As public awareness of river degradation has grown in recent years, the number of stream restoration activities has increased dramatically. Anthropogenic influences at a range of spatial scales from watershed landuse to riparian vegetation management to local channel morphology can have hierarchical relationships to local (meso- and macro-) in-stream habitat characteristics. This research examined these influences first by examining the influence of complex channel morphology on meso-scale brook trout (Salvelinus fontinalis) habitat in Shenandoah National Park, VA, and then by examining the combined influence of watershed urbanization and riparian vegetation (100-200 m reaches) on stream temperature. Moving beyond one-dimensional (1D) averaged representations of fish habitat, this research explored the distribution of two-dimensional (2D) flow complexity metrics at the meso-habitat scale as explanatory variables for brook trout habitat preferences and as potential metrics to evaluate habitat restoration design. Spatial hydraulic complexity metrics, including area-weighted circulation and kinetic energy gradients, were calculated based on 2D depth averaged modeled velocity distributions in two 100-m reaches on the Staunton River. While there were no statistically significant correlations between kinetic energy gradients or area-weighted circulation and fish density, fish density was positively correlated to the percent of the channel dominated by protruding boulders. The structural complexity of areas with protruding boulders create complex flow patterns suggesting that flow complexity plays an important role in available brook trout habitat preferences at the local scale, although the 2D depth averaged model may not have adequately represented this complexity. The 2D distribution of flow characteristics was then investigated further to quantify areas of flow refugia (low velocity shelters) and the relationship between these areas, traditional measures of habitat quality, and fish biomass. Flow complexity in the vicinity of flow obstructions (in this case, boulders) was investigated further using patch classification and landscape ecology metrics. The relative influence of riparian vegetation on stream temperature (another important habitat characteristic) in urban and nonurban watersheds was investigated in 27 paired forested and nonforested reaches in PA, MD, and DE. Riparian vegetation and watershed-scale urbanization both influence stream temperature, which can have profound impacts on in-stream ecosystems. Generally, increased urbanization and removal of riparian forest influenced maximum stream temperatures resulting in higher maximum summer stream temperatures (up to 1.8°C); however, the influence of riparian forests (at at 100-200 m reach scale) decreased with increasing urbanization. Extreme maximum summer temperatures, which are a concern for aquatic biota, increased in both frequency and duration in urban nonforested reaches relative to forested reaches indicating that the addition of a forested 100-200 m long buffer partially mitigated these temperature extremes even in urban watersheds. Overall, changes to channel morphology and riparian vegetation had measurable local effects on stream habitat (temperature and hydraulic complexity) yet the implications of restoration efforts at the local scale on ecosystem services at a larger (km +) scale requires further study. / Ph. D.

In the United States, the annual cost of on-site soil erosion problems such as soil and nutrient losses, and off-site soil erosion problems such as sedimentation of lakes and river, loss of navigable waterways, flooding and water quality impairment, has been estimated at 44 billion USD (Pimentel, 1995; Telles, 2011). While eroding sediment sources can either be from land or from stream/river systems, the erosion from streambanks can be quite significant, reaching up to 80% of sediment leaving a watershed (Simon et al 2002; Simon and Rinaldi 2006). Despite many decades of research one the erosion of cohesive soils by flowing water (fluvial erosion), this significant aspect of environmental sustainability and engineering is still poorly understood. While past studies have given invaluable insight into fluvial erosion, this process is still poorly understood. Therefore, the objective of this dissertation was to examine the relationship between time and erosion resistance of remolded cohesive soils, and to quantify and model the effects soil and water temperature on the fluvial erosion of cohesive soils First, erosion tests were performed to investigate how soil erosion resistance develops over time using three natural soils and testing in a laboratory water channel. Results showed that the erosion rate of the soils decreased significantly over the time since the soils were wetted. This study indicates researchers need to report their sample preparation methods in detail, including the time between sample wetting and sample testing. Second, erosion tests were performed at multiple soil and water temperatures. Results showed that increases in water temperature led to increased erosion rates while increases in soil temperature resulted in decreased erosion rate. When soil and water temperatures were equal, erosion results were not significantly different. Results also showed a linear relationship between erosion rate and the difference between soil and water temperatures, indicating erosion resistance decreased as heat energy was added to the soil. Lastly, two common erosion models (the excess shear stress and the Wilson models) were evaluated, and were modified to account for soil and water temperature effects. Results showed that, compared to the original models, the modified models were better in predicting erosion rates. However, significant error between model predictions and measured erosion rates still existed. Overall, these results improve the current state of knowledge of how erosion resistance of remolded cohesive soils evolves with time, showing the importance of this factor in the design of cohesive erosion experiments. Also, the results show that by accounting for thermal effects on erosion rate, the usability of erosion models can be improved in their use for erosion predictions in soil and water conservation and engineering practice. / PHD / In the United States, the annual cost of on-site soil erosion problems such as soil and nutrient losses, and off-site soil erosion problems such as sedimentation of lakes and river, loss of navigable waterways, flooding and water quality impairment, has been estimated at 44 billion USD (Pimentel, 1995; Telles, 2011). While eroding sediment sources can either be from land or from stream/river systems, the erosion from streambanks can be quite significant, reaching up to 80% of sediment leaving a watershed (Simon et al 2002; Simon and Rinaldi 2006). Despite many decades of research one the erosion of cohesive soils by flowing water (fluvial erosion), this significant aspect of environmental sustainability and engineering is still poorly understood. While past studies have given invaluable insight into fluvial erosion, this process is still poorly understood. Therefore, the objective of this dissertation was to examine the relationship between time and erosion resistance of remolded cohesive soils, and to quantify and model the effects soil and water temperature on the fluvial erosion of cohesive soils First, erosion tests were performed to investigate how soil erosion resistance develops over time using three natural soils and testing in a laboratory water channel. Results showed that the erosion rate of the soils decreased significantly over the time since the soils were wetted. This study indicates researchers need to report their sample preparation methods in detail, including the time between sample wetting and sample testing. Second, erosion tests were performed at multiple soil and water temperatures. Results showed that increases in water temperature led to increased erosion rates while increases in soil vi temperature resulted in decreased erosion rate. When soil and water temperatures were equal, erosion results were not significantly different. Results also showed a linear relationship between erosion rate and the difference between soil and water temperatures, indicating erosion resistance decreased as heat energy was added to the soil. Lastly, two common erosion models (the excess shear stress and the Wilson models) were evaluated, and were modified to account for soil and water temperature effects. Results showed that, compared to the original models, the modified models were better in predicting erosion rates. However, significant error between model predictions and measured erosion rates still existed. Overall, these results improve the current state of knowledge of how erosion resistance of remolded cohesive soils evolves with time, showing the importance of this factor in the design of cohesive erosion experiments. Also, the results show that by accounting for thermal effects on erosion rate, the usability of erosion models can be improved in their use for erosion predictions in soil and water conservation and engineering practice.

The SNTEMP (U.S. Fish and Wildlife Service), QUAL2E (U.S. Environmental Protection Agency), and RQUAL (Tennessee Valley Authority) stream temperature prediction models were evaluated. All models had high predictive ability with the majority of predictions, >80% for Back Creek (Roanoke County, VA) and >90% for the Smith River tailwater (SRT) (Patrick County, VA), within 3°C of the measured water temperature. Sensitivity of model input parameters was found to differ between model, stream system, and season. The most sensitive of assessed parameters, dependent on model and stream, were lateral inflow, starting-water, air, and wet-bulb temperature. All three models predicted well, therefore, selecting a model to assess alternative water management scenarios was based on model capabilities. The RQUAL model, used to predict SRT temperatures under alternative hydropower release regimes, illustrated potential thermal habitat improvement for brown trout (Salmo trutta) compared to existing conditions. A 7-day/week morning 1 hr release was determined to best concurrently increase occurrence of brown trout optimal growth temperatures (+10.2% mean), decrease 21°C (state standard) exceedances (99% prevention), and decrease hourly changes in temperature (-1.6°C mean) compared to existing thermal conditions. The SNTEMP model was used to assess thermal habitat under flow, shade, and channel width changes occurring from future urbanization within the Back Creek watershed. Predictions reveal that additional urban development could limit thermal habitat for present fish species by elevating summer mean daily temperature up to 1°C and cause 31°C (state standard) exceedances compared to existing conditions. Temperature impacts were lessened by single rather than cumulative changes suggesting mitigation measures may maintain suitable thermal habitat. / Master of Science

Water temperature in rivers and streams is an important factor for aquatic ecosystem health. Measurement of stream temperature has traditionally been accomplished by point temperature measurements, continuous point temperature loggers, and more recently, airborne remote sensing techniques such as Forward-Looking Infrared Radar (FLIR) or Thermal Infrared Radiometry. While each of these measurement techniques has certain advantages, none allows for the combined spatial and temporal information provided by Distributed Temperature Sensing (DTS). DTS employs fiber optic signals to measure temperature and is a relatively new temperature measurement technology for hydrologic sensing applications. Nine DTS stream temperature datasets were collected in the Middle Fork John Day River (MFJDR) as part of a basin-wide stream monitoring effort. The datasets encompassed five 1-3 kilometer long reaches, some monitored over three summers (2009-2011). In contrast to existing stream temperature measurement technologies, DTS can provide stream temperature data in both the spatial and temporal domains. Techniques and challenges of interpreting DTS stream temperature data were documented, and three applications of the technology to stream temperature monitoring were explored. Cold water patches, potentially used by fish as thermal refugia during stream temperature maximums, were located using DTS. No identified cold patch exceeded 2.31°C cooler than ambient stream temperature. Tributary inflows provided some of the most temperature-differentiated cold patches. These findings provide a reference for the degree of thermal heterogeneity in the MFJDR system and beg the question of whether fish respond to small (<3°C) spatial temperature variations. Theoretical predictions of stream mixing potential (Richardson number and cavity flow mixing predictions) suggested that increasing stream thermal heterogeneity would require channel modification to decrease stream flow velocity in select areas. The combined spatial and temporal coverage of a DTS stream temperature dataset on the Oxbow Conservation Area allowed diagnosis of a 2°C longitudinal stream temperature decrease observed in multiple Thermal Infrared Radiometry (TIR) and Forward-Looking Infrared Radiometry (FLIR) datasets collected on that reach. Advection velocity and channel depth, rather than groundwater or tributary inflows, were the main cause of the decrease, and the magnitude of the decrease peaked in the early afternoon, disappearing completely by evening. This finding suggests caution for interpretation of FLIR and TIR stream temperature datasets, which represent "snapshot" temperature measurements. For these datasets, knowledge of flow conditions (velocity and depth) may help avoid misinterpretation of temporally-transient temperature anomalies. Diurnal slope periodicity was observed in linear-like spatial trends in four DTS datasets, and an analysis was made to examine this subtle spatially and temporally varying phenomenon. The phase of the diurnal slope variation differed between river reaches, suggesting that propagation of larger-scale thermal waves might be one driving mechanism. Temporally-constant offsets between slope magnitudes within reaches suggested some intra-reach differences in heat fluxes. / Graduation date: 2012

Les espèces de poissons migrateurs (saumon atlantique, Salmo salar, en particulier) requièrent des conditions thermiques bien spécifiques. Ils sont très sensibles aux températures de l’eau et aux fortes variations estivales. Sur les trente dernières années, l’étude menée sur la Garonne (France) révèle une augmentation des températures estivales associée à un allongement de la durée des périodes chaudes. L’impact de cette modification du régime thermique sur la survie et la reproduction des espèces migratoires est également mis en évidence. Cette étude est menée sur un tronçon de Garonne, situé entre l’amont de Toulouse et l’amont de la retenue deMalause. Ce secteur est fortement touché par cette problématique avec en moyenne 2°C d’écart entre l’amont et l’aval et des températures supérieures à 25°C régulièrement atteintes. Le régime hydrologique de ce tronçon est fortement déficitaire (selon le SDAGE Adour-Garonne), la sensibilité au flux de surface est forte à cause de son lit large et peu profond, les pressions anthropiques sont importantes, ce sont autant de pistes dont l’impact sur le régime thermique est étudié. Une large collection de données hydrologiques et climatiques est exploitée afin de déterminer les processus en jeu dans l’évolution du régime thermique de ce tronçon de fleuve. Des études en tendances et corrélations et des modèles statistiques permettent de mettre en évidence d’une part la relation forte qui existe entre les températures de l’air et les températures de l’eau et d’autre part l’importance des faibles débits durant les périodes estivales. L’estimation des moyennes journalières de température de l’eau à Malause au moyen de modèles statistiques et déterministes donne de bons résultats pour les températures élevées ainsi que pour les franchissements de seuils liés aux conditions de migrations des amphilalins.Enfin un modèle numérique monodimensionnel de résolution de l’équation de transport thermique et des équations de St-Venant est développé. La physique du modèle tant au niveau hydraulique (prise en compte de fortes variabilités de pente, d’ouvrages, etc.) que thermique (apports latéraux, flux de surfaces, flux de conduction avec le lit) permet d’analyser l’évolution des différents flux qui participent au réchauffement du cours d’eau. Une évolution future à l’aide des sorties des modèles de l’IPCC est explorée et des méthodes éventuelles de restauration des conditions de températures favorables pour les espèces piscicoles sont analysées. / Fish species with strong thermal requirements (i.e. Atlantic salmon) are very sensitive to temperature evolution and particularly to large increases. An investigation conducted on the Garonne River (France) during the last three decades revealed global water warming along with an increase of the high temperature period duration. Large impact of this evolution on the survival and breeding of migrating fish species was also reported. Study was thus conducted on a specific reach of the Garonne River located between the immediate upstream of Toulouse and the upstream of the Malause dam. The issue of water temperature warming is particularly relevant on this reach, with an average increase of 2°C between upstream and downstream and temperatures above 25°C frequently reported. Potential causes are numerous: drastic low-flow regime (quoting SDAGE Adour-Garonne), impacts of surface fluxes that are important due to bed shape (wide and shallow), anthropogenic impacts, etc. Large amount of climatic and hydraulic data are used to make a clear determination of the processes involved in the thermal regime evolution of this reach. Trend and correlation analyses and use of statistical models indicate the strong relation between stream temperature and climate. Low flows also seem to be related to water temperatures during summer periods. Statistic and deterministic models give good results in estimating high daily mean water temperatures (RMSE ranging from 0.99°C to 1.22°C) and predicting water temperatures threshold crossings related to the migrating conditions of Atlantic salmon.Finally, a one-dimensional numerical model that solves both shallow water and thermal equations is developed. Both the formulation of the St-Venant equations (high variability in slope, gates …) and the phenomena taken into account in the water temperature model (lateral influx, surface fluxes, bed conduction …) allows studying the evolution of fluxes driving water temperature evolution. Future evolution of the water temperature at the 2050 horizon is also evaluated using IPCC models output and potential solutions to restore favorable stream temperatures conditions for fishes are analyzed.

Human impacts from land and water development have degraded water quality and altered the physical, chemical, and biological integrity of Nevada's Walker River. Reduced instream flows and increased nutrient concentrations affect native fish populations through warm daily stream temperatures and low nightly dissolved oxygen concentrations. Environmental water purchases are being considered to maintain instream flows, improve water quality, and enhance habitat for native fish species, such as Lahontan cutthroat trout. This study uses the River Modeling System (RMSv4), an hourly, physically-based hydrodynamic and water quality model, to estimate streamflows, temperatures, and dissolved oxygen concentrations in the Walker River. Stream temperature and dissolved oxygen changes were simulated from potential environmental water purchases to prioritize the time periods and locations that water purchases most enhance stream temperatures and dissolved oxygen concentrations for aquatic habitat. Environmental water purchases ranged from 0.03 cms to 1.41 cms average daily increases. Modeling results indicate that increased water purchases generally affect dissolved oxygen in two ways. First, environmental water purchases increase the thermal mass of the river, cooling daily stream temperatures and warming nightly temperatures. This prevents conditions that cause the lowest nightly dissolved oxygen concentrations (moderate production impairment thresholds are

The intensive nature of land uses in the Strzelecki Ranges poses significant threats to landscape values and water quality. A comprehensive catchment strategy was developed based on sustainability science concepts incorporating the careful management of landscape values, proper land management approaches, and government policy and legislative change to ensure that agriculture, forestry and other land uses become sustainable in this sensitive environment. The readily measurable water quality indicators of turbidity, flow, electrical conductivity, and water temperature were used to determine the impacts of the major land uses in the Strzeleckis. From a water quality perspective, there was a trend of decreasing water quality with increasing intensity in land management. However, from a total sediment load perspective, the forest area contributed the highest total sediment load due to higher volumes of steam flow suggesting that natural processes in the Strzeleckis may remain the principal mechanisms for sediment movement within the catchment. An incidental but significant finding was extensive bioturbation along the riparian zone of the plantation area, the extent of which was not observed in the other catchments. This finding suggested that bioturbation may have been the most significant contributor to poorer water quality flowing from in the plantation catchment. The project developed insights into the major environmental processes active in the upper catchment of the Morwell River. Understanding of the contributions to total sediment loads from natural erosional processes and bioturbation, findings related to the impacts on water quality from agricultural practices, and encountering negligible impacts from conservative timber harvesting practices demonstrate that catchment management approaches need to be tailored to achieve sustainability in land uses across the landscape. Key recommendations include the re-establishment and protection of riparian zones in agricultural catchments, the careful assessment and setting of stream buffer zone widths for timber harvesting operations, and the need for further work to map the extent of natural processes such as bioturbation and stream bank erosion. To mitigate these issues, government policy and legislation will need to focus on the preservation and enhancement of the Crown land riparian zones. Recommended changes to current administrative land management arrangements for these sensitive areas include a move from licensing riparian zones for agricultural practices such as grazing to conservation.

Exotic species alter the streamside plant community by changing the resources available to the stream food web, causing cascading changes throughout the entire aquatic ecosystem. To better understand the impacts of exotic litter species on stream communities, investigations were made at global and local levels. A meta-analysis was performed to understand which environmental and litter quality factors impact native and exotic litter decay rates on the global scale. It was found that exotic species are likely to decay faster than native species at larger mesh sizes, and in warm temperature environments because high quality exotic leaves have a lower C:N ratio than native leaves. An urban litter decay experiment in Victoria, B.C. streams contrasting Alnus rubra, Salix sitchensis, Hedera sp., Rubus armeniacus and plastic trash found that trash decays more slowly than leaf litter, but leaf species all decay at the same rate, and stream invertebrates colonize all litter types equally. Significant differences in litter decay rates and invertebrate community alpha and Shannon diversities were also observed across the four different streams. The more that is learned about the impacts of exotic leaf litter, the better we are able to respond to keep streams as healthy and as biodiverse as possible. / Graduate / 2017-08-10 / 0329 / 0793 / kimkenn@uvic.ca

Cette étude correspond au développement de deux approches de modélisation à base physique basées sur le concept de température d’équilibre pour simuler la température des cours d’eau à l’échelle du bassin de la Loire (105 km²). La performance de ces deux approches de modélisation est analysée via des chroniques horaires issues du réseau national thermique associé aux cours d’eau (RNT), mis en place par l’ONEMA en 2008. Une première partie est consacrée à l’étude de l’approche de modélisation stationnelle qui résout un bilan énergétique à l’échelle de la station. Cette approche a été testée selon une discrétisation simplifiée par ordre de Strahler puis selon une discrétisation à l’échelle du tronçon hydrographique. Elles simulent avec une très bonne précision la température horaire et journalière pour les grands cours d’eau où l’influence des conditions aux limites amont devient limitée. Une seconde approche dite « par propagation » basée sur une topologie de réseau est développée dans le but d’intégrer, à haute résolution spatiale et temporelle la propagation du signal thermique de l’amont vers l’aval des cours d’eau à une échelle régionale ce qui améliore la performance sur les cours d’eau situés en amont et de bien restituer la dynamique des profils thermiques longitudinaux des grands cours d’eau. / This work corresponds to the development of two physically based modeling approaches based on the equilibrium temperature concept to simulate the stream temperature at the Loire basin scale (105 km²). The performances of these two approaches are analyzed with hourly temperatures provided by the national thermal network associated with rivers (RNT), set up by the ONEMA in 2008. A first part focuses on the study of the 0D approach which solves the heat budget at the local scale. This approach has been tested with a simplified discretization by Strahler order and then with a discretization at the hydrographical reach scale. They simulated accurately hourly and daily temperatures for large rivers where the upstream influence becomes limited. The second part focuses on the approach by propagation based on a network topology in order to integrate the upstream-downstream propagation of the thermal signal with high spatial and temporal resolution at a regional scale which improves performances of rivers located near headwaters and to well reproduces the dynamics of longitudinal thermal profiles for large rivers.

The Middle Fork John Day Basin in Northeastern Oregon is prime habitat for spring Chinook salmon and Steelhead trout. In 2008, a major tributary supporting rearing habitat, Big Boulder Creek, was restored to its historic mid-valley channel along a 1 km stretch of stream 800 m upstream of the mouth. Reduction of peak summer stream temperatures was among the goals of the restoration. Using Distributed Temperature Sensing (DTS) Fiber Optic Technology, stream temperature was monitored prior to restoration in June 2008, and after restoration in September 2008, July 2009, and August 2009. Data gathered was used to determine locations of groundwater and hyporheic inflow and to form a stream temperature model of the system. The model was used both to develop an evaluation method to interpret components of model performance, and to better understand the physical processes important to the study reach. A very clear decreasing trend in surface temperature was seen throughout each of the DTS stream temperature datasets in the downstream 500 m of the study reach. Observed reduction in temperature was 0.5°C (±0.10) in June 2008, 0.3°C (±0.37) in September 2008, 0.6°C (±0.25) in July 2009, and 0.2°C (±0.08) in August 2009. Groundwater inflow was calculated to be 3% of the streamflow for July 2009 and 1% during the August 2009 installation. Statistically significant locations of groundwater and hyporheic inflow were also determined. July 2009 data was used to model stream temperature of the 1 km (RMSE 0.28°C). The developed model performance evaluation method measures timelag, offset, and amplitude at a downstream observed or simulated point compared with the boundary condition, rather than evaluating the model based on error. These measures are particularly relevant to small scale models in which error may not be a true reflection of the ability of a model to correctly predict temperature. Breaking down model performance into these three predictive measures was a simple and graphic method to show the model's predictive capability without sorting through large amounts of data. To better understand the model and the stream system, a sensitivity analysis was conducted showing high sensitivity to streamflow, air temperature, groundwater inflow, and relative humidity. Somewhat surprisingly, solar radiation was among the lowest sensitivity. Furthermore, three model scenarios were run: a 25% reduction in water velocity, a 5°C increase in air temperature, and no groundwater inflow. Simulations of removal of groundwater inflows resulted in a 0.5°C increase in average temperature over the modeled time period at the downstream end, further illustrating the importance of groundwater in this stream system to reduce temperatures. / Graduation date: 2012