Thesis advisor: Noah P. Snyder / Substrate size and mobility are important to Atlantic salmon (Salmo salar) spawning and rearing success. Channel geometry is a control on bedload mobility in streams. It is believed that channel morphology in many Maine rivers has been altered by land use practices, creating wider and shallower channels, and lowering stream competence. If correct, these changes may be partially responsible for the limited number of returning salmon currently observed in Maine coastal rivers. To evaluate the magnitude of these changes, I performed a statistical comparison of channel morphology between two Atlantic coastal streams: the Narraguagus River in Downeast Maine and the Jacquet River in northern New Brunswick, Canada. Compared to the Narraguagus River, the Jacquet River has relatively healthy returns of adult salmon. Both watersheds have similar drainage areas (Narraguagus 588 km²; Jacquet 510 km²;) and mean annual precipitation (1244 mm; 1200 mm), but differing average channel gradients (0.16%; 0.51%) and longitudinal profiles. During the summer of 2007, I surveyed a 13.6-km section of the Narraguagus with a drainage area range of 129-247 km², and a 10.4-km section of the Jacquet with a drainage area range of 94-265 km². I made measurements of active and bankfull width and depth, and channel gradient at 100-m intervals, and performed grain-size counts at 200-m intervals. I also measured gradient and width in a GIS-based analysis. Results of my analysis show that channel gradient is likely the most influential factor on Atlantic salmon habitat as it relates to sediment size. The two rivers exhibit no significant difference in width-to-depth ratio, when low-gradient outliers in the Narraguagus River are removed. Predicted median riverbed grain sizes were calculated using two methods: (1) from the empirical relationship between basal shear stress and measured grain size; and (2) using the Shields parameter and remote sensing data only. Measured and predicted grain sizes reveal finer river-bed sediments on the Narraguagus River, however, Shields parameter calculations show that sediment should be mobile in both streams. I compare these predictions to field-based habitat mapping on the Narraguagus River. Based on predicted grain sizes, I expect nearly continuous Atlantic salmon spawning (28-95%) and rearing (95-100%) habitat on the Jacquet, and much less spawning (47-62%) and rearing (57-68%) habitat on the Narraguagus. This is likely because the Narraguagus River is segmented into reaches of steeper gradient (S < 0.002) with potentially good habitat, and flatter reaches (S < 0.0005) of poor habitat. The long flat reaches (several km) likely act as sediment sinks, preventing the continuity of downstream sediment transport and causing sediment to be sourced from localized glacial deposits. / Thesis (MS) — Boston College, 2009. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Geology and Geophysics.

The spawning habitat associated with fall chinook salmon (Oncorhynchus tshawytscha) redd clusters was investigated in the Hanford Reach of the Columbia River. A conceptual spawning habitat model is proposed that describes how geomorphic features of river channels create hydraulic processes, including hyporheic flows, that influence where salmon spawn in unconstrained reaches of large mainstem alluvial rivers. Spatial point pattern analysis of redds showed that redd clusters averaged approximately 10 hectares in area and their locations were consistent from year to year. The tendency to spawn in clusters suggests fall chinook salmon's use of spawning habitat is highly selective. Hydraulic characteristics of the redd clusters were significantly different than the habitat surrounding them. Velocity and lateral slope of the river bottom were the most important habitat variables in predicting redd site selection. While these variables explained a large proportion of the variance in redd site selection (86 to 96%), some unmeasured factors still accounted for a small percentage of actual spawning site selection. Further investigation showed that the magnitude and chemical characteristics of hyporheic discharge were different between and within two spawning areas. Apparently, fall chinook salmon used chemical and physical cues from the discharge to locate spawning areas. Traditional spawning habitat models could be improved if they: used spawning area-specific, rather than river-specific; spawning characteristics; incorporated hyporheic discharge measurements; and gave further consideration to the geomorphic features that are present in the unconstrained segments of large alluvial rivers. Ultimately the recovery of endangered fall chinook salmon will depend on how well we are able to recreate the characteristics once common in alluvial floodplains of large rivers. The results from this research can be used to better define the relationship between these physical habitat characteristics and fall chinook salmon spawning site selection, and provide more efficient use of limited recovery resources. / Graduation date: 1999

I examined habitat electivity and movement patterns of adult spring chinook salmon at microhabitat and channel unit spatial scales, and seasonal to annual temporal scales in seven streams in the Grande Ronde, John Day, and Imnaha basins. The objective was to compare habitat use and availability among streams, channel units, and microhabitats, and to assess chinook salmon fidelity to those habitats using radio-telemetry. The analyses showed that habitat quality and availability in the seven study streams varied. Each stream posed different physical constraints on adult chinook salmon habitat; this was reflected by the differential use of habitat by salmon among streams. Salmon elected pools almost exclusively in the John Day Basin, whereas pools and riffles were elected in near equal proportion in the Grande Ronde and Inmaha basins. Within streams, use was similar between years. Almost all salmon were observed in association with cover, but the type of cover largely reflected availablity. Chinook salmon elected the deepest depths within channel units (microhabitat scale), but not necessarily the deepest channel units among streams (channel unit scale). Chinook salmon did not elect cooler stream temperatures within channel units in any study stream, except the Middle Fork John Day River. Radio-tagged chinook showed a high fidelity to habitats, except when stream temperatures approached lethal limits. Due to stream specific differences in habitat availability and use, multiscale habitat assessments for individual streams are recommended to increase the success of watershed restoration activities. / Graduation date: 1999

Thesis (M. Sc.)--Acadia University, 1999. / Includes bibliographical references (leaves 143-150). Also available on the Internet via the World Wide Web.

Thesis (M. Sc.)--Acadia University, 1999. / Includes bibliographical references (leaves 143-150). Also available on the Internet via the World Wide Web.

The macro-algae Nereocystis luetkeana or bull kelp is an important canopy-forming species in the rocky nearshore ecosystems of the Salish Sea. It provides structural habitat for many fish and invertebrates including juvenile salmon. In the Pacific Northwest, major declines in Chinook and Coho salmon populations have led to increased scientific efforts to determine the causes behind these losses. High mortality of juvenile salmon during their first months in the marine environment may be linked to loss of habitat such as kelp beds, which can provide shelter, concentration of prey and energetically favorable conditions. This work seeks to understand the role of kelp habitat in the early marine growth period of juvenile salmon. Initially, methods using satellite imagery were developed for mapping the location of kelp beds adjacent to a salmon bearing river in Cowichan Bay, on the West Coast of British Columbia. These methods were then applied to a time series of imagery from 2004 to 2017, to determine how kelp beds are changing over time and the possible drivers of those changes. The results found spatial and temporal variability in kelp beds with a decline from a high in 2015 to the lowest levels in 2017. The observed changes were over a short period considering the natural variability of Nereocystis and continued long term monitoring will help to determine if the declines are permanent. Spatial and temporal variability were found to relate to substrate type, current strengths and potential lag effects of declines due to warmer than average sea surface temperatures. Lastly, the maps created through satellite-based methods served to inform surveys investigating the importance of kelp habitat to the declining populations of Chinook and Coho salmon. To address this, remote underwater video and visual snorkel surveys were used to determine the presence and absence of juvenile salmon in paired kelp and no-kelp sites throughout the season when the fish are known to be present in the region. Higher densities of juvenile salmon were detected in kelp-associated areas; however, this effect was detected both before kelp growth in early spring and during kelp presence. Transects conducted on the inner edge of kelp beds, adjacent to rocky shorelines were determined to have the highest salmon densities indicating that physical factors such as substrate type and wave energy associated with these areas may be preferential to juvenile salmon. / Graduate

Hydropower production has advantages but also negative ecological consequences. Thisstudy analyzes the degree of flow variations downstream Viforsen's power plant to investigate how well the regulated flow is re-regulated towards a more natural flow pattern. The studyalso examine effects of the regulation on valuable salmon habitats in the section from Viforsen's power plant down to the sea and whether there is a downstream gradient in the presence of different fish species. Data on water level changes was obtained by installingthree pressure loggers in a gradient downstream of the Viforsen power plant. Collection of hourly flow-data in Viforsen and Vindelälven have been part of the data in the survey. The presence of different species of fish was determined by examination of the Swedish electrofishing registry. Results showed a strong correlation between flow and water level at all three sites in Ljungan and there is no ecologically significant dampening of water level fluctuations downstream Viforsen. The current requirement for a minimum discharge of 30 m3/s is too low as important salmon habitats risk being drained. The strong correlation between water levels and flow that this study shows make it possible to map in more detail the risks of valuable salmon habitats drying up. The results also showed that typically marine species” of fish are much more common in Viforsen than in Vindelälven. This study emphasizes that ecologically sustainable flows are complex and relevant field investigations at each watercourse are necessary when reconsidering and designing the new environmental conditions.

Habitats for juvenile chinook salmon (Oncorhynchus tshawytscha) were observed at a high flow during the spring of 1989 and at a low flow during the spring of 1991 in the lower American River of California. Parameters of microhabitats in eight macrohabitats were measured. Mean column water velocity and total water depth variables were used to statistically compare juvenile chinook salmon microhabitat distributions between and among macrohabitat type/reach and flow combinations. Using mean column water velocity and total water depth as independent variables, each macrohabitat type/reach appeared to be unique. Mean column water velocity seemed to be a better descriptor of juvenile chinook salmon habitat selection than was total water depth. Riffles appeared to be the preferred macrohabitats for large non-schooling chinook salmon at both flow levels. Root wads, woody debris, and submerged terrestrial vegetation were utilized extensively and provided a significant cover for schooling chinook salmon during the high flow period. Habitat utilization by chinook salmon appears to be influenced by nonhydraulic variables. Application of models in current instream flow studies need to include factors such as water temperature and aquatic insect production. / Graduation date: 1993

Lateral instability exerts considerable influence on the sedimentology, planform, and hydraulic characteristics of gravel-bed rivers. Because Atlantic salmon (Salmo salar) tolerate a narrow range of depths, velocities and substrate sizes, the quality and quantity of habitat available to salmon should vary with level of river instability. In the Riviere Nouvelle, a Gaspe river destabilized by deforestation and past channelization projects, the effect of lateral instability on habitat was variable. Fines content in riffle substrates did not show a significant relationship to local bank erosion rates, even where the rate was as high as 10 myr$ sp{-1}$ and the proportion of fines entering the channel was much higher than that found in riffles substrates (an excess of fines in potential spawning riffles reduces spawning success among salmonids). For juveniles, availability of hydraulically suitable habitat was largest where lateral instability resulted in aggradation of the river bed and development of a braided pattern. Hydraulic habitat availability was lowest where erosion patterns led to high planform curvature levels and to scouring of bed materials. In general, because of the relatively high power of the Riviere Nouvelle, structures or processes leading to diminishment of depths or velocities (e.g. aggradation) resulted in an increase in the amount of juvenile habitat available.

Although the watersheds of the Petite Cascapedia and Bonaventure Rivers, Gaspe Peninsula, have broadly similar geology and land use, their segment-scale river geomorphology is contrasted by subtle differences in valley characteristics that are a legacy of their individual geomorphic histories. These differences have consequences on the distribution of Atlantic salmon habitat such as boulder abundance (for parr rearing and overwintering habitats) and spawning substrate quality. Parr preference for boulder-rich river segments (1--5 km) was observed in the Bonaventure River. In the study systems redd distribution was sensitive to relatively small changes in the fines content of riffle substrate. River segments flowing through moderately narrow semi-alluvial valleys present better overall parr habitat (high boulder abundance) and better spawning substrate quality (percentage of sand) than wider valley sections. These differences are due to additional sources of coarse sediment, higher shear stresses, and lower bank erosion rates in such valleys.