Stream flowline delineation from high-resolution digital elevation models (HRDEMs) can be problematic due to the fine representation of terrain features as well as anthropogenic drainage structures (e.g., bridges, culverts) within the grid surface. The anthropogenic drainage structures (ADS) may create digital dams while delineating stream flowlines from HRDEMs. The study assessed the effects of ADS locations, spatial resolution (ranged from 1m to 10m), depression processing methods, and flow direction algorithms (D8, D-Infinity, and MFD-md) on hydrologic connectivity through digital dams using HRDEMs in Nebraska. The assessment was conducted based on the offset distances between modeled stream flowlines and original ADS locations using kernel density estimation (KDE) and calculated frequency of ADS samples within offset distances. Three major depression processing techniques (i.e., depression filling, stream breaching, and stream burning) were considered for this study. Finally, an automated method, constrained burning was proposed for HRDEMs which utilizes ancillary datasets to create underneath stream crossings at possible ADS locations and perform DEM reconditioning. The results suggest that coarser resolution DEMs with depression filling and breaching can produce better hydrologic connectivity through ADS compared with finer resolution DEMs with different flow direction algorithms. It was also found that stream burning with known stream crossings at ADS locations outperformed depression filling and breaching techniques for HRDEMs in terms of hydrologic connectivity. The flow direction algorithms combining with depression filling and breaching techniques do not have significant effects on the hydrologic connectivity of modeled stream flowlines. However, for stream burning methods, D8 was found as the best performing flow direction algorithm in HRDEMs with statistical significance. The stream flowlines delineated using the proposed constrained burning method from the HRDEM was found better than depression filling and breaching techniques. This method has an overall accuracy of 78.82% in detecting possible ADS locations within the study area.

Floodplains, and the sediment accumulating naturally on them, are important to maintain stream water quality and serve as sinks for organic and inorganic carbon. Newer theories contend that land use and hydrologic connectivity (water-mediated transport of matter, energy, and/or organisms within or between elements of the hydrologic cycle) play important roles in determining sediment accumulation on floodplains. This study hypothesizes that changes in hydrologic connectivity have a greater impact on floodplain sediment accumulation than changes in land use. Nine sediment cores from seven sub-basins were collected from the Savannah River Site (SRS), South Carolina, and processed for grain-size, radionuclide dating (7Be, 137Cs, 210Pb), particulate organic carbon (POC), and microscopy. Historical records, including aerial and satellite imagery, were used to identify anthropogenic disturbances in the sub-basins, as well as to calculate the percentages of natural vegetation land cover at the SRS in 1951, and 2014. LiDAR and field survey data identified 251 flow impediments, measured elevation, and recorded standard stream characteristics (e.g., bank height) that can affect hydrologic connectivity. Radionuclide dating was used to calculate sediment mass accumulation rates (MARs) and linear accumulation rates (LARs) for each core. Results indicate that sedimentation rates have increased across all SRS sub-basins over the past 40-50 years, shortly after site restoration and recovery efforts began. Findings show that hydrologic connectivity proxies (i.e., stream characteristics and impediments) have stronger relationships to MARs and LARs than the land use proxy (i.e., vegetation cover), confirming the hypothesis. As stream channel depth and the number of impediments increase, floodplain sedimentation rates also increase. This knowledge can help future stream restoration efforts by focusing resources to more efficiently attain stated goals, particularly in terms of floodplain sediment retention.

For this dissertation I studied groundwater and surface water interactions in the Kenai Lowlands, Alaska. In particular, I examine two important aspects of groundwater and surface water interactions: 1) Groundwater's influence on surface-water temperature; and 2) Groundwater's role in forming hydrologic flow paths that can connect uplands to streamside wetlands and streams. Chapter 2 investigates the controls on stream temperature in salmon-bearing headwater streams in two common hydrogeologic settings: 1) drainage-ways, which are low-gradient streams that flow through broad valleys; and 2) discharge-slopes, which are high gradient streams that flow through narrow valleys. The results from chapter 2 showed significant differences in stream temperatures between the two hydrogeologic settings. Observed stream temperatures were higher in drainage-way sites than in discharge-slope sites, and showed strong correlations as a continuous function with the calculated topographic metric flow-weighted slope. Additionally, modeling results indicated that the potential for groundwater discharge to moderate stream temperature is not equal between the two hydrogeologic settings, with groundwater having a greater moderating effect on stream temperature at the low gradient drainage-way sites. Chapter 3 examines the influence of groundwater on juvenile coho salmon winter habitat along the Anchor River. Two backwater habitats were selected from the larger set of 25 coho overwintering sites from a previous study for an in-depth hydrologic analysis. The results from chapter 3 showed that the type of groundwater discharge (i.e., focused versus diffuse groundwater discharge) can play an important role in determining habitat suitability in these backwater sites. During winter, focused discharge from a local groundwater seep maintained higher surface-water temperatures and higher concentrations of dissolved oxygen compared to the site with more diffuse groundwater discharge. Chapter 4 investigates the linkages along hydrologic flow paths among alder (Alnus spp.) stands, streamside wetlands, and headwater streams. Chapter 4 tested four related hypotheses: 1) groundwater nitrate concentrations are greater along flow paths with alder compared to flow paths without alder; 2) on hillslopes with alder, groundwater nitrate concentrations are highest when alder stands are located near the streamside wetlands at the base of the hillslope; 3) primary production of streamside wetland vegetation is N limited and wetlands are less N limited when alder stands are located nearby along flow paths; and 4) stream reaches at the base of flow paths with alder have higher nitrate concentrations than reaches at the base of flow paths without alder. The results from chapter 4 showed that groundwater nitrate concentrations were highest along flow paths with alder, however no difference was observed between flow paths with alder located near versus alder located further from streamside wetlands. Vegetation had a greater response to N fertilization in streamside wetlands that were connected to flow paths without alder and less when alder stands were near. Finally, higher nitrate concentrations were measured in streams at the base of flow paths with alder. The combined results of this dissertation showed that, in the Kenai Lowlands, groundwater and surface water interactions have a direct influence on the local ecology and that a fundamental understanding of the hydrology can aid in the successful management and protection of this unique and important ecosystem.

How much groundwater flows to boreal streams depends on the relative contributions from each landscape unit (forested uplands, lakes, and peatlands) within a catchment along with its hydrogeologic setting. Although there is an understanding of the hydrologic processes that regulate groundwater outputs from individual landscape units to their underlying aquifers (both coarse- and fine-textured) in the boreal forest, less understood is how the topography, typology, and topology (i.e. hydrologic connectivity) of the landscape units regulates groundwater flow to streams. Improved understanding of groundwater-stream interactions in the Boreal Plain of Alberta and Saskatchewan is critical as this region is undergoing substantial environmental change from land cover disturbances for energy and forestry industries and climate change. This thesis determines groundwater-stream interactions during the autumn low-flow period in a 97 km2 glacial outwash sub-catchment of White Gull Creek Research Basin, Boreal Ecosystem Research and Modelling Site, Saskatchewan. The catchment (Pine Fen Creek) is comprised of a large (30 km2) valley-bottom peatland, two lakes, and jack pine (Pinus banksiana) uplands. The pine uplands are important areas of annual groundwater recharge for the catchment. Vertical hydraulic gradients (VHGs) show frequent flow reversals between the lakes and sand aquifer, and spatially diverse VHGs between the peatland and sand aquifer. Groundwater flow nets and lateral hydraulic gradients indicate the stream receives groundwater along its length. Isotopic samples of end members corroborate the hydrometric data. Catchment streamflow response during the 2011 low flow period was not simply the addition of net groundwater inputs from each landscape unit. Instead, the large size, valley-bottom position, and short water ‘memory’ of the peatland were the critical factors in regulation of catchment streamflow during low flow periods. Peatland hydrologic function alternated between a source and sink of runoff (surface and subsurface) to the stream, dependent on the position of the water table; a value of 0.15 m below peat surface was the critical functional tipping point. Given the high percentage of peatlands (21%) within the Boreal Plain, incorporating their runoff threshold is required in parameterizing runoff generation in hydrological models, and thus predicting impacts of peatland degradation and forest clearing on streamflow.

Restoring hydrologic connectivity between the channel and floodplain is a common practice in stream and river restoration. Floodplain hydrology and hydrogeology impact biogeochemical processing and potential nutrient removal, yet rigorous field evaluations of surface and groundwater flows during overbank floods are rare. We conducted five sets of experimental floods to mimic floodplain reconnection. Experimental floods entailed pumping stream water onto an existing floodplain swale, and were conducted throughout the year to capture seasonal variation. Each set of experimental floods entailed two replicate floods occurring on successive days to test the effect of varying antecedent moisture. Water levels and specific conductivity were measured in surface water, shallow soils, and deep soils, along with surface flow into and out of the floodplain. Total flood water storage increased as vegetation density increased and or antecedent moisture decreased. Hydrologic flow mechanisms were spatially and temporally heterogeneous in surface water, in groundwater, as well as in exchange between the two and appeared to coexist in small areas. Immediate propagation of hydrostatic pressure into deep soils was suggested at some locations. Preferential groundwater flow was suggested in locations where the pressure and electrical conductivity signals propagated too fast for bulk Darcy flow through porous media. Preferential flow was particularly obvious where the pressure signal bypassed an intermediate depth but was observed at a deeper depth. Bulk Darcy flow in combination with preferential flow was suggested at locations where the flood pressure and electrical conductivity signal propagated more slowly yet arrived too quickly to be described using Darcy's Law. Finally, other areas exhibited no transmission of pressure or conductivity signals, indicating a complete lack of groundwater flow. Antecedent moisture affected the flood pulse arrival time and in some cases vertical connectivity with deeper sediments while vegetation density altered surface water storage volume. Understanding the variety of exchange mechanisms and their spatial variability will help understand the observed variability of floodplain impacts on water quality, and ultimately improve the effectiveness of floodplain restoration in reducing excess nutrient in river basins. / Master of Science

<p dir="ltr">Excess nitrogen loading to surface waters and groundwater from intensive agriculture threatens human and ecosystem health and economic prosperity within and downstream of the Mississippi River Basin. Restoring wetlands and floodplains reduces nitrogen export, but nitrogen export from the Mississippi River Basin remains elevated. Engineering restored wetlands and floodplains to have higher areal denitrification rates is necessary to advance toward nitrogen reduction goals. Environmental controls of denitrification in restored ecosystems must be further investigated to determine under what conditions denitrification is highest and to link these optimal conditions to restoration approaches. Yet, restoration efforts to reduce nitrogen export may inadvertently increase phosphorus export and greenhouse gas emissions. We evaluated different restoration design approaches and identified environmental controls of denitrification, phosphorus release, and greenhouse gas production to advance knowledge of how floodplain and wetland restorations can be designed and managed to maximize denitrification while also constraining phosphorus release and greenhouse gas production. Comparisons of different restoration design approaches in the Wabash River Basin in Indiana, U.S.A., demonstrated that a hydrologically connected floodplain with row crop agriculture provides limited N treatment. Floodplain restorations that involved structural modifications to enhance hydrologic connectivity supported higher denitrification than restorations that only reestablished native vegetation. Investigations of the plot- and field-scale drivers of denitrification indicated that enhanced hydrologic connectivity and specific native wetland and prairie vegetation types were associated with soil conditions that supported high denitrification potential, mainly sufficient soil moisture and bioavailable organic matter. These same soil conditions were associated with increased risks of phosphorus release and greenhouse gas production. However, artificial flooding experiments showed that preventing prolonged flooding has a strong potential to reduce phosphorus export from floodplains with limited impacts on nitrogen treatment. Microcosm experiments with plant litter and wetland soils indicated that certain wetland vegetation types may reduce greenhouse gas production without sacrificing nitrogen removal capacity based on differences in plant biomass composition.</p>

This research investigated hydrologic connectivity, the intricate network of water pathways linking waterbodies, and its implications for biodiversity exchange in floodplains. Chapter 1 provides an exhaustive literature review encompassing factors influencing hydrologic connectivity, assessment approaches, scales, challenges, and management tools. Existing research often focuses on single scales and short-term periods, revealing a need for comprehensive multi-scale and extended temporal analyses. The absence of standardized definitions and methodologies in this field is also considered. Chapter 2 presents an innovative approach quantifying eight key connectivity metrics using remote sensing and GIS within the Lower Mississippi Alluvial Valley (LMAV). This adaptable method assesses connectivity between oxbow lakes and varying stream sizes, revealing spatial variability within the LMAV and enhancing scientific understanding of connectivity dynamics while ensuring portability. This research is crucial for effective ecosystem management and targeted conservation efforts, particularly regarding invasive species like the bigheaded carps (Hypophthalmichthys spp.).

Alors que certains mécanismes pourtant jugés cruciaux pour la transformation de la pluie en débit restent peu ou mal compris, le concept de connectivité hydrologique a récemment été proposé pour expliquer pourquoi certains processus sont déclenchés de manière épisodique en fonction des caractéristiques des événements de pluie et de la teneur en eau des sols avant l’événement. L’adoption de ce nouveau concept en hydrologie reste cependant difficile puisqu’il n’y a pas de consensus sur la définition de la connectivité, sa mesure, son intégration dans les modèles hydrologiques et son comportement lors des transferts d’échelles spatiales et temporelles. Le but de ce travail doctoral est donc de préciser la définition, la mesure, l’agrégation et la prédiction des processus liés à la connectivité hydrologique en s’attardant aux questions suivantes : 1) Quel cadre méthodologique adopter pour une étude sur la connectivité hydrologique ?, 2) Comment évaluer le degré de connectivité hydrologique des bassins versants à partir de données de terrain ?, et 3) Dans quelle mesure nos connaissances sur la connectivité hydrologique doivent-elles conduire à la modification des postulats de modélisation hydrologique ? Trois approches d’étude sont différenciées, soit i) une approche de type « boite noire », basée uniquement sur l’exploitation des données de pluie et de débits sans examiner le fonctionnement interne du bassin versant ; ii) une approche de type « boite grise » reposant sur l’étude de données géochimiques ponctuelles illustrant la dynamique interne du bassin versant ; et iii) une approche de type « boite blanche » axée sur l’analyse de patrons spatiaux exhaustifs de la topographie de surface, la topographie de subsurface et l’humidité du sol. Ces trois approches sont ensuite validées expérimentalement dans le bassin versant de l’Hermine (Basses Laurentides, Québec). Quatre types de réponses hydrologiques sont distingués en fonction de leur magnitude et de leur synchronisme, sachant que leur présence relative dépend des conditions antécédentes. Les forts débits enregistrés à l’exutoire du bassin versant sont associés à une contribution accrue de certaines sources de ruissellement, ce qui témoigne d’un lien hydraulique accru et donc d’un fort degré de connectivité hydrologique entre les sources concernées et le cours d’eau. Les aires saturées couvrant des superficies supérieures à 0,85 ha sont jugées critiques pour la genèse de forts débits de crue. La preuve est aussi faite que les propriétés statistiques des patrons d’humidité du sol en milieu forestier tempéré humide sont nettement différentes de celles observées en milieu de prairie tempéré sec, d’où la nécessité d’utiliser des méthodes de calcul différentes pour dériver des métriques spatiales de connectivité dans les deux types de milieux. Enfin, la double existence de sources contributives « linéaires » et « non linéaires » est mise en évidence à l’Hermine. Ces résultats suggèrent la révision de concepts qui sous-tendent l’élaboration et l’exécution des modèles hydrologiques. L’originalité de cette thèse est le fait même de son sujet. En effet, les objectifs de recherche poursuivis sont conformes à la théorie hydrologique renouvelée qui prône l’arrêt des études de particularismes de petite échelle au profit de l’examen des propriétés émergentes des bassins versants telles que la connectivité hydrologique. La contribution majeure de cette thèse consiste ainsi en la proposition d’une définition unifiée de la connectivité, d’un cadre méthodologique, d’approches de mesure sur le terrain, d’outils techniques et de pistes de solution pour la modélisation des systèmes hydrologiques. / As core processes of the transformation of rainfall into runoff are not fully understood, the concept of hydrologic connectivity has been put forward to explain why some processes occur episodically, in a very discrete short-lived manner, as a response to intermittent atmospheric water input, storm characteristics and soil moisture storage. Even though emerging as a very powerful tool for explaining the growing numbers of nonlinear hydrologic behaviours documented around the world, the hydrologic connectivity concept raises major issues for future research in catchment hydrology in terms of its definition, its measure, its integration into hydrological models and its scaling in the space and the time domains. The aim of this doctoral work is to precise the definition, the measure, the scaling and the prediction of processes underlying hydrologic connectivity while focusing on the following research questions: (1) What methodological framework should guide investigations of hydrologic connectivity?, (2) How to assess hydrologic connectivity from field data?, and (3) To what extent can the ongoing knowledge acquisition on hydrologic connectivity be used to improve success with hydrological modeling? Three study approaches are discriminated, namely: (i) a black box approach that only relies on rainfall and runoff data without examining the internal catchment behaviour; (ii) a grey box approach based on punctual geochemical data illustrating the catchment internal state; and (iii) a white box approach involving exhaustive spatial patterns of surface and subsurface topographic variables and soil moisture. These three approaches are then tested against field data from the Hermine catchment (Lower Laurentians, Quebec). It is possible to classify the Hermine catchment hydrological responses with regards to their magnitude and their timing, the switching from one response type to another depending on antecedent conditions. It is revealed that high discharge values monitored at the catchment outlet are produced by increased contributions from specific runoff sources, thus hinting towards a reinforced hydraulic linkage and an enhanced degree of connectivity between runoff sources and the stream channel. It is established that saturated areas whose spatial extent exceeds 0.85 ha are critical for high runoff generation. Soil moisture spatial patterns in temperate humid forested catchments are shown to have statistical properties that are very different from those encountered in temperate rangelands; hence the necessity of using different spatial connectivity metrics in these contrasted environments. The co-existence of “linear” and “nonlinear” contributing sources is also illustrated in the Hermine catchment. These results suggest that some concepts should be revised for hydrological modeling purposes. The originality of the present thesis is mainly inherited from its prime focus. The pursued research objectives are in accordance with the future trend in catchment hydrology, especially as hydrologists are urged to move from site-specific experiments and results to more easily generalizable concepts that favour the study of emergent catchment properties such as connectivity. Thus, the major contribution of this thesis is the proposal of a unified definition of connectivity, a comprehensive methodological framework, technical tools and operational ideas for the better performance of hydrological models.

Dans un bassin versant, la connectivité hydrologique constitue un état hydrologique qui lie le versant à la zone riveraine. Ses impacts sur la production du débit et le transfert des éléments dissous vers le cours d’eau sont présumés substantiels. L’étude vise à 1) détecter les hydrotopes et les connexions hydrologiques à l’aide d’un réseau de puits qui permet la mesure des fluctuations de la nappe phréatique (NP); 2) identifier la variabilité spatio-temporelle et la signature géochimique des sources potentielles en eau à l’aide des éléments majeurs et traces et 3) examiner la contribution spatio-temporelle respective des sources en eau du bassin lors d’un événement de précipitation. L’étude s’effectue dans un bassin versant forestier du Bouclier canadien (l’Hermine). Nous démontrons l’existence de quatre hydrotopes représentant un gradient de convergence de l’eau, soulignant la diversité de comportement de NP. Les connexions hydrologiques se caractérisent par des coefficients de Spearman élevés des relations entre la profondeur de la NP et le débit, dans leur partie en aval, et s’enclenchent par le fill and spill. Le comportement de NP est influencé par la distance aux limites du bassin, l’horizonation du sol et la topographie souterraine. En somme, trois sources en eau se connectent à partir du versant vers la zone riveraine durant l’événement pluvial de manière chronologique: 1) les horizons B et la NP de l’ensemble du bassin (Sr); 2) les horizons LFH des zones de convergence (Ba et Zn) et 3) une dépression de sol humide sur le versant nord (Co et Mn). / In watersheds, hydrologic connectivity consists of a hydrologic state that links the upper part of a hillslope to the riparian zone. Its impacts on streamflow generation and transfer of dissolved elements towards the stream are considered substantial. This study aims to 1) detect hydrotops and hydrologic connections with a network of wells that allow measurements of water table (WT) fluctuations; 2) identify spatial and temporal variability and the geochemical signature of potential sources of water with major and trace elements and 3) examine the spatial and temporal contribution of sources of water within the watershed during a storm event. The study takes place in a small forested watershed of the Canadian Shield (the Hermine). We demonstrate the existence of four hydrotops representing a water convergence gradient, highlighting diversity of behavior of the WT. Hydrological connections are characterized by high Spearman coefficients of the relationship between WT depth and streamflow in their downstream portion. Some hydrological connections are engaged by the fill and spill mechanism. WT behavior is influenced by the distance limits of the basin, soil horizonation and subsurface topography. In sum, three water sources connect the hillslope to the riparian zone during the storm event in chronological order: 1) WT and B horizons of the entire basin (Sr), 2) LFH horizons of convergence zones (Ba and Zn) and 3) a depression of wet soil on north hillslope (Co and Mn).

Topographic depressions are naturally occurring low land areas surrounded by areas of high elevations, also known as “pits” or “sinks”, on terrain surfaces. Traditional watershed modeling often neglects the potential effects of depressions by implementing removal (mostly filling) procedures on the digital elevation model (DEM) prior to the simulation of physical processes. The assumption is that all the depressions are either spurious in the DEM or of negligible importance for modeling results. However, studies suggested that naturally occurring depressions can change runoff response and connectivity in a watershed based on storage conditions and their spatial arrangement, e.g., shift active contributing areas and soil moisture distributions, and timing and magnitude of flow discharge at the watershed outlet. In addition, recent advances in remote sensing techniques, such as LiDAR, allow us to examine this modeling assumption because naturally occurring depressions can be represented using high-resolution DEM. This dissertation provides insights on the effects of depressions on overland flow processes at multiple spatial scales, from internal depression areas to the watershed scale, based on hydrologic connectivity metrics. Connectivity describes flow pathway connectedness and is assessed using geostatistical measures of heterogeneity in overland flow patterns, i.e., connectivity function and integral connectivity scale lengths. A new algorithm is introduced here to upscale connectivity metrics to large gridded patterns (i.e., with > 1,000,000 cells) using GPU-accelerated computing. This new algorithm is sensitive to changes of connectivity directions and magnitudes in spatial patterns and is robust for large DEM grids with depressions. Implementation of the connectivity metrics to overland flow patterns generated from original and depression filled DEMs for a study watershed indicates that depressions typically decrease overland flow connectivity. A series of macro connectivity stages based on spatial distances are identified, which represent changes in the interaction mechanisms between overland flow and depressions, i.e., the relative dominance of fill and spill, and the relative speed of fill and formation of connected pathways. In addition, to study the role of spatial resolutions on such interaction mechanisms at watershed scale, two revised functional connectivity metrics are also introduced, based on depressions that are hydraulically connected to the watershed outlet and runoff response to rainfall. These two functional connectivity metrics are sensitive to connectivity changes in overland flow patterns because of depression removal (filling) for DEMs at different grid resolutions. Results show that these two metrics indicate the spatial and statistical characteristics of depressions and their implications on overland flow connectivity, and may also relate to storage and infiltration conditions. In addition, grid resolutions have a more significant impact on overland flow connectivity than depression removal (filling).