The segmenting of gravel-bed rivers into 'sedimentary links', characterized by single-sediment sources and downstream fining of alluvial sediments, is a relatively new technique which has had limited application. The sedimentary link concept has been primarily applied to alpine river environments where link formations are supplied by coarse sediment from active point sources. The purpose of this study is to apply the sedimentary link concept on the Ste Marguerite River in the Saguenay region of the Canadian Shield, where valley-segment deposits of coarse sediment from ancient glacial processes are dominant in forming links. / Specifically, this study examines link-scale trends in surface grain size and channel slope. This study also uses the sedimentary link concept within an ecological context to explain the spatial organization and quality of Atlantic salmon spawning and rearing habitat. (Abstract shortened by UMI.)

Changes in channel morphology in response to two flood events were measured within three reaches on the Sainte Marguerite River, Quebec. The first event was the spring freshet---peaking in mid-May, 1996---while the second event---peaking on July 20, 1996---was the largest flood on record for the region. The resultant channel adjustments can be classified as either bedform evolution---in which a clear, systematic pattern of adjustment is evident---or as bedform change, in which local hydraulic and sedimen tologic conditions produce a seemingly random pattern of channel mobilization. Where bedform evolution has occurred, it is consistent with the existing paradigm for meander development. Sediment transport calculations based on the 'inverse' or 'morphologic' method were strongly correlated to reach average mobility ratios. The average rate of transport in response to the larger flood approached those reported by others for a braided system (Goff and Ashmore, 1994). Potential spawning zones within the three reaches were all subjected to significant net scour and/or fill following the second event; several potential spawning zones were significantly affected by the first event The presence of bank protection upstream of a potential spawning zone seems to be a determinant 10 the severity of the impact by promoting erosion of these zones.

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In response to the increasing need for ecosystem services throughout the Southeast Alaska region, decision makers are tasked with balancing the need for natural resources with salmon conservation. However, accurate historical and current information on salmonid population abundance, freshwater distribution, and habitat quality are sparse with limited resolution for large portions of this remote and rugged landscape. Here, I created Intrinsic Potential (IP) models for chum and pink salmon to predict the potential for portions of coastal rivers to provide high-quality spawning habitat. I developed IP models for both species from field redd surveys and synthetic habitat variables derived from 1-m resolution digital elevation models. The surveys were performed at 49 study reaches in five coastal drainage basins on the north end of Chichagof Island, Southeast Alaska. I used a spatially balanced random sampling design that included field surveys for redds during two field seasons with contrasting precipitation patterns and disparate adult salmon escapements. The IP models predict probable spawning habitat for both species based on persistent landform characteristics and hydrologic processes that control the formation and distribution of spawning habitat across the landscape. Selection of persistent reach variables for both species IP models was informed by principal component analysis (PCA), resource selection ratios, random forest modeling, and regression models of field and synthetic variable comparisons. I observed primarily one spawning strategy by chum salmon associated with mainstem channels, and two distinct spawning strategies for pink salmon related to small moderate-gradient channels and tributaries, and lower drainage basin mainstem channels. The relationships suggest that chum and pink salmon primarily selected for unconstrained channel types in large-and small-size channels, with chum salmon being more selective toward the larger mainstem channels, and pink salmon selecting for smaller channels and tributaries. The prediction of chum salmon redd presence within a specific reach for both high and low streamflow regimes was explained by channel gradient, floodplain width, and mean annual flow in order of importance. In general, chum salmon redds were observed in larger unconstrained low-gradient floodplain reaches where accumulation of deposited gravels and adequate flow produce habitat heterogeneity suitable for spawning. Pink salmon redd presence for both survey years was explained by channel gradient, reach elevation, and mean annual flow, in order of importance. Specifically, when flows allowed upstream access, spawning pink salmon utilized smaller moderate-gradient channels where substrate size and flows were better suited to their smaller body size. Remotely sensed persistent fish habitat data is valuable information for helping understand fish population distributions across the landscape. These synthetic metrics enabled the identification and evaluation of persistent landscape features as probable predictors of IP. Validation of LiDAR-derived channel characteristics indicated channel lengths measured from the DEM were 12% longer than field measured channel length, primarily for channels wider than 10 meters. Thus, understanding the limitations of the data is important so that decision makers do not unintentionally set unrealistic objectives. This research highlights the utility of using IP models with high resolution remote sensing to expand known distributions and quality of spawning habitat for these two species in Southeast Alaska coastal streams.

Forested lands of western Oregon provide aquatic habitat for many fish and riparian dependent species, including a wide variety of salmon species. Current policies set riparian protections using fixed buffers on streams for federal and private lands based on stream type or size. These buffers can create a series of disjointed riparian protections, as federal lands require buffers that are much larger than private lands. In addition, the fixed buffer approach is neither flexible nor tailored to aquatic ecosystem values. This thesis presents a framework for comprehensively assessing stream networks using site specific watershed features and then suggests riparian conservation strategies that key stream and riparian protection to aquatic ecosystem values. Seven study watersheds were used in this analysis, totaling over 2.5 million acres of forested lands in western Oregon. Employing a set of geospatial tools, called NetMap, streams in each watershed were classified into higher and lower priorities using criteria of intrinsic potential, erosion/debris flow susceptibility, and thermal loading potential. Results demonstrated the inherent variability within and among watersheds based on the geomorphic and ecological processes determined important for selected salmon species. Within each watershed, both federal and non-federal lands had many miles of higher priority fish-bearing and non-fish bearing streams, suggesting the need for comprehensive, holistic watershed conservation strategies. Based on the partitioning of streams into higher and lower priorities, an alternative riparian conservation strategy was then modeled for federal lands that allocate protection on the basis of the ecological context of a stream segment’s potential and particular location while still meeting federal aquatic conservation goals and objectives. Possible increases to the land base for long-term timber production were then identified if this strategy were applied to federal Matrix lands. Results demonstrated that 8-30 percent of the current riparian buffers could be reallocated to the land base for long-term timber production. An additional 26-45 percent of current buffers could be managed simultaneously for both timber production and aquatic ecosystem goals. Results also provided a framework for targeting of conservation and restoration efforts towards higher priority streams within each watershed. As many of the most ecologically important streams were located on non-federal lands, riparian conservation policies focused on streams classified as higher priority on those lands may be needed to protect aquatic species and their environments. / Graduation date: 2013

Early life stages of many marine and diadromous fish species use sandy beach surf zones, which occur along >50% of the world's marine coastlines. This extensive habitat can provide juvenile fishes with an abundant supply of potential prey and the ability to hide from predators in its shallow turbid waters. Chinook salmon is an anadromous species that migrates to the ocean during their first (subyearlings) or second (yearlings) year of life. The majority of subyearlings reside in estuaries during their first summer season; however, a small number of juveniles also use surf zones. Early marine residence is considered a critical period for Chinook salmon due to high mortality rates; however the role of surf zones in Chinook salmon life history is unclear. Therefore, I determined the distribution of juvenile Chinook salmon on beaches of the eastern North Pacific, compared the migration and growth patterns observed in surf zones and estuaries, identified the factors that accounted for variation in juvenile surf zone catch, explored the factors that influence growth rate variation in surf zones and estuaries, and modeled how growth rates in these coastal habitats may vary in the near future with predicted changes in climate. The majority (94%) of juveniles were caught in surf zones adjacent to estuaries with trough areas, which are beach sections where sand moved by currents and waves produce a trench-like shape. Surf zone fish were collected in significantly lower numbers than estuarine juveniles but entered brackish/ocean waters at similar sizes. Juveniles in surf zones consumed similar organisms (gammarid amphipods, crustacean larvae and insects) as in estuaries. Furthermore, stomach fullness indices (average = 2% of body weight) and growth rates (average = 0.4 mm day�����) were similar in surf zones and estuaries. At one surf zone, juvenile catch was positively correlated to short-term specific growth rates (14 days prior to capture). A bioenergetics modeling approach indicated that given current conditions, consumption rates accounted for more of the variation in growth than prey energetic content and temperature. Climate models predict future increases in fresh water temperature (1.5 to 5.8��C), sea surface temperature (1.2��C) and wave height (0.75 m) that could influence estuarine and surf zone use. Therefore, I developed a local mixing model based on these predictions to estimate future surf zone and estuarine water temperatures in two of the watersheds studied. Based on these temperature projections and the bioenergetics model, I predicted how juvenile specific growth rates would vary in both habitats. I determined that increases in water temperature in both habitats would reduce specific growth rates by 9 to 40% in surf zones and estuaries if diet composition and consumption rates remain similar to present conditions. To compensate for the decline in growth, juveniles may increase their consumption rates or consume more energetically rich prey, if available. If they are not able to compensate, their size at the end of the season may be reduced, which could reduce their overall survival. These results confirm that a small number of suyearling Chinook salmon use sandy beach surf zones, mostly adjacent to estuary mouths, where they experience growth conditions comparable to estuaries. My findings indicate that, in certain situations, juvenile Chinook salmon surf zone use can be influenced by surf zone growth conditions, while variation in growth rates are themselves most strongly influenced by variation in consumption rates in surf zones and estuaries. Predicted changes in coastal western North American climate will likely modify juvenile growth conditions in the next 50 years, and potentially reduce overall survival. Additional insights into the potential impacts of climate change on juvenile salmon will require estimates of changes in the composition, energetic quality and abundance of prey communities inhabiting coastal environments. / Graduation date: 2013