Pathogenic contamination is a significant factor contributing to the degradation of surface water both globally and within the United States. This leads to negative economic impacts, sickness, and, in severe cases, fatalities. As the world's population grows, pollution increases, placing more stress on water resources, particularly in arid regions. The situation is made worse by climate change. The forecasted expansion of arid and semi-arid land areas and alterations in precipitation patterns could have a significant impact on those living in poverty and dry regions. This dissertation aims to investigate previously undocumented threats to water quality through understanding pathogen drivers in arid and semi-arid environments and documenting wastewater infrastructure on Tribal lands. Specifically, I first investigated how ephemeral streams (common in arid and semiarid areas) impact the presence of pathogens in surface waters by identifying the main drivers of E. coli concentration from a series of proposed predictors. Second, I identified unknown potential sources of water quality impairments on Tribal lands, which are mainly rural and in arid or semiarid areas, focusing on wastewater infrastructure in these systems. I specifically quantified populations served by wastewater treatment plants and then used a remote sensing approach to identify possible unpermitted wastewater lagoons that often serve as the only wastewater infrastructure in some areas. The findings revealed unique insights that could help aid water management in arid and semiarid regions as well as in rural areas.

Approximately 71% of the great lakes, lakes, reservoirs, and ponds, together with 51% of rivers and streams assessed in the US are impaired or threatened by pollution or do not meet the minimum water quality requirements. Pathogens, sediments, and nutrients are leading causes of impairment, with agriculture being a top source of pollution. Agricultural pollution has become a global concern overtaking urban contamination as the major factor of inland and coastal waters degradation in many parts of the world. High-yielding crop production has been achieved by the intensive use of inorganic fertilizers that are mainly composed of Nitrogen (N) and Phosphorus (P). N and P are essential nutrients for ecosystem structure, processes, and functions. However, N and P in excess can be problematic to the environment. One of the major impacts of the increasing amount of these nutrients in the environment is the global expansion of harmful algal blooms (HABs). Major agricultural nutrient pollution sources and climate change can exacerbate these risks. This dissertation aims to guide future policies to mitigate issues linked to excess nutrient loads in the U.S. by evaluating the impact of climate change on nutrient loads and assessing the environmental impact as well as the spatial patterns of one of the major agricultural sources of nutrient pollution - Concentrated Animal Feeding Operations (CAFOs). Specifically, I first investigated the impact of bias correction techniques when modeling mid-century nutrient loads in a watershed heavily impacted by CAFOs. Second, I evaluated the role of CAFOs in land use change and subsequent environmental degradation of the surrounding environment. Finally, I assessed the spatial organization of CAFOs and its links to water quality conditions. The findings revealed unique insights for future nutrient management strategies in the U.S.