In freshwater networks, the sources, movement, and cycling of carbon and nutrients are shaped both by in-stream processes and the surrounding landscape. Streams receive and transport materials from upstream and terrestrial sources that support in-stream ecosystem processes and regulate downstream water quality. Understanding how these processes within a stream alter downstream carbon and nutrient fluxes is needed to assess the functional role of lotic ecosystems on the landscape. Further, predictions of how materials cycle and move throughout freshwater networks are derived from measurements at the stream reach scale which deliberately avoid complex geomorphology such as stream confluences. As a result, the impact of stream confluences on in-stream ecosystem processes and the fate of carbon and nutrients in freshwater networks has been overlooked. In this dissertation, I seek to address the following questions: (1) How are coupled carbon and nitrogen cycles altered by land use? (2) To what extent can rates of in-stream organic carbon removal inform our understanding of the role of streams in landscape carbon fluxes? (3) How are carbon metabolism and nutrient uptake altered downstream of a stream confluence? (4) How do confluences alter the transport and fate of carbon and nutrients within a freshwater network? In Chapter 2, I showed that the fate of organic carbon and nitrate are similar in headwater streams across the United States. Organic carbon travels longer distances before being respired in agricultural and urban streams compared to reference streams, suggesting that human modifications to landscapes impact carbon cycling and transport in streams. In Chapter 3, I demonstrated how rates of in-stream organic carbon removal can be used to quantify terrestrial-aquatic linkages and showed that laboratory bioassays systematically underestimate ecosystem organic carbon fluxes compared to whole-stream metabolism measurements. In Chapter 4, I conducted whole-ecosystem manipulation experiments to assess how ecosystem processes are altered by a confluence. I found that carbon metabolism and phosphorus uptake are suppressed downstream of a confluence and that rates of organic carbon uptake are spatially variable throughout a confluence mixing zone. In Chapter 5, I examined potential reach-scale and watershed-scale drivers to explain patterns of organic matter and nutrient chemistry downstream of confluences throughout a stream network. Reaches downstream of confluences were geomorphically and biogeochemically distinct from upstream reaches, and differences in upstream and tributary reach chemistry or drainage area did not explain patterns of biologically reactive parameters at confluences. My dissertation highlights the importance of in-stream ecosystem processes in driving the cycling and downstream fate of carbon and nutrients. I show how rates of whole-stream carbon metabolism can be used to better constrain terrestrial-aquatic organic carbon fluxes. I investigate the potentially disproportionate role of ecosystem interfaces, namely stream confluences, in determining the cycling and fate of carbon and nutrients in freshwater networks. This work challenges assumptions around controls over water quality in freshwater networks and asserts that by ignoring (1) contributions of all in-stream processes to whole-ecosystem function and (2) how confluences alter those processes, we risk misrepresenting the role of running waters in determining the fluxes and fate of carbon and nutrients from the reach- to the network-scale. / Doctor of Philosophy / Streams receive and use materials from upstream and the surrounding landscape to fuel in-stream ecosystem processes (e.g. carbon and nutrient cycling). Understanding how these processes within a stream alter concentrations of carbon and other nutrients is needed to assess how the ecosystem is functioning and what the consequences are on water quality downstream. Further, predictions of how materials cycle and move at the scale of streams networks are derived from measurements at the stream reach scale. As a result, the impact of stream confluences (i.e., where two streams meet and mix) on in-stream carbon and nutrient cycling and the consequences on downstream water quality has been overlooked. In this dissertation, I seek to address the following questions: (1) How are carbon and nitrogen cycles linked in streams and how those links altered by land use? (2) How can rates of in-stream carbon cycling inform our understanding of the role of streams in landscape carbon budgets? (3) How are carbon and nutrient removal altered downstream of a stream confluence? (4) How do confluences alter water chemistry within a freshwater network? In Chapter 2, I showed that organic carbon and nitrate shared similar fates in streams across the United States. Organic carbon traveled longer distances before being respired in agricultural and urban streams compared to natively-vegetated streams, suggesting that human modifications to landscapes impact carbon cycling and transport in streams. In Chapter 3, I demonstrated how rates of in-stream organic carbon removal can be used to understand land-stream connections. In Chapter 4, I conducted whole-ecosystem experiments to assess how carbon and nutrient removal are altered by a confluence. I showed that carbon metabolism and phosphorus removal are suppressed downstream of a confluence and that rates of organic carbon removal are spatially variable throughout where water from the two streams are mixing. In Chapter 5, I examined potential drivers to explain patterns of organic matter and nutrient chemistry downstream of confluences throughout a stream network. Reaches downstream of confluences were physically, chemically, and biologically distinct from upstream reaches and differences in upstream and tributary reach chemistry or drainage area did not explain patterns of water chemistry downstream of confluences. Overall, my dissertation highlights the importance of processes within a stream in driving carbon and nutrient cycling, and how rates of whole-stream carbon cycling can be used to better understand connections between streams and the surrounding landscape. I investigate the role of stream confluences in determining the cycling and downstream fate of carbon and nutrients in freshwater networks. This work shows that ecosystem functioning and downstream water quality in freshwater networks are affected by processes occurring within streams and by the interfaces between streams and other ecosystems (e.g., land-water interfaces, stream confluences).