Watershed features, physiographic setting, geology, climate, and hydrologic processes combine to produce a time-variant nutrient concentration signal at the watershed outlet. Anthropogenic influences, such as increased agricultural pressures and urbanization, have increased overall nutrient loadings delivered to the fluvial network. The impact of such increased nutrient loadings on Kentucky’s drinking water remains a potential threat to the region. By coupling spatial sampling of nitrate concentrations in surface water with contemporary nutrient and water quality sensor technology, a decomposition of the Upper South Elkhorn watershed’s nitrate signal and an estimation of source timing and loading in the watershed was completed. The goal of the project was the decomposition of the integrated nitrate signal observed at the outlet of the Upper South Elkhorn watershed into contributing runoff and groundwater sources from agricultural/pasture and urban/suburban land-uses. Decomposing the watershed’s nitrate signal yielded new knowledge learned about nitrate source, fate and transport in immature fluviokarst. This thesis discusses how mean, seasonal, and fluctuating nitrate behavior is related to soil processes, groundwater transfer, streambed removal, and event dynamics. It is expected that the decomposition of the nitrate signal will allow for the targeting of both the timing and sources for nutrient reductions in a watershed.

Salinity (S) and temperature (T) control every facet of the eastern oyster (Crassostrea virginica) life cycle, principally reproduction, development, growth, and mortality. Previous studies conducted in in the Breton Sound (BR) and Barataria (BA) estuaries have reported differences in growth and mortality rates between the basins. In the present study, environmental conditions were synchronized to compare growth and mortality rates between basins at similar combinations of T and S. Results indicate that when T and S are the same (synchronized), seasonal oyster growth and mortality rates differ between BR and BA. Seasonal analyses revealed that as salinities increased in both estuaries, growth rates generally increased, while mortality rates generally decreased. These findings suggest that basin-wide adaptations to local environmental conditions may exist.

I evaluated the effectiveness of plant roots to increase infiltration rates within stormwater bioretention facilities (SBFs), roadside planter compartments that filter stormwater. SBFs attenuate harmful effects of stormwater by reducing peak flow and retaining pollutants, with increased infiltration that improves both these functions. Researchers have shown that roots can increase infiltration within greenhouse, lab, field, and test SBF settings. However, no researchers have yet measured either the extent to which different root characteristics can increase infiltration or the variation in root characteristics and their effect on infiltration rates among plant assemblages within currently functioning SBFs. To determine if root-enhanced infiltration was occurring within SBFs, I hypothesized 1) there is a relationship between root characteristics and infiltration during late spring, and 2) seasonal root growth increases infiltration rates. Within Portland, OR, I measured infiltration rate from January 2014 to February 2015 and root characteristics from January-February (J-F) and May-June (M-J) 2014 in ten SBFs with "Elk Blue" rush (Juncus patens) and 1 or 2 trees of less than 8.4 cm stem diameter. During M-J, four root characteristics showed a positive relationship with infiltration rate, and two root characteristics showed a strong positive relationship with infiltration rate within the topsoil. Also, a relationship was shown between the increase (J-F to M-J 2014) in three root characteristics and the increase in infiltration rate. To determine if root morphology and infiltration rates differed among SBFs with two different dominant vegetation taxa (small and large root biomass), I hypothesized 3) Juncus patens and tree dominant assemblage (greater root biomass) exhibits greater infiltration compared to the Carex dominant assemblage, 4) the increase in infiltration rate and root characteristics from J-F to M-J is greater in the Juncus compared to the Carex assemblage, and 5) root surface area density (RSAD) within Juncus SBFs shows a positive relationship with infiltration rate in late spring. I measured infiltration rate from January 2014 to February 2015 and root characteristics from January-February (J-F) and May-June (M-J) 2014 among five large-root (Juncus and tree) and five small-root biomass (Carex sp) SBFs. Juncus SBFs showed greater values for three root characteristics during J-F and five root characteristics during M-J 2014 compared to Carex SBFs. Also, Juncus SBFs showed an increase from J-F to M-J 2014 for five root characteristics while Carex SBFs showed no root increase. Juncus SBFs showed a relationship with four root characteristics and Carex SBFs a showed relationship with one root characteristic and infiltration rate. This work strongly suggests plant roots increase infiltration, and thus the primary functions of SBFs. Different root characteristics appear to increase infiltration rate at different depths. Data also show larger-root biomass plants increase infiltration rate to a greater degree than smaller-root biomass plants. I recommend considering several site and facility characteristics when determining the potential for root-enhanced infiltration. When selecting plant species to enhance infiltration, I recommend using several criteria, determining root characteristic values at certain depths, considering installation approaches, and accounting for regional climate changes.

This study conducts a dam-scale cost versus benefit analysis in order to explore the feasibility of each the 13 U.S. Army Corps of Engineers (USACE) commissioned dams in Oregon’s Willamette River network. Constructed between 1941 and 1969, these structures function in collaboration to comprise the Willamette River Basin Reservoir System (WRBRS). The motivation for this project derives from a growing awareness of the biophysical impacts that dam structures can have on riparian habitats. This project compares each of the 13 dams being assessed, to prioritize their level of utility within the system. The study takes the metrics from the top three services (flood regulation, hydropower generation and recreation) and disservices (fish mortality, structural risk and water temperature hazards) and creates a rubric that scores the feasibility of each dam within the system. Within a range between 0 to 3 for three dam services and 0 to -4.5 for two disservices, the overall calculated score elucidates for each structure whether its contribution to the WRBRS is positive or negative. Further analysis searches for spatiotemporal trends such as anomalous tributaries or magnified structural risk for structures exceeding a certain age. GIS data from the National Inventory of Dams (NID), U.S. Geologic Survey (USGS) water measurements, raw data from USACE, and peer-reviewed studies comprise the statistics that generate results for this analysis. The computed scores for each dam yield an average overall score of -1.31, and nine of the 13 structures have negative results, indicating that the WRBRS faces challenges going forward. The study seeks to contribute to the increasingly relevant examination of dam networks at the watershed scale.

The Tigris River is one of two primary rivers in Iraq and is, along with the Euphrates, the main source for drinking and irrigation water in the country. The Tigris River originates in the Taurus Mountains in Turkey, and is 1850 km long. The majority of the river lies within Iraq. The river passes through, and is the primary drinking water source for major cities such as Mosul, Baeji, Samarra, Baghdad (the capital), and Kut. The Tigris River joins the Euphrates River in Qurna city within Basra province to form the Shatt Al-Arab River which eventually discharges into the Persian Gulf. As a result of fluctuations in flow rate along the Tigris River that cause both potential flooding and drought, Mosul Dam was built on the mainstem of the Tigris River upstream of the city of Mosul and was operated starting in July 1986 to control the river flow and to generate hydroelectricity. Some canals were also constructed to divert excess fresh water from the mainstem of the river at Samarra Barrage located 125 km north (upstream) of Baghdad to Tharthar Lake, an artificial lake located 100 km northwest Baghdad city. The Tigris-Tharthar canal, 75 km long, was constructed in 1956 to divert excess water from Samarra Barrage to Tharthar Lake and to prevent potential flooding in Baghdad. During dry seasons, high total dissolved solids (TDS) water is diverted from Tharthar Lake into the mainstem of the Tigris River through the 65 km long Tharthar-Tigris canal, which is located 25 km upstream Baghdad. Due to rapid population growth and increasing industrial activates, the Tigris River is also facing many water quality challenges from inflows of contaminated wastewater from treatment plant stations. A water quality model that simulates the Tigris River system is therefore needed to study the effects of these discharges and how water quality of the Tigris River could be managed. To address this issue, CE-QUAL-W2 was used to develop a 2-D (longitudinal and vertical) hydrodynamic and water quality model of the mainstem Tigris River from Mosul Dam (Rkm 0) to Kut Barrage (Rkm 880). In addition, Tharthar Lake and its canals were modeled. A full suite of hydrodynamic and water quality variables were simulated for the year 2009, including flowrates, water level, and water temperature. Additionally, water quality constituents such as total dissolved solids (TDS), phosphate (PO4), ammonium (NH4), nitrate (NO3), biochemical oxygen demand (BOD), chlorophyll-a (Chl-a), and dissolved oxygen (DO) were also simulated. Bathymetry of the Tigris River and field data such as flowrate, water level, TDS, NO3 were obtained from the Ministry of Water Resources in Iraq, while surface water temperatures of the Tigris River were estimated remotely using Landsat satellites. These satellites provided a continuous observation record of remote sites. Other water quality field data, such as PO4, NH4, BOD, and DO, were estimated from literature values. Meteorological data, including, wind speed, wind direction, air and dew point temperatures, cloud cover, and solar radiation were obtained from the Iraqi Ministry of Transportation, the General Organization for Meteorology and Seismic Monitoring. Model predictions of flow and water level were compared to field data at three stations along the mainstem of the Tigris River, including Baeji, downstream of Samarra Barrage, and Baghdad. The absolute mean error in the flow varied from 12.6 to 3.4 m3/s and the water level absolute mean error varied from 0.036 to 0.018 m. The percentage error of the overall flowrate at Baeji, downstream Samarra Barrage and Baghdad was 1.9%, 0.8%, and 0.8% respectively. Injecting a conservative tracer at Mosul Dam showed that a parcel of water reaches to Baeji, Samarra Barrage, Baghdad, and Kut Barrage after approximately 3 days, 5 days, 10 days, and 19 days, respectively. Water temperature field data in Iraq are limited and there was no archive of existing field data. Therefore, I obtained estimates of surface water temperature on the Tigris River using the thermal band of the Landsat satellite, one of a series of satellites launched by the National Aeronautics and Space Administration (NASA). The calibration between satellite data and water temperature was validated using sparse field data from 2004, and the calibration then applied to 82 Landsat images from the year 2009. Landsat estimates showed a bias of -2°C compared to model results in winter months, possibly due to uncertainty in Landsat estimations. The absolute mean errors of the CE-QUAL-W2 model predictions of water temperature compared to Landsat estimated temperatures were 0.9 and 1.0°C at Baeji and Baghdad respectively. Temperature calibration in the Tigris River system was highly sensitive to meteorological input data. Landsat Images were also used to estimate longitudinal variation in surface water temperature of Tharthar Lake. It was found that surface water temperature in Tharthar Lake varied longitudinally along the North-South axis with warmer temperatures in the lower part compared with the upper part of the lake. Total dissolved solids concentrations in the Tigris River significantly increased from Mosul Dam to Kut Barrage with peak concentrations of 900 mg/l and 1050 mg/l at Baghdad and Kut, respectively, due to high TDS water diverted from Tharthar Lake, irrigation return flow, urban runoff, and uncontrolled discharge of wastewater effluents. NO3 concentrations did not significantly increase between Samarra Barrage and Baghdad city. BOD concentrations within Baghdad were extremely high due to direct discharge of industrial wastewater into the mainstem of the Tigris River from outlets located within the city. Management scenarios were simulated with the model of the Tigris River system and were compared with the base model. The main scenarios implemented on the Tigris River system were altering upstream hydrology, increasing air temperature due to the effect of climate change, disconnecting Tharthar Lake from the Tigris River system, and simulating long-term effects on Tharthar Lake. Increasing upstream inflows caused a decrease in TDS concentrations from 495 mg/l to 470 mg/l over all the mainstem of the river. In addition, CBOD concentrations decreased somewhat from 5.9 mg/l to 5.74 mg/l. On the other hand, decreasing upstream flows caused a significant increase in average TDS concentrations over the entire Tigris mainstem from 495 mg/l to 527 mg/l. Also, an increase in CBOD concentrations from 5.9 mg/l to 6.2 mg/l was predicted over all the mainstem of the river. Implementing the climate change scenario on the base model of the Tigris River system showed a 5% increase in annually averaged water temperature from 20.7°C to 21.68°C over the mainstem river. Climate change scenarios produced no significant impacts on TDS and CBOD concentrations in the mainstem, while DO concentrations decreased from 8.15 mg/l to 7.98 mg/l with a slight increase in Chl-a concentration from 1.97 µg/l to 2 µg/l in the mainstem. Disconnecting Tharthar Lake from the system showed a remarkable 25% decrease in TDS concentrations, with an average concentration changed from 495 mg/l to 397 mg/l in the mainstem due to an extra 36% increase in flow discharged downstream of Samarra Barrage. Also, Chl-a concentration significantly decreased by 40% with an average concentration changed from 2 µg/l to 1.2 µg/l. Additionally, a 6-year model simulation of the Tigris River system was performed to evaluate the long-term effects on Tharthar Lake. No significant impact was observed in the average temperature of the lake. TDS concentrations in the lake decreased from 1239 mg/l to 1041 mg/l. PO4, NH4 and NO3 concentrations decreased by 2%, 66% and 26%, respectively. Chl-a concentration in Tharthar Lake decreased from 2.0 µg/l to 1.61 µg/l. After decreasing BOD concentrations of the Tigris River by 50%, BOD concentrations in the mainstem decreased by 24%, while DO concentrations increased by 2.8%. There were no significant impacts on Chl-a concentrations in the mainstem of the river. Finally, for a scenario where extremely low dissolved oxygen release from Mosul Dam in the summer, it was found that approximately 50 km below Mosul Dam was affected before DO concentrations reached an equilibrium concentration. For further work on the Tigris River system, it is recommended to model the Tigris River from Kut Barrage to the confluence with the Euphrates River, about 400 km long, and connect it with the current model to have a complete model of the Tigris River system from Mosul Dam to the confluence with the Euphrates River. This is necessary to manage water the entire system of the Tigris River and also to provide enough water with good quality in Basra.

Cyanobacterial blooms in lakes impact human health, the economy, and ecosystem health. It is predicted that climate change will promote and increase the frequency and intensity of cyanobacterial blooms due to unique physiological adaptions that allow cyanobacteria to exploit warm stable water bodies. Key cyanobacteria physiological adaptions include nitrogen fixation, buoyancy regulation and higher optimum growth temperatures. The largest uncertainty of predicting the effect of climate change is in understanding how the interactions among species will change. Adding to the ambiguity, cyanobacteria physiological adaptions can vary based on lakespecific ecotypes and can have different sensitivities to temperature. It is critical to understand how cyanobacterial physiological adaptions impact species interactions in order to improve and devise adaptable, short‐term management methods for bloom control. This study investigated how weather patterns and algal buoyancy regulation influence the competition and accumulation of two bloom‐forming buoyant cyanobacteria species (Aphanizomenon flos‐aquae (APFA) and toxin‐forming Microcystis aeruginosa (MSAE)) in Upper Klamath Lake (UKL), Oregon. The focus was confirming the buoyancy rate of the APFA in Upper Klamath Lake and exploring whether short‐term weather conditions could lead to dangerous accumulations of APFA or MSAE. A sensitivity analysis was conducted on the model's buoyancy terms and growth curves to see if the outcome of competition was influenced by these parameters. UKL specific buoyancy rates were measured on APFA from samples taken directly from the lake in the summer of 2015. Tracking software was used to measure APFA movement through water, and individual colony movement was averaged to obtain a single buoyancy rate. There was a high degree of agreement between the calculated APFA buoyancy rate in UKL (0.89 ± 0.34 m hr-1) with the rate published by Walsby (1995; 0.9 ± 0.5 m hr-1). This study investigated how weather patterns and buoyancy regulation influenced the outcome of competition between APFA and MSAE. Weather and water column temperature data were collected from UKL in the summer of 2016. A onedimensional hydrodynamic model was used to calculate the lake's thermal and turbulence structure on days with contrasting weather patterns (hot/cool and windy/calm). A competition model was used to calculate the accumulation of APFA and MSAE cells in regular intervals through the water column under the various weather scenarios. MSAE accumulation was significantly influenced by the thermal and turbulence regimes, but APFA maintained high accumulations under every regime and was the better competitor under every thermal and turbulence regime. MSAE was more negatively impacted by high turbulence than low temperatures. APFA's optimum temperature growth curve was found to be important in determining the outcome of competition between APFA and MSAE. Surprisingly, competition was not sensitive to changes in buoyancy rates. Buoyancy was not found to be a function of algal accumulation under any thermal and turbulence regime. The impacts of climate change and human‐induced enrichment has the potential to change existing patterns of species interactions in lentic systems. Restoration and management efforts should consider the significance of cascading ecological responses to climate change. Understanding how key physiological adaptions operate is the first step to assessing the scope of this impact. While buoyancy might not play a large role in competition in UKL, it might be possible to use mixing to suppress MSAE because it is negatively impacted by high turbulence. If MSAE hot spots become a reoccurring problem in UKL, lakes managers might be able to use localized mixing to suppress MSAE blooms in these problem areas.

This study encompasses 25 kilometers of the Chehalis River in Washington, USA that currently has sections under a Total Maximum Daily Load (TMDL) plan for stream temperature impairments that exceed 18°C, a regulatory standard set at the time of the listing to protect salmonid spawning, rearing, and migration. Using information integrated from stationary data loggers (n=22) that collected stream temperature information from August 4-September 10, 2017, and longitudinal thermal profiling performed on July 29-30, August 4-5, and September 9-10, 2017, this study aimed to quantify the spatial distribution of stream temperature, evaluate relative consistencies of the riverine thermal regime over time, and identify which independent variables (land cover, aspect, canopy cover, impervious surfaces, channel width, discharge and air temperature) are correlated with stream temperature metrics using Spearman's rank correlation and stepwise linear regression modeling. Stream temperature was found to be strongly correlated with all air temperature metrics. The strongest model from stepwise linear regression (R2 = 0.711) found width, shrub/scrub, mixed forest, and cultivated crop land cover to be the strongest explanatory variables with the seven day average of the daily maximum stream temperature (7DADMaxTw) at the 22 sites. Tributaries had overall cooler average maximum stream temperatures than main stem sites. Thermal profiling identified seven cold-water patches (defined as the cumulative stream temperature ≥1°C cooler than the surrounding water). Integrating longitudinal thermal profiling and stationary data loggers allows resource managers to understand spatiotemporal stream temperature trends and influences and can assess more effective mitigation strategies to combat rising stream temperatures.

Agricultural runoff is one of largest contributors of phosphorus (P), nitrogen (N), and sediment affecting freshwater systems in watersheds across the Northeastern U.S., including the Lake Champlain Basin in Vermont. Agricultural cropping systems, such as corn silage and haylands, used for dairy feed production have been shown to impact watershed hydrology and water quality. Agricultural best management practices (BMPs) have the potential to decrease runoff volumes and flow rates and the associated export of nutrients and sediment from agricultural fields. Many states in the Northeastern U.S., including Vermont, are beginning to require farmers to implement water quality BMPs and further improve risk evaluation of export of P in runoff using evolving P site assessment tools, such as the Phosphorus Index (P-Index). Quantifying the effects of BMPs on hydrologic and nutrient exports from fields is critical for informing site assessment tools that aid in the development of nutrient management plans and to help design agroecosystems that do not degrade water quality. However, there is a lack of data on the effects of BMPs on edge-of-field hydrologic and nutrient fluxes, especially in cold-climate regions with snow-melt induced runoff events. This thesis consists of four chapters, Chapter 1 is a comprehensive literature review on agricultural hydrology and water quality, BMP effectiveness, and P site assessment tools. Chapters 2 and 3 address research objectives related to the evaluation of BMP and P site assessment tool effectiveness. Chapter 4 is a summary of the conclusions drawn from the work done in Chapters 2 and 3, and suggestions for future work. Chapter 2 evaluates the effects of soil aeration prior to manure application on edge-of-field hydrology, water quality, and P fluxes in haylands with clay soils during both precipitation and snow-melt induced runoff events. Edge-of-field water quality monitoring techniques and passive-capillary lysimeter systems were used to continuously measure the losses of surface runoff, subsurface leachate, and the associated export of nutrients (total phosphorus, total dissolved phosphorus, total nitrogen, and total dissolved nitrogen) and total suspended solids resulting from runoff events year-round from 2012 to 2018. Annual P fluxes in the form of vegetative uptake and removal, manure additions, and soil test P were also recorded. Results from this study indicated that soil aeration had the potential to reduce nutrient and sediment exports from haylands with poorly-drained, high runoff producing soils in the Northeastern U.S. where winter freeze-thaw conditions exist. However, potential increases in surface and subsurface hydrologic flows can accompany these reductions; these implications should be considered before implementation. Chapter 3 identifies potential P-Index improvements through the representation of topographic controls on phosphorus (P) transport by comparing results from the Vermont P-Index (VT P-Index) and a more complex process-based model, TopoSWAT, across topographic regions in a small agricultural watershed (360 ha) in the Lake Champlain Basin. Scenarios of varying P management strategies were modeled for corn silage production fields with poorly-drained soils and rolling topography. Modeled outputs of P risk assessments and edge-of-field dissolved and particulate P losses were compared. Results from this study suggest that the VT P-Index could improve its ability to support farm nutrient management planning and other P-based management decisions by incorporating topographic controls of runoff production into its estimation of P transport.

Population growth, coupled with changing weather patterns, is straining water supplies, especially in the American Southwest. A multitude of tools, including additional storage, will be needed to meet water demand and supply gaps. The Animas-La Plata Project, a reservoir in southwest Colorado, provides a case study of how groups worked for nearly 70 years to solve a water problem: insufficient irrigation for agriculture. This qualitative case study addressed a lack of first-person narratives from those most involved. Its purpose was to gather stakeholder narratives and analyze them using Kingdon's three streams theory to address the extent to which the problem, policy, and political streams converged to open policy windows that resulted in a built facility. Purposeful sampling identified 11 organizational stakeholders with the highest seniority and longest association with the project. Transcribed data from structured interview questions were inductively coded and thematically analyzed. Key findings include identification of a major federal policy change in the late 1970s to 1980s that excluded escalated benefits of water projects. Within this same timeframe, necessary elements were present to open a policy window, the Colorado Ute Indian Water Rights Settlement, which resulted in project construction. If strategists can learn to predict the opening of policy windows "when the problem, policy, and political streams join" water resource planning and policy can be improved. Retrospective narrative analysis is a promising ex post audit and evaluation tool that policy analysts can use to assess program performance and lessons learned. Social change implications of the study are that its findings on the need for positive collaboration may prove valuable to those in management who seek to address water scarcity issues.

Advanced wastewater treatment plants have complex biological kinetics, time variant influent rates and long processing times. The modeling and operation control of wastewater treatment plant gets complicated due to these characteristics. However, a robust operational system for a wastewater treatment plant is necessary to increase the efficiency of the plant, reduce energy cost and achieve environmental discharge limits. These discharge limits are set by the National Pollutant Discharge Elimination System (NPDES) for municipal and industrial wastewater treatment plants to limit the amount of nutrients being discharged into the aquatic systems. This document summarizes the research to develop a supervisory operational and control system for the Valrico Advanced Wastewater Treatment Plant (AWWTP) in the Hillsborough County, Florida. The Valrico AWWTP uses biological treatment process and has four oxidation ditches with extended aeration where simultaneous nitrification and denitrification (SND) takes place. Each oxidation ditch has its own anaerobic basin where in the absence of oxygen, the growth of microorganisms is controlled and which in return also helps in biological phosphorus removal. The principle objective of this research was to develop a working model for the Valrico AWWTP using BioWin which mimics the current performance of the plant, predicts the future effluent behavior and allows the operators to take control actions based on the effluent results to maintain the discharge permit limits. Influent and experimental data from online and offline sources were used to tune the BioWin model for the Valrico Plant. The validation and optimization of the BioWin model with plant data was done by running a series of simulations and carrying out sensitivity analysis on the model which also allowed the development of operation policies and control strategies. The control strategies were developed for the key variables such as aeration requirements in the oxidation ditch, recycle rates and wastage flow rates. A controller that manipulates the wasting flow rate based on the amount of mixed liquor suspended solids (MLSS) was incorporated in the model. The objective of this controller was to retain about 4500-4600 mg/L of MLSS in the oxidation ditch as it is maintained by the Valrico Plant. The Valrico AWWTP recycles around 80% of their effluent and hence, the split ratios were adjusted accordingly in the model to recycle the desired amount. The effluent concentrations from the BioWin model for the parameters such as Total Nitrogen (TN), Ammonia, Nitrate, Nitrite, Total Kjeldahl Nitrogen (TKN) complied with the discharge limits which is usually less than 2 mg/L for all the parameters.