Excess nitrogen (N) and phosphorus (P) from agricultural and urban lands cause numerous water quality problems in freshwater ecosystems, including eutrophication, reduced biodiversity, and drinking water contamination. As N and P are transferred from terrestrial to marine ecosystems via river networks, they are assimilated by autotrophs (i.e., algae, macrophytes) and heterotrophs (i.e., fungi, bacteria) or transformed via dissimilatory processes (i.e., denitrification). As such, nutrient processing may mitigate the effects of nutrient pollution on downstream ecosystems, either by removing nutrients prior to export, or buffering the timing and form of nutrient export. Watershed models of nutrient dynamics either assume that rivers are pipes, transporting nutrients downstream without any biological activity, or that rivers are oversized streams, and the biological processes occurring in streams also occur in rivers. Nutrient dynamics in streams are controlled by benthic (i.e., bottom) processes, whereas water column processes are ignored in all but the largest rivers. My dissertation research examined the role of the water column in nutrient dynamics of rivers, with a focus on how human land use may alter these dynamics. I found that water column nutrient uptake occurs across a variety of streams and rivers. However, across fifteen similarly sized rivers, water column nutrient uptake and the water column contribution to reach-scale uptake increased with human land use. I also found that human land use influenced nutrient limitation in benthic biofilms. I used novel techniques to measure denitrification in the sediment and water column of five Midwestern rivers, and found that the water column can be an important contributor to denitrification. Finally, I developed a hydrologic-biogeochemical model to predict the effect of dams on downstream N retention and transport. I found that hydrologic variation induced through dam management may make the river downstream of the dam more of a N sink. Overall, my dissertation shows that the water column can be an important and previously unaccounted for contributor to whole-river nutrient dynamics. Due to the biogeochemical activity of the sediment and the water column, rivers can process nutrients at rates comparable to headwater streams.