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Upland catchments play an outsized role in the processing and export of water, sediments, nutrients, and organic matter, thus strongly influencing downstream water quality. In Chapter 1, an overview of biogeochemical cycling within upland fluvial sediments is presented, focusing on key regional biogeochemical cycling patterns and solute export processes. Additionally, anthropogenic influences on this environment, such as historical mining activities and climate change, are briefly reviewed in this chapter.Chapter 2 explores the relationship between spatial hydrologic heterogeneity and microbial community assembly and functional potential within the hyporheic zone. The region of groundwater and river water mixing, known as the hyporheic zone, is a hotspot of microbial activity that influences solute export and cycling in rivers. Hyporheic mixing patterns can vary over small spatial scales, leading to heterogeneity in fluid chemistry and microbial community composition and function. Here, we integrate new mass-spectrometry data, metagenomic insights, and ecological models with previous analyses of microbial community composition and dissolved organic matter (DOM) quality to understand spatial relationships between hyporheic flow and microbial community assembly, metabolism, and DOM processing at high-resolution (100 locations) along a 200 m meander of East River, Colorado (USA). Ecological modeling revealed a strong linkage between community assembly patterns and underlying hydrologic and geochemical drivers, including the impact of physical heterogeneity (riverbed grain size) on microbial community structure. Geochemical profiles associated with upwelling groundwater suggest the influence of underlying geology, specifically Mancos-derived solutes, in driving community assembly. Distinct microbial community profiles and functional potential in zones of upwelling groundwater suggest that groundwater chemistry may have a greater influence on biogeochemical cycling within the river channel as periods of baseflow increase in both frequency and duration under future climate change scenarios.Chapter 3 investigates the seasonal impacts of snowmelt-dominated hydrology on hyporheic microbial community dynamics and associated biogeochemistry. Terrestrial and aquatic elemental cycles are tightly linked in upland fluvial networks. Biotic and abiotic mineral weathering, microbially-mediated degradation of organic matter, and anthropogenic influences all result in the movement of solutes (e.g., carbon, metals, nutrients) through these catchments, with implications for downstream water quality. Within the river channel, the region of hyporheic mixing represents a hotspot of microbial activity, exerting significant control over solute cycling. To investigate how snowmelt-driven seasonal changes in river discharge affect microbial community assembly and carbon biogeochemistry, depth-resolved pore water samples were recovered from multiple locations around a representative meander on the East River near Crested Butte, CO, USA. Vertical temperature sensor arrays were also installed in the streambed to enable seepage flux estimates. Snowmelt-driven high river discharge led to an expanding zone of vertical hyporheic mixing and introduced dissolved oxygen into the streambed that stimulated aerobic microbial respiration. These physicochemical processes contributed to microbial communities undergoing homogenizing selection, in contrast to other ecosystems where lower permeability may limit the extent of mixing. Conversely, lower river discharge conditions led to a greater influence of upwelling groundwater within the streambed and a decrease in microbial respiration rates. Associated with these processes, microbial communities throughout the streambed exhibited increasing dissimilarity between each other, suggesting that the earlier onset of snowmelt and longer periods of base flow may lead to changes in the composition (and associated function) of streambed microbiomes, with consequent implications for the processing and export of solutes from upland catchments.Chapter 4 explores the metal mobilization patterns that occurred as a result of a mine waste spill. The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amended with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO42--reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.Finally, Chapter 5 summarizes key findings and conclusions as well as outlines remaining questions that may be addressed in future work. The results presented in this study highlight the importance of seasonal and spatial hydrologic heterogeneity in upland watershed biogeochemistry. In collecting this information, I have expanded current knowledge of hyporheic hydrobiogeochemistry in upland fluvial systems. Particularly, I conclude that seasonally-driven dynamic water mixing patterns within the hyporheic zone create unique geochemical profiles that drive differences in microbial community composition, assembly, and functional potential. Our results provide insights into the relationship between hydrology and microbial community and metabolisms within river corridors, information which is critical to understanding water resources, particularly in our rapidly changing climate.