Large rivers in semiarid regions provide valuable resources for municipalities, agriculture, and adjacent ecosystems, yet the limited nature of the resource requires a concerted effort to understand the controls on water quality. To address this issue I continued and adapted biannual geochemical synoptic sampling of the Rio Grande from Del Norte, CO to Elephant Butte Reservoir between August 2003 and 2006 which had started in 2001. During average to drought conditions, river discharge was derived primarily from snowmelt in the headwaters region, total dissolved solutes increased downstream, and wastewater treatment plants were the largest source of nitrogen to the river. Surprisingly, return flows of river water diverted for agriculture had lower average nitrogen concentrations than the original river water, indicating that the agricultural system is a sink for nitrogen. When summer climatic conditions changed to a persistent monsoon regime, both the water and solute sources changed as the river was reconnected to its uplands and floodplain. Stable isotope data indicate that monsoon precipitation represented 10-50% of surface flow and that discharge increases were entirely due to ephemeral flows. An analysis of solute concentrations suggested that 80-100% of the increases in sulfate, chloride, DOC and nitrate were due to ephemeral flows. Ephemeral flows replaced wastewater treatment plants as the largest source of nitrogen to the river.

Using data from the synoptic sampling, I developed both a simple chloride mixing model and a dynamic simulation model of nitrate to evaluate the controls on nutrient cycling within the Rio Grande. Results from the chloride mixing model indicate that both abiotic hydrologic processes and biotic processes provide important controls on nutrient concentrations. River characteristics that increase surface water/groundwater exchange are important for determining nutrient retention, a result commonly identified in smaller streams, but never before quantified in a large river. Dynamic simulation modeling indicates that both plant uptake and denitrification remove nitrate within the Middle Rio Grande with denitrification accounting for 55-100% of the nitrate removal downstream of Albuquerque. The results of this dissertation provide a conceptual model for the hydrologic and biologic controls on nutrient concentrations in a heavily managed large semiarid river.