocean-type chinook salmon (Oncorhynchus tshawytscha), coho salmon (0. kisutch), coastal cutthroat trout (0. clarki) and winter-run steelhead (0. mykiss) comprised the salmonid assemblage. Habitat selection was quantified at stream system, valley segment, and channel unit scales by selection ratios estimated with bootstrapping methods. Unconstrained valleys in tributaries and pools in the mainstem were typically selected by each species except steelhead, which often avoided these. Valley segment types generally did not differ for characteristics routinely assessed in stream surveys. Thus, fish probably perceived other biotic or abiotic differences among valley segment types. Evidence suggested competition may have influenced selection by coho and chinook salmon. Discriminant analysis indicated that level of use by juvenile chinook salmon appeared related to valley segment type and spatial position. Unconstrained valleys, nearby valley segments, and valley segments with larger, deeper pools, containing more wood were most highly used by chinook salmon. Mean volume and maximum depth of pools were each directly related to catchment area, which explained more variation than landscape characteristics summarized at any of five spatial scales. At each scale except the most spatially extensive, wood density in valley segments was negatively related to the percent area in resistant rock types and positively related to the percent area in mature to old forests. The most variation was explained with these landscape variables summarized at an intermediate spatial scale (i.e., sub-catchment). Although spatial scales appeared similar in processes affecting wood density, finer scales omitted key source areas for wood delivery, and coarser scales included source areas less tightly coupled to wood dynamics in surveyed channels. If only 1 or 2 years of data or one spatial scale had been examined, as commonly occurs, conclusions may have differed substantially from those in this study. Close

• 8. [Article] Systematics, variation, distribution, and biology of lampreys of the genus Lampetra in Oregon

  Based on the number of velar tentacles and the form of longitudinal lingual laminae found in Lampetra (Entosphenus) t. tridentata and its closely related forms, the taxon Entosphenus should not be considered ...

  Citation × Citation Citation Abstract Copy Title: Systematics, variation, distribution, and biology of lampreys of the genus Lampetra in Oregon Author: Kan, Ting Tien Based on the number of velar tentacles and the form of longitudinal lingual laminae found in Lampetra (Entosphenus) t. tridentata and its closely related forms, the taxon Entosphenus should not be considered as a genus as commonly adopted, but, along with the taxa Lethenteron and Lampetra, should be regarded as a subgenus of the genus Lampetra. The genus Lampetra is distinct for various reasons, including particularly the character that no cusps are present in the area distal to the lateral circumorals. Six nominal species, belonging to the subgenera Entosphenus and Lampetra, have been known to occur in four of the seven major drainage systems of Oregon. The anadromous L. (E.) t.tridentata, is widespread in the Columbia River and Coastal drainage systems, occurring in most streams with access to the ocean regardless of distance to the ocean, as long as suitable spawning grounds and ammocoete habitats are present. Morphometrics and dentitional features vary little over its geographical range. The number of trunk myomeres and the adult body size vary appreciably so that two categories of regional forms, coastal and inland, may be recognized. The coastal forms are generally smaller and have fewer trunk myomeres compared to those of the larger inland forms. The spawning migration begins from the late spring to late summer for the coastal forms but may occur much earlier for the inland forms. The adult body size appears to be positively correlated with absolute fecundity, but is negatively correlated with relative fecundity. Duration of the larval period is from four to six years. Metamorphosis usually takes place in the fall. Macrophthalmia are known to enter the ocean over a long period, those descending coastal streams enter salt water in the late fall and early winter, whereas the peak of emigration from inland streams is in the early spring. Duration of its marine parasitic phase appears to be from 20 to 40 months. The small landlocked L. (E.) t. kawiaga n. subsp., found only in the Klamath and Goose Lake drainage systems in southern Oregon and northern California, differs from t. tridentata in body size and various meristic and morphometric characters. Its lacustrine parasitic phase is about 12 months long. L. (E.) lethophaga, the nonparasitic derivative of tridentata, occurs in the Klamath and probably also the Goose Lake drainage system. It is characterized by an extension of the larval phase and by a greatly reduced post-larval period. The presumably extinct L. (E. ) minima, a parasitic derivative of tridentata, found formerly only in Miller Lake, Oregon, possessed a number of characters that were concomitants of dwarfism, the distinctive feature of the species. Relationships and evolution among the subgenus Entosphenus were discussed. Distributional records of L. ayresii and L. richardsoni of the subgenus Lampetra in Oregon were given. Evidence indicates that a complex of clinal races, including L. pacifica Vladykov, 1973, may exist in the latter species. Title: Systematics, variation, distribution, and biology of lampreys of the genus Lampetra in Oregon Author: Kan, Ting Tien Based on the number of velar tentacles and the form of longitudinal lingual laminae found in Lampetra (Entosphenus) t. tridentata and its closely related forms, the taxon Entosphenus should not be considered as a genus as commonly adopted, but, along with the taxa Lethenteron and Lampetra, should be regarded as a subgenus of the genus Lampetra. The genus Lampetra is distinct for various reasons, including particularly the character that no cusps are present in the area distal to the lateral circumorals. Six nominal species, belonging to the subgenera Entosphenus and Lampetra, have been known to occur in four of the seven major drainage systems of Oregon. The anadromous L. (E.) t.tridentata, is widespread in the Columbia River and Coastal drainage systems, occurring in most streams with access to the ocean regardless of distance to the ocean, as long as suitable spawning grounds and ammocoete habitats are present. Morphometrics and dentitional features vary little over its geographical range. The number of trunk myomeres and the adult body size vary appreciably so that two categories of regional forms, coastal and inland, may be recognized. The coastal forms are generally smaller and have fewer trunk myomeres compared to those of the larger inland forms. The spawning migration begins from the late spring to late summer for the coastal forms but may occur much earlier for the inland forms. The adult body size appears to be positively correlated with absolute fecundity, but is negatively correlated with relative fecundity. Duration of the larval period is from four to six years. Metamorphosis usually takes place in the fall. Macrophthalmia are known to enter the ocean over a long period, those descending coastal streams enter salt water in the late fall and early winter, whereas the peak of emigration from inland streams is in the early spring. Duration of its marine parasitic phase appears to be from 20 to 40 months. The small landlocked L. (E.) t. kawiaga n. subsp., found only in the Klamath and Goose Lake drainage systems in southern Oregon and northern California, differs from t. tridentata in body size and various meristic and morphometric characters. Its lacustrine parasitic phase is about 12 months long. L. (E.) lethophaga, the nonparasitic derivative of tridentata, occurs in the Klamath and probably also the Goose Lake drainage system. It is characterized by an extension of the larval phase and by a greatly reduced post-larval period. The presumably extinct L. (E. ) minima, a parasitic derivative of tridentata, found formerly only in Miller Lake, Oregon, possessed a number of characters that were concomitants of dwarfism, the distinctive feature of the species. Relationships and evolution among the subgenus Entosphenus were discussed. Distributional records of L. ayresii and L. richardsoni of the subgenus Lampetra in Oregon were given. Evidence indicates that a complex of clinal races, including L. pacifica Vladykov, 1973, may exist in the latter species. Close

• 9. [Article] An economic analysis of alternative water allocations and habitat investments for anadromous fish production, John Day Basin, Oregon

  This thesis focuses on the economic efficiency of alternative habitat, streamfiow, and land use allocations within a major drainage of the Pacific Northwest. Specifically, productivity of present habitat and ...

  Citation × Citation Citation Abstract Copy Title: An economic analysis of alternative water allocations and habitat investments for anadromous fish production, John Day Basin, Oregon Author: Cerda, Arcadio Alberto This thesis focuses on the economic efficiency of alternative habitat, streamfiow, and land use allocations within a major drainage of the Pacific Northwest. Specifically, productivity of present habitat and streamfiow conditions is evaluated with respect to anadromous fish species (chinook salmon and steelhead trout) in the John Day River Basin, a high-desert system in the Pacific Northwest. Alternative water allocations and fish habitat enhancements to improve anadromous fish productivity are also examined. This biophysical information is combined with economics concepts to evaluate comparative benefits and economic efficiency of selected technically feasible habitat/streamflow alternatives. The John Day River Basin is used as a case study because it provides one of the most significant runs of wild summer steelhead trout and spring chinook salmon in the Columbia River Basin. Specific categories of alternative enhancements included water transfers to instream flow, habitat vegetation improvements, and habitat structural measures. The benefits of changes in fish numbers are valued through the travel cost method. Costs of habitat investments are derived from a synthesis of cost data for similar investments for the region. For most lower-reach stream sections, benefits of habitat investments/streamflow alternatives do not equal costs. However, changes in water allocations and habitat do appear economically efficient to some upper reaches. The main results suggest that economic efficiency varies greatly within the system, indicating the need for site-specific proposals for streamfiow or habitat alterations within this or similar high desert streams. In addition to providing preliminary estimates of the economic efficency of streamfiow and habitat investments, this thesis serves as a methodological template for future integrated bioeconomic evaluations of water and fishery management issues. Title: An economic analysis of alternative water allocations and habitat investments for anadromous fish production, John Day Basin, Oregon Author: Cerda, Arcadio Alberto This thesis focuses on the economic efficiency of alternative habitat, streamfiow, and land use allocations within a major drainage of the Pacific Northwest. Specifically, productivity of present habitat and streamfiow conditions is evaluated with respect to anadromous fish species (chinook salmon and steelhead trout) in the John Day River Basin, a high-desert system in the Pacific Northwest. Alternative water allocations and fish habitat enhancements to improve anadromous fish productivity are also examined. This biophysical information is combined with economics concepts to evaluate comparative benefits and economic efficiency of selected technically feasible habitat/streamflow alternatives. The John Day River Basin is used as a case study because it provides one of the most significant runs of wild summer steelhead trout and spring chinook salmon in the Columbia River Basin. Specific categories of alternative enhancements included water transfers to instream flow, habitat vegetation improvements, and habitat structural measures. The benefits of changes in fish numbers are valued through the travel cost method. Costs of habitat investments are derived from a synthesis of cost data for similar investments for the region. For most lower-reach stream sections, benefits of habitat investments/streamflow alternatives do not equal costs. However, changes in water allocations and habitat do appear economically efficient to some upper reaches. The main results suggest that economic efficiency varies greatly within the system, indicating the need for site-specific proposals for streamfiow or habitat alterations within this or similar high desert streams. In addition to providing preliminary estimates of the economic efficency of streamfiow and habitat investments, this thesis serves as a methodological template for future integrated bioeconomic evaluations of water and fishery management issues. Close

• 10. [Article] Aspects of the early life history of juvenile salmonids in the Dungeness River Estuary

  The decline of many Pacific salmon stocks has stimulated interest in the early life history and habitat requirements of juvenile salmon. Although estuarine habitat associations of juvenile salmon have ...

  Citation × Citation Citation Abstract Copy Title: Aspects of the early life history of juvenile salmonids in the Dungeness River Estuary Author: Sather, Nichole K. The decline of many Pacific salmon stocks has stimulated interest in the early life history and habitat requirements of juvenile salmon. Although estuarine habitat associations of juvenile salmon have been investigated in many coastal areas of the eastern Pacific Ocean, until recently, little was known about juvenile salmonid ecology within the Straits of Juan de Fuca. During the Spring/Summer outmigration period in 2006 and 2007, I examined the early life history of the five species of anadromous salmon in the Dungeness River estuary on the north Olympic Peninsula, Washington. I sampled multiple spatial scales within several habitat types to characterize salmon distribution and habitat use. My results presented in this thesis are segregated into two components: 1) tidal marsh ecology of juvenile salmonids in the Dungeness River estuary, and 2) the landscape-scale distribution of juvenile salmonids within the Dungeness River estuary. I examined the population of juvenile salmonids within blind tidal sloughs near the vicinity of the Dungeness River delta. Salmonids were present within the tidal marshes throughout the entire outmigration period (e.g., March through July). Juvenile Chinook salmon (Oncorhynchus tshawytscha) were the most abundant salmonid species within the marshes. Based on the temporal distribution and size structure of juvenile Chinook salmon in the estuary I identified at least four life history types: 1) a fry strategy included a large pulse of fish emigrating from the river at a small size (e.g., 35-45mm FL) during late winter and early spring months; 2) the second group of fish was the least abundant group emigrating from the river from April through mid May at sizes ranging from 50-75mm FL; 3) the third group of migrants entered the estuary between from late spring through the summer months at larger sizes than the initial groups (e.g., 60-90mm FL); and 4) the final group of Chinook salmon included a stream-type yearling strategy. In addition to the four life history strategies identified for Chinook salmon, I detected at least three groups of chum salmon migrating into the estuary. These groups were distinguished by their size and timing of migration and are further described according to different rearing strategies. The distribution of juvenile salmonids was most strongly influenced by the degree of connectivity (i.e., distance) between the tidal marshes and the mouth of the Dungeness River. Habitat complexity and opportunity also governed the distribution of juvenile salmonids within the tidal marshes. I also sampled three regions of the estuary with a beach seine to investigate the nearshore distribution of juvenile salmonids within the Dungeness River estuary: the delta face, inner Bay, and outer Bay. Among the three regions, species composition was highly variable between 2006 and 2007. The most common salmonids encountered within the beach seine sites included Chinook salmon, chum salmon (O. kisutch), and pink salmon (O. gorbuscha). The relative abundance of salmonids was highest near the delta face and lowest within the outer bay area. The landscape-scale distribution and habitat use of juvenile salmonids within the Dungeness River estuary is largely influenced by ecosystem connectivity, but is also linked to biotic characteristics of the fish (e.g., life history type and fish size). Although the Dungeness includes hydrogeomorphic characteristics (e.g., steep river gradient, composition of sand spits in the estuary) unique to other Pacific Northwest watersheds, this system produces a variety of life history types comparable to other estuaries. Understanding the mechanisms that drive the distribution of juvenile salmonids within the Dungeness will supply local resource managers with a baseline with which to establish ecosystem restoration goals. Title: Aspects of the early life history of juvenile salmonids in the Dungeness River Estuary Author: Sather, Nichole K. The decline of many Pacific salmon stocks has stimulated interest in the early life history and habitat requirements of juvenile salmon. Although estuarine habitat associations of juvenile salmon have been investigated in many coastal areas of the eastern Pacific Ocean, until recently, little was known about juvenile salmonid ecology within the Straits of Juan de Fuca. During the Spring/Summer outmigration period in 2006 and 2007, I examined the early life history of the five species of anadromous salmon in the Dungeness River estuary on the north Olympic Peninsula, Washington. I sampled multiple spatial scales within several habitat types to characterize salmon distribution and habitat use. My results presented in this thesis are segregated into two components: 1) tidal marsh ecology of juvenile salmonids in the Dungeness River estuary, and 2) the landscape-scale distribution of juvenile salmonids within the Dungeness River estuary. I examined the population of juvenile salmonids within blind tidal sloughs near the vicinity of the Dungeness River delta. Salmonids were present within the tidal marshes throughout the entire outmigration period (e.g., March through July). Juvenile Chinook salmon (Oncorhynchus tshawytscha) were the most abundant salmonid species within the marshes. Based on the temporal distribution and size structure of juvenile Chinook salmon in the estuary I identified at least four life history types: 1) a fry strategy included a large pulse of fish emigrating from the river at a small size (e.g., 35-45mm FL) during late winter and early spring months; 2) the second group of fish was the least abundant group emigrating from the river from April through mid May at sizes ranging from 50-75mm FL; 3) the third group of migrants entered the estuary between from late spring through the summer months at larger sizes than the initial groups (e.g., 60-90mm FL); and 4) the final group of Chinook salmon included a stream-type yearling strategy. In addition to the four life history strategies identified for Chinook salmon, I detected at least three groups of chum salmon migrating into the estuary. These groups were distinguished by their size and timing of migration and are further described according to different rearing strategies. The distribution of juvenile salmonids was most strongly influenced by the degree of connectivity (i.e., distance) between the tidal marshes and the mouth of the Dungeness River. Habitat complexity and opportunity also governed the distribution of juvenile salmonids within the tidal marshes. I also sampled three regions of the estuary with a beach seine to investigate the nearshore distribution of juvenile salmonids within the Dungeness River estuary: the delta face, inner Bay, and outer Bay. Among the three regions, species composition was highly variable between 2006 and 2007. The most common salmonids encountered within the beach seine sites included Chinook salmon, chum salmon (O. kisutch), and pink salmon (O. gorbuscha). The relative abundance of salmonids was highest near the delta face and lowest within the outer bay area. The landscape-scale distribution and habitat use of juvenile salmonids within the Dungeness River estuary is largely influenced by ecosystem connectivity, but is also linked to biotic characteristics of the fish (e.g., life history type and fish size). Although the Dungeness includes hydrogeomorphic characteristics (e.g., steep river gradient, composition of sand spits in the estuary) unique to other Pacific Northwest watersheds, this system produces a variety of life history types comparable to other estuaries. Understanding the mechanisms that drive the distribution of juvenile salmonids within the Dungeness will supply local resource managers with a baseline with which to establish ecosystem restoration goals. Close