Earth’s hydrology is made up of complex systems which are spatially varied and influence a number of ecosystem processes. Complex ecosystems, in this case, are defined as those involving multiple bodies of water and land masses which are seasonally connected to one another through various processes, resulting in an intricate aquatic and terrestrial relationship in a single area. There have been advances in how we study these environments, yet it remains important to determine the most efficient tools in order to accurately monitor ecosystem health in these regions. Monitoring water quality in freshwater-dominated, wetland systems is costly and often impractical due to the remote locations of areas of interest. By exploring the methods of analysis in which remotely sensed data can be used to monitor changes in the spatial patterns of water quality, it is possible to study these complex ecosystems in a more frequent and effective manner.

Diatom analyses were carried out on sediment cores collected from two low-lying, closed-drainage basins (PAD 9 - 58??46. 46?N, 111??19. 48?W; PAD 12 - 58??57. 29?, 111??19. 74?) in the Peace sector of the Peace-Athabasca Delta (PAD), Alberta, Canada, to provide >1000 year long records of hydro-ecological change. Results from diatom analyses were compared with macrofossil and stable isotope records from the same cores and assessed within the framework of an Athabasca River headwater climate record inferred from isotope dendroclimate data. Results from PAD 9 and PAD 12 sediment cores indicated closed-drainage conditions during the Medieval Warm Period (MWP) and the post-Little Ice Age and high water conditions during the Little Ice Age (LIA). High water levels at PAD 9 and PAD 12 reflected high water conditions on Lake Athabasca and the Rivi??re des Rochers or possibly the Peace River during the LIA (~AD 1600-1900). High water conditions were also observed at low-lying sites in the central and southern regions of the PAD (PAD 31 and PAD 37), and corresponded with evidence of high streamflows on the North Saskatchewan River. In contrast, desiccation evident at PAD 5, a site largely isolated from river influence, reflected atmospherically dry conditions during the LIA. Consistent with changes observed at PAD 5, sediment records at PAD 15, an oxbow lake off the Revillion Coup??, demonstrated low flood frequency during the early to mid-1700s. Increased water levels evident at low-lying sites located in proximity to the central open-drainage network of lakes and rivers were likely due to higher flows on the Athabasca River and potentially on the Peace River. High flows on rivers of the PAD may be attributed to snowmelt-dominated runoff during the LIA relative to the rainfall-dominated runoff during MWP (prior to ~AD 1600) and the post-LIA period (~AD 1900 to present).

Microbial biodegradation is the primary mechanism by which petrogenic hydrocarbons (PHCs) are removed from the environment. Though hydrocarbon biodegradation is widely studied in marine systems, knowledge of how it occurs in freshwater systems is still lacking. The Peace-Athabasca Delta (PAD), located in northeastern Alberta, is an ideal location to study microbial hydrocarbon degradation since it has a long history of exposure to PHCs. What’s more, these PHCs are predominately sourced from bituminous deposits and are therefore relevant to the Canadian Oil Sands Industry. This thesis investigated the genetic potential for hydrocarbon degradation of PHCs via metagenomic reconstruction of microbial communities in lakes of the Peace and Athabasca Deltas, as well as reference lakes in the nearby boreal uplands. In order to properly evaluate the microbial community and its potential for hydrocarbon degradation, a comprehensive analysis of PHCs (including n-alkanes, polycyclic aromatic compounds (PACs), and petroleum biomarkers of terpanes, hopanes, and steranes) was performed. PHC analysis showed that n-alkanes in lake sediments from all three regions were highly similar and predominately biogenic, while PAC composition was significantly different in each region. Restricted-drainage lakes of the Athabasca Delta had the highest concentrations of PACs from petrogenic sources. Closed-drainage lakes in the Peace Delta had lower concentrations of PACs that likely originated from a mixture of pyrogenic and petrogenic sources. Closed-drainage lakes in the boreal upland region had the lowest concentrations of PACs likely sourced from pyrogenic wood combustion with traces of petrogenic PACs, possibly from atmospheric deposition of dust. Petroleum biomarkers of terpanes, hopanes, and steranes were successfully used to identify the long-range fluvial, and possibly atmospheric, transport of bituminous compounds more than one hundred kilometers from their potential source. This validates the future use of these biomarkers in environmental forensics. Microbial communities in all three regions under study were highly diverse, and their composition was significantly different in both sediment and water. Targeted gene analysis identified a total of 3885 genes involved in the degradation of n-alkanes and PACs in sediment and water. The results show that organic carbon, nitrogen, and sulfur content, as well as PAC and short-chain alkane concentrations were important chemical predictors of change in degradation gene composition. Furthermore, genes for anaerobic degradation of PHCs were identified in syntrophic bacteria, methanogens, nitrate and sulfate reducers, demonstrating the potential for syntrophic hydrocarbon degradation in PAD lakes. Though this thesis confirms the genetic potential for hydrocarbon degradation in PAD and boreal upland lakes, further research is necessary to determine whether these microbial communities can actively degrade the PHCs present in these lakes.

One of the world’s largest freshwater deltas (~4000 km2), the Peace-Athabasca Delta (PAD), is located at the convergence of the Peace and Athabasca rivers and Lake Athabasca in northern Alberta, Canada. Since the early 1970s, there has been increasing concern regarding the ecological impacts on the PAD after flow regulation of the Peace River began in 1968, decreased discharge in the Peace and Athabasca rivers as a result of hydroclimatic changes in Western Canada, and increased Athabasca River water usage by oil sands development to the south. This thesis is part of an ongoing, multi-disciplinary project assessing current and past hydrological and ecological conditions in the PAD. Research conducted in this thesis aims to better understand the processes controlling water balance of lakes in the PAD using mainly stable water isotope data collected from lakes and their input sources. Isotope data are used to describe and quantify hydrological processes for individual lakes (seasonal and annual) and across the delta and are supported by other chemical and hydrometric data. An isotopic framework in d18O-d2H-space is developed for the PAD using evaporation-flux-weighted local climate data, and isotopic data collected from a reference basin, lakes throughout the PAD, and lake input sources (i.e., snowmelt, rainfall, and river water). The framework is comprised of two reference lines, the Local Meteoric Water Line, which is based on measured isotopic composition of precipitation, and the Local Evaporation Line, which is based on modelled isotopic composition of reference points. Evaporation pan data is used to assess short-term variations in key isotopic reference values, which are important for addressing short-term changes in the isotopic signature of shallow basins. This framework is used in subsequent chapters including assessment of seasonal and annual water balance of two hydrologically-contrasting shallow lakes, and to quantify the impacts of flood water and snowmelt on a set of 45 lakes in spring 2003. Five years of isotope data using time-series analysis and the isotopic framework suggested that a perched (isolated) lake and its catchment (forest and bedrock) in the northern, relict Peace sector captured sufficient rain, snow, and runoff to maintain a relatively stable water balance, and also that a low-lying lake in the southern, active Athabasca sector was regularly replenished with river water in both spring and summer. Snowmelt and rainfall were found to have diluted the perched basin by an average of 16% and 28 % respectively, while spring and summer floods were found to almost completely flush the low-lying lake. Using the spring 2003 regional dataset, flooded lakes were separated from snowmelt-dominated lakes through use of suspended sediment concentrations, isotope data, and field observations. Application of an isotope mixing model translated d18O values into a range of replenishment amount by either river water or snowmelt, which compared well with hydrological conditions at the time of sampling and previously classified drainage types of the lakes. Spatial mapping of replenishment amounts illustrated flooding of much of the Athabasca sector due to ice-jams, except for two sub-regions isolated from flooding by artificial and natural northern diversion of flow from the Athabasca River. It is also shown that most of the relict landscape of the Peace sector was replenished by snowmelt except for a few low-lying lakes close to the Peace River and its tributaries. Overall, improved understanding of lake and regional hydrology in the PAD, especially the ability to quantify the affects of various lake inputs, will improve the ability to develop effective guidelines and management practices in the PAD as lakes respond to future changes in climate and river discharge.

One of the world’s largest freshwater deltas (~4000 km2), the Peace-Athabasca Delta (PAD), is located at the convergence of the Peace and Athabasca rivers and Lake Athabasca in northern Alberta, Canada. Since the early 1970s, there has been increasing concern regarding the ecological impacts on the PAD after flow regulation of the Peace River began in 1968, decreased discharge in the Peace and Athabasca rivers as a result of hydroclimatic changes in Western Canada, and increased Athabasca River water usage by oil sands development to the south. This thesis is part of an ongoing, multi-disciplinary project assessing current and past hydrological and ecological conditions in the PAD. Research conducted in this thesis aims to better understand the processes controlling water balance of lakes in the PAD using mainly stable water isotope data collected from lakes and their input sources. Isotope data are used to describe and quantify hydrological processes for individual lakes (seasonal and annual) and across the delta and are supported by other chemical and hydrometric data. An isotopic framework in d18O-d2H-space is developed for the PAD using evaporation-flux-weighted local climate data, and isotopic data collected from a reference basin, lakes throughout the PAD, and lake input sources (i.e., snowmelt, rainfall, and river water). The framework is comprised of two reference lines, the Local Meteoric Water Line, which is based on measured isotopic composition of precipitation, and the Local Evaporation Line, which is based on modelled isotopic composition of reference points. Evaporation pan data is used to assess short-term variations in key isotopic reference values, which are important for addressing short-term changes in the isotopic signature of shallow basins. This framework is used in subsequent chapters including assessment of seasonal and annual water balance of two hydrologically-contrasting shallow lakes, and to quantify the impacts of flood water and snowmelt on a set of 45 lakes in spring 2003. Five years of isotope data using time-series analysis and the isotopic framework suggested that a perched (isolated) lake and its catchment (forest and bedrock) in the northern, relict Peace sector captured sufficient rain, snow, and runoff to maintain a relatively stable water balance, and also that a low-lying lake in the southern, active Athabasca sector was regularly replenished with river water in both spring and summer. Snowmelt and rainfall were found to have diluted the perched basin by an average of 16% and 28 % respectively, while spring and summer floods were found to almost completely flush the low-lying lake. Using the spring 2003 regional dataset, flooded lakes were separated from snowmelt-dominated lakes through use of suspended sediment concentrations, isotope data, and field observations. Application of an isotope mixing model translated d18O values into a range of replenishment amount by either river water or snowmelt, which compared well with hydrological conditions at the time of sampling and previously classified drainage types of the lakes. Spatial mapping of replenishment amounts illustrated flooding of much of the Athabasca sector due to ice-jams, except for two sub-regions isolated from flooding by artificial and natural northern diversion of flow from the Athabasca River. It is also shown that most of the relict landscape of the Peace sector was replenished by snowmelt except for a few low-lying lakes close to the Peace River and its tributaries. Overall, improved understanding of lake and regional hydrology in the PAD, especially the ability to quantify the affects of various lake inputs, will improve the ability to develop effective guidelines and management practices in the PAD as lakes respond to future changes in climate and river discharge.

Diatom analyses were carried out on sediment cores collected from two low-lying, closed-drainage basins (PAD 9 - 58º46. 46?N, 111º19. 48?W; PAD 12 - 58º57. 29?, 111º19. 74?) in the Peace sector of the Peace-Athabasca Delta (PAD), Alberta, Canada, to provide >1000 year long records of hydro-ecological change. Results from diatom analyses were compared with macrofossil and stable isotope records from the same cores and assessed within the framework of an Athabasca River headwater climate record inferred from isotope dendroclimate data. Results from PAD 9 and PAD 12 sediment cores indicated closed-drainage conditions during the Medieval Warm Period (MWP) and the post-Little Ice Age and high water conditions during the Little Ice Age (LIA). High water levels at PAD 9 and PAD 12 reflected high water conditions on Lake Athabasca and the Rivière des Rochers or possibly the Peace River during the LIA (~AD 1600-1900). High water conditions were also observed at low-lying sites in the central and southern regions of the PAD (PAD 31 and PAD 37), and corresponded with evidence of high streamflows on the North Saskatchewan River. In contrast, desiccation evident at PAD 5, a site largely isolated from river influence, reflected atmospherically dry conditions during the LIA. Consistent with changes observed at PAD 5, sediment records at PAD 15, an oxbow lake off the Revillion Coupé, demonstrated low flood frequency during the early to mid-1700s. Increased water levels evident at low-lying sites located in proximity to the central open-drainage network of lakes and rivers were likely due to higher flows on the Athabasca River and potentially on the Peace River. High flows on rivers of the PAD may be attributed to snowmelt-dominated runoff during the LIA relative to the rainfall-dominated runoff during MWP (prior to ~AD 1600) and the post-LIA period (~AD 1900 to present).

Periodic flooding has been widely believed to serve an important role in maintaining water levels and productivity of aquatic basins in floodplain landscapes. Here, I analyze four basins of contrasting flood frequencies (one through-flow, one pulse-flooded, two non-flooded) and two adjacent river sites in the PAD were sampled during the open-water season of 2007 and spring of 2008 to characterize linkages between hydrological processes (using O and H stable isotopes) and limnological conditions, and to assess how these linkages affect trophic interactions involving the aquatic flora and fauna (using C and N stable isotopes). The water balance and water chemistry of the through-flow basin was dominated at all times by the input of river water which reduced concentrations of nutrients and ions. In contrast, evaporation played an important role in the water balance and concentrated nutrients and ions in the non-flooded basins. Surprisingly, pulse-flood events had short-lived effects on the water balance and carbon stable isotopic signatures of biota. Hydrological and limnological conditions in the pulse-flooded basin were similar to those of the river water shortly after spring flooding. After flooding, evaporation caused rapid increase of δ18O of the water comparable to patterns observed in the non-flooded basins, but recovery of water chemistry variables was delayed. In the non-flooded and pulse-flooded basins, δ13CDIC declined due to atmospheric CO2 invasion under conditions of high primary productivity and pH that generated strong kinetic fractionation. This decline in δ13CDIC values produced the opposite effect compared to when photosynthesis occurs under non-limiting carbon conditions, as occurred in the through-flow basin. This feature provides important new knowledge to improve paleolimnological interpretation of δ13C values of organic matter in sediment cores to track past changes in flooding regimes. Importantly, this study shows that pulse floods exert short-lived transient (~1-2 months) effects of the water balance and carbon dynamics of aquatic food-webs and do not elevate aquatic production, but exert longer lasting (at least an entire open-water season) on water chemistry conditions. This contrasts with previous beliefs that the effects of pulse flooding are more profound and longer lasting.

Periodic flooding has been widely believed to serve an important role in maintaining water levels and productivity of aquatic basins in floodplain landscapes. Here, I analyze four basins of contrasting flood frequencies (one through-flow, one pulse-flooded, two non-flooded) and two adjacent river sites in the PAD were sampled during the open-water season of 2007 and spring of 2008 to characterize linkages between hydrological processes (using O and H stable isotopes) and limnological conditions, and to assess how these linkages affect trophic interactions involving the aquatic flora and fauna (using C and N stable isotopes). The water balance and water chemistry of the through-flow basin was dominated at all times by the input of river water which reduced concentrations of nutrients and ions. In contrast, evaporation played an important role in the water balance and concentrated nutrients and ions in the non-flooded basins. Surprisingly, pulse-flood events had short-lived effects on the water balance and carbon stable isotopic signatures of biota. Hydrological and limnological conditions in the pulse-flooded basin were similar to those of the river water shortly after spring flooding. After flooding, evaporation caused rapid increase of δ18O of the water comparable to patterns observed in the non-flooded basins, but recovery of water chemistry variables was delayed. In the non-flooded and pulse-flooded basins, δ13CDIC declined due to atmospheric CO2 invasion under conditions of high primary productivity and pH that generated strong kinetic fractionation. This decline in δ13CDIC values produced the opposite effect compared to when photosynthesis occurs under non-limiting carbon conditions, as occurred in the through-flow basin. This feature provides important new knowledge to improve paleolimnological interpretation of δ13C values of organic matter in sediment cores to track past changes in flooding regimes. Importantly, this study shows that pulse floods exert short-lived transient (~1-2 months) effects of the water balance and carbon dynamics of aquatic food-webs and do not elevate aquatic production, but exert longer lasting (at least an entire open-water season) on water chemistry conditions. This contrasts with previous beliefs that the effects of pulse flooding are more profound and longer lasting.

Floodplain lakes are strongly regulated by river connectivity because floodwaters exert strong influence on the water balance, the physical, chemical and biological limnological conditions, and the influx of contaminants. The Peace-Athabasca Delta (PAD) in northern Alberta (Canada) is a hydrologically complex landscape and is an important node in the upper Mackenzie River Drainage Basin. The ecological integrity of the PAD is potentially threatened by multiple environmental stressors, yet our understanding of the hydroecology of this large floodplain remains underdeveloped. Indeed, ever since the planning and construction of the WAC Bennett Dam (1960s), concerns have grown over the effects of upstream human activities on the lakes of the PAD. More recently, concerns over the health of the PAD have intensified and come to the fore of national and international dialogue due to water abstraction and mining and processing activities by the rapidly expanding oil sands industry centred in Fort McMurray Alberta. Currently, widespread perception is that upstream human activities have reduced water levels and frequency of flooding at the PAD, which have lowered nutrient availability and productivity of perched basin lakes, and have increased supply of pollutants from oil sands. However, these perceptions remain based on insufficient knowledge of pre-impact conditions and natural variability. Current and past relations between hydrology and limnology of PAD lakes are mostly undocumented, particularly during the important spring freshet period when the effects of river flood waters are strongest. Similarly, knowledge of the deposition of oil-sands- related contaminants in the PAD remains insufficient to determine whether anthropogenic activities have increased the deposition of important oil-sands-related contaminants such as polycyclic aromatic compounds (PACs) relative to natural processes. Such knowledge gaps must be filled to achieve effective monitoring, policy and governance concerning impacts of industrial development and the protection of human and environmental health within the PAD and Mackenzie drainage basin. This thesis examines the effects of river flooding (and the lack of) on water clarity, nutrients, chemistry, phytoplankton abundance, epiphyton community composition and the deposition of polycyclic aromatic compounds (PACs) in lakes of the Peace-Athabasca Delta. To determine the role of flooding on contemporary epiphytic diatom communities (an abundant and diverse guild of primary producers in PAD lakes), a field experiment was conducted examining the community composition and abundance of epiphytic diatoms in four PAD lakes. Two of these four lakes had received floodwaters that spring and two had not. Epiphytic diatom communities in each lake were sampled during the peak macrophyte biomass period (summer) from two macrophyte taxa (Potamogeton zosteriformis, P. perfoliatus var. richardsonii) and from polypropylene artificial substrates previously deployed that spring. A two-way analysis of similarity (ANOSIM) test identified that epiphytic diatom community composition differed between lakes that flooded and those that did not flood. From the use of similarity percentage (SIMPER) analysis, diatom taxa were identified that discriminate between flooded and non-flooded lakes. The relative abundance of ‘strong flood indicator taxa’ was used to construct an event-scale flood record spanning the past ~180 years using analyses of sedimentary diatom assemblages from a closed-drainage lake (PAD 5). Results were verified by close agreement with an independent paleo-flood record from a nearby flood-prone oxbow lake (PAD 54) and historical records. Comparison of epiphytic diatoms in flooded and non-flooded lakes in this study provides a promising approach to detect changes in flood frequency, and may have applications for reconstructing other pulse-type disturbances such as hurricanes and pollutant spills. Additionally, this study demonstrates that artificial substrates can provide an effective bio-monitoring tool for lakes of the PAD and elsewhere. To improve our understanding of the hydrolimnological responses of lake in the PAD to flooding, repeated measurements over three years (2003-05) were made on a series of lakes along a hydrological gradient. This allowed the role of river flooding to be characterized on limnological conditions of lakes and to identify the patterns and timescales of limnological change after flooding. River floodwaters elevate lake water concentrations of suspended sediment, total phosphorus (TP), SO4 and dissolved Si (DSi), and reduce concentrations of total Kjeldahl nitrogen (TKN), DOC and most ions. River flooding increases limnological homogeneity among lakes, because post-flood conditions are strongly affected by the river water properties. After floodwaters recede, limnological conditions become more heterogeneous among lakes in response to diversity of local basin influences (geology, slope, vegetation, depth, fetch, and biological communities and processes), and limnological changes occur at two distinct timescales. In the weeks to months after flooding, water clarity increases as suspended sediments and TP settle out of the water column. In the absence of flooding for many years to decades, evaporative concentration leads to an increase in most nutrients (TKN, inorganic N, and dissolved P), DOC and ions. Contrary to a prevailing paradigm, these results suggest that regular flooding is not required to maintain high nutrient concentrations. In light of anticipated declines in river discharge, limnological conditions in the southern Athabasca sector will become increasingly less dominated by the short-term effects of flooding, and resemble nutrient- and solute-rich lakes in the northern Peace sector that are infrequently flooded. To determine the roles of the Athabasca River and atmospheric transport as vectors for the deposition of PACs in the PAD, sediment cores spanning the last ~200 years were collected from three lakes within the delta. A closed-drainage basin elevated well above the floodplain (PAD 18) was selected to determine temporal patterns of change in PAC concentration due to atmospheric deposition and within-basin production of PACs. Known patterns of paleohydrological changes at the other two lakes (PAD 23 and 31) were used to assess the role of the Athabasca River in delivering PACs to the Athabasca Delta during the ~200 year. Well- dated sediment core samples were analysed for 52 alkylated and non-alkylated PACs (method EPA 3540/8270-GC/MS). Sediments deposited in the non-flood prone lake (PAD 18) contained lower concentrations of total PACs compared to sediments deposited during flood-prone periods in the other study lakes, and were dominated by PACs of a pyrogenic rather than bitumen origin. Multivariate analysis of similarity tests identified that the composition of PACs differs between sediments deposited during not flood-prone and flood-prone periods. Subsequent Similarities Percentage (SIMPER) analysis was used and identified seven PACs that are preferentially deposited during flood-prone periods. These seven PACs are bitumen-associated, river-transported and account for 51% of the total PACs found in oil-sands sediment. At PAD 31, which has been flood-prone both before and since onset of Athabasca oil sands development, identified no measureable differences in both the proportion and concentration of the river-transported indicator PACs in sediments deposited pre-1940s versus post-1982. Our findings suggest that natural erosion of exposed bitumen along the banks of the Athabasca River and its tributaries is the main process delivering PACs to the Athabasca Delta, and that the spring freshet is a key period for contaminant mobilization and transport. Such key baseline environmental information is essential for informed management of natural resources and human-health concerns by provincial and federal regulatory agencies and industry, and for designing effective long-term monitoring and surveillance programs for the lower Athabasca River watershed in the face of future oil sands development. Further monitoring activities and additional paleolimnological studies of the depositional history of PACs and other oil-sands- and non-oil-sands-related contaminants is strongly recommended. Overall, results of this research identify that river flooding exerts strong control on physical, chemical and biological conditions of lakes within the PAD. However, contrary to prevailing paradigms, the PAD is not a landscape that has been adversely and permanently affected by regulation of the Peace River and industrial development of the oil sands along the Athabasca River. Instead, data from contemporary and paleolimnological studies identify that natural processes continue to dominate the delivery of water and contaminants to the delta. Regular and frequent flooding is not essential to maintain the supply of nutrients and productivity of delta lakes, which has been a widespread paradigm that developed in the absence of objective scientific data. Instead, nutrient concentrations rise over years to decades after flooding and lake productivity increases. During the thesis research, novel approaches were developed and demonstrated to be effective. Namely, new artificial substrate samplers were designed for aquatic biomonitoring that accrue periphyton and can identify the occurrence of flood events. Also, paleolimnological methods were employed to characterize the composition and concentration of PACs supplied by natural processes prior to oil sands industrial activity, which serves as an important benchmark for assessing industrial impacts. These are effective methods that can be employed to improve monitoring programs and scientific understanding of the factors affecting this world-renowned landscape, as well as floodplains elsewhere.